bluuebunny/crossref_metadata_2025_split huggingface dataset:
B‐cell activating factor, a predictor of antibody mediated rejection in kidney transplantation recipients
Authors: Pongpirul Wannarat , Chancharoenthana Wiwat , Pongpirul Krit , Leelahavanichkul Asada , Kittikowit Wipawee , Jutivorakool Kamonwan , Nonthasoot Bunthoon , Avihingsanon Yingyos , Eiam‐Ong Somchai , Praditpornsilpa Kearkiat , Townamchai Natavudh 
Published: November 2016

AbstractAimDonor‐specific antibody (DSA) is a widely‐used biomarker for antibody‐mediated rejection (ABMR) but correctly indicates only 30–40% of patients with ABMR. Additional biomarkers of ABMR in kidney transplant recipients are needed.MethodsAll 68 kidney transplanted‐recipients enrolled in this study were negative for graft rejection as determined by surveillance‐biopsy ELISA at day 7 post‐transplantation. Allograft biopsy was then performed at 6 months post‐transplantation for subclinical‐ABMR detection. Recipients were stratified by pre‐transplant DSA and BAFF at day 7 into four groups.ResultsDuring the study period, 13.2% of the recipients demonstrated subclinical‐ABMR at 6 months, without patient with clinical ABMR presentations. Overall mean BAFF at day 7 was 393 pg/mL (95% CI = 316–471 pg/mL). The optimal cut‐off value for low vs. high BAFF level was 573 pg/mL, with sensitivity and specificity at 77.8% and 88.1%, respectively. Fifty percent of recipients with high BAFF at day 7 (14 patients) and only 3.7% of patients with low BAFF demonstrated ABMR (P < 0.05). Indeed, ABMR was more common in patients high BAFF level (hazard ratio = 7.30; 95% CI = 3.77–14.15). The prevalence of ABMR among negative pre‐transplant DSA/low BAFF, positive DSA/low BAFF, negative DSA/high BAFF, and positive DSA/ high BAFF recipients were 4.4, 0, 37.5 and 66.7%, respectively (P < 0.05).ConclusionsPost‐transplant ABMR can be predicted by perioperative serum BAFF level. Together with DSA testing, BAFF provides additional predictive value for ABMR.
Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice
Authors: Brozynska Marta , Copetti Dario , Furtado Agnelo , Wing Rod A. , Crayn Darren , Fox Glen , Ishikawa Ryuji , Henry Robert J. 
Published: November 2016

SummaryThe related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
Development and field performance of nitrogen use efficient rice lines for Africa
Authors: Selvaraj Michael Gomez , Valencia Milton Orlando , Ogawa Satoshi , Lu Yingzhi , Wu Liying , Downs Christopher , Skinner Wayne , Lu Zhongjin , Kridl Jean C. , Ishitani Manabu , van Boxtel Jos 
Published: November 2016

SummaryNitrogen (N) fertilizers are a major input cost in rice production, and its excess application leads to major environmental pollution. Development of rice varieties with improved nitrogen use efficiency (NUE) is essential for sustainable agriculture. Here, we report the results of field evaluations of marker‐free transgenic NERICA4 (New Rice for Africa 4) rice lines overexpressing barley alanine amino transferase (HvAlaAT) under the control of a rice stress‐inducible promoter (pOsAnt1). Field evaluations over three growing seasons and two rice growing ecologies (lowland and upland) revealed that grain yield of pOsAnt1:HvAlaAT transgenic events was significantly higher than sibling nulls and wild‐type controls under different N application rates. Our field results clearly demonstrated that this genetic modification can significantly increase the dry biomass and grain yield compared to controls under limited N supply. Increased yield in transgenic events was correlated with increased tiller and panicle number in the field, and evidence of early establishment of a vigorous root system in hydroponic growth. Our results suggest that expression of the HvAlaAT gene can improve NUE in rice without causing undesirable growth phenotypes. The NUE technology described in this article has the potential to significantly reduce the need for N fertilizer and simultaneously improve food security, augment farm economics and mitigate greenhouse gas emissions from the rice ecosystem.
Petal micromorphology and its relationship to pollination
Authors: Costa V. B. S. , Pimentel R. M. M. , Chagas M. G. S. , Alves G. D. , Castro C. C. 
Published: November 2016

Abstract

The characteristics of petal epidermal conical cells affect the quality of the signals perceived by various pollinators. This study aimed to identify variations in micromorphological characteristics of flower petals and their relationship to melittophily, ornithophily and chiropterophily pollination systems.

