bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the global transcriptome for Pyropia haitanensis(Bangiales, Rhodophyta) and development of cSSR markers
Authors: Xie Chaotian , Li Bing , Xu Yan , Ji Dehua , Chen Changsheng 
Published: February 2013

Abstract

Background

Pyropia haitanensis is an economically important mariculture crop in China and is also valuable in life science research. However, the lack of genetic information of this organism hinders the understanding of the molecular mechanisms of specific traits. Thus, high-throughput sequencing is needed to generate a number of transcriptome sequences to be used for gene discovery and molecular marker development.

Results
In this study, high-throughput sequencing was used to analyze the global transcriptome of P. haitanensis. Approximately 103 million 90 bp paired-end reads were generated using an Illumina HiSeq 2000. De novo assembly with paired-end information yielded 24,575 unigenes with an average length of 645 bp. Based on sequence similarity searches with known proteins, a total of 16,377 (66.64%) genes were identified. Of these annotated unigenes, 5,471 and 9,168 unigenes were assigned to gene ontology and clusters of orthologous groups, respectively. Searching against the KEGG database indicated that 12,167 (49.51%) unigenes mapped to 124 KEGG pathways. Among the carbon fixation pathways, almost all the essential genes related to the C3- and C4-pathways for P. haitanensis were discovered. Significantly different expression levels of three key genes (Rubisco, PEPC and PEPCK) in different lifecycle stages of P. haitanensis indicated that the carbon fixation pathway in the conchocelis and thallus were different, and the C4-like pathway might play important roles in the conchocelis stage. In addition, 2,727 cSSRs loci were identified in the unigenes. Among them, trinucleotide SSRs were the dominant repeat motif (87.17%, 2,377) and GCC/CCG motifs were the most common repeats (60.07%, 1,638). High quality primers to 824 loci were designed and 100 primer pairs were randomly evaluated in six strains of P. haitanensis. Eighty-seven primer pairs successfully yielded amplicons.

Conclusion
This study generated a large number of putative P. haitanensis transcript sequences, which can be used for novel gene discovery and gene expression profiling analyses under different physiological conditions. A number of the cSSR markers identified can be used for molecular markers and will facilitate marker assisted selection in P. haitanensis breeding. These sequences and markers will provide valuable resources for further P. haitanensis studies.
Identification of genes involved in serum tolerance in the clinical strain Cronobacter sakazakiiES5
Authors: Schwizer Sarah , Tasara Taurai , Zurfluh Katrin , Stephan Roger , Lehner Angelika 
Published: February 2013

Abstract

Background

Cronobacter spp. are opportunistic pathogens that can cause septicemia and infections of the central nervous system primarily in premature, low-birth weight and/or immune-compromised neonates. Serum resistance is a crucial virulence factor for the development of systemic infections, including bacteremia. It was the aim of the current study to identify genes involved in serum tolerance in a selected Cronobacter sakazakii strain of clinical origin.

Results
Screening of 2749 random transposon knock out mutants of a C. sakazakii ES 5 library for modified serum tolerance (compared to wild type) revealed 10 mutants showing significantly increased/reduced resistance to serum killing. Identification of the affected sites in mutants displaying reduced serum resistance revealed genes encoding for surface and membrane proteins as well as regulatory elements or chaperones. By this approach, the involvement of the yet undescribed Wzy_C superfamily domain containing coding region in serum tolerance was observed and experimentally confirmed. Additionally, knock out mutants with enhanced serum tolerance were observed. Examination of respective transposon insertion loci revealed regulatory (repressor) elements, coding regions for chaperones and efflux systems as well as the coding region for the protein YbaJ. Real time expression analysis experiments revealed, that knock out of the gene for this protein negatively affects the expression of the fimA gene, which is a key structural component of the formation of fimbriae. Fimbriae are structures of high immunogenic potential and it is likely that absence/truncation of the ybaJ gene resulted in a non-fimbriated phenotype accounting for the enhanced survival of this mutant in human serum.

