bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bulked sample analysis in genetics, genomics and crop improvement
Authors: Zou Cheng , Wang Pingxi , Xu Yunbi 
Published: March 2016

SummaryBiological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high‐throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker‐assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
Shoot tolerance mechanisms to iron toxicity in rice (Oryza sativa L.)
Authors: Wu Lin‐Bo , Ueda Yoshiaki , Lai Shang‐Kun , Frei Michael 
Published: March 2016

AbstractIron toxicity frequently affects lowland rice and leads to oxidative stress via the Fenton reaction. Tolerance mechanisms were investigated in contrasting genotypes: the intolerant IR29 and the tolerant recombinant inbred line FL483. Seedlings were exposed to 1000 mg L‐1 ferrous iron, and the regulation of genes involved in three hypothetical tolerance mechanisms was investigated (I) Iron uptake, partitioning and storage. The iron concentration and speciation in different plant tissues did not differ significantly between genotypes. Sub‐cellular iron partitioning genes such as vacuolar iron transporters or ferritin showed no genotypic differences. (II) Antioxidant biosynthesis. Only one gene involved in carotenoid biosynthesis showed genotypic differences, but carotenoids are unlikely to scavenge the reactive oxygen species (ROS) involved in Fe toxicity, i.e. H2O2 and hydroxyl radicals. (III) Enzymatic activities for ROS scavenging and antioxidants turnover. In shoots, glutathione‐S‐transferase and ascorbate oxidase genes showed genotypic differences, and consistently, the tolerant FL483 had lower dehydroascorbate reductase and higher ascorbate oxidase activity, suggesting that high rates ascorbate reduction confer sensitivity. This hypothesis was confirmed by application of exogenous reduced ascorbate or L‐galactono‐1,4‐lactone, which increased lipid peroxidation under iron toxic conditions. Our results demonstrate in planta pro‐oxidant activity of reduced ascorbate in the presence of iron.
Comparison of D1´‐ and D1‐containing PS II reaction centre complexes under different environmental conditions in Synechocystis sp. PCC 6803
Authors: Crawford Tim S. , Hanning Kyrin R. , Chua Jocelyn P.S. , Eaton‐Rye Julian J. , Summerfield Tina C. 
Published: March 2016

AbstractIn oxygenic photosynthesis, the D1 protein of Photosystem II is the primary target of photodamage and environmental stress can accelerate this process. The cyanobacterial response to stress includes transcriptional regulation of genes encoding D1, including low‐oxygen‐induction of psbA1 encoding the D1´ protein in Synechocystis sp. PCC 6803. The psbA1 gene is also transiently up‐regulated in high light, and its deletion has been reported to increase ammonium‐induced photoinhibition. Therefore we investigated the role of D1´‐containing PS II centres under different environmental conditions. A strain containing only D1´‐PS II centres under aerobic conditions exhibited increased sensitivity to ammonium chloride and high light compared to a D1‐containing strain. Additionally a D1´‐PS II strain was outperformed by a D1‐PS II strain under normal conditions; however, a strain containing low‐oxygen‐induced D1´‐PS II centres was more resilient under high light than an equivalent D1 strain. These D1´‐containing centres had chlorophyll a fluorescence characteristics indicative of altered forward electron transport and back charge recombination with the donor side of PS II. Our results indicate D1´‐PS II centres are important in the reconfiguration of thylakoid electron transport in response to high light and low oxygen.
Factors affecting N‐terminal pro‐brain natriuretic peptide elevation in the acute phase of Kawasaki disease
Authors: Yanagisawa Daisuke , Ayusawa Mamoru , Kato Masataka , Watanabe Hirofumi , Komori Akiko , Abe Yuriko , Nakamura Takahiro , Kamiyama Hiroshi , Takahashi Shori 
Published: March 2016

