bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples
Authors: Zhang Eileen Z , Bartels Doug J , Frantz JDan , Seepersaud Sheila , Lippke Judith A , Shames Benjamin , Zhou Yi , Lin Chao , Kwong Ann , Kieffer Tara L
Published: February 2013

Background

Direct-acting antiviral (DAAs) agents for hepatitis C virus (HCV) span a variety of targets, including proteins encoded by the NS3/4A, NS4B, NS5A, and NS5B genes. Treatment with DAAs has been shown to select variants with sequence changes in the HCV genome encoding amino acids that may confer resistance to the treatment. In order to assess these effects in patients, a Reverse Transcription Polymerase Chain Reaction (RT-PCR) method was developed to sequence these regions of HCV from patient plasma.

Methods

A method was developed to amplify and sequence genotype 1 HCV RNA from patient plasma. Optimization of HCV RNA isolation, cDNA synthesis, and nested PCR steps were performed. The optimization of HCV RNA isolation, design of RT-PCR primers, optimization of RT-PCR amplification conditions and reagents, and the evaluation of the RT-PCR method performance is described.

Results

The optimized method is able to successfully, accurately, and reproducibly amplify near full-length genotype 1 HCV RNA containing a wide range of concentrations (103to 108IU/mL) with a success rate of 97%. The lower limit of detection was determined to be 1000 IU/mL HCV RNA.

Conclusions

This assay allows viral sequencing of all regions targeted by the most common DAAs currently in development, as well as the possibility to determine linkage between variants conferring resistance to multiple DAAs used in combination therapy.
Hevea brasiliensis cell suspension peroxidase: purification, characterization and application for dye decolorization
Authors: Chanwun Thitikorn , Muhamad Nisaporn , Chirapongsatonkul Nion , Churngchow Nunta
Published: February 2013

Peroxidases are oxidoreductase enzymes produced by most organisms. In this study, a peroxidase was purified from Hevea brasiliensis cell suspension by using anion exchange chromatography (DEAE-Sepharose), affinity chromatography (Con A-agarose) and preparative SDS-PAGE. The obtained enzyme appeared as a single band on SDS-PAGE with molecular mass of 70 kDa. Surprisingly, this purified peroxidase also had polyphenol oxidase activity. However, the biochemical characteristics were only studied in term of peroxidase because similar experiments in term of polyphenol oxidase have been reported in our pervious publication. The optimal pH of the purified peroxidase was 5.0 and its activity was retained at pH values between 5.0–10.0. The enzyme was heat stable over a wide range of temperatures (0–60°C), and less than 50% of its activity was lost at 70°C after incubation for 30 min. The enzyme was completely inhibited by β-mercaptoethanol and strongly inhibited by NaN3; in addition, its properties indicated that it was a heme containing glycoprotein. This peroxidase could decolorize many dyes; aniline blue, bromocresol purple, brilliant green, crystal violet, fuchsin, malachite green, methyl green, methyl violet and water blue. The stability against high temperature and extreme pH supported that the enzyme could be a potential peroxidase source for special industrial applications.
Additive value of blood neutrophil gelatinase-associated lipocalin to clinical judgement in acute kidney injury diagnosis and mortality prediction in patients hospitalized from the emergency department
Authors: Di Somma Salvatore , Magrini Laura , De Berardinis Benedetta , Marino Rossella , Ferri Enrico , Moscatelli Paolo , Ballarino Paola , Carpinteri Giuseppe , Noto Paola , Gliozzo Biancamaria , Paladino Lorenzo , Di Stasio Enrico
Published: February 2013

Introduction

Acute kidney injury (AKI) is a common complication among hospitalized patients. The aim of this study was to evaluate the utility of blood neutrophil gelatinase-associated lipocalin (NGAL) assessment as an aid in the early risk evaluation for AKI development in admitted patients.

Methods

This is a multicenter Italian prospective emergency department (ED) cohort study in which we enrolled 665 patients admitted to hospital from the ED.

Results

Blood NGAL and serum creatinine (sCr) were determined at ED presentation (T0), and at: 6 (T6), 12 (T12), 24 (T24) and 72 (T72) hours after hospitalization. A preliminary assessment of AKI by the treating ED physician occurred in 218 out of 665 patients (33%), while RIFLE AKI by expert nephrologists was confirmed in 49 out of 665 patients (7%). The ED physician's initial judgement lacked sensitivity and specificity, overpredicting the diagnosis of AKI in 27% of the cohort, while missing 20% of those with AKI as a final diagnosis.

The area under the receiver operating characteristic curve (AUC), obtained at T0, for blood NGAL alone in the AKI group was 0.80. When NGAL at T0 was added to the ED physician's initial clinical judgment the AUC was increased to 0.90, significantly greater when compared to the AUC of the T0 estimated glomerular filtration rate (eGFR) obtained either by modification of diet in renal disease (MDRD) equation (0.78) or Cockroft-Gault formula (0.78) (P = 0.022 and P = 0.020 respectively). The model obtained by combining NGAL with the ED physician's initial clinical judgement compared to the model combining sCr with the ED physician's initial clinical judgement, resulted in a net reclassification index of 32.4 percentage points. Serial assessment of T0 and T6 hours NGAL provided a high negative predictive value (NPV) (98%) in ruling out the diagnosis of AKI within 6 hours of patients' ED arrival. NGAL (T0) showed the strongest predictive value for in-hospital patient's mortality at a cutoff of 400 ng/ml.

