bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global small RNA analysis in fast-growing Arabidopsis thaliana with elevated concentrations of ATP and sugars
Authors: Liang Chao , Liu Xuan , Sun Yuzhe , Yiu Siu-Ming , Lim Boon Leong 
Published: February 2014

Abstract

Background
In higher eukaryotes, small RNAs play a role in regulating gene expression. Overexpression (OE) lines of Arabidopsis thaliana purple acid phosphatase 2 (AtPAP2) were shown to grow faster and exhibit higher ATP and sugar contents. Leaf microarray studies showed that many genes involved in microRNAs (miRNAs) and trans-acting siRNAs (tasiRNAs) biogenesis were significantly changed in the fast-growing lines. In this study, the sRNA profiles of the leaf and the root of 20-day-old plants were sequenced and the impacts of high energy status on sRNA expression were analyzed.

Results
9-13 million reads from each library were mapped to genome. miRNAs, tasiRNAs and natural antisense transcripts-generated small interfering RNAs (natsiRNAs) were identified and compared between libraries. In the leaf of OE lines, 15 known miRNAs increased in abundance and 9 miRNAs decreased in abundance, whereas in the root of OE lines, 2 known miRNAs increased in abundance and 9 miRNAs decreased in abundance. miRNAs with increased abundance in the leaf and root samples of both OE lines (miR158b and miR172a/b) were predicted to target mRNAs coding for Dof zinc finger protein and Apetala 2 (AP2) proteins, respectively. Furthermore, a significant change in the miR173-tasiRNAs-PPR/TPR network was observed in the leaves of both OE lines.

Conclusion
In this study, the impact of high energy content on the sRNA profiles of Arabidopsis is reported. While the abundance of many stress-induced miRNAs is unaltered, the abundance of some miRNAs related to plant growth and development (miR172 and miR319) is elevated in the fast-growing lines. An induction of miR173-tasiRNAs-PPR/TPR network was also observed in the OE lines. In contrast, only few cis- and trans-natsiRNAs are altered in the fast-growing lines.
Does Low-intensity pulsed ultrasound treatment repair articular cartilage injury? A rabbit model study
Authors: Yang Shan-Wei , Kuo Chien-Lin , Chang Shwu Jen , Chen Po-Chou , Lin Yen Ting , Manousakas Ioannis , Kuo Shyh Ming 
Published: February 2014

Abstract

Background
Low-intensity pulsed ultrasound (LIPUS) regiment has been used to treat fractures with non-union and to promote bone union in general. The effect of LIPUS on articular cartilage metabolism has been characterized. Yet, the effect of LIPUS to repair articular cartilage injury remains unclear in vivo.

Methods
We designed a study to investigate the effect of LIPUS on articular cartilage repairing in a rabbit severe cartilage injury model. Eighteen rabbits were divided into three groups: Sham-operated group, operated group without-LIPUS-treatment, operated group with-LIPUS-treatment (a daily 20-minute treatment for 3 months). Full-thickness cartilage defects were surgically created on the right side distal femoral condyle without intending to penetrate into the subchondral bone, which mimicked severe chondral injury. MR images for experimental joints, morphology grading scale, and histopathological Mankin score were evaluated.

Results
The preliminary results showed that the operated groups with-LIPUS-treatment and without-LIPUS-treatment had significantly higher Mankin score and morphological grading scale compared with the sham-operated group. However, there was no significant difference between the with-LIPUS-treatment and without-LIPUS-treatment groups. Cartilage defects filled with proliferative tissue were observed in the with-LIPUS-treatment group grossly and under MR images, however which presented less up-take under Alcian blue stain. Furthermore, no new deposition of type II collagen or proliferation of chondrocyte was observed over the cartilage defect after LIPUS treatment.