AbstractBackgroundThe aim of this study was to investigate the clinical significance and factors that affect N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) elevation in the acute phase of Kawasaki disease (KD) despite the absence of apparent cardiac complications.MethodsThe laboratory and echocardiography results of 44 KD patients in the acute and subacute phases were reviewed.ResultsWith preserved cardiac function, median NT‐proBNP was significantly elevated in the acute phase compared with the subacute phase (343 pg/mL, IQR, 162–1182 pg/mL vs 98 pg/mL, IQR, 61–205 pg/mL, respectively; P < 0.0001). The respective levels of tumor necrosis factor (TNF)‐α, soluble TNF receptor (sTNFR)1, and sTNFR2 were also significantly elevated in the acute phase compared with the subacute phase: TNF‐α, 3.3 pg/mL (IQR, 2.6–4.8 pg/mL) versus 2.4 pg/mL (IQR 1.9–4.0 pg/mL; P < 0.01), sTNFR1, 2741 pg/mL (IQR, 2080–3183 pg/mL) versus 976 pg/mL (IQR, 814–1247 pg/mL; P < 0.0001), sTNFR2, 5644 pg/mL (IQR, 4693–7520 pg/mL) versus 3169 pg/mL (IQR, 2132–3878 pg/mL; P < 0.0001). Log‐transformed NT‐proBNP was correlated with TNF‐α (r = 0.29, P = 0.056), sTNFR1 (r = 0.60, P < 0.0001), and sTNFR2 (r = 0.65, P < 0.0001). TNF‐α was correlated with sTNFR1 (r = 0.35, P = 0.02) and sTNFR2 (r = 0.51, P < 0.001).ConclusionTumor necrosis factor‐α may cause NT‐proBNP elevation in the acute phase of KD, and NT‐proBNP level may be an indicator of TNF‐α activity.
Autoimmune hepatitis in a child presenting with hepatopulmonary syndrome (HPS)
Authors: Grabinski Zoe , Beg Mirza , Wali Prateek 
Published: March 2016

AbstractHPS has been described in 9–20% of children with end‐stage liver disease. We present a case of a previously, asymptomatic nine‐yr‐old incidentally found to have low oxygen saturation. Physical exam was remarkable for digital clubbing, splenomegaly and orthodeoxia. Laboratory evaluation revealed a low platelet count, hyperammonemia, and prolonged coagulation studies. Sonography showed evidence of splenomegaly and portal venous hypertension. High resolution CT thorax and CTA were normal. HPS was confirmed by agitated saline contrast enhanced echocardiography and Tc‐99m MAA scan with evidence of intrapulmonary vascular dilatations. Liver biopsy was performed and consistent with autoimmune hepatitis. A high clinical index of suspicion should be maintained for HPS in pediatric patients who have unexplained hypoxemia as typical signs and symptoms of severe liver disease are often absent. In this report, we discuss a case of HPS complicated AIH in a pediatric patient and review the relevant literature.
Ultrasound assessment of diaphragmatic function in patients with amyotrophic lateral sclerosis
Authors: Fantini Riccardo , Mandrioli Jessica , Zona Stefano , Antenora Federico , Iattoni Andrea , Monelli Marco , Fini Nicola , Tonelli Roberto , Clini Enrico , Marchioni Alessandro 
Published: March 2016