Conclusion
By using a transposon knock out approach we were able to identify genes involved in both increased and reduced serum tolerance in Cronobacter sakazakii ES5. This study reveals first insights in the complex nature of serum tolerance of Cronobacter spp.
Single cell transcriptomic analysis of prostate cancer cells
Authors: Welty Christopher J , Coleman Ilsa , Coleman Roger , Lakely Bryce , Xia Jing , Chen Shu , Gulati Roman , Larson Sandy R , Lange Paul H , Montgomery Bruce , Nelson Peter S , Vessella Robert L , Morrissey Colm 
Published: February 2013

Abstract

Background
The ability to interrogate circulating tumor cells (CTC) and disseminated tumor cells (DTC) is restricted by the small number detected and isolated (typically <10). To determine if a commercially available technology could provide a transcriptomic profile of a single prostate cancer (PCa) cell, we clonally selected and cultured a single passage of cell cycle synchronized C4-2B PCa cells. Ten sets of single, 5-, or 10-cells were isolated using a micromanipulator under direct visualization with an inverted microscope. Additionally, two groups of 10 individual DTC, each isolated from bone marrow of 2 patients with metastatic PCa were obtained. RNA was amplified using the WT-Ovation™ One-Direct Amplification System. The amplified material was hybridized on a 44K Whole Human Gene Expression Microarray. A high stringency threshold, a mean Alexa Fluor® 3 signal intensity above 300, was used for gene detection. Relative expression levels were validated for select genes using real-time PCR (RT-qPCR).

Results
Using this approach, 22,410, 20,423, and 17,009 probes were positive on the arrays from 10-cell pools, 5-cell pools, and single-cells, respectively. The sensitivity and specificity of gene detection on the single-cell analyses were 0.739 and 0.972 respectively when compared to 10-cell pools, and 0.814 and 0.979 respectively when compared to 5-cell pools, demonstrating a low false positive rate. Among 10,000 randomly selected pairs of genes, the Pearson correlation coefficient was 0.875 between the single-cell and 5-cell pools and 0.783 between the single-cell and 10-cell pools. As expected, abundant transcripts in the 5- and 10-cell samples were detected by RT-qPCR in the single-cell isolates, while lower abundance messages were not. Using the same stringency, 16,039 probes were positive on the patient single-cell arrays. Cluster analysis showed that all 10 DTC grouped together within each patient.

Conclusions
A transcriptomic profile can be reliably obtained from a single cell using commercially available technology. As expected, fewer amplified genes are detected from a single-cell sample than from pooled-cell samples, however this method can be used to reliably obtain a transcriptomic profile from DTC isolated from the bone marrow of patients with PCa.
The eCALM Trial-eTherapy for cancer appLying mindfulness: online mindfulness-based cancer recovery program for underserved individuals living with cancer in Alberta: protocol development for a randomized wait-list controlled clinical trial
Authors: Zernicke Kristin A , Campbell Tavis S , Speca Michael , McCabe-Ruff Kelley , Flowers Steven , Dirkse Dale A , Carlson Linda E 
Published: February 2013

Abstract

Background
Elevated stress can exacerbate cancer symptom severity, and after completion of primary cancer treatments, many individuals continue to have significant distress. Mindfulness-Based Cancer Recovery (MBCR) is an 8-week group psychosocial intervention consisting of training in mindfulness meditation and yoga designed to mitigate stress, pain, and chronic illness. Efficacy research shows face-to-face (F2F) MBCR programs have positive benefits for cancer patients; however barriers exist that impede participation in F2F groups. While online MBCR groups are available to the public, none have been evaluated. Primary objective: determine whether underserved patients are willing to participate in and complete an online MBCR program. Secondary objectives: determine whether online MBCR will mirror previous efficacy findings from F2F MBCR groups on patient-reported outcomes.

Method/design
The study includes cancer patients in Alberta, exhibiting moderate distress, who do not have access to F2F MBCR. Participants will be randomized to either online MBCR, or waiting for the next available group. An anticipated sample size of 64 participants will complete measures online pre and post treatment or waiting period. Feasibility will be tracked through monitoring numbers eligible and participating through each stage of the protocol.

Discussion
47 have completed/completing the intervention. Data suggest it is possible to conduct a randomized waitlist controlled trial of online MBCR to reach underserved cancer survivors.