Conclusion
LIPUS has no significant therapeutic potential in treating severe articular cartilage injury in our animal study.
Selection of peptides binding to metallic borides by screening M13 phage display libraries
Authors: Ploss Martin , Facey Sandra J , Bruhn Carina , Zemel Limor , Hofmann Kathrin , Stark Robert W , Albert Barbara , Hauer Bernhard 
Published: February 2014

Abstract

Background
Metal borides are a class of inorganic solids that is much less known and investigated than for example metal oxides or intermetallics. At the same time it is a highly versatile and interesting class of compounds in terms of physical and chemical properties, like semiconductivity, ferromagnetism, or catalytic activity. This makes these substances attractive for the generation of new materials. Very little is known about the interaction between organic materials and borides. To generate nanostructured and composite materials which consist of metal borides and organic modifiers it is necessary to develop new synthetic strategies. Phage peptide display libraries are commonly used to select peptides that bind specifically to metals, metal oxides, and semiconductors. Further, these binding peptides can serve as templates to control the nucleation and growth of inorganic nanoparticles. Additionally, the combination of two different binding motifs into a single bifunctional phage could be useful for the generation of new composite materials.

Results
In this study, we have identified a unique set of sequences that bind to amorphous and crystalline nickel boride (Ni3B) nanoparticles, from a random peptide library using the phage display technique. Using this technique, strong binders were identified that are selective for nickel boride. Sequence analysis of the peptides revealed that the sequences exhibit similar, yet subtle different patterns of amino acid usage. Although a predominant binding motif was not observed, certain charged amino acids emerged as essential in specific binding to both substrates. The 7-mer peptide sequence LGFREKE, isolated on amorphous Ni3B emerged as the best binder for both substrates. Fluorescence microscopy and atomic force microscopy confirmed the specific binding affinity of LGFREKE expressing phage to amorphous and crystalline Ni3B nanoparticles.

Conclusions
This study is, to our knowledge, the first to identify peptides that bind specifically to amorphous and to crystalline Ni3B nanoparticles. We think that the identified strong binding sequences described here could potentially serve for the utilisation of M13 phage as a viable alternative to other methods to create tailor-made boride composite materials or new catalytic surfaces by a biologically driven nano-assembly synthesis and structuring.
How mindfulness changed my sleep: focus groups with chronic insomnia patients
Authors: Hubbling Amber , Reilly-Spong Maryanne , Kreitzer Mary Jo , Gross Cynthia R 
Published: February 2014

Abstract

Background
Chronic insomnia is a major public health problem affecting approximately 10% of adults. Use of meditation and yoga to develop mindful awareness (‘mindfulness training’) may be an effective approach to treat chronic insomnia, with sleep outcomes comparable to nightly use of prescription sedatives, but more durable and with minimal or no side effects. The purpose of this study was to understand mindfulness training as experienced by patients with chronic insomnia, and suggest procedures that may be useful in optimizing sleep benefits.

Methods
Adults (N = 18) who completed an 8-week mindfulness-based stress reduction (MBSR) program as part of a randomized, controlled clinical trial to evaluate MBSR as a treatment for chronic insomnia were invited to participate in post-trial focus groups. Two groups were held. Participants (n = 9) described how their sleep routine, thoughts and emotions were affected by MBSR and about utility (or not) of various mindfulness techniques. Groups were audio-recorded, transcribed and analyzed using content analysis.

Results
Four themes were identified: the impact of mindfulness on sleep and motivation to adopt a healthy sleep lifestyle; benefits of mindfulness on aspects of life beyond sleep; challenges and successes in adopting mindfulness-based practices; and the importance of group sharing and support. Participants said they were not sleeping more, but sleeping better, waking more refreshed, feeling less distressed about insomnia, and better able to cope when it occurred. Some participants experienced the course as a call to action, and for them, practicing meditation and following sleep hygiene guidelines became priorities. Motivation to sustain behavioral changes was reinforced by feeling physically better and more emotionally stable, and seeing others in the MBSR class improve. The body scan was identified as an effective tool to enable falling asleep faster. Participants described needing to continue practicing mindfulness to maintain benefits.

