bluuebunny/crossref_metadata_2025_split huggingface dataset:
Productivity and botanical composition of orchardgrass–white clover swards in a cool‐temperate hill land region of the eastern United States
Authors: Malinowski Dariusz P. , Belesky David P. , Ruckle Joyce M. , Fedders James M. 
Published: November 2012

AbstractUnderstanding the growth dynamics of grass–legume swards is critical as pastoral management practices are adapted to varying economic constraints and emerging environmental considerations. Efficient management must synchronize the use of accumulated herbage with the needs of grazing livestock. This must be accomplished against the dynamic background of within and among year weather patterns interacting with herbage growth and grazing animal behavior. In the Appalachian region of the eastern United States, pastures often are dominated by orchardgrass (Dactylis glomerata L.) and white clover (Trifolium repens L.). We determined botanical composition and herbage productivity of orchardgrass and white clover swards during four consecutive years when managed as a function of canopy development and regrowth interval. Productivity was influenced by defoliation practices when mixtures were managed according to canopy development. Productivity was greatest when swards were managed as hay or when clipped to a 5‐cm residue each time mean canopy height reached 20 cm. White clover declined and orchardgrass increased in the sward irrespective of defoliation treatment. Botanical composition of mixtures with the erect growing orchardgrass tended to be more stable, whereas swards including the decumbent orchardgrass tended to be invaded by weeds. Some increase in productivity occurred during the first growing season when mixtures were clipped at either 2‐ or 4‐week intervals. Regardless of defoliation practice, white clover, and in some instances orchardgrass, presence declined during two consecutive growing seasons with various other volunteer grasses and forbs contributing to productivity. Productivity and persistence of sown sward components may be less dependent on management practices than on the expression of interactions responding to within and among year weather patterns.
Laboratory evaluation of sample collection methods (organs vs swabs) for Tasmanian salmon reovirus detection in farmed Atlantic salmon, Salmo salar L.
Authors: Zainathan S C , Carson J , Crane M St J , Nowak B F 
Published: November 2012

AbstractThe use of swabs relative to organs as a sample collection method for the detection of Tasmanian salmon reovirus (TSRV) in farmed Tasmanian Atlantic salmon, Salmo salar L., was evaluated by RT‐qPCR. Evaluation of individual and pooled sample collection (organs vs swabs) was carried out to determine the sensitivity of the collection methods and the effect of pooling of samples for the detection of TSRV. Detection of TSRV in individual samples was as sensitive when organs were sampled compared to swabs, and in pooled samples, organs demonstrated a sensitivity of one 10‐fold dilution higher than sampling of pooled swabs. Storage of swabs at 4 °C for t = 24 h demonstrated results similar to those at t = 0. Advantages of using swabs as a preferred sample collection method for the detection of TSRV compared to organ samples are evident from these experimental trials.
Construction of gene regulatory networks mediated by vegetative and reproductive stage‐specific small RNAs in rice (Oryza sativa)
Authors: Meng Yijun , Shao Chaogang , Wang Huizhong , Ma Xiaoxia , Chen Ming 
Published: November 2012

Summary

Although huge amounts of high‐throughput sequencing (HTS) data are available, limited systematic analyses have been performed by integrating these valuable resources. Based on small RNA (sRNA), RNA and degradome HTS data, the sRNAs specifically expressed at vegetative and reproductive stages were identified separately in rice.

Two distinct groups of sRNA HTS data, which were prepared during the vegetative and the reproductive stages, were utilized to extract stage‐specific sRNAs. Degradome sequencing data were employed for sRNA target validation. RNA sequencing data were used to construct expression‐based, sRNA‐mediated networks.

As a result, 26 microRNAs and 413 sRNAs were specifically expressed at the vegetative stage, and 79 microRNAs and 539 sRNAs were specifically expressed at the reproductive stage. In addition to the microRNAs, numerous stage‐specific sRNAs enriched in ARGONAUTE1 showed great potential to perform cleavage‐based repression on the targets. Several stage‐specific sRNAs were indicated to result from the wobble effect of Dicer‐like 1‐mediated processing of microRNA precursors. The expression patterns of the sRNA targets, and the stage‐specific cleavage signals strongly indicated the reliability of the constructed networks.

