bluuebunny/crossref_metadata_2025_split huggingface dataset:
PASmiR: a literature-curated database for miRNA molecular regulation in plant response to abiotic stress
Authors: Zhang Shihua , Yue Yi , Sheng Liang , Wu Yunzhi , Fan Guohua , Li Ao , Hu Xiaoyi , ShangGuan Mingzhu , Wei Chaoling 
Published: March 2013

Abstract

Background
Over 200 published studies of more than 30 plant species have reported a role for miRNAs in regulating responses to abiotic stresses. However, data from these individual reports has not been collected into a single database. The lack of a curated database of stress-related miRNAs limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application.

Description

PASmiR, a literature-curated and web-accessible database, was developed to provide detailed, searchable descriptions of miRNA molecular regulation in different plant abiotic stresses. PASmiR currently includes data from ~200 published studies, representing 1038 regulatory relationships between 682 miRNAs and 35 abiotic stresses in 33 plant species. PASmiR’s interface allows users to retrieve miRNA-stress regulatory entries by keyword search using plant species, abiotic stress, and miRNA identifier. Each entry upon keyword query contains detailed regulation information for a specific miRNA, including species name, miRNA identifier, stress name, miRNA expression pattern, detection method for miRNA expression, a reference literature, and target gene(s) of the miRNA extracted from the corresponding reference or miRBase. Users can also contribute novel regulatory entries by using a web-based submission page. The PASmiR database is freely accessible from the two URLs of http://hi.ustc.edu.cn:8080/PASmiR, and http://pcsb.ahau.edu.cn:8080/PASmiR.

Conclusion
The PASmiR database provides a solid platform for collection, standardization, and searching of miRNA-abiotic stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses for the plant stress physiology community.
CD64-Neutrophil expression and stress metabolic patterns in early sepsis and severe traumatic brain injury in children
Authors: Fitrolaki Diana-Michaela , Dimitriou Helen , Kalmanti Maria , Briassoulis George 
Published: March 2013

Abstract

Background
Critical illness constitutes a serious derangement of metabolism. The aim of our study was to compare acute phase metabolic patterns in children with sepsis (S) or severe sepsis/septic shock (SS) to those with severe traumatic brain injury (TBI) and healthy controls (C) and to evaluate their relations to neutrophil, lymphocyte and monocyte expressions of CD64 and CD11b.

Methods
Sixty children were enrolled in the study. Forty-five children with systemic inflammatory response syndrome (SIRS) were classified into three groups: TBI (n = 15), S (n = 15), and SS (n = 15). C consisted of 15 non- SIRS patients undergoing screening tests for minor elective surgery. Blood samples were collected within 6 hours after admission for flow cytometry of neutrophil, lymphocyte and monocyte expression of CD64 and CD11b (n = 60). Procalcitonin (PCT), C-reactive protein (CRP), glucose, triglycerides (TG), total cholesterol (TC), high (HDL) or low-density-lipoproteins (LDL) were also determined in all groups, and repeated on day 2 and 3 in the 3 SIRS groups (n = 150).

Results
CRP, PCT and TG (p < 0.01) were significantly increased in S and SS compared to TBI and C; glucose did not differ among critically ill groups. Significantly lower were the levels of TC, LDL, and HDL in septic groups compared to C and to moderate changes in TBI (p < 0.0001) but only LDL differed between S and SS (p < 0.02). Among septic patients, PCT levels declined significantly (p < 0.02) with time, followed by parallel decrease of HDL (p < 0.03) and increase of TG (p < 0.02) in the SS group. Neutrophil CD64 (nCD64) expression was higher in patients with SS (81.2%) and S (78.8%) as compared to those with TBI (5.5%) or C (0.9%, p < 0.0001). nCD64 was positively related with CRP, PCT, glucose, and TG (p < 0.01) and negatively with TC, LDL, and HDL (p < 0.0001), but not with severity of illness, hematologic indices, length of stay or mechanical ventilation duration.