The petals of 11 species were analysed using scanning electron microscopy and optical microscopy and the micromorphological traits were described, measured and compared using Tukey's test, PCA and cluster analysis.

Unlike chiropterophily, all melittophilous and some ornithophilous species possessed adaxial epidermal conical cells. Cluster grouping separated chiropterophilous flowers from melittophilous and ornithophilous. PCA analysis showed that the two morphometric profile of conical cells was the attribute that most strongly influenced the grouping of species. When considering the data set of the three pollination systems, melittophilous and ornithophilous plants were more similar to each other than they were to chriopterophilous species. The distance between conical cell apices is an important parameter in interactions with pollinators.

This study facilitated recognition of smoothing pollinator resource access through petal micromorphological characteristics. Further research regarding the biometry of micromorphological traits related to pollination is required.
Patterns of local and global redox variability during the Cenomanian–Turonian Boundary Event (Oceanic Anoxic Event 2) recorded in carbonates and shales from central Italy
Authors: Owens Jeremy D. , Lyons Timothy W. , Hardisty Dalton S. , Lowery Chris M. , Lu Zunli , Lee Bridget , Jenkyns Hugh C. 
Published: November 2016

AbstractCareful evaluation of the local geochemical conditions in past marine settings can provide a window to the average redox state of the global ocean during episodes of extensive organic carbon deposition. These comparisons aid in identifying the interplay between climate and biotic feedbacks contributing to and resulting from these events. Well‐documented examples are known from the Mesozoic Era, which is characterized by episodes of widespread organic carbon deposition known as Oceanic Anoxic Events. This organic carbon burial typically leads to coeval positive carbon‐isotope excursions. Geochemical data are presented here for several palaeoredox proxies (Cr/Ti, V, Mo, Zn, Mn, Fe speciation, I/Ca and sulphur isotopes) from a section exposed at Furlo in the Marche–Umbrian Apennines of Italy that spans the Cenomanian–Turonian boundary. Here, Oceanic Anoxic Event 2 is represented by a ca 1 m thick radiolarian‐rich millimetre‐laminated organic‐rich shale known locally as the Bonarelli Level. Iron speciation data for thin organic‐rich intervals observed below the Bonarelli Level imply a local redox shift going into the Oceanic Anoxic Event, with ferruginous conditions (i.e. anoxic with dissolved ferrous iron) transiently developed prior to the event and euxinia (i.e. anoxic and sulphidic bottom waters) throughout the event itself. Pre‐Oceanic Anoxic Event enrichments of elements sensitive to anoxic water columns were due to initial development of locally ferruginous bottom waters as a precursor to the event. However, the greater global expanse of dysoxic to euxinic conditions during the Oceanic Anoxic Event greatly reduced redox‐sensitive trace‐metal concentrations in seawater. Pyrite sulphur isotopes document a positive excursion during the Oceanic Anoxic Event. Carbonate I/Ca ratios were generally low, suggesting locally reduced bottom‐water oxygen conditions preceding the event and relatively increased oxygen concentrations post‐event. Combined, the Furlo geochemical data suggest a redox‐stratified water column with oxic surface waters and a shallow chemocline overlying locally ferruginous bottom waters preceding the event, globally widespread euxinic bottom waters during the Oceanic Anoxic Event, followed by chemocline shallowing but sustained local redox stratification following the event.
Oceanic tectonic islands
Authors: Palmiotto Camilla , Corda Laura , Bonatti Enrico 
Published: November 2016