A set of rice stage‐specific sRNAs along with the regulatory cascades, which have great potential in regulating specific developmental stages, were provided for further investigation.
Preventing Cervical Cancer Globally
Authors: Schmeler Kathleen M. 
Published: November 2012

Abstract
Cervical cancer is one of the leading causes of cancer and cancer-related deaths among women worldwide. More than 85% of cases and deaths occur in the developing world where the availability of effective screening is limited. In this issue of the journal, Pierce and colleagues (beginning on page 1273) describe a novel technique using a high-resolution microendoscope (HRME) to diagnose cervical dysplasia. This perspective reviews the limitations of existing cervical cancer screening methods currently in use in low-resource settings and the potential for HRME imaging to contribute to cervical cancer prevention in the developing world. Cancer Prev Res; 5(11); 1257–9. ©2012 AACR.
Maximum voluntary ventilation is more strongly associated with energy expenditure during simple activities of daily living than measures of airflow obstruction or respiratory muscle strength in patients with COPD
Authors: Cavalheri Vinicius , Hill Kylie , Donaria Leila , Camillo Carlos Augusto , Pitta Fabio 
Published: November 2012

This is a retrospective analysis of data in which we explored the association between energy expenditure (EE) and lung function in patients with chronic obstructive pulmonary disease (COPD). A total of 36 participants ( 20 males; forced expiratory volume in 1 second (FEV1) of 48 ± 15% predicted) underwent measures of indirect calorimetry whilst performing five simple activities of daily living. Maximal voluntary ventilation was the only lung function parameter associated with EE. These data highlight the limited extent to which the FEV1 is related to the functional performance of patients with COPD.
MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling
Authors: Kitchen James L , Moore Jonathan D , Palmer Sarah A , Allaby Robin G 
Published: November 2012

Abstract

Background
Next generation sequencing technologies often require numerous primer designs that require good target coverage that can be financially costly. We aimed to develop a system that would implement primer reuse to design degenerate primers that could be designed around SNPs, thus find the fewest necessary primers and the lowest cost whilst maintaining an acceptable coverage and provide a cost effective solution. We have implemented Metropolis-Hastings Markov Chain Monte Carlo for optimizing primer reuse. We call it the Markov Chain Monte Carlo Optimized Degenerate Primer Reuse (MCMC-ODPR) algorithm.

Results
After repeating the program 1020 times to assess the variance, an average of 17.14% fewer primers were found to be necessary using MCMC-ODPR for an equivalent coverage without implementing primer reuse. The algorithm was able to reuse primers up to five times. We compared MCMC-ODPR with single sequence primer design programs Primer3 and Primer-BLAST and achieved a lower primer cost per amplicon base covered of 0.21 and 0.19 and 0.18 primer nucleotides on three separate gene sequences, respectively. With multiple sequences, MCMC-ODPR achieved a lower cost per base covered of 0.19 than programs BatchPrimer3 and PAMPS, which achieved 0.25 and 0.64 primer nucleotides, respectively.

Conclusions
MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base.
The adhesion modulation protein, AmpA localizes to an endocytic compartment andinfluences substrate adhesion, actin polymerization and endocytosis invegetative Dictyostelium cells
Authors: Noratel Elizabeth F , Petty Chere’ L , Kelsey Jessica S , Cost Hoa N , Basappa Nisha , Blumberg Daphne D 
Published: November 2012

Abstract

Background
AmpA is a secreted 24Kd protein that has pleiotropic effects onDictyostelium development. Null mutants delay development atthe mound stage with cells adhering too tightly to the substrate. Prestalkcells initially specify as prespore cells and are delayed in their migrationto the mound apex. Extracellular AmpA can rescue these defects, but AmpA isalso necessary in a cell autonomous manner for a nteriorl ike c ells (ALCs) to migrate to the upper cup. The ALCsare only 10% of the developing cell population making it difficult to studythe cell autonomous effect of AmpA on the migration of these cells. AmpA isalso expressed in growing cells, but, while it contains a hydrophobic leadersequence that is cleaved, it is not secreted from growing cells. This makesgrowing cells an attractive system for studying the cell autonomous functionof AmpA.

Results
In growing cells AmpA plays an environment dependent role in cell migration.Excess AmpA facilitates migration on soft, adhesive surfaces but hindersmigration on less adhesive surfaces. AmpA also effects the level of actinpolymerization. Knockout cells polymerize less actin while over expressingcells polymerize more actin than wild type. Overexpression of AmpA alsocauses an increase in endocytosis that is traced to repeated formation ofmultiple endocytic cups at the same site on the membrane. Immunofluorescenceanalysis shows that AmpA is found in the Golgi and colocalizes with calnexinand the slow endosomal recycling compartment marker, p25, in a perinuclearcompartment. AmpA is found on the cell periphery and is endocyticallyrecycled to the perinuclear compartment.

