bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and Analysis of Resistance‐like Genes in the Tomato Genome
Authors: Ni Xiaoxun , Yang Jingjing , Sun Silong , Yang Wencai 
Published: August 2013

AbstractTomato (Solanum lycopersicum L.) is one of the most important vegetable crops in the world. However, the tomato production is severely affected by many diseases. The use of host resistance is believed to be the most effective approach to control the pathogens. In this study, a total of 1003 resistance‐like genes were identified from the tomato genome using individual full‐length search and conserved domain verification approach. Of the predicted resistance genes, serine/threonine protein kinase was the largest class with 384 genes followed by 212 genes encoding receptor‐like kinase, 107 genes encoding receptor‐like proteins, 68 genes encoding coiled‐coil–nucleotide‐binding site (NBS)–leucine‐rich repeat (LRR) and 19 genes encoding Toll interleukin‐1 receptor domain‐NBS‐LRR. Physical map positions established for all predicted genes using the tomato WGS chromosomes SL2.40 information indicated that most resistance‐like genes clustered on certain chromosomal regions. Comparisons of the sequences from the same resistance‐like genes in S. pimpinellifolium and S. lycopersicum showed that 93.5% genes contained single nucleotide polymorphisms and 19.7% genes contained insertion/deletion. The data obtained here will facilitate isolation and characterization of new resistance genes as well as marker‐assisted selection for disease resistance breeding in tomato.
Gene expression patterns associated with caste and reproductive status in ants: worker‐specific genes are more derived than queen‐specific ones
Authors: Feldmeyer B. , Elsner D. , Foitzik S. 
Published: August 2013

AbstractVariation in gene expression leads to phenotypic diversity and plays a central role in caste differentiation of eusocial insect species. In social Hymenoptera, females with the same genetic background can develop into queens or workers, which are characterized by divergent morphologies, behaviours and lifespan. Moreover, many social insects exhibit behaviourally distinct worker castes, such as brood‐tenders and foragers. Researchers have just started to explore which genes are differentially expressed to achieve this remarkable phenotypic plasticity. Although the queen is normally the only reproductive individual in the nest, following her removal, young brood‐tending workers often develop ovaries and start to reproduce. Here, we make use of this ability in the ant Temnothorax longispinosus and compare gene expression patterns in the queens and three worker castes along a reproductive gradient. We found the largest expression differences between the queen and the worker castes (~2500 genes) and the smallest differences between infertile brood‐tenders and foragers (~300 genes). The expression profile of fertile workers is more worker‐like, but to a certain extent intermediate between the queen and the infertile worker castes. In contrast to the queen, a high number of differentially expressed genes in the worker castes are of unknown function, pointing to the derived status of hymenopteran workers within insects.
NtProRP1, a novel proline‐rich protein, is an osmotic stress‐responsive factor and specifically functions in pollen tube growth and early embryogenesis in Nicotiana tabacum
Authors: CHEN JUNYI , ZHAO JING , NING JUE , LIU YUAN , XU JING , TIAN SHUJUAN , ZHANG LIYAO , SUN MENG‐XIANG 
Published: August 2013

AbstractProline‐rich proteins (PRPs) are known to play important roles in sexual plant reproduction. Most of the known proteins in the family were found in styles or pollen and modulate pollen tube growth. Here, we identified a novel member of the gene family, NtProRP1, which is preferentially expressed in tobacco pollen grains, pollen tubes and zygotes. NtProRP1 could be secreted into the extracellular space including the cell wall, and the predicted N‐terminal signal peptide is crucial for its secretion. In NtProRP1‐RNAi plants, pollen germination and pollen tube growth were significantly slower and showed zigzag or swell morphology in vitro. Early embryogenesis also exhibited aberrant development, indicative of its critical role in both pollen tube growth and early embryogenesis. Further investigation revealed that NtProRP1 plays a crucial role in osmotic stress response during pollen tube growth and is likely regulated by Tsi, a stress‐responsive gene, suggesting that the regulatory mechanism is also involved in the stress response during sexual plant reproduction. These data provide evidence that NtProRP1 functions as a downstream factor of Tsi1 in the stress response and converges the stress signal into the modulation of pollen tube growth and early embryogenesis.
Perinatal factors in patent ductus arteriosus in very low‐birthweight infants
Authors: Chen Ying‐Yao , Wang Hsiao‐Ping , Chang Jenn‐Tzong , Chiou Yee‐Hsuan , Huang Yung‐Feng , Hsieh Kai‐Sheng ,   Taiwan Premature Infant Development Collaborative Study Group
Published: August 2013