Conclusions
First-person accounts are consistent with published trial results of positive impacts of MBSR on sleep measured by sleep diary, actigraphy, and self-report sleep scales. Findings indicate that mindfulness training in a group format, combined with sleep hygiene education, is important for effective application of MBSR as a treatment for chronic insomnia.
Photocurrent response and semiconductor characteristics of Ce-Ce2O3-CeO2-modified TiO2 nanotube arrays
Authors: Tan Yu , Zhang Shenghan , Liang Kexin 
Published: February 2014

Abstract
We reported Ce and its oxide-modified TiO2 nanotube arrays (TNTs) and their semiconductor properties. The TNTs were prepared by anodic oxidation on pure Ti and investigated by electrochemical photocurrent response analysis. Then, the TNT electrodes were deposited of Ce by cathodic reduction of Ce(NO3)3 6H2O. After deposition, the TNT electrodes were fabricated by anodic oxidation at E = 1.0 V(SCE) for various electricity as Ce-Ce2O3-CeO2 modification. The Ce-deposited TNTs (band gap energy E
g = 2.92 eV) exhibited enhanced photocurrent responses under visible light region and indicated more negative flat band potential (E
fb) compared with the TNTs without deposition. After anodic oxidation, the mixed Ce and its oxide (Ce2O3-CeO2)-modified TNT photoelectrodes exhibited higher photocurrent responses under both visible and UV light regions than the TNTs without deposition. The photocurrent responses and E
fb were found to be strongly dependent on the contents of Ce2O3 and CeO2 deposited on TNTs. A new characteristic of E
g = 2.1 ± 0.1 eV was investigated in the Ce2O3- and CeO2-modified photoelectrodes. X-ray diffraction (XRD), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS) were also employed to characterize various modified TNTs photoelectrodes.
Protein signatures of oxidative stress response in a patient specific cell line model for autism
Authors: Chiocchetti Andreas G , Haslinger Denise , Boesch Maximilian , Karl Thomas , Wiemann Stefan , Freitag Christine M , Poustka Fritz , Scheibe Burghardt , Bauer Johann W , Hintner Helmut , Breitenbach Michael , Kellermann Josef , Lottspeich Friedrich , Klauck Sabine M , Breitenbach-Koller Lore 
Published: February 2014

Abstract

Background
Known genetic variants can account for 10% to 20% of all cases with autism spectrum disorders (ASD). Overlapping cellular pathomechanisms common to neurons of the central nervous system (CNS) and in tissues of peripheral organs, such as immune dysregulation, oxidative stress and dysfunctions in mitochondrial and protein synthesis metabolism, were suggested to support the wide spectrum of ASD on unifying disease phenotype. Here, we studied in patient-derived lymphoblastoid cell lines (LCLs) how an ASD-specific mutation in ribosomal protein RPL10 (RPL10[H213Q]) generates a distinct protein signature. We compared the RPL10[H213Q] expression pattern to expression patterns derived from unrelated ASD patients without RPL10[H213Q] mutation. In addition, a yeast rpl10 deficiency model served in a proof-of-principle study to test for alterations in protein patterns in response to oxidative stress.

Methods
Protein extracts of LCLs from patients, relatives and controls, as well as diploid yeast cells hemizygous for rpl10, were subjected to two-dimensional gel electrophoresis and differentially regulated spots were identified by mass spectrometry. Subsequently, Gene Ontology database (GO)-term enrichment and network analysis was performed to map the identified proteins into cellular pathways.

Results
The protein signature generated by RPL10[H213Q] is a functionally related subset of the ASD-specific protein signature, sharing redox-sensitive elements in energy-, protein- and redox-metabolism. In yeast, rpl10 deficiency generates a specific protein signature, harboring components of pathways identified in both the RPL10[H213Q] subjects’ and the ASD patients’ set. Importantly, the rpl10 deficiency signature is a subset of the signature resulting from response of wild-type yeast to oxidative stress.

