bluuebunny/crossref_metadata_2025_split huggingface dataset:
A coherent feedforward loop design principle to sustain robustness of biological networks
Authors: Le Duc-Hau , Kwon Yung-Keun 
Published: January 2013

AbstractMotivation: Many studies have investigated the relationship between structural properties and dynamic behaviors in biological networks. In particular, feedback loop (FBL) and feedforward loop (FFL) structures have received a great deal of attention. One interesting and common property of FBL and FFL structures is their coherency of coupling. However, the role of coherent FFLs in relation to network robustness is not fully known, whereas that of coherent FBLs has been well established.Results: To establish that coherent FFLs are abundant in biological networks, we examined gene regulatory and signaling networks and found that FFLs are ubiquitous, and are in a coherently coupled form. This result was also observed in the species-based signaling networks that are integrated from KEGG database. By using a random Boolean network model, we demonstrated that these coherent FFLs can improve network robustness against update-rule perturbations. In particular, we found that coherent FFLs increase robustness because these structures induce downstream nodes to be robust against update-rule perturbations. Therefore, coherent FFLs can be considered as a design principle of human signaling networks that improve network robustness against update-rule perturbations.Contact: kwonyk@ulsan.ac.krSupplementary information: Supplementary data are available at Bioinformatics online.
PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information
Authors: Li Tao , Li Qian-Zhong , Liu Shuai , Fan Guo-Liang , Zuo Yong-Chun , Peng Yong 
Published: January 2013

AbstractMotivation: Protein–DNA interactions often take part in various crucial processes, which are essential for cellular function. The identification of DNA-binding sites in proteins is important for understanding the molecular mechanisms of protein–DNA interaction. Thus, we have developed an improved method to predict DNA-binding sites by integrating structural alignment algorithm and support vector machine–based methods.Results: Evaluated on a new non-redundant protein set with 224 chains, the method has 80.7% sensitivity and 82.9% specificity in the 5-fold cross-validation test. In addition, it predicts DNA-binding sites with 85.1% sensitivity and 85.3% specificity when tested on a dataset with 62 protein–DNA complexes. Compared with a recently published method, BindN+, our method predicts DNA-binding sites with a 7% better area under the receiver operating characteristic curve value when tested on the same dataset. Many important problems in cell biology require the dense non-linear interactions between functional modules be considered. Thus, our prediction method will be useful in detecting such complex interactions.Availability: The PreDNA webserver is freely available at: http://202.207.14.178/predna/index.aspxContact: qzli@imu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online
Transport of misfolded endoplasmic reticulum proteins to the cell surface by MHC class II molecules
Authors: Jiang Yan , Arase Noriko , Kohyama Masako , Hirayasu Kouyuki , Suenaga Tadahiro , Jin Hui , Matsumoto Maki , Shida Kyoko , Lanier Lewis L. , Saito Takashi , Arase Hisashi 
Published: January 2013

Abstract
Nascent MHC class II molecules are associated with the invariant chain and are transported to the endolysosomal pathway, where MHC class II molecules acquire peptide antigens. On the other hand, misfolded endoplasmic reticulum (ER) proteins are generally degraded in the cells and are neither expressed on the cell surface nor secreted. Here, we found that MHC class II molecules associate with some misfolded ER proteins via the peptide-binding groove in competition with invariant chain. The misfolded proteins associated with MHC class II molecules are transported intact to the cell surface without processing to peptides. Furthermore, these complexes efficiently stimulate antigen-specific B cells. These findings reveal that MHC class II molecules function as a chaperone for the cell surface expression of misfolded ER proteins. In addition, we suggest that MHC class II molecules present not only peptides but also intact host-cell-derived proteins on the cell surface. These findings provide new insights into the function of MHC class II molecules.
Impact of Entropy Monitoring on Volatile Anesthetic Uptake
Authors: El Hor Tarek , Van Der Linden Philippe , De Hert Stephan , Mélot Christian , Bidgoli Javad 
Published: January 2013

Abstract

Background:
Electroencephalogram-derived monitoring to assess anesthetic depth may allow more accurate hypnotic drug administration, resulting in decreased anesthetic drug consumption. The authors hypothesized that the use of M-Entropy monitoring (Datex-Ohmeda, Helsinki, Finland) is associated with reduced sevoflurane uptake (primary outcome) in patients undergoing major abdominal surgery.