Conclusions
In sepsis, the early stress-metabolic pattern is characterized by a high (nCD64, glucose, TG) - low (TC, HDL, LDL) combination in contrast to the moderate pattern of TBI in which only glucose increases combined with a moderate cholesterol - lipoprotein decrease. These early metabolic patterns persist the first 3 days of acute illness and are associated with the acute phase CD64 expression on neutrophils.
Abnormalities of cortical-limbic-cerebellar white matter networks may contribute to treatment-resistant depression: a diffusion tensor imaging study
Authors: Peng Hong-jun , Zheng Hui-rong , Ning Yu-ping , Zhang Yan , Shan Bao-ci , Zhang Li , Yang Hai-chen , Liu Jun , Li Ze-xuan , Zhou Jian-song , Zhang Zhi-jun , Li Ling-jiang 
Published: March 2013

Abstract

Background
White matter abnormalities can cause network dysfunction that underlies major depressive disorder (MDD). Diffusion tensor imaging (DTI) is used to examine the neural connectivity and integrity of the white matter. Previous studies have implicated frontolimbic neural networks in the pathophysiology of MDD. Approximately 30% of MDD patients demonstrate treatment-resistant depression (TRD). However, the neurobiology of TRD remains unclear.

Methods
We used a voxel-based analysis method to analyze DTI data in young patients with TRD (n = 30; 19 males, 11 females) compared with right-handed, age- and sex-matched healthy volunteers (n = 25; 14 males, 11 females).

Results
We found a significant decrease in fractional anisotropy (FA) (corrected, cluster size >50) in the left middle frontal gyrus (peak coordinates [−18 46–14]), left limbic lobe uncus (peak coordinates [−18 2–22]), and right cerebellum posterior lobe (peak coordinates [26–34 -40]). There was no increase in FA in any brain region in patients. We also found a significant negative correlation between mean regional FA values in the three areas and Beck Depression Inventory symptom scores.

Conclusions
We found significant differences in white matter FA in the frontal lobe, limbic lobe and cerebellum between TRD patients and controls. These data suggest that abnormalities of cortical-limbic-cerebellar white matter networks may contribute to TRD in young patients.
In vitro biological effects of two anti-diabetic medicinal plants used in Benin as folk medicine
Authors: Bothon Fifa TD , Debiton Eric , Avlessi Felicien , Forestier Christiane , Teulade Jean-Claude , Sohounhloue Dominique KC 
Published: March 2013

Abstract

Background
Extracts from Polygonum senegalensis (Polygonaceae) and Pseudocedrela kotschyi (Meliaceae) are two important traditionally used medicinal plants in rural Benin to treat many diseases and notably type 2 diabetes. The aim of the study was to investigate the α-glucosidase inhibition, antioxidant and antibacterial activities of those plants extract: Polygonum senegalensis leaves, and Pseudocedrela kotschyi root.

Methods
Hydro-alcoholic (50%) extracts were analyzed for their phytochemical content and tested for their inhibition potency on α-glucosidase from Saccharomyces cerevisiae. Antioxidant activities were assessed using the DPPH, ORAC, FRAP and DCFH-DA (cell based) assay. Finally, the antibacterial activity was evaluated using MIC determination on four Gram-positive cocci (Bacillus subtilis, Clostridium difficile, Enterococcus faecalis, Staphylococcus aureus), three Gram-negative bacilli (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae), and the yeast Candida albicans.

Results
Each extract presented significant α-glucosidase inhibition and antioxidant activities. Polygonum senegalensis leaf extracts were the most active in each in vitro assay with an IC50 = 1.5 μg/ml for α-glucosidase inhibition and an IC50 = 6.8 μg/ml for DPPH scavenging, - 4.5 μmol Fe II/g of dry matter - 9366 μmol Trolox / g DW - for FRAP and ORAC values, respectively. IC50 = 2.3 μg GA / ml for DCFH-DA assay. Concerning its antibacterial activity, a growth inhibitory effect was observed only against three Gram negative bacilli: B. subtilis, E. faecalis, S. aureus and the yeast C. albicans at high concentration.