AbstractBackgroundThe relationship between hemoglobin and patent ductus arteriosus (PDA) has not been discussed before. The aim of this study was to assess the influence of hemoglobin and perinatal factors on PDA in very low‐birthweight (VLBW) infants.MethodsUsing data from the Premature Baby Foundation of Taiwan (PBFA), the characteristics, perinatal factors, and hemoglobin of VLBW infants with and without PDA and treatment were compared.ResultsBetween January 2008 and December 2010, 89 VLBW infants were admitted to hospital. The overall survival rate was 87.6%. Twelve infants were excluded. Compared to those without PDA, the 34 infants with PDA received oral indomethacin or surgery, had smaller mean gestational age (GA; 27.93 ± 1.818 weeks, P = 0.000003), lower mean birthweight (BW; 1031 ± 259 g, P = 0.0001), significantly lower Apgar score at 5 min, more severe respiratory distress syndrome (RDS; grade 3 or 4), greater use of surfactants, and lower mean hemoglobin (P = 0.018) after birth than those without PDA. Compared to those with indomethacin, the seven infants with surgery had lower mean GA (26.43 ± 1.718 weeks, P = 0.011), significantly lower Apgar scores at 1 min, but higher platelet count (P = 0.002) after birth, and more red blood cell transfusions (P = 0.039).ConclusionsSmaller GA, lower BW, lower Apgar score at 5 min, more severe RDS, greater use of surfactants, and lower hemoglobin after birth place VLBW infants at greater risk of PDA. Proper prenatal care, and prevention of premature labor and delivery may be the most important preventative factors. The appropriate hemoglobin level for PDA closure requires further investigation.
Association of problem behavior with sleep problems and gastroesophageal reflux symptoms
Authors: Sakaguchi Katsuyoshi , Yagi Takakazu , Maeda Aya , Nagayama Kunihiro , Uehara Sawako , Saito‐Sakoguchi Yoko , Kanematsu Kyoko , Miyawaki Shouichi 
Published: August 2013

AbstractBackgroundThere are few large‐scale epidemiologic studies examining the associations between sleep problems, gastroesophageal reflux disease (GERD) symptoms, lifestyle and food habits and problem behaviors (PB) in adolescents. The aim of this study was to evaluate the associations among these factors in Japanese adolescents.MethodsA cross‐sectional survey of 1840 junior high school students was carried out using questionnaires. The subjects were classified into PB or normal behavior (NB) groups using the Pediatric Symptom Checklist (PSC). The scores of the sleep‐related factors, sleep bruxism, lifestyle and food habits, and GERD symptoms were compared. Logistic regression analysis was used to determine the factors related to PB.ResultsMean subject age was 13.3 ± 1.8 years. The PB group had significantly longer sleep latency and higher GERD symptom score (P < 0.001). Furthermore, the PB group was significantly more likely to experience absence of the mother at dinner time, skip breakfast, and have <30 min of conversation among family at dinner time. The PB group had significantly higher frequencies of sleep bruxism, difficulty falling asleep within 30 min, nightmares, feeling of low sleep quality, daytime somnolence, and daytime lack of motivation. Feelings of low sleep quality had the strongest association with PB, with an adjusted odds ratio of 12.88 (95% confidence interval: 8.99–18.46).ConclusionsPB in adolescents are associated with sleep problems, including sleep bruxism, as well as lifestyle and food habits and GERD symptoms.
Fluid–rock interactions associated with regional tectonics and basin evolution
Authors: Fontana Simone , Nader Fadi Henri , Morad Sadoon , Ceriani Andrea , Al‐Aasm Ihsan Shakir , Daniel Jean‐Marc , Mengus Jean‐Marie 
Published: August 2013