AbstractThe origin of oceanic islands has been the subject of much speculation, starting with Darwin almost two centuries ago. Two classes of oceanic islands can be identified: ‘volcanic islands’, which form due to excess volcanism caused by melting anomalies in the suboceanic mantle, and ‘tectonic islands’, which form due to transpressive and/or transtensional tectonics of blocks of oceanic lithosphere along transform faults. Modern and sunken tectonic islands from the Atlantic Ocean and Indian Ocean and the Caribbean Sea and Red Sea expose mantle and lower‐crust lithologies and display an elongated narrow morphology; in contrast, volcanic islands expose basalts and have near‐circular morphology. Both are often capped by carbonate platforms. The life cycle of tectonic islands tends to be more complex than that of most volcanic islands; their elongated narrow morphology, together with their tectonic instability and high seismicity, affect the architecture of the carbonate platforms capping them, limiting coral reef development and favouring rhodalgal–foramol biota associations.
Records of palaeo‐sea level and eruption duration in a coastal tuff ring, Jeju Island, Korea
Authors: Yoon Woo Seok , Yoon Seok Hoon , Sohn Chanwoo , Sohn Young Kwan 
Published: November 2016

AbstractPhreatomagmatic volcanoes and their sedimentary products can preserve high‐resolution records of earth surface processes because of their high deposition rate. Songaksan, Jeju Island, Korea, is a phreatomagmatic volcano, which erupted c. 3.7 ka BP in a coastal setting. Its tuff ring preserves a record of intertidal to supratidal facies transition in the basal part, which reveals the position of palaeo‐high‐tide level for at least 13 high‐tide events, and a record of a storm‐surge event in the middle part of the tuff ring, which lasted approximately three tidal cycles. Based on these features, the phreatomagmatic eruption of Songaksan is estimated to have taken place over a month. The sea level at the time was almost identical to that at present. This study shows that coastal phreatomagmatic volcanoes can preserve high‐resolution records of eruption duration and palaeo‐sea level, and can provide accurately levelled and dated data points to the Quaternary sea‐level curve.
Interplay between stress permutations and overpressure to cause strike‐slip faulting during tectonic inversion
Authors: Peacock David C. P. , Tavarnelli Enrico , Anderson Mark W. 
Published: November 2016

AbstractField data from an orogenic foreland and an orogenic belt (the Mesozoic rocks of southern England and the Umbria‐Marche Apennines of Italy respectively) indicate the following. Firstly, stress evolution during the tectonic cycle, between maximum compressive stress (σ1) being vertical during extension and least compressive stress (σ3) being vertical during contraction, can involve phases when the intermediate compressive stress (σ2) is vertical, promoting strike‐slip deformation. Secondly, variations in the relative magnitudes of the stress axes are caused by variations in overburden and tectonic forces. Thirdly, overpressure can develop because of compaction during burial, and, as overburden is reduced during uplift and erosion, the vertical stress (σV) reduces but fluid pressure (Pf) remains approximately constant. Brittle deformation, including transient strike‐slip faults, reverse‐reactivated normal faults and normal‐reactivated thrusts, is preferentially developed in overpressured areas because high Pf promotes faulting.
Towards a whole‐genome sequence for rye (Secale cereale L.)
Authors: Bauer Eva , Schmutzer Thomas , Barilar Ivan , Mascher Martin , Gundlach Heidrun , Martis Mihaela M. , Twardziok Sven O. , Hackauf Bernd , Gordillo Andres , Wilde Peer , Schmidt Malthe , Korzun Viktor , Mayer Klaus F.X. , Schmid Karl , Schön Chris‐Carolin , Scholz Uwe 
Published: November 2016

SummaryWe report on a whole‐genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole‐genome shotgun sequencing of the 7.9‐Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low‐copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high‐density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high‐density genetic map and establishing a synteny‐based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome‐wide map of selection signals differentiating the divergent gene pools. This rye whole‐genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome‐based breeding in rye.
Chitin receptor CERK1 links salt stress and chitin‐triggered innate immunity in Arabidopsis
Authors: Espinoza Catherine , Liang Yan , Stacey Gary 
Published: November 2016