Conclusions

Our study demonstrated that assessment of a patient's initial blood NGAL when admitted to hospital from the ED improved the initial clinical diagnosis of AKI and predicted in-hospital mortality. Blood NGAL assessment coupled with the ED physician's clinical judgment may prove useful in deciding the appropriate strategies for patients at risk for the development of AKI.

See related commentary by Legrand et al.,http://ccforum.com/content/17/2/132
Translational control of human neutrophil responses by MNK1
Authors: Fortin Carl F , Mayer Thomas Z , Cloutier Alexandre , McDonald Patrick P
Published: February 2013

A growing number of inflammatory and immune processes in vivo have been shown to be influenced by neutrophil-derived cytokines. Whereas the underlying transcriptional mechanisms are increasingly well understood, the translational regulation of this neutrophil response remains largely unexplored. Here, we show that the MNK1, which participates in translational control in several cell types, is activated in response to physiological neutrophil agonists (LPS, TNF-α) in the cytoplasmic and nuclear compartments. With the use of various pharmacological inhibitors, we found that MNK1 activation takes place downstream of the TAK1-p38 MAPK axis in neutrophils, whereas the MEK/ERK, JNK, PI3K, and PKC pathways are not involved. Pharmacological blockade of MNK1, as well as overexpression experiments, established that cytokine protein synthesis (but not gene expression) is under the control of MNK1 in neutrophils. Likewise, MNK1 inhibition reversed the antiapoptotic effect of LPS and TNF-α in neutrophils, and this was accompanied by a decreased expression of the antiapoptotic protein Mcl-1. Thus, MNK1 appears to be an important regulator of neutrophil responses. Although MNK1 inhibition did not affect protein recruitment to mRNA caps, it decreased the phosphorylation of molecules implicated in translation initiation control, such as S6K, S6, and hyperphosphorylated 4E-BP1. These molecular targets of MNK1 are shared with those of PI3K in neutrophils, and accordingly, MNK1 inhibition partially impaired the belated PI3K/Akt activation elicited by LPS or TNF in these cells. Given the importance of neutrophils and their products in numerous chronic inflammatory disorders, MNK1 could represent an attractive therapeutic target.
Preterm neonates display altered plasmacytoid dendritic cell function and morphology
Authors: Schüller S S , Sadeghi K , Wisgrill Lukas , Dangl A , Diesner S C , Prusa A R , Klebermasz-Schrehof K , Greber-Platzer S , Neumüller J , Helmer H , Husslein P , Pollak A , Spittler A , Förster-Waldl E
Published: February 2013

Functionality and morphology of pDCs of preterm newborns, with emphasis on TLR9 triggered IFN-α production.

Bacterial and viral infections cause high rates of morbidity and mortality in premature newborns. In the setting of viral infection, pDCs play a key role as strong producers of IFN-α upon TLR9 activation. We analyzed pDC frequency, phenotype, morphology, and function in CB of preterm and term newborns in comparison with adults. Whereas all age groups show similar pDC numbers, BDCA-2, CD123, and TLR9 levels, the expression of BDCA-4 and capacity to produce IFN-α upon TLR9 challenge were decreased significantly in preterm neonates. Furthermore, we show by means of electron microscopy that pDCs from preterm newborns exhibit a distinct, “immature” morphology. Taken together, these findings suggest decreased functionality of pDCs in the premature newborn. The reduced capacity to produce IFN-α is likely to render such infants more susceptible to viral infections.
Maintenance Chemotherapy for Advanced Non–Small-Cell Lung Cancer: New Life for an Old Idea
Authors: Gerber David E. , Schiller Joan H.
Published: February 2013

Although well established for the treatment of certain hematologic malignancies, maintenance therapy has only recently become a treatment paradigm for advanced non–small-cell lung cancer. Maintenance therapy, which is designed to prolong a clinically favorable state after completion of a predefined number of induction chemotherapy cycles, has two principal paradigms. Continuation maintenance therapy entails the ongoing administration of a component of the initial chemotherapy regimen, generally the nonplatinum cytotoxic drug or a molecular targeted agent. With switch maintenance (also known as sequential therapy), a new and potentially non–cross-resistant agent is introduced immediately on completion of first-line chemotherapy. Potential rationales for maintenance therapy include increased exposure to effective therapies, decreasing chemotherapy resistance, optimizing efficacy of chemotherapeutic agents, antiangiogenic effects, and altering antitumor immunity. To date, switch maintenance therapy strategies with pemetrexed and erlotinib have demonstrated improved overall survival, resulting in US Food and Drug Administration approval for this indication. Recently, continuation maintenance with pemetrexed was found to prolong overall survival as well. Factors predicting benefit from maintenance chemotherapy include the degree of response to first-line therapy, performance status, the likelihood of receiving further therapy at the time of progression, and tumor histology and molecular characteristics. Several aspects of maintenance therapy have raised considerable debate in the thoracic oncology community, including clinical trial end points, the prevalence of second-line chemotherapy administration, the role of treatment-free intervals, quality of life, economic considerations, and whether progression-free survival is a worthy therapeutic goal in this disease setting.
Direct and indirect roles of Fgf3 and Fgf10 in innervation and vascularisation of the vertebrate hypothalamic neurohypophysis
Authors: Liu Fang , Pogoda Hans-Martin , Pearson Caroline Alayne , Ohyama Kyoji , Löhr Heiko , Hammerschmidt Matthias , Placzek Marysia
Published: February 2013

