bluuebunny/crossref_metadata_2025_split huggingface dataset:
Schizosaccharomyces japonicus: the fission yeast is a fusion of yeast and hyphae
Authors: Niki Hironori 
Published: December 2013

AbstractThe clade of Schizosaccharomyces includes 4 species: S. pombe, S. octosporus, S. cryophilus, and S. japonicus. Although all 4 species exhibit unicellular growth with a binary fission mode of cell division, S. japonicus alone is dimorphic yeast, which can transit from unicellular yeast to long filamentous hyphae. Recently it was found that the hyphal cells response to light and then synchronously activate cytokinesis of hyphae. In addition to hyphal growth, S. japonicas has many properties that aren't shared with other fission yeast. Mitosis of S. japonicas is referred to as semi‐open mitosis because dynamics of nuclear membrane is an intermediate mode between open mitosis and closed mitosis. Novel genetic tools and the whole genomic sequencing of S. japonicas now provide us with an opportunity for revealing unique characters of the dimorphic yeast. © 2013 The Author. Yeast Published by John Wiley & Sons Ltd.
R1 Hepatectomy With Exposure of Tumor Surface for Centrally Located Hepatocellular Carcinoma
Authors: Yu Weibo , Rong Weiqi , Wang Liming , Wu Fan , Xu Quan , Wu Jianxiong 
Published: December 2013

AbstractBackgroundHepatectomy with exposure of tumor surface (a special type of R1 resection) provides a chance of cure for selected patients with centrally located hepatocellular carcinoma (HCC) that is adherent to or compresses major vessels. However, the operative indications, safety, and patient outcomes are not well defined.MethodsWe performed hepatectomy for removal of complex centrally located HCC using a selective and dynamic region‐specific vascular occlusion technique. Between May 2006 and March 2012, a total of 118 patients underwent resection with exposure of tumor surface (exposure group) and 169 underwent conventional hepatectomy (without exposure of the tumor and vascular surface). The short‐ and long‐term outcomes of patients were evaluated and compared.ResultsThe postoperative recovery of liver function was comparable between the two groups. Bile leakage occurred in five patients, all in the exposure group. The 1‐, 3‐, and 5‐year recurrence‐free survival rates were 74.4, 45.6, and 30.1 % in the exposure group and 80.9, 57.2, and 31.7 % in the control group (p = 0.041). Corresponding overall survival rates were 92.3, 70.3, and 44.9 % in the exposure group and 97.8, 81.4, and 53.1 % in the control group (p = 0.094).ConclusionsHepatectomy with exposure of tumor surface is technically demanding, but can be performed safely. It is also associated with a risk of tumor recurrence. Multidisciplinary combined therapy would be the solution and can contribute to improve overall survival.
Optimization of Lipase‐Catalyzed Fractionation of Two Conjugated Linoleic Acid (CLA) Isomers
Authors: Jafari Maryam , Kadivar Mahdi , Goli Sayed Amir Hossein , Ghiaci Mehran 
Published: December 2013

AbstractThe separation of two isomers of conjugated linoleic acid is highly significant since each exhibits different biochemical properties. The aim of this study was to investigate and optimize several factors affecting the esterification of l‐menthol with the c9,t11‐CLA isomer in an organic solvent‐free system using lipase from Candida rugosa (Lipase AY‐30). D‐optimal design with 5 factors and 3 levels were employed to evaluate the effects of synthesis parameters; reaction time (8–24 h), temperature (30–50 °C), enzyme content (2–20 U/ml), substrate molar ratio of conjugated linoleic acid oil to l‐menthol (2:1–1:2) and pH (6–8) on esterification of c9,t11‐CLA with l‐menthol. Based on the analysis of the residual amount of c9,t11‐CLA in the free fatty acid fraction after just one‐step esterification, the optimum synthesis conditions were as follows: reaction time 23.12 h, temperature 32.65 °C, enzyme amount 135.40 U, molar ratio of CLA oil to l‐menthol at 1:1.7 and pH at 7.7; the lowest purity of c9,t11‐CLA in free fatty acid fraction based on the total content of c9,t11 and t10,c12‐CLA isomers was 8.6 %.
Associations among sleep, daily experiences, and loneliness in adolescence: Evidence of moderating and bidirectional pathways
Authors: Doane Leah D. , Thurston Emily C. 
Published: December 2013