SummaryIn nature, plants need to respond to multiple environmental stresses that require the involvement and fine‐tuning of different stress signaling pathways. Cross‐tolerance, in which plants pre‐treated with chitin (a fungal microbe‐associated molecular pattern) have improved salt tolerance, was observed in Arabidopsis, but is not well understood. Here, we show a unique link between chitin and salt signaling mediated by the chitin receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1). Transcriptome analysis revealed that salt stress‐induced genes are highly correlated with chitin‐induced genes, although this was not observed with other microbe‐associated molecular patterns (MAMPs) or with other abiotic stresses. The cerk1 mutant was more susceptible to NaCl than was the wild type. cerk1 plants had an irregular increase of cytosolic calcium ([Ca2+]cyt) after NaCl treatment. Bimolecular fluorescence complementation (BiFC) and co‐immunoprecipitation experiments indicated that CERK1 physically interacts with ANNEXIN 1 (ANN1), which was reported to form a calcium‐permeable channel that contributes to the NaCl‐induced [Ca2+]cyt signal. In turn, ann1 mutants showed elevated chitin‐induced rapid responses. In short, molecular components previously shown to function in chitin or salt signaling physically interact and intimately link the downstream responses to fungal attack and salt stress.
Differentiation of induced pluripotent stem cell–derived neutrophil granulocytes from common marmoset monkey (Callithrix jacchus)
Authors: Schrimpf Christopher , Wrede Christoph , Glage Silke , Hegermann Jan , Backhaus Samantha , Blasczyk Rainer , Heuft Hans‐Gert , Müller Thomas 
Published: November 2016

BACKGROUNDInherited and acquired marrow failure syndromes most commonly lead to defect in myeloid and/or neutrophil differentiation and/or function. Besides this, neutropenia induced by cancer‐adjusted chemotherapy is a frequent clinical problem. In both cases, cell replacement therapy is a well‐established, but due to necessity of donors limited and perilous procedure. Therefore, autologous cell replacement from patients' own marrow‐derived cells lowers risk and bares new possibilities for therapy. Since the immune system of the marmoset monkey is known to show high similarity to humans, preclinical studies with these animals bare high hopes for immunologic research and cell replacement therapy.STUDY DESIGN AND METHODSMarmoset‐induced pluripotent stem (iPS) cells (cj‐iPSC) were first cultivated on mouse embryonic feeder cells in medium containing recombinant human vascular endothelial growth factor. After 13 days, CD34+/vascular endothelial growth factor receptor‐2 (VEGFR2)– cells were sorted, treated with interleukin (IL‐3), thrombopoietin, and stem cell factor for 20 days and further cultivated with granulocyte–colony‐stimulating factor (G‐CSF) and IL‐3 for 10 days.RESULTSCD34+/VEGFR2– cells could be generated in high amounts (39.65 ± 6.01%; 2.31 × 105 cells). Afterward, these hematopoietic progenitors could be successfully differentiated into mature cj‐iPSC–derived neutrophils showing similar morphology, specific surface antigens, and neutrophil‐specific gene products and in vitro phagocytic activity.CONCLUSIONcj‐iPSC–derived neutrophils bare high hopes in hematologic cell replacement therapy. They exhibit high morphologic similarity to native neutrophils and present neutrophil‐specific surface antigens, antimicrobial proteins, and gene products yielding an auspicious approach for continuative experiments including tests in living animals.
EFFECT OF CHEMICAL AND ENZYMATIC INTERESTERIFICATION ON THE PHYSICOCHEMICAL PROPERTIES OF PALM OIL AND. PALM KERNEL OIL BLENDS
Authors: Abd Rashid Norizzah , Kamarulzaman Nur Azimah , Omar Zaliha 
Published: November 2016