The neurohypophysis is a crucial component of the hypothalamo-pituitary axis, serving as the site of release of hypothalamic neurohormones into a plexus of hypophyseal capillaries. The growth of hypothalamic axons and capillaries to the forming neurohypophysis in embryogenesis is therefore crucial to future adult homeostasis. Using ex vivo analyses in chick and in vivo analyses in mutant and transgenic zebrafish, we show that Fgf10 and Fgf3 secreted from the forming neurohypophysis exert direct guidance effects on hypothalamic neurosecretory axons. Simultaneously, they promote hypophyseal vascularisation, exerting early direct effects on endothelial cells that are subsequently complemented by indirect effects. Together, our studies suggest a model for the integrated neurohemal wiring of the hypothalamo-neurohypophyseal axis.
The transcriptional co-factor RIP140 regulates mammary gland development by promoting the generation of key mitogenic signals
Authors: Nautiyal Jaya , Steel Jennifer H. , Mane Meritxell Rosell , Oduwole Olayiwola , Poliandri Ariel , Alexi Xanthippi , Wood Nicholas , Poutanen Matti , Zwart Wilbert , Stingl John , Parker Malcolm G.
Published: February 2013

Nuclear receptor interacting protein (Nrip1), also known as RIP140, is a co-regulator for nuclear receptors that plays an essential role in ovulation by regulating the expression of the epidermal growth factor-like family of growth factors. Although several studies indicate a role for RIP140 in breast cancer, its role in the development of the mammary gland is unclear. By using RIP140-null and RIP140 transgenic mice, we demonstrate that RIP140 is an essential factor for normal mammary gland development and that it functions by mediating oestrogen signalling. RIP140-null mice exhibit minimal ductal elongation with no side-branching, whereas RIP140-overexpressing mice show increased cell proliferation and ductal branching with age. Tissue recombination experiments demonstrate that RIP140 expression is required in both the mammary epithelial and stromal compartments for ductal elongation during puberty and that loss of RIP140 leads to a catastrophic loss of the mammary epithelium, whereas RIP140 overexpression augments the mammary basal cell population and shifts the progenitor/differentiated cell balance within the luminal cell compartment towards the progenitors. For the first time, we present a genome-wide global view of oestrogen receptor-α (ERα) binding events in the developing mammary gland, which unravels 881 ERα binding sites. Unbiased evaluation of several ERα binding sites for RIP140 co-occupancy reveals selectivity and demonstrates that RIP140 acts as a co-regulator with ERα to regulate directly the expression of amphiregulin (Areg), the progesterone receptor (Pgr) and signal transducer and activator of transcription 5a (Stat5a), factors that influence key mitogenic pathways that regulate normal mammary gland development.
The tiptop/teashirt genes regulate cell differentiation and renal physiology in Drosophila
Authors: Denholm Barry , Hu Nan , Fauquier Teddy , Caubit Xavier , Fasano Laurent , Skaer Helen
Published: February 2013

The physiological activities of organs are underpinned by an interplay between the distinct cell types they contain. However, little is known about the genetic control of patterned cell differentiation during organ development. We show that the conserved Teashirt transcription factors are decisive for the differentiation of a subset of secretory cells, stellate cells, in Drosophila melanogaster renal tubules. Teashirt controls the expression of the water channel Drip, the chloride conductance channel CLC-a and the Leukokinin receptor (LKR), all of which characterise differentiated stellate cells and are required for primary urine production and responsiveness to diuretic stimuli. Teashirt also controls a dramatic transformation in cell morphology, from cuboidal to the eponymous stellate shape, during metamorphosis. teashirt interacts with cut, which encodes a transcription factor that underlies the differentiation of the primary, principal secretory cells, establishing a reciprocal negative-feedback loop that ensures the full differentiation of both cell types. Loss of teashirt leads to ineffective urine production, failure of homeostasis and premature lethality. Stellate cell-specific expression of the teashirt paralogue tiptop, which is not normally expressed in larval or adult stellate cells, almost completely rescues teashirt loss of expression from stellate cells. We demonstrate conservation in the expression of the family of tiptop/teashirt genes in lower insects and establish conservation in the targets of Teashirt transcription factors in mouse embryonic kidney.
The Ntcheu derotation splint for lower limb traction
Authors: Doorgakant Ashtin , Parmar Rishee , Ngulube Christopher
Published: February 2013

The Ntcheu derotation splint is recommended as a tool to improve the care of patients in lower limb traction. It avoids the various problems associated with the traditional plaster boot that is routinely used (stiffness, pressure sores, cost and time). It is easy to make, is relatively low cost and uses widely available materials.
Clinical profile of children with moderate-to-severe eosinophilia presenting to a tertiary hospital in Nepal
Authors: Shrestha Shrijana , Timila Dipsal , Karki Utkarsh , Shrestha Ashis , Bhandary Shital
Published: February 2013

Fifty children (mean age 8 years) with an absolute eosinophil count ranging from 1956 to 28,500 were studied in a tertiary hospital in Nepal. Most had multisystem involvement: 47 had constitutional symptoms; 38 had gastrointestinal symptoms; and 37 had respiratory symptoms. Abdominal pain, fever, cough and weight loss were the most common presentations while pleural effusion, ascites, pericardial effusion, abdominal nodes and high erythrocyte sedimentation rates were the common investigational findings.
Salmonella typhi presenting as acute glomerulonephritis in twin siblings
Authors: Bhatt Girish Chandra , Nandan Devki
Published: February 2013