AbstractAn integrated approach consisting of fracture analysis, petrography, carbon, oxygen and strontium‐isotope analyses, as well as fluid‐inclusion micro‐thermometry, led to a better understanding of the evolution of fluid–rock interactions and diagenesis of the Upper Permian to Upper Triassic carbonates of the United Arab Emirates. The deposited carbonates were first marked by extensive early dolomitization. During progressive burial, the carbonates were affected by dolomite recrystallization as well as precipitation of vug and fracture‐filling dolomite, quartz and calcite cements. After considerable burial during the Middle Cretaceous, sub‐vertical north–south oriented fractures (F1) were cemented by dolomite derived from mesosaline to hypersaline fluids. Upon the Late Cretaceous maximum burial and ophiolite obduction, sub‐vertical east–west fractures (F2) were cemented by dolomite (Dc2) and saddle dolomite (Ds) derived from hot, highly saline fluids. Then, minor quartz cement has precipitated in fractures from hydrothermal brines. Fluid‐inclusion analyses of the various diagenetic phases imply the involvement of increasingly hot (200°C) saline brines (20 to 23% NaCl eq.). Through one‐dimensional burial history numerical modelling, the maximum temperatures reached by the studied rocks are estimated to be in the range of 160 to 200°C. Tectonically‐driven flux of hot fluids and associated diagenetic products are interpreted to have initiated during the Late Cretaceous maximum burial and lasted until the Oligocene–Miocene compressional tectonics and related uplift. The circulation of such hydrothermal brines led to partial dissolution of dolomites (Dc2 and Ds) and to precipitation of hydrothermal calcite C1 in new (mainly oriented north–south; F3) and pre‐existing, reactivated fractures. The integration of the obtained data confirms that the diagenetic evolution was controlled primarily by the interplay of the burial thermal evolution of the basin and the regional tectonic history. Hence, this contribution highlights the impacts of regional tectonics and basin history on diagenetic processes, which may subsequently affect reservoir properties.
Detectable urogenital schistosome DNA and cervical abnormalities 6 months after single‐dose praziquantel in women with Schistosoma haematobium infection
Authors: Downs Jennifer A. , Kabangila Rodrick , Verweij Jaco J. , Jaka Hyasinta , Peck Robert N. , Kalluvya Samuel E. , Changalucha John M. , Johnson Warren D. , van Lieshout Lisette , Fitzgerald Daniel W. 
Published: August 2013

AbstractWe explored response to single‐dose praziquantel therapy in a cohort of 33 women with Schistosoma haematobium infection in rural Mwanza, Tanzania. Women with S. haematobium infection confirmed both by eggs in urine and by polymerase chain reaction (PCR) received single‐dose praziquantel and treatment of concomitant sexually transmitted infections. Macroscopic cervical abnormalities were also quantified. After 6 months, microscopically detectable egg excretion was eliminated, but 8 of 33 women (24%) were persistently positive for S. haematobium by PCR, and 11 (33%) had cervical abnormalities potentially attributable to schistosomiasis. This suggests that praziquantel treatment more frequently than every 6 months may be necessary for complete elimination of the parasite and prevention of genital tissue pathology. This aggressive therapy may in turn play a key role decreasing HIV susceptibility in millions of people living in regions in which S. haematobium is endemic.
Getting antimalarials on target: impact of national roll‐out of malaria rapid diagnostic tests on health facility treatment in three regions of Tanzania
Authors: Bruxvoort Katia , Kalolella Admirabilis , Nchimbi Happy , Festo Charles , Taylor Mark , Thomson Rebecca , Cairns Matthew , Thwing Julie , Kleinschmidt Immo , Goodman Catherine , Kachur S. Patrick 
Published: August 2013

