bluuebunny/crossref_metadata_2025_split huggingface dataset:
C-mii: a tool for plant miRNA and target identification
Authors: Numnark Somrak , Mhuantong Wuttichai , Ingsriswang Supawadee , Wichadakul Duangdao 
Published: December 2012

Abstract

Background
MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of tools tailored towards plants is limited, and those that are available have specific functionality, lack graphical user interfaces, and restrict the number of input sequences. Large-scale computational identifications of miRNAs and/or targets of several plants have been also reported. Their methods, however, are only described as flow diagrams, which require programming skills and the understanding of input and output of the connected programs to reproduce.

Results
To overcome these limitations and programming complexities, we proposed C-mii as a ready-made software package for both plant miRNA and target identification. C-mii was designed and implemented based on established computational steps and criteria derived from previous literature with the following distinguishing features. First, software is easy to install with all-in-one programs and packaged databases. Second, it comes with graphical user interfaces (GUIs) for ease of use. Users can identify plant miRNAs and targets via step-by-step execution, explore the detailed results from each step, filter the results according to proposed constraints in plant miRNA and target biogenesis, and export sequences and structures of interest. Third, it supplies bird's eye views of the identification results with infographics and grouping information. Fourth, in terms of functionality, it extends the standard computational steps of miRNA target identification with miRNA-target folding and GO annotation. Fifth, it provides helper functions for the update of pre-installed databases and automatic recovery. Finally, it supports multi-project and multi-thread management.

Conclusions
C-mii constitutes the first complete software package with graphical user interfaces enabling computational identification of both plant miRNA genes and miRNA targets. With the provided functionalities, it can help accelerate the study of plant miRNAs and targets, especially for small and medium plant molecular labs without bioinformaticians. C-mii is freely available at http://www.biotec.or.th/isl/c-mii for both Windows and Ubuntu Linux platforms.
Whole-genome sequencing and identification of Morganella morganii KT pathogenicity-related genes
Authors: Chen Yu-Tin , Peng Hwei-Ling , Shia Wei-Chung , Hsu Fang-Rong , Ken Chuian-Fu , Tsao Yu-Ming , Chen Chang-Hua , Liu Chun-Eng , Hsieh Ming-Feng , Chen Huang-Chi , Tang Chuan-Yi , Ku Tien-Hsiung 
Published: December 2012

Abstract

Background
The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. M. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts, wound infection, and septicaemia. M. morganii infection is associated with a high mortality rate, although most patients respond well to appropriate antibiotic therapy. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, we used Illumina technology to sequence the genome of the KT strain and compared its sequence with the genome sequences of related bacteria.

Results
The 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in the other non-Proteeae enterobacterial genomes.

Conclusions
This is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen.
Maxillary nerve compression in cynomolgus monkey Macaca fascicularis: altered somatic sensation and peripheral nerve firing
Authors: Guo Ning , Gu Xiyao , Zhao Jun , Zhao Guoping , Jin Meilei , Zou Hong , Zhang Yuqiu , Zhao Zhiqi , Jin Gang Jason , Yu Lei 
Published: December 2012

Abstract

Background
Trigeminal nerve is a major source of the sensory input of the face, and trigeminal neuropathology models have been reported in rodents with injury to branches of the maxillary or mandibular division of the trigeminal nerve. Non-human primates are neuroanatomically more closely related to human than rodents; however, nerve injury studies in non-human primates are limited.

Results
We describe here a nerve injury model of maxillary nerve compression (MNC) in the cynomolgus macaque monkey, Macaca fascicularis, and the initial characterization of the consequences of damage to this trigeminal nerve branch. The nerve injury from the compression appeared to be mild, as we did not observe overt changes in home-cage behavior in the monkeys. When mechanical stimulation was applied to the facial area, monkeys with MNC displayed increased mechanical sensitivity, as the avoidance response scores were lower than those from the control animals. Such a change in mechanical sensitivity appeared to be somewhat bilateral, as the contralateral side also showed increased mechanical sensitivity, although the change on the ipsilateral side was more robust. Multiple-unit recording of the maxillary nerve showed a general pattern of increasing responsiveness to escalating force in mechanical stimulation on the contralateral side. Ipsilateral side of the maxillary nerve showed a lack of responsiveness to escalating force in mechanical stimulation, possibly reflecting a maximum stimulation threshold effect from sensitized nerve due to MNC injury.