Acute glomerulonephritis occurring during the course of enteric fever is a rare entity and only a few cases have been reported in the published literature. We describe two interesting cases of acute glomerulonephritis occurring in twin siblings.
The value of health partnerships: a practical approach to evidence
Authors: Ritman Dan , Zegeye Hana
Published: February 2013

Your April editorial 1 points out that there is little strong evidence of the effectiveness and impact of health links – or health partnerships, as they are often known – in terms of the processes and particularly the outcomes of health care. We believe this reflects the inherent complexity of the health systems and the consequent challenges for robust measurement. However, health partnerships use a range of evaluation methods that provide valuable, qualitative and descriptive information about change and performance management, which can help demonstrate the effectiveness of health partnerships.
Structure of caa
3 cytochrome c oxidase – a nature-made enzyme-substrate complex
Authors: Noor Mohamed Radzi , Soulimane Tewfik
Published: February 2013

Aerobic respiration, the energetically most favorable metabolic reaction, depends on the action of terminal oxidases that include cytochrome c oxidases. The latter forms a part of the heme-copper oxidase superfamily and consists of three different families (A, B, and C types). The crystal structures of all families have now been determined, allowing a detailed structural comparison from evolutionary and functional perspectives. The A2-type oxidase, exemplified by the Thermus thermophilus caa
3 oxidase, contains the substrate cytochrome c covalently bound to the enzyme complex. In this article, we highlight the various features of caa
3 enzyme and provide a discussion of their importance, including the variations in the proton and electron transfer pathways.
Allele Identification for Transcriptome-Based Population Genomics in the Invasive PlantCentaurea solstitialis
Authors: Dlugosch Katrina M , Lai Zhao , Bonin Aurélie , Hierro José , Rieseberg Loren H
Published: February 2013

Transcriptome sequences are becoming more broadly available for multiple individuals of the same species, providing opportunities to derive population genomic information from these datasets. Using the 454 Life Science Genome Sequencer FLX and FLX-Titanium next-generation platforms, we generated 11−430 Mbp of sequence for normalized cDNA for 40 wild genotypes of the invasive plant Centaurea solstitialis, yellow starthistle, from across its worldwide distribution. We examined the impact of sequencing effort on transcriptome recovery and overlap among individuals. To do this, we developed two novel publicly available software pipelines: SnoWhite for read cleaning before assembly, and AllelePipe for clustering of loci and allele identification in assembled datasets with or without a reference genome. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries. We find that modest applications of sequencing effort recover most of the novel sequences present in the transcriptome of this species, including single-copy loci and a representative distribution of functional groups. In contrast, the coverage of variable sites, observation of heterozygosity, and overlap among different libraries are all highly dependent on sequencing effort. Nevertheless, the information gained from overlapping regions was informative regarding coarse population structure and variation across our small number of population samples, providing the first genetic evidence in support of hypothesized invasion scenarios.
Tissue-Specific Transcriptomics in the Field CricketTeleogryllus oceanicus
Authors: Bailey Nathan W , Veltsos Paris , Tan Yew-Foon , Millar A Harvey , Ritchie Michael G , Simmons Leigh W
Published: February 2013

Field crickets (family Gryllidae) frequently are used in studies of behavioral genetics, sexual selection, and sexual conflict, but there have been no studies of transcriptomic differences among different tissue types. We evaluated transcriptome variation among testis, accessory gland, and the remaining whole-body preparations from males of the field cricket, Teleogryllus oceanicus. Non-normalized cDNA libraries from each tissue were sequenced on the Roche 454 platform, and a master assembly was constructed using testis, accessory gland, and whole-body preparations. A total of 940,200 reads were assembled into 41,962 contigs, to which 36,856 singletons (reads not assembled into a contig) were added to provide a total of 78,818 sequences used in annotation analysis. A total of 59,072 sequences (75%) were unique to one of the three tissues. Testis tissue had the greatest proportion of tissue-specific sequences (62.6%), followed by general body (56.43%) and accessory gland tissue (44.16%). We tested the hypothesis that tissues expressing gene products expected to evolve rapidly as a result of sexual selection—testis and accessory gland—would yield a smaller proportion of BLASTx matches to homologous genes in the model organism Drosophila melanogaster compared with whole-body tissue. Uniquely expressed sequences in both testis and accessory gland showed a significantly lower rate of matching to annotated D. melanogaster genes compared with those from general body tissue. These results correspond with empirical evidence that genes expressed in testis and accessory gland tissue are rapidly evolving targets of selection.
A Compendium of Caenorhabditis elegans RNA Binding Proteins Predicts Extensive Regulation at Multiple Levels
Authors: Tamburino Alex M , Ryder Sean P , Walhout Albertha J M
Published: February 2013