AbstractObjectivesParasitological confirmation of malaria prior to treatment is recommended for patients of all ages, with malaria rapid diagnostic tests (mRDTs) an important tool to target artemisinin‐based combination therapies (ACTs) to patients with malaria. To evaluate the impact on case management practices of routine government implementation of mRDTs, we conducted large‐scale health facility surveys in three regions of Tanzania before and after mRDT roll‐out.MethodsFebrile patients at randomly selected health facilities were interviewed about care received at the facility, and blood samples were collected for reference blood smears. Health facility staff were interviewed about their qualifications and availability of malaria diagnostics and drugs.ResultsThe percentage of febrile patients tested for malaria at the facility increased from 15.8% in 2010 to 54.9% in 2012. ACTs were obtained by 65.8% of patients positive by reference blood smear in 2010 and by 50.2% in 2012 (P = 0.0675); no antimalarial was obtained by 57.8% of malaria‐negative patients in 2010 and by 82.3% in 2012 (P < 0.0001). Overall, ACT use decreased (39.9–21.3%, P < 0.0001) and antibiotic use increased (31.2–48.5%, P < 0.0001).ConclusionRoll‐out of mRDTs in Tanzania dramatically improved diagnostic testing for malaria and reduced overuse of ACTs for patients without parasitemia. However, post–roll‐out almost 50% of febrile patients did not receive a diagnostic test, and almost 50% of patients testing positive did not receive ACTs. Stock‐outs of ACTs and mRDTs were important problems. Further investigation is needed to determine reasons for not providing ACTs to patients with malaria and potential for inappropriate antibiotic use.
Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB‐LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Authors: Jupe Florian , Witek Kamil , Verweij Walter , Śliwka Jadwiga , Pritchard Leighton , Etherington Graham J. , Maclean Dan , Cock Peter J. , Leggett Richard M. , Bryan Glenn J. , Cardle Linda , Hein Ingo , Jones Jonathan D.G. 
Published: August 2013

SummaryRenSeq is a NB‐LRR (nucleotide binding‐site leucine‐rich repeat) gene‐targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB‐LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB‐LRRs and can be accessed through a genome browser that we provide. We compared these NB‐LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum ‘Heinz 1706’ extended the NB‐LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co‐segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi‐ber2) and S. ruiz‐ceballosii (Rpi‐rzc1), we were able to apply RenSeq successfully to identify markers that co‐segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy‐to‐adapt Galaxy pipelines.
An integrative model of the control of ovule primordia formation
Authors: Galbiati Francesca , Sinha Roy Dola , Simonini Sara , Cucinotta Mara , Ceccato Luca , Cuesta Candela , Simaskova Maria , Benkova Eva , Kamiuchi Yuri , Aida Mitsuhiro , Weijers Dolf , Simon Rüdiger , Masiero Simona , Colombo Lucia 
Published: August 2013

SummaryUpon hormonal signaling, ovules develop as lateral organs from the placenta. Ovule numbers ultimately determine the number of seeds that develop, and thereby contribute to the final seed yield in crop plants. We demonstrate here that CUP‐SHAPED COTYLEDON 1 (CUC1), CUC2 and AINTEGUMENTA (ANT) have additive effects on ovule primordia formation. We show that expression of the CUC1 and CUC2 genes is required to redundantly regulate expression of PINFORMED1 (PIN1), which in turn is required for ovule primordia formation. Furthermore, our results suggest that the auxin response factor MONOPTEROS (MP/ARF5) may directly bind ANT, CUC1 and CUC2 and promote their transcription. Based on our findings, we propose an integrative model to describe the molecular mechanisms of the early stages of ovule development.
Segmentation of the mouse fourth deep lumbrical muscle connectome reveals concentric organisation of motor units
Authors: Hirst Theodore C. , Ribchester Richard R. 
Published: August 2013