Methods:
A total of 50 patients with an American Society of Anesthesiology score of II–III, scheduled for elective laparoscopic rectosigmoidectomy were randomized into two groups in this randomized controlled trial. In the control group, the target expiratory fraction of sevoflurane was adapted according to standard clinical practice. In the study group, the target expiratory fraction of sevoflurane was adapted to maintain state entropy values between 40 and 60. State entropy values were continuously recorded in both groups but were not available to the anesthesiologist in the control group. In both groups, patients were ventilated using the auto-control mode of the Zeus® (Dräger, Lübeck, Germany) respirator, which allows precise measurements of sevoflurane uptake. Sufentanil was administered using a target-controlled infusion system.

Results:
Demographics did not differ between groups. During the anesthesia maintenance phase, state entropy values were lower in the control group than the study group (P < 0.0001). Sevoflurane uptake was higher in the control group than the study group (5.2 ± 1.4 ml/h vs. 3.8 ± 1.5 ml/h; P = 0.0012). Three patients in the control group developed intraoperative hypotension compared with none in the study group (P = 0.03).

Conclusions:
Monitoring the depth of anesthesia using M-Entropy was associated with a significant reduction in sevoflurane uptake.
RootScape: A Landmark-Based System for Rapid Screening of Root Architecture in Arabidopsis
Authors: Ristova Daniela , Rosas Ulises , Krouk Gabriel , Ruffel Sandrine , Birnbaum Kenneth D. , Coruzzi Gloria M. 
Published: January 2013

Abstract
The architecture of plant roots affects essential functions including nutrient and water uptake, soil anchorage, and symbiotic interactions. Root architecture comprises many features that arise from the growth of the primary and lateral roots. These root features are dictated by the genetic background but are also highly responsive to the environment. Thus, root system architecture (RSA) represents an important and complex trait that is highly variable, affected by genotype × environment interactions, and relevant to survival/performance. Quantification of RSA in Arabidopsis (Arabidopsis thaliana) using plate-based tissue culture is a very common and relatively rapid assay, but quantifying RSA represents an experimental bottleneck when it comes to medium- or high-throughput approaches used in mutant or genotype screens. Here, we present RootScape, a landmark-based allometric method for rapid phenotyping of RSA using Arabidopsis as a case study. Using the software AAMToolbox, we created a 20-point landmark model that captures RSA as one integrated trait and used this model to quantify changes in the RSA of Arabidopsis (Columbia) wild-type plants grown under different hormone treatments. Principal component analysis was used to compare RootScape with conventional methods designed to measure root architecture. This analysis showed that RootScape efficiently captured nearly all the variation in root architecture detected by measuring individual root traits and is 5 to 10 times faster than conventional scoring. We validated RootScape by quantifying the plasticity of RSA in several mutant lines affected in hormone signaling. The RootScape analysis recapitulated previous results that described complex phenotypes in the mutants and identified novel gene × environment interactions.
Elevated Early Callose Deposition Results in Complete Penetration Resistance to Powdery Mildew in Arabidopsis
Authors: Ellinger Dorothea , Naumann Marcel , Falter Christian , Zwikowics Claudia , Jamrow Torsten , Manisseri Chithra , Somerville Shauna C. , Voigt Christian A. 
Published: January 2013