Palm oil (PO) and palm kernel oil (PKO) have different chemical composition and physical properties. Both oils have limited application in their natural form. To widen their commercial values, PO and PKO were modified by blending and subsequently followed by interesterification (IE). Interesterification is the rearrangement of fatty acids within and among different triacylglycerols, using enzyme or chemical as the catalysts. Palm oil with iodine value (IV) of 52.6 and PKO (IV = 17.5) were mixed in different ratios from 25:75 to 75:25 (%wt/wt) at 25% increment. The blends were subjected to chemical and enzymatic interesterification using sodium methoxide and Lipozyme TL IM as catalysts, respectively. The effects of chemical and enzymatic interesterification on the triacylglycerols (TAG) composition, thermal properties, solid fat content (SFC) and slip melting point (SMP) were investigated. Chemical interesterification (CIE) caused significant changes in the TAG composition of the oil blend compared to enzymatic interesterification (EIE). This changes led to a significantly higher (p<0.05) SMP for the chemically-interesterified than the enzymatically-interesterified blends. The differential scanning calorimetry (DSC) melting thermograms confirmed that harder product with higher final complete melting temperature was obtained from the chemically-interesterified blends. Similar SFC profiles for all oil blends were observed with steep SFC slopes for blend with high proportion of PKO. Chemical interesterification reduced the eutectic interactions that occurred at 5 to 25°C in the non-interesterified and enzymatically-interesterified blends. Thus, CIE caused significant changes in physicochemical properties of the PO and PKO blends compared to EIE. Results from this study could improve the existing PO and PKO properties and widen their usage in food and non-food applications.
BIODEGRADABLE FILM FROM Pleurotus sajor-caju WASTE
Authors: Husain Hazwani , Rahman Ahmad Yazid , Senawi Norshazila , A/P Kuthiah Yamunasri , Khairudin Syaliyana , A/P Nadarajah Thivya 
Published: November 2016

The accumulation of waste is a growing environmental concern on the issues all around the world. One green option is to convert waste into valuable materials. This study aims to recycle mushroom waste from Pleurotus sajor-caju from ‘Rumah Cendawan’, Politeknik Nilai to develop biofilm which has the potential to be molded into a variety of products. Forty two formulations have been molded and 14 best formulations have been tested. The tensile strengths of these 14 biofilms have been determined by using Shimadzu Universal Testing Machine and the biodegradability characteristics of the films have been tested. In a conclusion, biodegradable films from Pleurotus sajor-caju waste can be developed as a better alternative to the existing plastics in the market.
EFFECTS OF SOLID STATE FERMENTATION BY Monascus purpureus ON PHENOLIC CONTENT AND BIOLOGICAL ACTIVITIES OF COCONUT TESTA AND RICE BRAN
Authors: Jamaluddin Anisah , Abd. Razak Dang Lelamurni , Abd. Rashid Nur Yuhasliza , Sharifudin Shaiful Adzni , Abd. Kahar Ainaa , Md. Saad Ainur Zunira , Long Kamariah 
Published: November 2016

Solid-state fermentation (SSF) is an alternative low cost useful process that has many important applications in the field of biotechnology. In this study, SSF has been employed as a process for the production of value-added agricultural by-product using coconut testa (CT), rice bran (RB) and the combination of both substrates (CT-RB). The effect of SSF by Monascus purpureus on total phenolic content (TPC), antioxidant, anti-tyrosinase and anti-elastase of the substrates were studied and compared with its non-fermented counterparts. The results showed that the SSF has improved the TPC up to three-fold higher in the studied substrates. Antioxidant potential evaluated using FRAP analysis also exhibited an enhancement in fermented substrates with the values ranging from 23.70 to 63.15 mg AAE/g sample. On the other hand, the radical scavenging activity evaluated using DPPH assay showed a different trend in comparison to the TPC and FRAP analyses. In another two analyses, tyrosinase and elastase inhibition activities were also enhanced in most substrates upon the fermentation. The changes in free phenolic acids content (p-coumaric, caffeic, ferulic, sinapic, vanillic, protocatechuic, gallic and 4-hydroxybenzoic and syringic acid) of the substrates after fungal fermentation was also examined through high performance liquid chromatography (HPLC) analysis. In summary, SSF offers a tool to further increase the bioactive potential of the studied substrate.