Trial registration
Clinical Trials.gov Identifier: NCT01476891
Spectral broadening effects of high-power amplifiers in MIMO–OFDM relaying channels
Authors: Ahmad Ishtiaq , Sulyman Ahmed Iyanda , Alsanie Abdulhameed , Alasmari Awad Kh , Alshebeili Saleh A 
Published: February 2013

Abstract
The combination of MIMO–OFDM is a very attractive solution for broadband wireless services. Thus, the two prominent fourth-generation (4G) cellular systems, WiMAX and LTE-advanced, have both adopted MIMO–OFDM transmission at the physical layer. OFDM signal however suffers from nonlinear distortions when passed through high-power amplifier (HPA) at the RF stage. This nonlinear distortion introduces out-of-band spectral broadening and in-band distortions on the transmitted signals. 4G cellular standards have placed strict limits on the allowable spectral broadening in their spectrum mask specifications, to insure that data transmission on a given channel is not interfering significantly with an adjacent channel user. In this article, we characterize the out-of-band spectral broadening introduced by HPA when MIMO–OFDM signals are transmitted over multiple relaying channels. Expressions for the power spectral density of MIMO–OFDM signals are derived over multiple relay channels, and the cumulative effects of HPA on the spectrum of the transmitted signals are estimated. It is shown that depending on the number of relays and the relaying configuration employed, it may happen that a transmitted MIMO–OFDM signal with the transmit spectrum mask initially within the allowable set limit at the source node arrives at the destination violating this limit due to the cumulative effects of the multiple HPA’s in a multihop relaying channel.
Pulmonary metastasis of a papillary thyroid carcinoma and primary lung adenocarcinoma: two coincident carcinomas at the same location
Authors: Xue Liyan , Luan Zhonghua , Liu Ying , Zou Shuangmei , Jiang Jun , Wu Ning , Lu Ning , Lin Dongmei 
Published: February 2013

Abstract
Tumor-to-tumor metastasis is a fairly rare phenomenon. The lung cancers are the most common donors, but are exceedingly rare as recipients. Here we report a case of a lung adenocarcinoma acting as the recipient of papillary thyroid carcinoma, with multiple spreading foci of the two cancers in the lung simultaneously. The morphology and immunohistochemisty (Napsin-A, Thyroglobulin) are very important in differential diagnosis of lung primary adenocarcinoma and metastatic papillary thyroid carcinoma.

Virtual Slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2069496615891134
Production of bacterial cellulose and enzyme from waste fiber sludge
Authors: Cavka Adnan , Guo Xiang , Tang Shui-Jia , Winestrand Sandra , Jönsson Leif J , Hong Feng 
Published: February 2013

Abstract

Background
Bacterial cellulose (BC) is a highly crystalline and mechanically stable nanopolymer, which has excellent potential as a material in many novel applications, especially if it can be produced in large amounts from an inexpensive feedstock. Waste fiber sludge, a residue with little or no value, originates from pulp mills and lignocellulosic biorefineries. A high cellulose and low lignin content contributes to making the fiber sludge suitable for bioconversion, even without a thermochemical pretreatment step. In this study, the possibility to combine production of BC and hydrolytic enzymes from fiber sludge was investigated. The BC was characterized using field-emission scanning electron microscopy and X-ray diffraction analysis, and its mechanical properties were investigated.

Results
Bacterial cellulose and enzymes were produced through sequential fermentations with the bacterium Gluconacetobacter xylinus and the filamentous fungus Trichoderma reesei. Fiber sludges from sulfate (SAFS) and sulfite (SIFS) processes were hydrolyzed enzymatically without prior thermochemical pretreatment and the resulting hydrolysates were used for BC production. The highest volumetric yields of BC from SAFS and SIFS were 11 and 10 g/L (DW), respectively. The BC yield on initial sugar in hydrolysate-based medium reached 0.3 g/g after seven days of cultivation. The tensile strength of wet BC from hydrolysate medium was about 0.04 MPa compared to about 0.03 MPa for BC from a glucose-based reference medium, while the crystallinity was slightly lower for BC from hydrolysate cultures. The spent hydrolysates were used for production of cellulase with T. reesei. The cellulase activity (CMCase activity) in spent SAFS and SIFS hydrolysates reached 5.2 U/mL (87 nkat/mL), which was similar to the activity level obtained in a reference medium containing equal amounts of reducing sugar.