Abstract
A common response by plants to fungal attack is deposition of callose, a (1,3)-β-glucan polymer, in the form of cell wall thickenings called papillae, at site of wall penetration. While it has been generally believed that the papillae provide a structural barrier to slow fungal penetration, this idea has been challenged in recent studies of Arabidopsis (Arabidopsis thaliana), where fungal resistance was found to be independent of callose deposition. To the contrary, we show that callose can strongly support penetration resistance when deposited in elevated amounts at early time points of infection. We generated transgenic Arabidopsis lines that express POWDERY MILDEW RESISTANT4 (PMR4), which encodes a stress-induced callose synthase, under the control of the constitutive 35S promoter. In these lines, we detected callose synthase activity that was four times higher than that in wild-type plants 6 h post inoculation with the virulent powdery mildew Golovinomyces cichoracearum. The callose synthase activity was correlated with enlarged callose deposits and the focal accumulation of green fluorescent protein-tagged PMR4 at sites of attempted fungal penetration. We observed similar results from infection studies with the nonadapted powdery mildew Blumeria graminis f. sp. hordei. Haustoria formation was prevented in resistant transgenic lines during both types of powdery mildew infection, and neither the salicylic acid-dependent nor jasmonate-dependent pathways were induced. We present a schematic model that highlights the differences in callose deposition between the resistant transgenic lines and the susceptible wild-type plants during compatible and incompatible interactions between Arabidopsis and powdery mildew.
Cell-to-Cell Movement of Two Interacting AT-Hook Factors inArabidopsisRoot Vascular Tissue Patterning
Authors: Zhou Jing , Wang Xu , Lee Jung-Youn , Lee Ji-Young 
Published: January 2013

AbstractThe xylem and phloem, major conducting and supporting tissues in vascular plants, are established by cell division and cell-type specification in the procambium/cambium. The organization of the xylem, phloem, and procambium/cambium is tightly controlled. However, the underlying regulatory mechanisms remain largely unknown. In this study, we report the discovery of two transcription factors, AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 3 (AHL3) and AHL4, which regulate vascular tissue boundaries in Arabidopsis thaliana roots. In either of the knockout mutants of AHL3 and AHL4, encoding closely related AT-hook transcription factors, a misspecification of tissue boundaries between the xylem and procambium occurred and ectopic xylem developed in the procambium domain. In plants, specific types of transcription factors can serve as direct intercellular signals by moving from one cell to another, playing crucial roles in tissue patterning. Adding to this paradigm, AHL4 moves actively from the procambium to xylem in the root meristem to regulate the tissue boundaries. When the intercellular movement of AHL4 was impaired, AHL4 could not complement the xylem phenotype in the ahl4. Furthermore, AHL4 revealed unique characteristics in that it interacts with AHL3 in vivo and that this interaction facilitates their intercellular trafficking. Taken together, this study uncovered a novel mechanism in vascular tissue patterning that requires the intercellular trafficking of two interacting transcription factors.
Transcription Repressor HANABA TARANU Controls Flower Development by Integrating the Actions of Multiple Hormones, Floral Organ Specification Genes, and GATA3 Family Genes inArabidopsis
Authors: Zhang Xiaolan , Zhou Yun , Ding Lian , Wu Zhigang , Liu Renyi , Meyerowitz Elliot M. 
Published: January 2013

AbstractPlant inflorescence meristems and floral meristems possess specific boundary domains that result in proper floral organ separation and specification. HANABA TARANU (HAN) encodes a boundary-expressed GATA3-type transcription factor that regulates shoot meristem organization and flower development in Arabidopsis thaliana, but the underlying mechanism remains unclear. Through time-course microarray analyses following transient overexpression of HAN, we found that HAN represses hundreds of genes, especially genes involved in hormone responses and floral organ specification. Transient overexpression of HAN also represses the expression of HAN and three other GATA3 family genes, HANL2 (HAN-LIKE 2), GNC (GATA, NITRATE-INDUCIBLE, CARBON-METABOLISM-INVOLVED), and GNL (GNC-LIKE), forming a negative regulatory feedback loop. Genetic analysis indicates that HAN and the three GATA3 family genes coordinately regulate floral development, and their expression patterns are partially overlapping. HAN can homodimerize and heterodimerize with the three proteins encoded by these genes, and HAN directly binds to its own promoter and the GNC promoter in vivo. These findings, along with the fact that constitutive overexpression of HAN produces an even stronger phenotype than the loss-of-function mutation, support the hypothesis that HAN functions as a key repressor that regulates floral development via regulatory networks involving genes in the GATA3 family, along with genes involved in hormone action and floral organ specification.
The Impact of Iron on the Bleaching Efficacy of Hydrogen Peroxide in Liquid Whey Systems
Authors: Jervis Suzanne M. , Drake MaryAnne 
Published: January 2013