Gene expression is regulated at multiple levels, including transcription and translation, as well as mRNA and protein stability. Although systems-level functions of transcription factors and microRNAs are rapidly being characterized, few studies have focused on the posttranscriptional gene regulation by RNA binding proteins (RBPs). RBPs are important to many aspects of gene regulation. Thus, it is essential to know which genes encode RBPs, which RBPs regulate which gene(s), and how RBP genes are themselves regulated. Here we provide a comprehensive compendium of RBPs from the nematode Caenorhabditis elegans (wRBP1.0). We predict that as many as 887 (4.4%) of C. elegans genes may encode RBPs ~250 of which likely function in a gene-specific manner. In addition, we find that RBPs, and most notably gene-specific RBPs, are themselves enriched for binding and modification by regulatory proteins, indicating the potential for extensive regulation of RBPs at many different levels. wRBP1.0 will provide a significant contribution toward the comprehensive delineation of posttranscriptional regulatory networks and will provide a resource for further studies regulation by RBPs.
Redundant Canonical and NoncanonicalCaenorhabditis elegansp21-Activated Kinase Signaling Governs Distal Tip Cell Migrations
Authors: Peters Eldon C , Gossett Andrea J , Goldstein Bob , Der Channing J , Reiner David J
Published: February 2013

p21-activated kinases (Paks) are prominent mediators of Rac/Cdc42-dependent and -independent signaling and regulate signal transduction and cytoskeletal-based cell movements. We used the reproducible migrations of the Caenorhabditis elegans gonadal distal tip cells to show that two of the three nematode Pak proteins, MAX-2 and PAK-1, function redundantly in regulation of cell migration but are regulated by very different mechanisms. First, we suggest that MAX-2 requires CED-10/Rac function and thus functions canonically. Second, PIX-1 and GIT-1 function in the same role as PAK-1, and PAK-1 interaction with PIX-1 is required for PAK-1 activity; thus, PAK-1 functions noncanonically. The human Pak-Pix-Git complex is central to noncanonical Pak signaling and requires only modest Rac/CDC-42 input. Unlike the human complex, our results suggest that the C. elegans Pak-Pix-Git complex requires PAK-1 kinase domain activity. This study delineates signaling network relationships in this cell migration model, thus providing potential further mechanistic insights and an assessment of total Pak contribution to cell migration events.
Caenorhabditis elegans POT-1 and POT-2 Repress Telomere Maintenance Pathways
Authors: Shtessel Ludmila , Lowden Mia Rochelle , Cheng Chen , Simon Matt , Wang Kyle , Ahmed Shawn
Published: February 2013

Telomeres are composed of simple tandem DNA repeats that protect the ends of linear chromosomes from replicative erosion or inappropriate DNA damage response mechanisms. The mammalian Protection Of Telomeres (POT1) protein interacts with single-stranded telomeric DNA and can exert positive and negative effects on telomere length. Of four distinct POT1 homologs in the roundworm Caenorhabditis elegans, deficiency for POT-1 or POT-2 resulted in progressive telomere elongation that occurred because both proteins negatively regulate telomerase. We created a POT-1::mCherry fusion protein that forms discrete foci at C. elegans telomeres, independent of POT-2, allowing for live analysis of telomere dynamics. Transgenic pot-1::mCherry repressed telomerase in pot-1 mutants. Animals deficient for pot-1, but not pot-2, displayed mildly enhanced telomere erosion rates in the absence of the telomerase reverse transcriptase, trt-1. However, trt-1; pot-1 double mutants exhibited delayed senescence in comparison to trt-1 animals, and senescence was further delayed in trt-1; pot-2; pot-1 triple mutants, some of which survived robustly in the absence of telomerase. Our results indicate that POT-1 and POT-2 play independent roles in suppressing a telomerase-independent telomere maintenance pathway but may function together to repress telomerase.
RNA Polymerase II Mutations Conferring Defects in Poly(A) Site Cleavage and Termination inSaccharomyces cerevisiae
Authors: Kubicek Charles E , Chisholm Robert D , Takayama Sachiko , Hawley Diane K
Published: February 2013

Transcription termination by RNA polymerase (Pol) II is an essential but poorly understood process. In eukaryotic nuclei, the 3′ ends of mRNAs are generated by cleavage and polyadenylation, and the same sequence elements that specify that process are required for downstream release of the polymerase from the DNA. Although Pol II is known to bind proteins required for both events, few studies have focused on Pol II mutations as a means to uncover the mechanisms that couple polyadenylation and termination. We performed a genetic screen in the yeast Saccharomyces cerevisiae to isolate mutations in the N-terminal half of Rpb2, the second largest Pol II subunit, that conferred either a decreased or increased response to a well-characterized poly(A) site. Most of the mutant alleles encoded substitutions affecting either surface residues or conserved active site amino acids at positions important for termination by other RNA polymerases. Reverse transcription polymerase chain reaction experiments revealed that transcript cleavage at the poly(A) site was impaired in both classes of increased readthrough mutants. Transcription into downstream sequences beyond where termination normally occurs was also probed. Although most of the tested readthrough mutants showed a reduction in termination concomitant with the reduced poly(A) usage, these processes were uncoupled in at least one mutant strain. Several rpb2 alleles were found to be similar or identical to published mutants associated with defective TFIIF function. Tests of these and additional mutations known to impair Rpb2−TFIIF interactions revealed similar decreased readthrough phenotypes, suggesting that TFIIF may have a role in 3′ end formation and termination.
Saccharomyces cerevisiaeGenetics Predicts Candidate Therapeutic Genetic Interactions at the Mammalian Replication Fork
Authors: van Pel Derek M , Stirling Peter C , Minaker Sean W , Sipahimalani Payal , Hieter Philip
Published: February 2013