ABSTRACTThe present study examined the dynamic associations among daily stress levels, affect, and objective sleep quality in adolescence. We also explored loneliness as a potential moderator of these associations. Seventy‐eight adolescents participated over three days. They completed diary reports of stressful experiences and affect five times a day while wearing an actigraph to obtain objective measurement of sleep. They also provided self‐reports of loneliness. High daily stress was associated with shorter sleep duration. Models testing bidirectional associations indicated that prior day stress was associated with shorter sleep duration, but poor sleep duration and sleep efficiency were also associated with greater stress the next day. Loneliness was a significant moderator of the associations between daily stress and sleep duration and latency such that lonely individuals had shorter sleep durations and sleep latencies after particularly stressful days. Results suggest daily dynamic associations among loneliness, daily stress, and objective measures of adolescent sleep.
Pubertal timing and vulnerabilities to depression in early adolescence: Differential pathways to depressive symptoms by sex☆
Authors: Hamilton Jessica L. , Hamlat Elissa J. , Stange Jonathan P. , Abramson Lyn Y. , Alloy Lauren B. 
Published: December 2013

ABSTRACTAlthough research implicates pubertal processes in the emergence of the sex difference in depression during adolescence, few studies have examined how cognitive and affective vulnerabilities influence the effect of pubertal timing on depressive symptoms. The current study prospectively examined whether early pubertal timing predicted increases in depressive symptoms among adolescents with more negative cognitive styles and lower emotional clarity, and whether this risk was specific to adolescent girls. In a diverse sample of 318 adolescents, early pubertal timing predicted increases in depressive symptoms among adolescent boys and girls with more negative cognitive styles and adolescent girls with poor emotional clarity. These findings suggest that earlier pubertal maturation may heighten the risk of depression for adolescents with pre‐existing vulnerabilities to depression, and that early maturing adolescent girls with lower levels of emotional clarity may be particularly vulnerable to depressive symptoms, representing one pathway through which the sex difference in depression may emerge.
Trust and social reciprocity in adolescence – A matter of perspective‐taking
Authors: Fett Anne‐Kathrin J. , Shergill Sukhi S. , Gromann Paula M. , Dumontheil Iroise , Blakemore Sarah‐Jayne , Yakub Farah , Krabbendam Lydia 
Published: December 2013

ABSTRACTChanges in social behaviour from childhood to adulthood have been suggested to be driven by an increased sensitivity to others' perspectives. Yet, the link between perspective‐taking and social processes, such as trust and reciprocity, has rarely been investigated during adolescence. Using two trust games with a cooperative and an unfair counterpart and an online perspective‐taking task with 50 adolescents, we show that those with a higher perspective‐taking tendency demonstrate greater trust towards others and higher levels of trust during cooperative interactions. Both low and high perspective‐takers adapted their levels of trust in response to unfair behaviour. However, high perspective‐takers reduced their trust more drastically and showed more malevolent and less benevolent tit‐for‐tat when they were treated unfairly by their counterpart. The findings suggest that a higher perspective‐taking tendency in adolescence is associated with specific mechanisms of trust and reciprocity, as opposed to undifferentiated increases in positive social behaviour towards others.
Preeclampsia alters milk neurotrophins and long chain polyunsaturated fatty acids
Authors: Dangat Kamini , Kilari Anitha , Mehendale Savita , Lalwani Sanjay , Joshi Sadhana 
Published: December 2013