Abstract Whey is a value‐added product that is utilized in many food and beverage applications for its nutritional and functional properties. Whey and whey products are generally utilized in dried ingredient applications. One of the primary sources of whey is from colored Cheddar cheese manufacture that contains the pigment annatto resulting in a characteristic yellow colored Cheddar cheese. The colorant is also present in the liquid cheese whey and must be bleached so that it can be used in ingredient applications without imparting a color. Hydrogen peroxide and benzoyl peroxide are 2 commercially approved chemical bleaching agents for liquid whey. Concerns regarding bleaching efficacy, off‐flavor development, and functionality changes have been previously reported for whey bleached with hydrogen peroxide and benzoyl peroxide. It is very important for the dairy industry to understand how bleaching can impact flavor and functionality of dried ingredients. Currently, the precise mechanisms of off‐flavor development and functionality changes are not entirely understood. Iron reactions in a bleached liquid whey system may play a key role. Reactions between iron and hydrogen peroxide have been widely studied since the reaction between these 2 relatively stable species can cause great destruction in biological and chemical systems. The actual mechanism of the reaction of iron with hydrogen peroxide has been a controversy in the chemistry and biological community. The precise mechanism for a given reaction can vary greatly based upon the concentration of reactants, temperature, pH, and addition of biological material. In this review, some hypotheses for the mechanisms of iron reactions that may occur in fluid whey that may impact bleaching efficacy, off‐flavor development, and changes in functionality are presented.Practical Application:  Cheese whey is bleached to remove residual carotenoid cheese colorant. Concerns regarding bleaching efficacy, off‐flavor development, and functionality changes have been reported for whey proteins bleached with hydrogen peroxide and benzoyl peroxide. It is very important for the dairy industry to understand how whey bleaching can impact flavor and functionality of dried ingredients. Proposed mechanisms of off‐flavor development and functionality changes are discussed in this hypothesis paper.
Prenatal diagnosis of abnormally invasive placenta reduces maternal peripartum hemorrhage and morbidity
Authors: Chantraine Frédéric , Braun Thorsten , Gonser Markus , Henrich Wolfgang , Tutschek Boris 
Published: January 2013

AbstractObjectiveAbnormally invasive placenta (AIP) poses diagnostic and therapeutic challenges. We analyzed clinical cases with confirmed placenta increta or percreta.DesignRetrospective case series.SettingMulticenter study.PopulationPregnant women with AIP.MethodsChart review.Main outcome measuresPrenatal detection rates, treatment choices, morbidity, mortality and short‐term outcome.ResultsSixty‐six cases were analyzed. All women and all but three fetuses survived; 57/64 women (89%) had previous uterine surgery. In 26 women (39%) the diagnosis was not known before delivery (Group 1), in the remaining 40 (61%) diagnosis had been made between 14 and 37 weeks of gestation (Group 2). Placenta previa was present in 36 women (54%). In Groups 1 and 2, 50% (13/26) and 62% (25/40) of the women required hysterectomy, respectively. In Group 1 (unknown at the time of delivery) 69% (9/13) required (emergency) hysterectomy for severe hemorrhage in the immediate peripartum period compared with only 12% (3/25) in Group 2 (p = 0.0004). Mass transfusions were more frequently required in Group 1 (46%, 12/26 vs. 20%, 8/40; p = 0.025). In 18/40 women (45%) from Group 2 the placenta was intentionally left in situ; secondary hysterectomies and infections were equally frequent (18%) among these differently treated women. Overall, postpartum infections occurred in 11% and 20% of women in Groups 1 and 2, respectively.ConclusionsAIP was known before delivery in more than half of the cases. Unknown AIP led to significantly more emergency hysterectomies and mass transfusions during or immediately after delivery. Prenatal diagnosis of AIP reduces morbidity. Future studies should also address the selection criteria for cases appropriate for leaving the placenta in situ.
Hysteroscopic resection of abnormally invasive placenta residuals
Authors: Nisolle Michelle , Delbecque Katty , Perrier D'Hauterive Sophie , Firquet Anne , Chantraine Frédéric 
Published: January 2013