Conclusions
It was shown that waste fiber sludge is a suitable raw material for production of bacterial cellulose and enzymes through sequential fermentation. The concept studied offers efficient utilization of the various components in fiber sludge hydrolysates and affords a possibility to combine production of two high value-added products using residual streams from pulp mills and biorefineries. Cellulase produced in this manner could tentatively be used to hydrolyze fresh fiber sludge to obtain medium suitable for production of BC in the same biorefinery.
Proposed roadmap to stepwise integration of genetics in family medicine and clinical research
Authors: Houwink Elisa JF , Sollie Annet W , Numans Mattijs E , Cornel Martina C 
Published: February 2013

AbstractWe propose A step‐by‐step roadmap to integrate genetics in the Electronic Patient Record in Family Medicine and clinical research. This could make urgent operationalization of readily available genetic knowledge feasible in clinical research and consequently improved medical care.Improving genomic literacy by training and education is needed first. The second step is the improvement of the possibilities to register the family history in such a way that queries can identify patients at risk. Adding codes to the ICPC chapters “A21 Personal/family history of malignancy” and “A99 Disease carrier not described further” is proposed. Multidisciplinary guidelines for referral must be unambiguous. Electronical patient records need possibilities to add (new) family history information, including links between individuals who are family members. Automatic alerts should help general practitioners to recognize patients at risk who satisfy referral criteria. We present a familial breast cancer case with a BRCA1 mutation as an example.
Does land abandonment decrease species richness and abundance of plants and animals in Mediterranean pastures, arable lands and permanent croplands?
Authors: Plieninger Tobias , Gaertner Mirijam , Hui Cang , Huntsinger Lynn 
Published: February 2013

AbstractBackgroundObscured by the more prevalent discussion of intensification and expansion of agricultural land, the impacts of the abandonment of many grasslands and croplands of the world in recent decades have received limited attention in the literature. Land abandonment is a common phenomenon in the Mediterranean Basin, a global biodiversity hotspot, but little is known about the impacts of this process on biodiversity. To upscale existing case-study insight to a Pan-Mediterranean level, we plan to perform a systematic review of the effects of land abandonment on plant and animal richness and abundance in pastures, arable lands and permanent crops of the Mediterranean Basin. In particular, we ask (1) which taxonomic groups are most affected by land abandonment; (2) whether different spatial and temporal scales of studies influence species richness and abundance outcomes; (3) whether previous land use and current anthropogenic impacts on abandoned lands determine differences in the number and abundance of species; and (4) whether landscape context modifies the impacts.MethodsOur review will be based on searching scientific databases as well as the internet for empirical studies on the effects of land abandonment on biodiversity in the Mediterranean Basin. Study selection follows a three-stage process and includes study quality assessment. Extracted data will be synthesized through meta-analysis. Results will be presented in the form of a quantitative (e.g. figures indicating effect sizes, tables summarizing heterogeneity statistics) and narrative synthesis. Additional aspects will be addressed through meta-regression and sub-group analyses.
Developmental Programming: Postnatal Steroids Complete Prenatal Steroid Actions to Differentially Organize the GnRH Surge Mechanism and Reproductive Behavior in Female Sheep
Authors: Jackson Leslie M. , Mytinger Andrea , Roberts Eila K. , Lee Theresa M. , Foster Douglas L. , Padmanabhan Vasantha , Jansen Heiko T. 
Published: February 2013

AbstractIn female sheep, estradiol (E2) stimulates the preovulatory GnRH/LH surge and receptive behavior, whereas progesterone blocks these effects. Prenatal exposure to testosterone disrupts both the positive feedback action of E2 and sexual behavior although the mechanisms remain unknown. The current study tested the hypothesis that both prenatal and postnatal steroids are required to organize the surge and sex differences in reproductive behavior. Our approach was to characterize the LH surge and mating behavior in prenatally untreated (Control) and testosterone-treated (T) female sheep subsequently exposed to one of three postnatal steroid manipulations: endogenous E2, excess E2 from a chronic implant, or no E2 due to neonatal ovariectomy (OVX). All females were then perfused at the time of the expected surge and brains processed for estrogen receptor and Fos immunoreactivity. None of the T females exposed postnatally to E2 exhibited an E2-induced LH surge, but a surge was produced in five of six T/OVX and all Control females. No surges were produced when progesterone was administered concomitantly with E2. All Control females were mounted by males, but significantly fewer T females were mounted by a male, including the T/OVX females that exhibited LH surges. The percentage of estrogen receptor neurons containing Fos was significantly influenced in a brain region-, developmental stage-, and steroid-specific fashion by testosterone and E2 treatments. These findings support the hypothesis that the feedback controls of the GnRH surge are sensitive to programming by prenatal and postnatal steroids in a precocial species.
GH-Releasing Hormone Induces Cardioprotection in Isolated Male Rat Heart via Activation of RISK and SAFE Pathways
Authors: Penna Claudia , Settanni Fabio , Tullio Francesca , Trovato Letizia , Pagliaro Pasquale , Alloatti Giuseppe , Ghigo Ezio , Granata Riccarda 
Published: February 2013