Conclusion
The results showed that the semi alcoholic extract of the two studied plants possess α-glucosidase inhibitory activity, antioxidant potency, and low antibacterial effect.
Antioxidant and antiproliferative activities of Abrus precatorius leaf extracts - an in vitro study
Authors: Gul Mir Z , Ahmad Farhan , Kondapi Anand K , Qureshi Insaf A , Ghazi Irfan A 
Published: March 2013

Abstract

Background
The use of traditional medicine at the primary health care level is widespread and plant-based treatments are being recommended for curing various diseases by traditional medical practitioners all over the world. The phytochemicals present in the fruits, vegetables and medicinal plants are getting attention day-by-day for their active role in the prevention of several human diseases. Abrus precatorius is a widely distributed tropical medicinal plant with several therapeutic properties. Therefore in the present study, A. precatorius leaf extracts were examined for their antioxidant and cytotoxic properties in vitro in order to discover resources for new lead structures or to improve the traditional medicine.

Methods
In this study, antioxidant and antiproliferative properties of the different leaf extracts (hexane, ethyl acetate, ethanol and water) from A. precatorius were investigated along with the quantification of the polyphenol and flavonoid contents. The ability of deactivating free radicals was extensively investigated with in vitro biochemical methods like DPPH•, •OH, NO, SO2- scavenging assays and inhibition capability of Fe(II)-induced lipid peroxidation. Furthermore, antiproliferative activities using different human cancer cell lines and primary cell line was carried out by MTT method.

Results
Total phenolic content and total flavonoid content of the extracts were found in the range of 1.65 ± 0.22 to 25.48 ± 0.62 GAE mg/g dw and 6.20 ± 0.41 to 17.16 ± 1.04 QE mg/g dw respectively. The experimental results further revealed that A. precatorius extracts showed strong antiradical properties, capable to chelate Fe2+ and possess good inhibition ability of lipid peroxidation. In addition, as a first step towards the identification of phytoconstituents endowed with potent chemopreventive activities, we evaluated the inhibitory effects of A. precatorius extracts on the proliferation of four different human tumour cell lines such as human colon adenocarcinoma cells (Colo-205), human retinoblastoma cancer cells (Y79), human hepatocellular carcinoma cells (HepG2) and Leukemia cells (SupT1). Ethanol extract (APA) and ethyl acetate extract (APE) of A. precatorius had apparent capabilities of inhibiting the survival of tested human cancer cell lines. Moreover, it was observed that the A. precatorius extracts did not inhibit the growth of mice peritoneal macrophages, thus confirming that plants extracts are selective against the cancer cell lines.

Conclusion
This work provides a scientific support for the high antioxidant and antiproliferative activity of this plant and thus it may find potential applications in the treatment of the diseases caused by ROS. Further studies are needed to confirm in vivo anti-tumorgenicity and subsequent chemical characterization of the active molecule(s).
Anti-allergic and anti-inflammatory effects of butanol extract from Arctium Lappa L
Authors: Sohn Eun-Hwa , Jang Seon-A , Joo Haemi , Park Sulkyoung , Kang Se-Chan , Lee Chul-Hoon , Kim Sun-Young 
Published: March 2013

Abstract

Background
Atopic dermatitis is a chronic, allergic inflammatory skin disease that is accompanied by markedly increased levels of inflammatory cells, including eosinophils, mast cells, and T cells. Arctium lappa L. is a traditional medicine in Asia. This study examined whether a butanol extract of A. lappa (ALBE) had previously unreported anti-allergic or anti-inflammatory effects.

Methods
This study examined the effect of ALBE on the release of β-hexosaminidase in antigen-stimulated-RBL-2H3 cells. We also evaluated the ConA-induced expression of IL-4, IL-5, mitogen-activated protein kinases (MAPKs), and nuclear factor (NF)-κB using RT-PCR, Western blotting, and ELISA in mouse splenocytes after ALBE treatment.