AbstractObjectiveTo present our experience in hysteroscopic removal of abnormally invasive placenta (AIP) residuals using bipolar energy.DesignCase series.SettingUniversity hospital.PopulationSixteen patients with AIP residuals after 17 pregnancies.MethodsCases were identified by ultrasound, treated with hysteroscopic bipolar electrosurgery and oral contraceptives, and followed up by ultrasound or hysteroscopy. Nine subsequent pregnancies were described.Main outcome measures and ResultsComplete removal of AIP residuals was achieved by hysteroscopic bipolar electrosurgery in all cases except one. No perioperative complications occurred. AIP residual recurred in one patient after a subsequent pregnancy and was successfully treated using the same procedure.ConclusionsAIP residual is a rare condition. Management by hysteroscopic resection using bipolar energy is safe and feasible.
Relationship of Δ6‐desaturase and Δ5‐desaturase activities with thyroid hormone status in adolescents with eating disorders and weight loss
Authors: Swenne Ingemar , Vessby Bengt 
Published: January 2013

AbstractAimIn starvation, there is down‐regulation of metabolism and changes in essential fatty acid (FA) status, which could be related to alterations of desaturase activities. Presently, the relationship between thyroid hormones and desaturase activities has been investigated in adolescents with eating disorders and weight loss.MethodsSerum triiodothyronine concentrations and proportions of polyunsaturated FA in plasma phospholipids were analysed in blood samples from 227 adolescents with ED. Δ6‐desaturase (D6D) activity was calculated as the FA ratio 20:3ω6/18:2ω6 and Δ5‐desaturase (D5D) activity as the ratio 20:4ω6/20:3ω6.ResultsSerum triiodothyronine concentrations were related to leanness and ongoing weight loss. The estimated D6D activity was positively correlated with serum triiodothyronine (R2 = 0.232; p < 0.001). D5D activity exhibited a strong inverse correlation with serum triiodothyronine (R2 = 0.410; p < 0.001).ConclusionChanges in desaturase activities during starvation cannot be explained by inhibition/disinhibition by essential FA only. It is possible that the effects of starvation on these enzyme activities, and hence on essential FA status, are mediated by triiodothyronine.
Impacts of an Invasive N2‐Fixing Tree on Hawaiian Stream Water Quality
Authors: Wiegner Tracy N. , Hughes Flint , Shizuma Lisa M. , Bishaw David K. , Manuel Mark E. 
Published: January 2013

AbstractN2‐fixing trees can affect stream water quality. This has been documented in temperate streams, but not in tropical ones, even though N2‐fixing trees are prevalent in the tropics. We investigated the effects of the introduced, invasive tree, Falcataria moluccana (albizia) on water quality of Hawaiian streams. Nutrient concentrations were measured in reaches above and below F. moluccana‐dominated riparian zones of four streams over 14 mo, and benthic algal nutrient limitation was examined in one stream. NO3−+NO2− concentrations were up to 600 percent higher in reaches below F. moluccana stands than in ones above them. In contrast, dissolved organic nitrogen concentrations were 24 percent lower in most reaches below F. moluccana stands, and NH4+ and particulate nitrogen concentrations were similar above and below the stands. Dissolved organic carbon concentrations were up to 30 percent lower below F. moluccana stands, but particulate carbon concentrations were similar between reaches. Total dissolved phosphorus concentrations were similar above and below F. moluccana stands, whereas H4SiO4 concentrations were higher below the stands. In the stream where benthic chlorophyll a was measured, concentrations were three times higher below the F. moluccana stand than above it. Benthic algae were co‐limited by nitrogen and phosphorus above the F. moluccana stand, and limited by phosphorus below it. These results suggest that F. moluccana's presence relieved nitrogen‐limitation and caused the benthic algae to become solely phosphorus‐limited. Overall, our results demonstrate that F. moluccana can strongly affect the chemistry and primary producers of these tropical streams.