The concept of synthetic lethality has gained popularity as a rational guide for predicting chemotherapeutic targets based on negative genetic interactions between tumor-specific somatic mutations and a second-site target gene. One hallmark of most cancers that can be exploited by chemotherapies is chromosome instability (CIN). Because chromosome replication, maintenance, and segregation represent conserved and cell-essential processes, they can be modeled effectively in simpler eukaryotes such as Saccharomyces cerevisiae. Here we analyze and extend genetic networks of CIN cancer gene orthologs in yeast, focusing on essential genes. This identifies hub genes and processes that are candidate targets for synthetic lethal killing of cancer cells with defined somatic mutations. One hub process in these networks is DNA replication. A nonessential, fork-associated scaffold, CTF4, is among the most highly connected genes. As Ctf4 lacks enzymatic activity, potentially limiting its development as a therapeutic target, we exploited its function as a physical interaction hub to rationally predict synthetic lethal interactions between essential Ctf4-binding proteins and CIN cancer gene orthologs. We then validated a subset of predicted genetic interactions in a human colorectal cancer cell line, showing that siRNA-mediated knockdown of MRE11A sensitizes cells to depletion of various replication fork-associated proteins. Overall, this work describes methods to identify, predict, and validate in cancer cells candidate therapeutic targets for tumors with known somatic mutations in CIN genes using data from yeast. We affirm not only replication stress but also the targeting of DNA replication fork proteins themselves as potential targets for anticancer therapeutic development.
Genome-Wide Copy Number Variant Analysis in Inbred Chickens Lines With Different Susceptibility to Marek’s Disease
Authors: Luo Juan , Yu Ying , Mitra Apratim , Chang Shuang , Zhang Huanmin , Liu George , Yang Ning , Song Jiuzhou
Published: February 2013

Breeding of genetically resistant chickens to Marek’s disease (MD) is a vital strategy to poultry health. To find the markers underlying the genetic resistance to MD, copy number variation (CNV) was examined in inbred MD-resistant and -susceptible chicken lines. A total of 45 CNVs were found in four lines of chickens, and 28 were potentially involved in immune response and cell proliferation, etc. Importantly, two CNVs related with MD resistance were transmitted to descendent recombinant congenic lines that differ in susceptibility to MD. Our findings may lead to better strategies for genetic improvement of disease resistance in poultry.
Effect of Iron Deficiency Anemia in Pregnancy on Child Mental Development in Rural China
Authors: Chang Suying , Zeng Lingxia , Brouwer Inge D. , Kok Frans J. , Yan Hong
Published: February 2013

OBJECTIVE:

To determine the impact of iron deficiency anemia (IDA) in pregnancy on young child development.

METHODS:

A 2-year follow-up of 850 children born to women who participated in a double-blind cluster randomized controlled trial of prenatal micronutrient supplementation in western rural China. These women were randomly assigned to receive either daily folic acid, iron/folic acid (60 mg iron), or multiple micronutrients (with 30 mg iron) during pregnancy. Children were categorized into the prenatal-IDA and prenatal–non-IDA groups based on the mother’s hemoglobin in the third trimester. Each group contained 3 subgroups based on mother’s treatment: folic acid, iron/folic acid, and multiple micronutrients. Bayley scales of infant development were administered to the children to assess their development at 3, 6, 12, 18, and 24 months of age.

RESULTS:

Compared with the prenatal–non-IDA group, the prenatal-IDA group showed a significantly lower mental development index at 12, 18, and 24 months of age. The adjusted mean difference was 5.8 (95% confidence interval [CI], 1.1–10.5), 5.1 (95% CI, 1.2–9.0), and 5.3 (95% CI, 0.9–9.7), respectively. Further analysis showed that the mental development indexes in the prenatal-IDA group and prenatal–non-IDA group were similar with supplementation of iron/folic acid but were significantly lower in the prenatal-IDA group with supplementation of folic acid or multiple micronutrients.

CONCLUSIONS:

Prenatal IDA in the third trimester is associated with mental development of the child. However, prenatal supplementation with sufficient iron protects child development even when the woman’s IDA was not properly corrected in pregnancy.
Cost-Effectiveness of the School-Based Asthma Therapy (SBAT) Program
Authors: Noyes Katia , Bajorska Alina , Fisher Susan , Sauer Joseph , Fagnano Maria , Halterman Jill S.
Published: February 2013

BACKGROUND AND OBJECTIVE:

Impoverished urban children suffer disproportionately from asthma and underuse preventive asthma medications. The objective of this study was to examine cost-effectiveness (CE) of the School-Based Asthma Therapy (SBAT) program compared with usual care (UC).

METHODS:

The analysis was based on the SBAT trial, including 525 children aged 3 to 10 years attending urban preschool or elementary school who were randomized to either UC or administration of 1 dose of preventive asthma medication at school by the school nurse each school day. The primary outcome was the mean number of symptom-free days (SFDs). The impact of the intervention on medical costs was estimated by using parent-reported child health services utilization data and average national reimbursement rates. We estimated the cost of running the program using wages for program staff. Productivity costs were estimated by using value of parent lost time due to child illness. CE of the SBAT program compared with UC was evaluated based on the incremental CE ratio.