AbstractObjectiveTo examine the levels of breast milk neurotrophins 1.5, 3.5, and 6 months of lactation and long chain polyunsaturated fatty acids (LCPUFA) at day 3, 1.5, 2.5, 3.5 and 6 months of lactation in mothers with preeclampsia and compare them with normotensive women. Their associations with growth parameters in children are also examined.MethodsWomen with preeclampsia (n = 101) and normotensive women (n = 144) with singleton pregnancies were recruited for this study. Milk samples were collected and anthropometry was recorded at the first 6 months. The LCPUFA composition of milk samples was analyzed by using gas chromatography at all time points and neurotrophins were analyzed at 1.5, 3.5 and 6 months by Emax Immuno Assay System using Promega kits.ResultsMilk DHA levels were higher at day 3 (9.5%), and 1.5 (23%) and 3.5 (40%) months in mothers with preeclampsia as compared to controls. Milk nerve growth factor (NGF) levels were lower in preeclampsia group as compared to control group at 1.5 (20%) and 3.5 months (27.7%). Milk brain derived neurotrophic factor (BDNF) levels were lower at 1.5 months (10.5%) in the preeclampsia group as compared to control group.ConclusionThe present study suggests that there is a differential regulation of DHA and neurotrophins in breast milk in preeclampsia and are associated with growth parameters of children. Future studies should explore the associations between milk LCPUFA, neurotrophins with neurodevelopment in children.
Spreading depression features and Iba1 immunoreactivity in the cerebral cortex of developing rats submitted to treadmill exercise after treatment with monosodium glutamate
Authors: Lima Cássia Borges , Soares Georgia de Sousa Ferreira , Vitor Suênia Marcele , Andrade‐da‐Costa Belmira Lara da Silveira , Castellano Bernardo , Guedes Rubem Carlos Araujo 
Published: December 2013

AbstractPhysical exercise and excessive consumption of monosodium glutamate (MSG) can affect the morphological and electrophysiological organization of the brain during development. However, the interaction of both factors remains unclear. We analyzed the effect of this interaction on the excitability‐related phenomenon known as cortical spreading depression (CSD) and the microglial reaction expressed as Iba1‐immunolabeled cells in the rat motor cortex. MSG (2 g/kg or 4 g/kg) was administered every other day during the first 14 postnatal days. Treadmill exercise started at 21–23 days of life and lasted 3 weeks, 5 days/week, for 30 min/day. At 45–60 days, CSD was recorded for 4 h at two cortical points and the CSD parameters (velocity, amplitude, and duration of the negative potential change) calculated. Confirming previous observations, exercised rats presented with lower CSD velocities (3.29 ± 0.18 mm/min) than the sedentary group (3.80 ± 0.18 mm/min; P < 0.05). MSG increased CSD velocities in the exercised rats compared to saline‐treated and exercised animals in a dose‐dependent manner (3.49 ± 0.19, 4.05 ± 0.18, and 3.27 ± 0.26 for 2 g/kg MSG, 4 g/kg MSG, and saline, respectively; P < 0.05). The amplitude (ranging from 14.3 ± 5.9 to 18.7 ± 6.2 mV) and duration (46.7 ± 11.1 to 60.5 ± 11.6 s) of the negative slow potential shift of the CSD were similar in all groups. Both exercise and MSG treatment increased Iba1 immunolabeling. The results confirm that physical exercise decelerates CSD propagation. However, it does not impede the CSD‐accelerating action of MSG. These effects were accompanied by a cortical microglia reaction. Therefore, the data suggest that treadmill exercise early in life can influence the development of cortical electrical activity.
LIM‐homeobox gene 2 promotes tumor growth and metastasis by inducing autocrine and paracrine PDGF‐B signaling
Authors: Kuzmanov Aleksandar , Hopfer Ulrike , Marti Patricia , Meyer-Schaller Nathalie , Yilmaz Mahmut , Christofori Gerhard 
Published: December 2013

An epithelial‐mesenchymal transition (EMT) is a critical process during embryonic development and the progression of epithelial tumors to metastatic cancers. Gene expression profiling has uncovered the transcription factor LIM homeobox gene 2 (Lhx2) with up‐regulated expression during TGFβ‐induced EMT in normal and cancerous breast epithelial cells. Loss and gain of function experiments in transgenic mouse models of breast cancer and of insulinoma in vivo and in breast cancer cells in vitro indicate that Lhx2 plays a critical role in primary tumor growth and metastasis. Notably, the transgenic expression of Lhx2 during breast carcinogenesis promotes vessel maturation, primary tumor growth, tumor cell intravasation and metastasis by directly inducing the expression of platelet‐derived growth factor (PDGF)‐B in tumor cells and by indirectly increasing the expression of PDGF receptor‐β (PDGFRβ) on tumor cells and pericytes. Pharmacological inhibition of PDGF‐B/PDGFRβ signaling reduces vessel functionality and tumor growth and Lhx2‐induced cell migration and cell invasion. The data indicate a dual role of Lhx2 during EMT and tumor progression: by inducing the expression of PDGF‐B, Lhx2 provokes an autocrine PDGF‐B/PDGFRβ loop required for cell migration, invasion and metastatic dissemination and paracrine PDGF‐B/PDGFRβ signaling to support blood vessel functionality and, thus, primary tumor growth.
Biological role of prolyl 3-hydroxylation in type IV collagen
Authors: Pokidysheva Elena , Boudko Sergei , Vranka Janice , Zientek Keith , Maddox Kerry , Moser Markus , Fässler Reinhard , Ware Jerry , Bächinger Hans Peter 
Published: December 2013