Conclusion
AmpA is processed through the secretory pathway and traffics to the cellperiphery where it is endocytosed and localizes to what has been defined asa slow endosomal recycling compartment. AmpA plays a role in actinpolymerization and cell substrate adhesion. Additionally AmpA influencescell migration in an environment dependent manner. Wild type cells show verylittle variation in migration rates under the different conditions examinedhere, but either loss or over expression of AmpA cause significant substrateand environment dependent changes in migration.
A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells
Authors: Kloster Maria Bro , Bilgrau Anders Ellern , Rodrigo-Domingo Maria , Bergkvist Kim Steve , Schmitz Alexander , Sønderkær Mads , Bødker Julie Støve , Falgreen Steffen , Nyegaard Mette , Johnsen Hans Erik , Nielsen Kåre Lehmann , Dybkaer Karen , Bøgsted Martin 
Published: November 2012

Abstract

Background
Malignant cells in tumours of B-cell origin account for 0.1% to 98% of the total cell content, depending on disease entity. Recently, gene expression profiles (GEPs) of B-cell lymphomas based on microarray technologies have contributed significantly to improved sub-classification and diagnostics. However, the varying degrees of malignant B-cell frequencies in analysed samples influence the interpretation of the GEPs. Based on emerging next-generation sequencing technologies (NGS) like tag sequencing (tag-seq) for GEP, it is expected that the detection of mRNA transcripts from malignant B-cells can be supplemented. This study provides a quantitative assessment and comparison of the ability of microarrays and tag-seq to detect mRNA transcripts from malignant B-cells. A model system was established by eight serial dilutions of the malignant B-cell lymphoma cell line, OCI-Ly8, into the embryonic kidney cell line, HEK293, prior to parallel analysis by exon microarrays and tag-seq.

Results
We identified 123 and 117 differentially expressed genes between pure OCI-Ly8 and HEK293 cells by exon microarray and tag-seq, respectively. There were thirty genes in common, and of those, most were B-cell specific. Hierarchical clustering from all dilutions based on the differentially expressed genes showed that neither technology could distinguish between samples with less than 1% malignant B-cells from non-B-cells. A novel statistical concept was developed to assess the ability to detect single genes for both technologies, and used to demonstrate an inverse proportional relationship with the sample purity. Of the 30 common genes, the detection capability of a representative set of three B-cell specific genes - CD74, HLA-DRA, and BCL6 - was analysed. It was noticed that at least 5%, 13% and 22% sample purity respectively was required for detection of the three genes by exon microarray whereas at least 2%, 4% and 51% percent sample purity of malignant B-cells were required for tag-seq detection.

Conclusion
A sample purity-dependent loss of the ability to detect genes for both technologies was demonstrated. Taq-seq, in comparison to exon microarray, required slightly less malignant B-cells in the samples analysed in order to detect the two most abundantly expressed of the selected genes. The results show that malignant cell frequency is an important variable, with fundamental impact when interpreting GEPs from both technologies.
Transcranial magnetic stimulation with a half-sine wave pulse elicits direction-specific effects in human motor cortex
Authors: Jung Nikolai H , Delvendahl Igor , Pechmann Astrid , Gleich Bernhard , Gattinger Norbert , Siebner Hartwig R , Mall Volker 
Published: November 2012

Abstract

Background
Transcranial magnetic stimulation (TMS) commonly uses so-called monophasic pulses where the initial rapidly changing current flow is followed by a critically dampened return current. It has been shown that a monophasic TMS pulse preferentially excites different cortical circuits in the human motor hand area (M1-HAND), if the induced tissue current has a posterior-to-anterior (PA) or anterior-to-posterior (AP) direction. Here we tested whether similar direction-specific effects could be elicited in M1-HAND using TMS pulses with a half-sine wave configuration.

Results
In 10 young participants, we applied half-sine pulses to the right M1-HAND which elicited PA or AP currents with respect to the orientation of the central sulcus.
Measurements of the motor evoked potential (MEP) revealed that PA half-sine stimulation resulted in lower resting motor threshold (RMT) than AP stimulation. When stimulus intensity (SI) was gradually increased as percentage of maximal stimulator output, the stimulus–response curve (SRC) of MEP amplitude showed a leftward shift for PA as opposed to AP half-sine stimulation. Further, MEP latencies were approximately 1 ms shorter for PA relative to AP half-sine stimulation across the entire SI range tested. When adjusting SI to the respective RMT of PA and AP stimulation, the direction-specific differences in MEP latencies persisted, while the gain function of MEP amplitudes was comparable for PA and AP stimulation.