Results
We observed significant inhibition of β-hexosaminidase release in RBL-2H3 cells and suppressed mRNA expression and protein secretion of IL-4 and IL-5 induced by ConA-treated primary murine splenocytes after ALBE treatment. Additionally, ALBE (100 μg/mL) suppressed not only the transcriptional activation of NF-κB, but also the phosphorylation of MAPKs in ConA-treated primary splenocytes.

Conclusions
These results suggest that ALBE inhibits the expression of IL-4 and IL-5 by downregulating MAPKs and NF-κB activation in ConA-treated splenocytes and supports the hypothesis that ALBE may have beneficial effects in the treatment of allergic diseases, including atopic dermatitis.
Transport through a strongly coupled graphene quantum dot in perpendicular magnetic field
Authors: Güttinger Johannes , Stampfer Christoph , Frey Tobias , Ihn Thomas , Ensslin Klaus 
Published: March 2013

AbstractWe present transport measurements on a strongly coupled graphene quantum dot in a perpendicular magnetic field. The device consists of an etched single-layer graphene flake with two narrow constrictions separating a 140 nm diameter island from source and drain graphene contacts. Lateral graphene gates are used to electrostatically tune the device. Measurements of Coulomb resonances, including constriction resonances and Coulomb diamonds prove the functionality of the graphene quantum dot with a charging energy of approximately 4.5 meV. We show the evolution of Coulomb resonances as a function of perpendicular magnetic field, which provides indications of the formation of the graphene specific 0th Landau level. Finally, we demonstrate that the complex pattern superimposing the quantum dot energy spectra is due to the formation of additional localized states with increasing magnetic field.
Multi-stream continuous hidden Markov models with application to landmine detection
Authors: Missaoui Oualid , Frigui Hichem , Gader Paul 
Published: March 2013

AbstractWe propose a multi-stream continuous hidden Markov model (MSCHMM) framework that can learn from multiple modalities. We assume that the feature space is partitioned into subspaces generated by different sources of information. In order to fuse the different modalities, the proposed MSCHMM introduces stream relevance weights. First, we modify the probability density function (pdf) that characterizes the standard continuous HMM to include state and component dependent stream relevance weights. The resulting pdf approximate is a linear combination of pdfs characterizing multiple modalities. Second, we formulate the CHMM objective function to allow for the simultaneous optimization of all model parameters including the relevance weights. Third, we generalize the maximum likelihood based Baum-Welch algorithm and the minimum classification error/gradient probabilistic descent (MCE/GPD) learning algorithms to include stream relevance weights. We propose two versions of the MSCHMM. The first one introduces the relevance weights at the state level while the second one introduces the weights at the component level. We illustrate the performance of the proposed MSCHMM structures using synthetic data sets. We also apply them to the problem of landmine detection using ground penetrating radar. We show that when the multiple sources of information are equally relevant across all training data, the performance of the proposed MSCHMM is comparable to the baseline CHMM. However, when the relevance of the sources varies, the MSCHMM outperforms the baseline CHMM because it can learn the optimal relevance weights. We also show that our approach outperforms existing multi-stream HMM because the latter one cannot optimize all model parameters simultaneously.
Supplementation of a grape seed and grape marc meal extract decreases activities of the oxidative stress-responsive transcription factors NF-κB and Nrf2 in the duodenal mucosa of pigs
Authors: Gessner Denise K , Fiesel Anja , Most Erika , Dinges Jennifer , Wen Gaiping , Ringseis Robert , Eder Klaus 
Published: March 2013

Abstract

Background
In pigs, enteric infections and the development of gut disorders such as diarrhoea are commonly observed, particularly after weaning. The present study investigated the hypothesis that feeding a grape seed and grape marc extract (GSGME) as a dietary supplement has the potential to suppress the inflammatory process in the small intestine of pigs by modulating the activities of NF-κB and Nrf2 due to its high content of flavonoids.