RESULTS:

The health benefit of the intervention was equal to ∼158 SFD gained per each 30-day period (P < .05) per 100 children. The programmatic expenses summed to an extra $4822 per 100 children per month. The net saving due to the intervention (reduction in medical costs and parental productivity, and improvement in school attendance) was $3240, resulting in the incremental cost-savings difference of $1583 and CE of $10 per 1 extra SFD gained.

CONCLUSIONS:

The SBAT was effective and cost-effective in reducing symptoms in urban children with asthma compared with other existing programs.
US Prevalence and Trends in Tobacco Smoke Exposure Among Children and Adolescents With Asthma
Authors: Kit Brian K. , Simon Alan E. , Brody Debra J. , Akinbami Lara J.
Published: February 2013

OBJECTIVE:

To examine exposure to tobacco smoke products (TSPs), environmental tobacco smoke (ETS), and in-home smoke among youth with asthma in the United States.

METHODS:

Nationally representative, cross-sectional data from 2250 youth aged 4 to 19 years with current asthma in the 1988–1994, 1999–2004, and 2005–2010 National Health and Nutrition Examination Survey (NHANES) were analyzed. Outcomes were use of TSPs (serum cotinine level >10 ng/mL or self-reported recent use of cigarettes, cigars, or pipes) and, among non-TSP users, ETS exposure (serum cotinine ≥0.05 ng/mL) and in-home smoke exposure (reported). Multiple logistic regression analyses assessed the associations between the outcomes and age, gender, race/ethnicity, and family income.

RESULTS:

Among adolescents (aged 12–19 years) with asthma in 2005–2010, 17.3% reported TSP use. Among youth (aged 4–19 years) with asthma who did not use TSPs, 53.2% were exposed to ETS and 17.6% had in-home smoke exposure. Among low-income youth, 70.1% and 28.1% had exposure to ETS and in-home smoke, respectively. After controlling for sociodemographic factors, higher prevalence of exposure to ETS and in-home smoke persisted among low-income youth. Between 1988–1994 and 2005–2010, there was a decline in ETS and in-home smoke exposure (both P < .001).

CONCLUSIONS:

ETS exposure among youth with asthma declined between 1988–1994 and 2005–2010, but a majority remained exposed in 2005–2010, with higher exposure among low-income youth. More than 1 in 6 youth with asthma in 2005–2010 were exposed to in-home smoke and a similar portion of adolescents used TSPs.
Comparative Effectiveness of Interventions for Children Exposed to Nonrelational Traumatic Events
Authors: Forman-Hoffman Valerie L. , Zolotor Adam J. , McKeeman Joni L. , Blanco Roberto , Knauer Stefanie R. , Lloyd Stacey W. , Fraser Jenifer Goldman , Viswanathan Meera
Published: February 2013

OBJECTIVES:

To assess the effectiveness of interventions targeting traumatic stress among children exposed to nonrelational traumatic events (eg, accidents, natural disasters, war).

METHODS:

We assessed research on psychological and pharmacological therapy as part of an Agency for Healthcare Research and Quality–commissioned comparative effectiveness review. We conducted focused searches of Medline, Cochrane Library, Embase, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, International Pharmaceutical Abstracts, and Web of Science. Two trained reviewers independently selected, extracted data from, and rated the risk of bias of relevant trials and systematic reviews. We used qualitative rather than quantitative analysis methods because of statistical heterogeneity, insufficient numbers of similar studies, and variation in outcome reporting.

RESULTS:

We found a total of 21 trials and 1 cohort study of medium or low risk of bias from our review of 6647 unduplicated abstracts. We generally did not find studies that attempted to replicate findings of effective interventions. In the short term, no pharmacotherapy intervention demonstrated efficacy, and only a few psychological treatments (each with elements of cognitive behavioral therapy) showed benefit. The body of evidence provides little insight into how interventions to treat children exposed to trauma might influence healthy long-term development.

CONCLUSIONS:

Our findings serve as a call to action: Psychotherapeutic intervention may be beneficial relative to no treatment in children exposed to traumatic events. Definitive guidance, however, requires far more research on the comparative effectiveness of interventions targeting children exposed to nonrelational traumatic events.
Effect of Model Parameters on Finite Element Analysis of Micromotions in Implant Dentistry
Authors: Winter Werner , Klein Daniel , Karl Matthias
Published: February 2013

Micromotion between dental implant and bony socket may occur in immediate-loading scenarios. Excessive micromotion surpassing an estimated threshold of approximately 150 μm may result in fibrous encapsulation instead of osseointegration of the implant. As finite element analysis (FEA) has been applied in this field, it was the aim of this study to evaluate the effect of implant-related variables and modeling parameters on simulating micromotion phenomena. Three-dimensional FEA models representing a dental implant within a bony socket were constructed and used for evaluating micromotion (global displacement) and stress transfer (von Mises equivalent stress) at the implant-bone interface when static loads were applied. A parametric study was conducted altering implant geometry (cylinder, screw), direction of loading (axial, horizontal), healing status (immediate implant, osseointegrated implant), and contact type between implant and bone (friction free, friction, rigid). Adding threads to a cylindrically shaped implant as well as changing the contact type between implant and bone from friction free to rigid led to a reduction of implant displacement. On the other hand, reducing the elastic modulus of bone for simulating an immediate implant caused a substantial increase in displacement of the implant. Altering the direction of loading from axial to horizontal caused a change in loading patterns from uniform loading surrounding the whole implant to localized loading in the cervical area. Implant-related and bone-related factors determine the degree of micromotion of a dental implant during the healing phase, which should be considered when choosing a loading protocol.
Horizontal Augmentation Through the Ridge-Split Procedure: A Predictable Surgical Modality in Implant Reconstruction
Authors: Tolstunov Len , Hicke Bruce
Published: February 2013