Significance
Prolyl 3-hydroxylation is a crucial posttranslational modification of collagens. To investigate the role of prolyl 3-hydroxylase 2 (P3H2) and function of 3-hydroxylation in type IV collagen, we created a KO mouse. Prolyl 3-hydroxylation of type IV collagen is required to avoid an aberrant interaction with the platelet-specific glycoprotein VI (GPVI), resulting in platelet aggregation, thrombosis of the maternal blood, and death of the embryo. Homozygous P3H2-null embryos die before embryonic day 8.5. The lethal phenotype can be rescued by producing double mutants of P3H2 and GPVI. Double nulls are viable and fertile. Thus, 3-hydroxylation of type IV collagen is indispensable for embryonic development in mice. We assign a molecular function for prolyl 3-hydroxyl groups in type IV collagen.
Ohnologs are overrepresented in pathogenic copy number mutations
Authors: McLysaght Aoife , Makino Takashi , Grayton Hannah M. , Tropeano Maria , Mitchell Kevin J. , Vassos Evangelos , Collier David A. 
Published: December 2013

Significance
Copy number variants (CNVs) have recently emerged as an important cause of human disorders. Most pathogenic CNVs are large and contain many genes, and identification of the specific disease-causing genes has proven to be challenging. Using an evolutionary genetic approach, we tried to identify such genes through the mapping of ohnologs, genes retained after ancestral whole-genome duplication events. Comparing the proportion of ohnologs between potentially pathogenic and nonpathogenic sets of CNVs, we found that ohnologs are significantly overrepresented in the pathogenic sets. Our results support the hypothesis that ohnologs are ancestral dosage-sensitive elements that may be responsible for some of the deleterious phenotypes observed for CNVs.
Rationale and mechanism for the low photoinactivation rate of bacteria in plasma
Authors: Chen Jie , Cesario Thomas C. , Rentzepis Peter M. 
Published: December 2013

Significance
Human plasma is often decontaminated by methylene blue (MB) photoexcitation; however, the rate of bacterial photoinactivation in plasma has been found to be lower by about an order of magnitude than that in PBS or water. We attribute this low inactivation rate to the bleaching of the 660-nm band of MB by the electrophilic attack of the S–H group of cysteine on the central nitrogen atom. Further investigations are aimed at the development of means that prevent bleaching of MB and allow its photoinactivation of bacteria and other pathogens.
The Opportunity Cost of Travel Time as a Noisy Wage Fraction
Authors: Larson Douglas M. , Lew Daniel K. 
Published: December 2013

AbstractFew issues are more important to welfare estimation with recreation demand models than the specification of the opportunity cost of travel time. The two most common approaches to specifying this cost treat it as a fixed fraction of the recreationist's wage, and either estimate the fraction (done infrequently) or assume it takes some value (done commonly), with references to results from the commute time literature used to justify the latter. However, these approaches lack firm conceptual rationales, and the consequences of using them are not fully understood. Recognizing that information limitations often preclude more general approaches, we use a joint recreation travel‐labor supply model to show that under relatively modest assumptions the opportunity cost of travel time can be expressed as a wage fraction with noise. This formulation is straightforward to implement as part of random parameters‐based recreation demand models. We then evaluate the welfare consequences of using the two approaches noted above, which are special cases of the noisy wage fraction specification. Our results suggest that the more critical restriction to relax in opportunity cost of travel time specifications is the absence of noise, rather than the specific level of the wage fraction.
Foreclosures and Invasive Insect Spread: The Case of Asian Citrus Psyllid
Authors: Richards Timothy J. , Shanafelt David W. , Fenichel Eli P. 
Published: December 2013