Conclusions
These results suggest that MNC may produce increased sensitivity of the ipsilateral maxillary nerve, and that this model may serve as a non-human primate model to evaluate the effect of injury to trigeminal nerve branches.
Volunteering in the care of people with severe mental illness: a systematic review
Authors: Hallett Claudia , Klug Günter , Lauber Christoph , Priebe Stefan 
Published: December 2012

Abstract

Background
Much of the literature to date concerning public attitudes towards people with severe mental illness (SMI) has focused on negative stereotypes and discriminatory behaviour. However, there also exists a tradition of volunteering with these people, implying a more positive attitude. Groups with positive attitudes and behaviours towards people with SMI have received relatively little attention in research. They merit further attention, as evidence on characteristics and experiences of volunteers may help to promote volunteering. The present paper aims to systematically review the literature reporting characteristics, motivations, experiences, and benefits of volunteers in the care of people with SMI.

Methods
In November 2010, a systematic electronic search was carried out in BNI, CINAHL, Embase, Medline, PsycINFO, Cochrane Registers and Web of Science databases, using a combination of ‘volunteer’, ‘mental health’ and ‘outcome’ search terms. A secondary hand search was performed in relevant psychiatric journals, grey literature and references.

Results
14 papers met the inclusion criteria for the review, with data on a total of 540 volunteers. The results suggest that volunteers are a mostly female, but otherwise heterogeneous group. Motivations for volunteering are a combination of what they can ‘give’ to others and what they can ‘get’ for themselves. Overall volunteers report positive experiences. The main benefit to persons with a psychiatric illness is the gaining of a companion, who is non-stigmatizing and proactive in increasing their social-community involvement.

Conclusions
The evidence base for volunteers in care of people with SMI is small and inconsistent. However there are potential implications for both current and future volunteering programmes from the data. As the data suggests that there is no ‘typical’ volunteer, volunteering programmes should recruit individuals from a variety of backgrounds. The act of volunteering can not only benefit people with SMI, but also the volunteers. Further research may specify methods of recruiting, training, supervising and using volunteers to maximise the benefit for all involved.
The optimal duration of progesterone supplementation in pregnant women after IVF/ICSI: a meta-analysis
Authors: Liu Xi-Ru , Mu Hua-Qiao , Shi Qi , Xiao Xiao-Qiu , Qi Hong-Bo 
Published: December 2012

Abstract

Background
Progesterone supplementation after in vitro fertilisation/intracytoplasmic sperm injection (IVF/ICSI) can improve the rates of clinical pregnancy and live birth, but the optimal duration of treatment remains controversial. The objective of this meta-analysis was to investigate the effects of early progesterone cessation on pregnancy outcomes in women undergoing IVF/ICSI.

Methods
We searched MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), the Chinese biomedicine (CBM) literature database, and the Wanfang database. The final search was performed in July 2012. All available randomised trials that compared the effects of early progesterone cessation with progesterone continuation during early pregnancy after IVF/ICSI were included. The main outcome measures were live birth rate, miscarriage rate and ongoing pregnancy rate. Fixed or random-effects models were chosen to calculate the risk ratio (RR).

Results
Six eligible studies with a total of 1,201 randomised participants were included in the final analysis. No statistically significant differences were detected between patients who underwent early progesterone cessation and those who received progesterone continuation for luteal phase support in terms of live birth rate (RR: 0.95, 95% CI: 0.86–1.05), miscarriage rate (RR: 1.01, 95% CI: 0.74–1.38) or ongoing pregnancy rate (RR: 0.97, 95% CI: 0.90–1.05). These results did not change after a sensitivity analysis.

Conclusions
The currently available evidence suggests that progesterone supplementation beyond the first positive hCG test after IVF/ICSI might generally be unnecessary, although large-scale randomised controlled trials are needed to strengthen this conclusion.
The production of concentrated dispersions of few-layer graphene by the direct exfoliation of graphite in organosilanes
Authors: Nuvoli Daniele , Alzari Valeria , Sanna Roberta , Scognamillo Sergio , Piccinini Massimo , Peponi Laura , Kenny Josè Maria , Mariani Alberto 
Published: December 2012

Abstract
We report the formation and characterization of graphene dispersions in two organosilanes, 3-glycidoxypropyl trimethoxysilane (GPTMS) and phenyl triethoxysilane (PhTES) as new reactive solvents. The preparation method was mild and easy and does not produce any chemical modification. The dispersions, which exhibit the Tyndall effect, were characterized by TEM and Raman spectroscopy to confirm the presence of few-layer graphene. Concentrations as high as 0.66 and 8.00 mg/ml were found for PhTES and GPTMS, respectively. The latter is one of the highest values reported for a dispersion of graphene obtained by any method. This finding paves the way for the direct synthesis of polymer nanofiller-containing composites consisting of graphene and reactive silanes to be used in sol–gel synthesis, without any need for solvent removal, thus preventing graphene reaggregation to form graphite flakes.
A novel approach to mapping load transfer from the plantar surface of the foot to the walls of the total contact cast: a proof of concept study
Authors: Begg Lindy , McLaughlin Patrick , Manning Leon , Vicaretti Mauro , Fletcher John , Burns Joshua 
Published: December 2012