Among alveolar ridge augmentation techniques, the ridge-split procedure demonstrates many benefits, including no need for a second (donor) surgical site, rare risk of inferior alveolar nerve injury, and less pain and swelling, and others. Lateral bone augmentation through the ridge-split works best in a localized lateral bony defect intended for 1 or 2 implants and where the ridge is vertically intact. In this article, the authors present a detailed description of the implant-driven technique of alveolar ridge-split procedure in small and large bone deficiencies, in maxilla and mandible, supplemented by multiple photographs. The authors emphasize the need for careful manipulation of the thin ridge based on knowledge of precise surgical principles and stress that a practitioner needs specialized training and experience to perform this type of alveolar bone augmentation.
Unique critical state characteristics in granular media considering fabric anisotropy
Authors: ZHAO J. , GUO N.
Published: February 2013

The concept of the critical state in granular soils needs to make proper reference to the fabric structure that develops at critical state. This study identifies a unique property associated with the fabric structure relative to the stresses at critical state. A unique relationship between the mean effective stress and a fabric anisotropy parameter, K, defined by the first joint invariant of the deviatoric stress tensor and the deviatoric fabric tensor, is found at critical state, and is path-independent. Numerical simulations using the discrete-element method under different loading conditions and intermediate principal stress ratios identify a unique power law for this relationship. Based on the findings, a new definition of critical state for granular media is proposed. In addition to the conditions of constant stress and unique void ratio required by the conventional critical state concept, the new definition imposes the additional constraint that K reaches a unique value at critical state. A unique spatial critical state curve in the three-dimensional space K–e–p′ is found for a granular medium, the projection of which onto the e–p′ plane turns out to be the conventional critical state line. The new critical state concept provides an important reference state for a soil to reach, based on which the key concepts in the constitutive modelling of granular media, including the choice of state parameters, dilatancy relation and non-coaxiality, are reassessed, and future exploratory topics are discussed.
Behaviour of air-entrained concrete under triaxial compression
Authors: Shang Huai-shuai , Song Yu-pu , Sun Hai-ming
Published: February 2013

The properties of air-entrained concrete under triaxial compressive loads with seven stress ratios were investigated. The strength and deformation in three principal directions were recorded and the crack patterns and failure modes were examined. Based on the test data, the influence of the stress ratio α1 = σ1:σ3 and the middle stress ratio α2 = σ2:σ3 on the ultimate compressive strength σ3 is analysed. The characteristics of the stress–strain relationship and the influence of intermediate principal stress on the peak stress and strain are analysed. The stress–volume strain relationships of air-entrained concrete under triaxial compression are discussed. This work will serve as a reference for the finite-element analysis and maintenance of air-entrained concrete structures in cold northern regions subject to complex load.
Constant properties of plant–frugivore networks despite fluctuations in fruit and bird communities in space and time
Authors: Plein Michaela , Längsfeld Laura , Neuschulz Eike Lena , Schultheiß Christina , Ingmann Lili , Töpfer Till , Böhning-Gaese Katrin , Schleuning Matthias
Published: February 2013

Human‐induced changes in anthropogenic landscapes are a predominant threat to biodiversity and have been documented to affect mutualistic interactions between plants and animals, such as avian seed dispersal. Interactions between fleshy‐fruited plants and frugivorous birds are highly seasonal in temperate ecosystems. Nevertheless, combined effects of landscape modification and seasonal variation on plant–frugivore interactions have never been assessed from a network perspective. Here, we present the first study that simultaneously investigates effects of landscape modification and seasonal variation on plant–frugivore interactions and on functional and interaction diversity of plant–frugivore networks. We recorded visitation rates of 39 frugivorous bird species to 28 fruiting‐plant species in Central Germany from early summer to late autumn in hedgerows within three landscape types arranged along a gradient of decreasing anthropogenic modification and increasing structural diversity (i.e., farmland, orchard, forest edge). We analyzed how species richness, abundance, and community composition, as well as functional and interaction diversity of fruiting plants and frugivorous birds changed with landscape type, fruit availability, and season. We found that visitation rates of frugivorous birds were lower in farmland, but only in summer. In autumn, visitation rates were similar in all landscape types and strongly increased with increasing local fruit availability. The functional diversity of fruits and frugivorous birds and their interaction diversity remained surprisingly constant in all landscape types. Due to seasonal changes in communities of fruiting plants and frugivorous birds, functional dispersion of fruiting plants was lower in autumn than in summer, whereas functional richness and dispersion of frugivorous birds was higher in autumn than in summer. Our results indicate that seasonal changes in fruit availability influence the abundance of frugivorous birds along gradients of structural diversity at the landscape scale. Although seasonal fluctuations influenced the functional diversity of avian frugivore communities, we found constant interaction diversity of plant–frugivore networks in space and time, probably due to the functional redundancy of frugivorous birds. These findings indicate a high robustness of avian frugivory to moderate levels of human‐induced landscape modification in temperate ecosystems and call for studies testing the generality of these findings for ultimate avian seed dispersal functions.