AbstractHuman economic activity is considered to be an important factor in exacerbating the speed of invasive species spread, but may also play an important role in preventing it. In this study, we investigate the role of home foreclosure in the spread of Asian Citrus Psyllid (ACP, Diaphorina citri Kuwayama) throughout residential areas of Southern California. We find that foreclosures are indeed a significant factor in explaining ACP spread, even after controlling for other human and environmental effects. Our results suggest that human economic activity may be more important in controlling the spread of invasive species than previously realized, and that the external costs of the foreclosure problem may also be underestimated.
Angel Investment and Collective Agricultural Marketing: The Case of the Minnesota Food Network
Authors: Damon Amy , Nicola Diego 
Published: December 2013

AbstractThe Minnesota Food Network is a limited liability company comprised of 52 farmers producing a variety of high‐quality, sustainably produced agricultural products in southern Minnesota. The network's goal is to develop a regional food system to provide locally grown food at a price that “is fair” to both consumers and producers. This case outlines the challenges that the network faces in their efforts to expand to take advantage of a market opportunity. One of their biggest challenges is that they face high operating costs because of their disaggregated distribution system and need to purchase a distribution and storage facility and two vehicles. They will fund the purchase of a building through an angel investor. An angel investor is necessary because the network cannot sustain traditional loan payments in its current form. Students are asked to consider a number of questions pertaining to the decisions in this case outlined in the final section of the case study.
Discriminative motif optimization based on perceptron training
Authors: Patel Ronak Y. , Stormo Gary D. 
Published: December 2013

Abstract
Motivation: Generating accurate transcription factor (TF) binding site motifs from data generated using the next-generation sequencing, especially ChIP-seq, is challenging. The challenge arises because a typical experiment reports a large number of sequences bound by a TF, and the length of each sequence is relatively long. Most traditional motif finders are slow in handling such enormous amount of data. To overcome this limitation, tools have been developed that compromise accuracy with speed by using heuristic discrete search strategies or limited optimization of identified seed motifs. However, such strategies may not fully use the information in input sequences to generate motifs. Such motifs often form good seeds and can be further improved with appropriate scoring functions and rapid optimization.
Results: We report a tool named discriminative motif optimizer (DiMO). DiMO takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. We use area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. Using DiMO, on a large test set of 87 TFs from human, drosophila and yeast, we show that it is possible to significantly improve motifs identified by nine motif finders. The motifs are generated/optimized using training sets and evaluated on test sets. The AUC is improved for almost 90% of the TFs on test sets and the magnitude of increase is up to 39%.
Availability and implementation: DiMO is available at http://stormo.wustl.edu/DiMO
Contact: rpatel@genetics.wustl.edu, ronakypatel@gmail.com
Quantitative analysis of genomic element interactions by molecular colony technique
Authors: Gavrilov Alexey A. , Chetverina Helena V. , Chermnykh Elina S. , Razin Sergey V. , Chetverin Alexander B. 
Published: December 2013

Abstract
Distant genomic elements were found to interact within the folded eukaryotic genome. However, the used experimental approach (chromosome conformation capture, 3C) enables neither determination of the percentage of cells in which the interactions occur nor demonstration of simultaneous interaction of >2 genomic elements. Each of the above can be done using in-gel replication of interacting DNA segments, the technique reported here. Chromatin fragments released from formaldehyde–cross-linked cells by sodium dodecyl sulfate extraction and sonication are distributed in a polyacrylamide gel layer followed by amplification of selected test regions directly in the gel by multiplex polymerase chain reaction. The fragments that have been cross-linked and separate fragments give rise to multi- and monocomponent molecular colonies, respectively, which can be distinguished and counted. Using in-gel replication of interacting DNA segments, we demonstrate that in the material from mouse erythroid cells, the majority of fragments containing the promoters of active β-globin genes and their remote enhancers do not form complexes stable enough to survive sodium dodecyl sulfate extraction and sonication. This indicates that either these elements do not interact directly in the majority of cells at a given time moment, or the formed DNA–protein complex cannot be stabilized by formaldehyde cross-linking.