Conclusions
Using half-sine pulse configuration, single-pulse TMS elicits consistent direction-specific effects in M1-HAND that are similar to TMS with monophasic pulses. The longer MEP latency for AP half-sine stimulation suggests that PA and AP half-sine stimulation preferentially activates different sets of cortical neurons that are involved in the generation of different corticospinal descending volleys.
Novel molecular, cytotoxical, and immunological study on promising and selective anticancer activity of Mung bean sprouts
Authors: Hafidh Rand R , Abdulamir Ahmed S , Bakar Fatimah Abu , Jalilian Farid Azizi , Abas Faridah , Sekawi Zamberi 
Published: November 2012

Abstract

Background
The anticancer and immunomodulatory activity of mung bean sprouts (MBS) and the underlying mechanisms against human cervical and hepatocarcinoma cancer cells were explored.

Methods
MBS cytotoxicity and MBS-induced anticancer cytokines, TNF-α and IFN-β from cancer cells, and immunological cytokines, IL-4, IFN-γ, and IL-10 from peripheral mononuclear cells (PMNC) were assessed by MTS and ELISA assays. Apoptotic cells were investigated by flow cytometry. The expression level of apoptotic genes (Bax, BCL-2, Capsases 7–9) and cell cycle regulatory genes (cyclin D, E, and A) and tumor suppressor proteins (p27, p21, and p53) was assessed by real-time qPCR in the cancer cells treated with extract IC50.

Results
The cytotoxicity on normal human cells was significantly different from HeLa and HepG2 cells, 163.97 ± 5.73, 13.3 ± 0.89, and 14.04 ± 1.5 mg/ml, respectively. The selectivity index (SI) was 12.44 ± 0.83 for HeLa and 11.94 ± 1.2 for HepG2 cells. Increased levels of TNF-α and IFN-β were observed in the treated HeLa and HepG2 culture supernatants when compared with untreated cells. MBS extract was shown to be an immunopolarizing agent by inducing IFNγ and inhibiting IL-4 production by PBMC; this leads to triggering of CMI and cellular cytotoxicity. The extract induced apoptosis, in a dose and time dependent manner, in treated HeLa and HepG2, but not in untreated, cells (P < 0.05). The treatment significantly induced cell cycle arrest in G0/G1 in HeLa cells. The percentage of cells in G0/G1 phase of the treated HeLa cells increased from 62.87 ± 2.1%, in untreated cells, to 80.48 ± 2.97%. Interestingly, MBS IC50 induced the expression of apoptosis and tumor suppressor related genes in both HeLa and HepG2 cells. MBS extract succeeded in inducing cdk-inhibitors, p21, p53, and p27 in HeLa cells while it induced only p53 in HepG2 cells (P < 0.05). This is a clue for the cell type- specific interaction of the studied extract. These proteins inhibit the cyclin-cdk complexes apart from the presence of some other components that might stimulate some cyclins such as cyclin E, A, and D.

Conclusion
MBS extract was shown to be a potent anticancer agent granting new prospects of anticancer therapy using natural products.
Relationship among coronary plaque compliance, coronary risk factors and tissue characteristics evaluated by integrated backscatter intravascular ultrasound
Authors: Ishihara Yoshiyuki , Kawasaki Masanori , Hattori Arihiro , Imai Hajime , Takahashi Shigekiyo , Sato Hironobu , Kubota Tomoki , Okubo Munenori , Ojio Shinsuke , Nishigaki Kazuhiko , Takemura Genzou , Fujiwara Hisayoshi , Minatoguchi Shinya 
Published: November 2012

Abstract

Background
The purpose of the present study was to evaluate the mechanical properties of coronary plaques and plaque behavior, and to elucidate the relationship among tissue characteristics of coronary plaques, mechanical properties and coronary risk factors using integrated backscatter intravascular ultrasound (IB-IVUS).