Abstract
GHRH stimulates GH synthesis and release from the pituitary and exerts direct effects in extrapituitary tissues. We have previously shown that pretreatment with GHRH reduces cardiomyocyte apoptosis and improves heart function in isolated rat hearts subjected to ischemia/reperfusion (I/R). Here, we determined whether GHRH given at reperfusion reduces myocardial reperfusion injury and investigated the molecular mechanisms involved in GHRH effects. Isolated rat hearts subjected to I/R were treated at the onset of reperfusion with: 1) GHRH; 2) GHRH+GHRH antagonist JV-1-36; 3) GHRH+mitochondrial ATP-dependent potassium channel inhibitor 5-hydroxydecanoate; 4) GHRH+mitochondrial permeability transition pore opener atractyloside; 5) GHRH+ phosphoinositide 3-kinase/Akt inhibitor Wortmannin (WM); and 6) GHRH+signal transducer and activator of transcription-3 inhibitor tyrphostin-AG490 (AG490). GHRH reduced infarct size at the end of reperfusion and reverted contractility dysfunction in I/R hearts. These effects were inhibited by either JV-1-36, 5-hydroxydecanoate, atractylosid, WM, or AG490. Western blot analysis on left ventricles showed GHRH-induced phosphorylation of either the reperfusion injury salvage kinases (RISK), phosphoinositide 3-kinase/Akt, ERK1/2, and glycogen synthase kinase-3β or signal transducer and activator of transcription-3, as part of the survivor activating factor enhancement (SAFE) pathway. GHRH-induced activation of RISK and SAFE pathways was blocked by JV-1-36, WM, and AG490. Furthermore, GHRH increased the phosphorylation of endothelial nitric oxide synthase and AMP-activated protein kinase and preserved postischemic nicotinamide adenine dinucleotide (NAD+) levels. These results suggest that GHRH protects the heart from I/R injury through receptor-mediated mechanisms, leading to activation of RISK and SAFE pathways, which converge on mitochondria and possibly on AMP-activated protein kinase.
Excess Androgen During Puberty Disrupts Circadian Organization in Female Rats
Authors: Sellix Michael T. , Murphy Zachary C. , Menaker Michael 
Published: February 2013

Abstract
Circadian clocks have been described in each tissue of the hypothalamo-pituitary-ovarian axis. Although a role for the clock in the timing of ovulation is indicated, the impact of diseases that disrupt fertility on clock function or the clocks' role in the etiology of these pathologies has yet to be fully appreciated. Polycystic ovary syndrome (PCOS) is a particularly devastating endocrinopathy, affecting approximately 10% of women at childbearing age. Common features of PCOS are a polycystic ovary, amenorrhea, and excess serum androgen. Approximately 40% of these women have metabolic syndrome, including hyperinsulinemia, dyslipidemia, and hyperleptinemia. It has been suggested that excess androgen is a critical factor in the etiology of PCOS. We have examined the effects of androgen excess during puberty on the phase of circadian clocks in tissues of the metabolic and hypothalamo-pituitary-ovarian axes. Female period1-luciferase (per1-luc) rats were exposed to androgen (5α-dihydrotestosterone [DHT]) or placebo for 4-6 weeks (short term) or 9-15 weeks (long term). As expected, DHT-treated animals gained more weight than controls and had disrupted estrous cycles. At the end of treatment, tissues, including the liver, lung, kidney, white adipose, cornea, pituitary, oviduct, and ovarian follicles, were cultured, and per1-luc expression in each was recorded. Analysis of per1-luc expression revealed that DHT exposure increased phase distribution of multiple oscillators, including ovarian follicles, liver, and adipose, and altered phase synchrony between animals. These data suggest that excess androgen during puberty, a common feature of PCOS, negatively affects internal circadian organization in both the reproductive and metabolic axes.