Conclusions
Redox-sensitive protein signatures mapping into cellular pathways with pathophysiology in ASD have been identified in both LCLs carrying the ASD-specific mutation RPL10[H213Q] and LCLs from ASD patients without this mutation. At pathway levels, this redox-sensitive protein signature has also been identified in a yeast rpl10 deficiency and an oxidative stress model. These observations point to a common molecular pathomechanism in ASD, characterized in our study by dysregulation of redox balance. Importantly, this can be triggered by the known ASD-RPL10[H213Q] mutation or by yet unknown mutations of the ASD cohort that act upstream of RPL10 in differential expression of redox-sensitive proteins.
A novel mechanism of regulating breast cancer cell migration via palmitoylation-dependent alterations in the lipid raft affiliation of CD44
Authors: Babina Irina S , McSherry Elaine A , Donatello Simona , Hill Arnold DK , Hopkins Ann M 
Published: February 2014

Abstract
Introduction
Most breast cancer-related deaths result from metastasis, a process involving dynamic regulation of tumour cell adhesion and migration. The adhesion protein CD44, a key regulator of cell migration, is enriched in cholesterol-enriched membrane microdomains termed lipid rafts. We recently reported that raft affiliation of CD44 negatively regulates interactions with its migratory binding partner ezrin. Since raft affiliation is regulated by post-translational modifications including palmitoylation, we sought to establish the contribution of CD44 palmitoylation and lipid raft affiliation to cell migration.

Methods
Recovery of CD44 and its binding partners from raft versus non-raft membrane microdomains was profiled in non-migrating and migrating breast cancer cell lines. Site-directed mutagenesis was used to introduce single or double point mutations into both CD44 palmitoylation sites (Cys286 and Cys295), whereupon the implications for lipid raft recovery, phenotype, ezrin co-precipitation and migratory behaviour was assessed. Finally CD44 palmitoylation status and lipid raft affiliation was assessed in primary cultures from a small panel of breast cancer patients.

Results
CD44 raft affiliation was increased during migration of non-invasive breast cell lines, but decreased during migration of highly-invasive breast cells. The latter was paralleled by increased CD44 recovery in non-raft fractions, and exclusive non-raft recovery of its binding partners. Point mutation of CD44 palmitoylation sites reduced CD44 raft affiliation in invasive MDA-MB-231 cells, increased CD44-ezrin co-precipitation and accordingly enhanced cell migration. Expression of palmitoylation-impaired (raft-excluded) CD44 mutants in non-invasive MCF-10a cells was sufficient to reversibly induce the phenotypic appearance of epithelial-to-mesenchymal transition and to increase cell motility. Interestingly, cell migration was associated with temporal reductions in CD44 palmitoylation in wild-type breast cells. Finally, the relevance of these findings is underscored by the fact that levels of palmitoylated CD44 were lower in primary cultures from invasive ductal carcinomas relative to non-tumour tissue, while CD44 co-localisation with a lipid raft marker was less in invasive ductal carcinoma relative to ductal carcinoma in situ cultures.

Conclusion
Our results support a novel mechanism whereby CD44 palmitoylation and consequent lipid raft affiliation inversely regulate breast cancer cell migration, and may act as a new therapeutic target in breast cancer metastasis.
Utility of thromboelastography and/or thromboelastometry in adults with sepsis: a systematic review
Authors: Müller Marcella C , Meijers Joost CM , Vroom Margreeth B , Juffermans Nicole P 
Published: February 2014

Abstract
Introduction
Coagulation abnormalities are frequent in sepsis. Conventional coagulation assays, however, have several limitations. A surge of interest exists in the use of point-of-care tests to diagnose hypo- and hypercoagulability in sepsis.
We performed a systematic review of available literature to establish the value of rotational thromboelastography (TEG) and thromboelastometry (ROTEM) compared with standard coagulation tests to detect hyper- or hypocoagulability in sepsis patients. Furthermore, we assessed the value of TEG/ROTEM to identify sepsis patients likely to benefit from therapies that interfere with the coagulation system.

Methods
MEDLINE, EMBASE, and the Cochrane Library were searched from 1 January 1980 to 31 December 2012. The search was limited to adults, and language was limited to English. Reference lists of retrieved articles were hand-searched for additional studies. Ongoing trials were searched on http://www.controlled-trials.com and http://www.clinicaltrials.gov. Studies addressing TEG/ROTEM measurements in adult patients with sepsis admitted to the ICU were considered eligible.