Methods
Non-targeted plaques with moderate stenosis (plaque burden at the minimal lumen site: 50-70%) located proximal to the site of the percutaneous coronary intervention target lesions were evaluated by IB-IVUS. Thirty-six plaques (less calcified group: an arc of calcification ≤10°) in 36 patients and 22 plaques (moderately calcified group: 10° < an arc of calcification ≤60°) in 22 patients were evaluated. External elastic membrane volume (EEMV) compliance, lumen volume (LV) compliance, plaque volume (PV) response (difference between PV in systole and diastole), EEM area stiffness index were measured at the minimal lumen site. Relative lipid volume (lipid volume/internal elastic membrane volume) was calculated by IB-IVUS.

Results
In the less calcified group, there was a significant correlation between EEMV compliance and the relative lipid volume (r = 0.456, p = 0.005). There was a significant inverse correlation between EEM area stiffness index and the relative lipid volume (p = 0.032, r = −0.358). The LV compliance and EEM area stiffness index were significantly different in the diabetes mellitus (DM) group than in the non-DM group (1.32 ± 1.49 vs. 2.47 ± 1.79%/10 mmHg, p =0.014 and 28.3 ± 26.0 vs. 15.7 ± 17.2, p =0.020). The EEMV compliance and EEM area stiffness index were significantly different in the hypertension (HTN) group than in the non-HTN group (0.77 ± 0.68 vs. 1.57 ± 0.95%/10 mmHg, p =0.012 and 26.5 ± 24.3 vs. 13.0 ± 16.7, p =0.020). These relationships were not seen in the moderately calcified group.

Conclusion
The present study provided new findings that there was a significant correlation between mechanical properties and tissue characteristics of coronary arteries. In addition, our results suggested that the EEMV compliance and the LV compliance were independent and the compliance was significantly impaired in the patients with DM and/or HTN. Assessment of coronary mechanical properties during PCI may provide us with useful information regarding the risk stratification of patients with coronary heart disease.
Some results on q-difference equations
Authors: Zhang Junchao , Wang Gang , Chen Junjie , Zhao Rongxiang 
Published: November 2012

Abstract
In this paper, we consider the q-difference analogue of the Clunie theorem. We obtain there is no zero-order entire solution of

f
n

(
z
)
+

(

∇
q

f
(
z
)
)

n

=
1

when

n
≥
2

; there is no zero-order transcendental entire solution of

f
n

(
z
)
+
P
(
z
)

(

∇
q

f
(
z
)
)

m

=
Q
(
z
)

when

n
>
m
≥
0

; and the equation

f
n

+
P
(
z
)

∇
q

f
(
z
)
=
h
(
z
)

has at most one zero-order transcendental entire solution f if f is not the solution of

∇
q

f
(
z
)
=
0

, when

n
≥
4

.

MSC:30D35, 30D30, 39A13, 39B12.
Consistent condom use increases spontaneous regression in high-risk non-HPV16 but not in HPV16 CIN2-3 lesions, a prospective population-based cohort study
Authors: Munk Ane Cecilie , Øvestad Irene Tveiterås , Gudlaugsson Einar , Løvslett Kjell , Fiane Bent , van Diermen-Hidle Bianca , Kruse Arnold-Jan , Skaland Ivar , Janssen Emiel AM , Baak Jan PA 
Published: November 2012

Abstract

Background
The major cause of cervical intraepithelial neoplasia (CIN) is persistent infection with human papillomavirus (HPV). Most CIN grade 2 and 3 lesions are treated with cone excision, although a substantial proportion (6-50%) of CIN2-3 lesions will regresses spontaneously. Predictors for regression of CIN2-3 are desirable in order to reduce this overtreatment.

Methods
In this prospective cohort study, 145 consecutive women with first-time onset CIN2-3 in colposcopy-directed biopsies and standardized biopsy-cone excision interval were included. The genotype of the high-risk human papillomaviruses (=hr HPV) and clinical factors including sexual behaviour, parity, contraception and smoking were assessed. Patients were divided into two groups according to lesions containing HPV16 (hr HPV16+) and high-risk non-HPV16 (hr HPV16-) genotypes.

Results
Women whose partners consistently used condoms showed a significantly higher regression rate than women using other types of contraception (53% versus 13%, p<0.0001). However, this effect was only seen in hr HPV16- patients (73% regression rate versus 13%, p<0.0001). Hr HPV16+ patients had a significantly higher number of sexual partners and more current smokers compared to hr HPV16- patients. The regression rate was not significantly different in CIN2-3 lesions containing HPV16 (hr HPV16+) versus hr HPV16- genotypes.

Conclusions
Heterogeneity among hr HPV genotypes excists. HPV-genotype analyses can identify women who significantly increase their chance of regression by consistent condom use.