AbstractBackgroundTotal contact casting is regarded as the gold standard treatment for plantar foot ulcers. Load transfer from the plantar surface of the foot to the walls of the total contact cast has previously been assessed indirectly. The aim of this proof of concept study was to determine the feasibility of a new method to directly measure the load between the cast wall and the lower leg interface using capacitance sensors.MethodsPlantar load was measured with pedar® sensor insoles and cast wall load with pliance® sensor strips as participants (n=2) walked along a 9 m walkway at 0.4±0.04 m/sec. The relative force (%) on the cast wall was calculated by dividing the mean cast wall force (N) per step by the mean plantar force (N) per step in the shoe‐cast condition.ResultsThe combined average measured load per step upon the walls of the TCC equated to 23‐34% of the average plantar load on the opposite foot. The highest areas of load on the lower leg were located at the posterior margin of the lateral malleolus and at the anterior ankle/extensor retinaculum.ConclusionsThese direct measurements of cast wall load are similar to previous indirect assessment of load transfer (30‐36%) to the cast walls. This new methodology may provide a more comprehensive understanding of the mechanism of load transfer from the plantar surface of the foot to the cast walls of the total contact cast.
Current status and implications of microRNAs in ovarian cancer diagnosis and therapy
Authors: Zaman Mohd Saif , Maher Diane M , Khan Sheema , Jaggi Meena , Chauhan Subhash C 
Published: December 2012

AbstractOvarian cancer is the fifth most common cancer among women and causes more deaths than any other type of female reproductive cancer. Currently, treatment of ovarian cancer is based on the combination of surgery and chemotherapy. While recurrent ovarian cancer responds to additional chemotherapy treatments, the progression-free interval becomes shorter after each cycle, as chemo-resistance increases until the disease becomes incurable. There is, therefore, a strong need for prognostic and predictive markers to help optimize and personalize treatment in order to improve the outcome of ovarian cancer. An increasing number of studies indicate an essential role for microRNAs in ovarian cancer progression and chemo-resistance. MicroRNAs (miRNAs) are small endogenous non-coding RNAs (~22bp) which are frequently dysregulated in cancer. Typically, miRNAs are involved in crucial biological processes, including development, differentiation, apoptosis and proliferation. Two families of miRNAs, miR-200 and let-7, are frequently dysregulated in ovarian cancer and have been associated with poor prognosis. Both have been implicated in the regulation of epithelial-to-mesenchymal transition, a cellular transition associated with tumor aggressiveness, tumor invasion and chemo-resistance. Moreover, miRNAs also have possible implications for improving cancer diagnosis; for example miR-200 family, let-7 family, miR-21 and miR-214 may be useful in diagnostic tests to help detect ovarian cancer at an early stage. Additionally, the use of multiple target O-modified antagomirs (MTG-AMO) to inhibit oncogenic miRNAs and miRNA replacement therapy for tumor suppressor miRNAs are essential tools for miRNA based cancer therapeutics. In this review we describe the current status of the role miRNAs play in ovarian cancer and focus on the possibilities of microRNA-based therapies and the use of microRNAs as diagnostic tools.
Autoantibody-mediated arthritis in the absence of C3 and activating Fcγ receptors: C5 is activated by the coagulation cascade
Authors: Auger Jennifer L , Haasken Stefanie , Binstadt Bryce A 
Published: December 2012

Abstract
Introduction
The effector functions of immunoglobulin G (IgG) are mediated by interaction of its Fc region with Fc receptors (FcγRs) and/or the complement system. The three main pathways of complement activation converge at C3. However, C3-independent pathways can activate C5 and other downstream complement components during IgG-initiated inflammatory responses. These C3-independent pathways of C5 activation are triggered by activating FcγRs in some systems or can be activated by factors of the coagulation cascade such as thrombin. Here we studied the interplay of C3, C5, and activating FcγRs in a model of spontaneous autoantibody-driven arthritis.

Methods
We utilized the K/BxN TCR transgenic mouse model of arthritis. We bred K/BxN mice bearing targeted or naturally-occurring mutations in one or more of the genes encoding complement components C3, C5, and FcRγ, the cytoplasmic signaling chain shared by the activating FcγRs. We measured arthritis development, the production of arthritogenic autoantibodies, T cell activation status and cytokine synthesis. In addition, we treated mice with anti-C5 monoclonal antibodies or with the thrombin inhibitor argatroban.