Key points
An accelerated image segmentation algorithm was developed and applied to analysis of motor unit arborisation and connectivity (the ‘connectome’) in fourth deep lumbrical muscles (4DL) of mice expressing fluorescent proteins as morphological reporters.
Mouse 4DL muscles contain between 4 and 9 motor units and motor unit size in these muscles ranged from 3 to 111 muscle fibres.
Small motor units were restricted in their arbors to the vicinity of the nerve entry point. Larger motor units concentrically occupied muscle fibres located progressively further from the nerve entry point.
Motor unit size was weakly correlated with motor endplate size, suggesting a hierarchy of motor unit sizes based on synaptic strength.
The data suggest a segregated organisation of motor units in cylindrical muscles that has not previously been appreciated and indicate the direction of future studies required to establish possible relationships between the strengths of synaptic connections and motor unit size.
Abstract  Connectomic analysis of the nervous system aims to discover and establish principles that underpin normal and abnormal neural connectivity and function. Here we performed image analysis of motor unit connectivity in the fourth deep lumbrical muscle (4DL) of mice, using transgenic expression of fluorescent protein in motor neurones as a morphological reporter. We developed a method that accelerated segmentation of confocal image projections of 4DL motor units, by applying high resolution (63×, 1.4 NA objective) imaging or deconvolution only where either proved necessary, in order to resolve axon crossings that produced ambiguities in the correct assignment of axon terminals to identified motor units imaged at lower optical resolution (40×, 1.3 NA). The 4DL muscles contained between 4 and 9 motor units and motor unit sizes ranged in distribution from 3 to 111 motor nerve terminals per unit. Several structural properties of the motor units were consistent with those reported in other muscles, including suboptimal wiring length and distribution of motor unit size. Surprisingly, however, small motor units were confined to a region of the muscle near the nerve entry point, whereas their larger counterparts were progressively more widely dispersed, suggesting a previously unrecognised form of segregated motor innervation in this muscle. We also found small but significant differences in variance of motor endplate length in motor units, which correlated weakly with their motor unit size. Thus, our connectomic analysis has revealed a pattern of concentric innervation that may perhaps also exist in other, cylindrical muscles that have not previously been thought to show segregated motor unit organisation. This organisation may be the outcome of competition during postnatal development based on intrinsic neuronal differences in synaptic size or synaptic strength that generates a territorial hierarchy in motor unit size and disposition.
Preparing for Generation Z: The Hippocampus Experiment at Ecole Centrale de Nantes
Authors: Evain Christine , Carolan Simon , Magnin Morgan 
Published: August 2013

Although social researchers who have written about Generation Z have found it difficult to classify the generation precisely, “Gen Z” is generally defined as the younger children of Generation X — in other words, Gen Z starts with today’s teenagers.
For the last fifteen years, technoculture theorists have been exploring the consequences of the wide availability of internet connectivity to the first generation of people born to it, who are referred to as “Digital Natives”. Their purpose is to address issues such as shifts in the concept of identity, privacy, content creation, activism, and piracy.
Our objective will be to apply the findings of generational experts to highlight possible avenues for pedagogical innovation in our University of science and engineering. We cover a range of questions:
What are the online behavioral differences between generation X, Y and Z?
What is our experience at ECN in terms of blended teacher and student driven pedagogies?
What is the role of Information and Communication Technologies (ICT) in education?
What are the expectations and contributions of the “Digital Natives” likely to be?
Our purpose will be to define the type pedagogical approach which has the potential to appeal to Gen Z and help them face the challenges of their generation.
This paper will be based on the research and testimonies of a wide range of experts: it will include the work of technoculture theorists such as John Palfrey, Urs Gasser and Cathy Davidson as well as our own practical experience at ECN, mainly the Hippocampus project.
Our purpose will be to determine how we — researchers and pedagogues — can draw on our present pedagogical experiences to prepare for generation Z1.
Gear Rattle Analysis Based on Wavelet Signal Decomposition
Authors: Brancati R. , Rocca E. , Savino S. , Farroni F. 
Published: August 2013

The “gear rattle” phenomenon is a research topic of great interest for the NVH (Noise, Vibration and Harshness) automotive sector, concerning driveline noise and vibrations coming from the manual gear boxes. It is due to the internal combustion engine variable torque producing impacts and rebounds, and consequently noise, between the teeth of the unloaded gear pairs of the gear box because of the unavoidable presence of backlashes.
Discrete Wavelet Transform (DWT) is used to decompose the angular relative motion signal and the wavelet decomposition details are adopted to analyze the dynamic behaviour of gears under rattle conditions. The DWT has been chosen because it is a particularly suitable instrument to recognize discontinuities, such as jumps or instantaneous changes in the slope of the signals, due to their localization in the time domain. Wavelet analysis allows to characterize an event by the localization, the kind, and the amplitude of the event. This technique enables, moreover, to define new indices for metrics of gear rattle especially useful in order to conduct comparisons among different operative conditions. Some examples of application of the proposed technique are reported in the paper. The theoretical investigations regard comparative analysis with respect to the amplitude and to the frequency of speed fluctuations and to the gears lubrication regime.