Methods
Twenty-four crossbred, 6 weeks old pigs were randomly assigned to 2 groups of 12 animals each and fed nutritionally adequate diets without or with 1% GSGME for 4 weeks.

Results
Pigs administered GSGME had a lower transactivation of NF-κB and Nrf2 and a lower expression of various target genes of these transcription factors in the duodenal mucosa than control pigs (P < 0.05). Concentrations of α-tocopherol and thiobarbituric acid reactive substances (TBARS) in liver and plasma and total antioxidant capacity of plasma and relative mRNA abundances of NF-κB and Nrf2 target genes in the liver did not differ between the two groups. However, the ratio of villus height:crypt depth and the gain:feed ratio was higher in the pigs fed GSGME than in control pigs (P < 0.05).

Conclusions
This study shows that dietary supplementation of a polyphenol rich GSGME suppresses the activity of NF-κB in the duodenal mucosa of pigs and thus might provide a useful dietary strategy to inhibit inflammation in the gut frequently occurring in pigs. Feeding GSGME did not influence vitamin E status and the antioxidant system of the pigs but improved the gain:feed ratio. In overall, the study suggests that polyphenol-rich plant extracts such GSGME could be useful feed supplements in pig nutrition, in order to maintain animal health and improve performance.
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats
Authors: Bonnet Eric , Calzone Laurence , Rovera Daniel , Stoll Gautier , Barillot Emmanuel , Zinovyev Andrei 
Published: March 2013

Abstract

Background
Public repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the formulation of new biological hypotheses to be tested, a fundamental principle of the systems biology approach. However, large-scale molecular maps are not always easy to mine and interpret.

Results
We have developed BiNoM (Biological Network Manager), a Cytoscape plugin, which provides functions for the import-export of some standard systems biology file formats (import from CellDesigner, BioPAX Level 3 and CSML; export to SBML, CellDesigner and BioPAX Level 3), and a set of algorithms to analyze and reduce the complexity of biological networks. BiNoM can be used to import and analyze files created with the CellDesigner software. BiNoM provides a set of functions allowing to import BioPAX files, but also to search and edit their content. As such, BiNoM is able to efficiently manage large BioPAX files such as whole pathway databases (e.g. Reactome). BiNoM also implements a collection of powerful graph-based functions and algorithms such as path analysis, decomposition by involvement of an entity or cyclic decomposition, subnetworks clustering and decomposition of a large network in modules.

Conclusions
Here, we provide an in-depth overview of the BiNoM functions, and we also detail novel aspects such as the support of the BioPAX Level 3 format and the implementation of a new algorithm for the quantification of pathways for influence networks. At last, we illustrate some of the BiNoM functions on a detailed biological case study of a network representing the G1/S transition of the cell cycle, a crucial cellular process disturbed in most human tumors.
Genetic variants and their interactions in disease risk prediction – machine learning and network perspectives
Authors: Okser Sebastian , Pahikkala Tapio , Aittokallio Tero 
Published: March 2013

Abstract
A central challenge in systems biology and medical genetics is to understand how interactions among genetic loci contribute to complex phenotypic traits and human diseases. While most studies have so far relied on statistical modeling and association testing procedures, machine learning and predictive modeling approaches are increasingly being applied to mining genotype-phenotype relationships, also among those associations that do not necessarily meet statistical significance at the level of individual variants, yet still contributing to the combined predictive power at the level of variant panels. Network-based analysis of genetic variants and their interaction partners is another emerging trend by which to explore how sub-network level features contribute to complex disease processes and related phenotypes. In this review, we describe the basic concepts and algorithms behind machine learning-based genetic feature selection approaches, their potential benefits and limitations in genome-wide setting, and how physical or genetic interaction networks could be used as a priori information for providing improved predictive power and mechanistic insights into the disease networks. These developments are geared toward explaining a part of the missing heritability, and when combined with individual genomic profiling, such systems medicine approaches may also provide a principled means for tailoring personalized treatment strategies in the future.