Results
We have previously shown that genetic deficiency of C5 protects K/BxN mice from the development of arthritis. We found here that C3-deficient K/BxN mice developed arthritis equivalent in severity to C3-sufficient animals. Arthritis also developed normally in K/BxN mice lacking both C3 and FcRγ, but could be ameliorated in these animals by treatment with anti-C5 monoclonal antibody or by treatment with argatroban. Production of arthritogenic autoantibodies, T cell activation, and T cell cytokine production were not affected by the absence of C3, C5, and/or FcRγ.

Conclusions
In K/BxN mice, C5-dependent autoantibody-driven arthritis can occur in the genetic absence of both complement C3 and activating FcγRs. Our findings suggest that in this setting, thrombin activates C5 to provoke arthritis.
Whole-genome reconstruction and mutational signatures in gastric cancer
Authors: Nagarajan Niranjan , Bertrand Denis , Hillmer Axel M , Zang Zhi Jiang , Yao Fei , Jacques Pierre-Étienne , Teo Audrey SM , Cutcutache Ioana , Zhang Zhenshui , Lee Wah Heng , Sia Yee Yen , Gao Song , Ariyaratne Pramila N , Ho Andrea , Woo Xing Yi , Veeravali Lavanya , Ong Choon Kiat , Deng Niantao , Desai Kartiki V , Khor Chiea Chuen , Hibberd Martin L , Shahab Atif , Rao Jaideepraj , Wu Mengchu , Teh Ming , Zhu Feng , Chin Sze Yung , Pang Brendan , So Jimmy BY , Bourque Guillaume , Soong Richie , Sung Wing-Kin , Tean Teh Bin , Rozen Steven , Ruan Xiaoan , Yeoh Khay Guan , Tan Patrick BO , Ruan Yijun 
Published: December 2012

Abstract
Background
Gastric cancer is the second highest cause of global cancer mortality. To explore the complete repertoire of somatic alterations in gastric cancer, we combined massively parallel short read and DNA paired-end tag sequencing to present the first whole-genome analysis of two gastric adenocarcinomas, one with chromosomal instability and the other with microsatellite instability.

Results
Integrative analysis and de novo assemblies revealed the architecture of a wild-type KRAS amplification, a common driver event in gastric cancer. We discovered three distinct mutational signatures in gastric cancer - against a genome-wide backdrop of oxidative and microsatellite instability-related mutational signatures, we identified the first exome-specific mutational signature. Further characterization of the impact of these signatures by combining sequencing data from 40 complete gastric cancer exomes and targeted screening of an additional 94 independent gastric tumors uncovered ACVR2A, RPL22 and LMAN1 as recurrently mutated genes in microsatellite instability-positive gastric cancer and PAPPA as a recurrently mutated gene in TP53 wild-type gastric cancer.

Conclusions
These results highlight how whole-genome cancer sequencing can uncover information relevant to tissue-specific carcinogenesis that would otherwise be missed from exome-sequencing data.
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development
Authors: Tervo Christopher J , Reed Jennifer L 
Published: December 2012

AbstractCurrent computational tools can generate and improve genome-scale models based on existing data; however, for many organisms, the data needed to test and refine such models are not available. To facilitate model development, we created the forced coupling algorithm, FOCAL, to identify genetic and environmental conditions such that a reaction becomes essential for an experimentally measurable phenotype. This reaction's conditional essentiality can then be tested experimentally to evaluate whether network connections occur or to create strains with desirable phenotypes. FOCAL allows network connections to be queried, which improves our understanding of metabolism and accuracy of developed models.
Nonstretching NMO correction of prestack time-migrated gathers using a matching-pursuit algorithm
Authors: Zhang Bo , Zhang Kui , Guo Shiguang , Marfurt Kurt J. 
Published: December 2012

Wide-azimuth, long-offset surveys are becoming increasingly common in unconventional exploration plays where one of the key routine processes is maintaining data fidelity at far offsets. The conventional NMO correction that processes the data sample-by-sample results in the well-known decrease of frequency content and amplitude distortion through stretch, which lowers the seismic resolution and hinders [Formula: see text] and amplitude variation with offset and azimuth (AVAz) analysis of the long-offset signal. To mitigate the stretch typically associated with large offsets, we use a matching-pursuit-based normal moveout correction (MPNMO) to reduce NMO-stretch effects in long-offset data. MPNMO corrects the data wavelet-by-wavelet rather than sample-by-sample, thereby avoiding stretch. We apply our technique (1) to a set of synthetic gathers and (2) as part of a residual velocity analysis workflow to a prestack time-migrated data volume acquired over the Northern Chicontepec Basin, Mexico. Test results show that MPNMO can produce relatively nonstretched events and generate higher temporal resolution prestack gathers.