Results
Of 680 screened articles, 18 studies were included, of which two were randomized controlled trials, and 16 were observational cohort studies. In patients with sepsis, results show both hyper- and hypocoagulability, as well as TEG/ROTEM values that fell within reference values. Both hyper- and hypocoagulability were to some extent associated with diffuse intravascular coagulation. Compared with conventional coagulation tests, TEG/ROTEM can detect impaired fibrinolysis, which can possibly help to discriminate between sepsis and systemic inflammatory response syndrome (SIRS). A hypocoagulable profile is associated with increased mortality. The value of TEG/ROTEM to identify patients with sepsis who could possibly benefit from therapies interfering with the coagulation system could not be assessed, because studies addressing this topic were limited.

Conclusion
TEG/ROTEM could be a promising tool in diagnosing alterations in coagulation in sepsis. Further research on the value of TEG/ROTEM in these patients is warranted. Given that coagulopathy is a dynamic process, sequential measurements are needed to understand the coagulation patterns in sepsis, as can be detected by TEG/ROTEM.
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Authors: Hoffmann Steve , Otto Christian , Doose Gero , Tanzer Andrea , Langenberger David , Christ Sabina , Kunz Manfred , Holdt Lesca M , Teupser Daniel , Hackermüller Jörg , Stadler Peter F 
Published: February 2014

AbstractNumerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool (http://www.bioinf.uni-leipzig.de/Software/segemehl/).
Follicular Thyroid Cancers Demonstrate Dual Activation of PKA and mTOR as Modeled by Thyroid-Specific Deletion of Prkar1a and Pten in Mice
Authors: Pringle Daphne R. , Vasko Vasily V. , Yu Lianbo , Manchanda Parmeet K. , Lee Audrey A. , Zhang Xiaoli , Kirschner Jessica M. , Parlow Albert F. , Saji Motoyasu , Jarjoura David , Ringel Matthew D. , La Perle Krista M. D. , Kirschner Lawrence S. 
Published: February 2014

Context:
Thyroid cancer is the most common form of endocrine cancer, and it is a disease whose incidence is rapidly rising. Well-differentiated epithelial thyroid cancer can be divided into papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC). Although FTC is less common, patients with this condition have more frequent metastasis and a poorer prognosis than those with PTC.

Objective:
The objective of this study was to characterize the molecular mechanisms contributing to the development and metastasis of FTC.

Design:
We developed and characterized mice carrying thyroid-specific double knockout of the Prkar1a and Pten tumor suppressor genes and compared signaling alterations observed in the mouse FTC to the corresponding human tumors.

Setting:
The study was conducted at an academic research laboratory. Human samples were obtained from academic hospitals.

Patients:
Deidentified, formalin-fixed, paraffin-embedded (FFPE) samples were analyzed from 10 control thyroids, 30 PTC cases, five follicular variant PTC cases, and 10 FTC cases.

Interventions:
There were no interventions.

Main outcome measures:
Mouse and patient samples were analyzed for expression of activated cAMP response element binding protein, AKT, ERK, and mammalian target of rapamycin (mTOR). Murine FTCs were analyzed for differential gene expression to identify genes associated with metastatic progression.

Results:
Double Prkar1a-Pten thyroid knockout mice develop FTC and recapitulate the histology and metastatic phenotype of the human disease. Analysis of signaling pathways in FTC showed that both human and mouse tumors exhibited strong activation of protein kinase A and mTOR. The development of metastatic disease was associated with the overexpression of genes required for cell movement

Conclusions:
These data imply that the protein kinase A and mTOR signaling cascades are important for the development of follicular thyroid carcinogenesis and may suggest new targets for therapeutic intervention. Mouse models paralleling the development of the stages of human FTC should provide important new tools for understanding the mechanisms of FTC development and progression and for evaluating new therapeutics.