AbstractBackground and objectiveEvaluation of diaphragm function in Amyotrophic Lateral Sclerosis (ALS) is critical in determining when to commence non‐invasive mechanical ventilation (NIV).Currently, forced vital capacity (FVC) and sniff nasal inspiratory pressure (SNIP) are volitional measures for this evaluation, but require collaboration and are poorly specific. The primary aim of this study was to assess whether diaphragmatic thickness measured by ultrasound (US) correlates with lung function impairment in ALS patients. The secondary aim was then to compare US diaphragm thickness index (ΔTdi) with a new parameter (ΔTmax index).Methods41 patients with ALS and 30 healthy subjects were enrolled in the study. All subjects underwent spirometry, SNIP and diaphragm US evaluation, while arterial blood gases were measured in some patients only. US assessed diaphragm thickness (Tdi) at tidal volume (Vt) or total lung capacity (TLC), and their ratio (ΔTmax) were recorded. Changes (Δ) in Tdi indices during tidal volume (ΔTdiVt) and maximal inspiration (ΔTdiTLC) were also assessed.ResultsΔTdiTLC (p <0.001) and ΔTmax (p = 0.007), but not ΔTdiVt, differed between patients and controls. Significant correlation (p < 0.05) was found between ΔTdiTLC, ΔTmax and FVC. The ROC curve analysis for comparison of individual testing showed better accuracy with Δtmax than with ΔtdiTLC for FVC (AUC 0.76 and 0.27) and SNIP (AUC 0.71 and 0.25).ConclusionDiaphragm thickness assessed by ultrasound significantly correlates with global respiratory alterations in patients with ALS. ΔTmax represents a new US index of early diaphragmatic dysfunction, better related with the routinely performed lung function tests.
Clinical features of usual interstitial pneumonia with anti‐neutrophil cytoplasmic antibody in comparison with idiopathic pulmonary fibrosis
Authors: Hosoda Chiaki , Baba Tomohisa , Hagiwara Eri , Ito Hiroyuki , Matsuo Norikazu , Kitamura Hideya , Iwasawa Tae , Okudela Koji , Takemura Tamiko , Ogura Takashi 
Published: March 2016

AbstractBackground and objectiveMyeloperoxidase anti‐neutrophil cytoplasmic antibody (MPO‐ANCA) is occasionally positive in patients with usual interstitial pneumonia (UIP). However, the differences from idiopathic pulmonary fibrosis (IPF/UIP) have not been well documented. We aimed to clarify the clinical, radiological and pathological features of UIP associated with MPO‐ANCA (ANCA/UIP).MethodsWe retrospectively reviewed the medical records of 12 consecutive ANCA/UIP patients not manifesting microscopic polyangiitis and 108 IPF/UIP patients with no autoantibodies, both diagnosed by surgical lung biopsy.ResultsThere was no significant difference in clinical background, laboratory results and pulmonary function tests between ANCA/UIP patients and IPF/UIP patients except for the percentage of bronchoalveolar lavage neutrophils. HRCT showed subpleural reticulation in both groups. Increased attenuation around honeycombing and cysts was significantly observed in ANCA/UIP. Pathologically, ANCA/UIP had more prominent inflammatory cell infiltration, lymphoid follicles with germinal centres and cellular bronchiolitis. During the disease course, three of 12 patients (25%) developed microscopic polyangiitis. Immunosuppressive treatment tended to be more effective in ANCA/UIP patients, and the survival time in ANCA/UIP patients tended to be longer than those with IPF/UIP.ConclusionANCA/UIP may be distinguishable from IPF/UIP with a combination of HRCT findings of increased attenuation around honeycombing and cysts and some of the characteristic pathological findings. In contrast to IPF/UIP, immunosuppressive treatment could be a therapeutic option for ANCA/UIP.
Tumour‐Associated Autoantibodies as Diagnostic Biomarkers for Breast Cancer: A Systematic Review and Meta‐Analysis
Authors: Xia J. , Shi J. , Wang P. , Song C. , Wang K. , Zhang J. , Ye H. 
Published: March 2016

AbstractTumour‐associated autoantibodies may be promising biomarkers that could facilitate breast cancer (BC) diagnosis and improve patient outcomes. This review aims to identify the tumour‐associated autoantibodies with the greatest diagnostic potential. Systematic searches were conducted using PubMed and Web of Science. The most studied tumour‐associated autoantibody was included in a meta‐analysis, and its clinical value was determined using Fagan's nomogram. The analysis included 84 studies regarding tumour‐associated autoantibodies with the diagnostic value. Anti‐p53 antibody was the most frequently studied autoantibody, followed by autoantibodies against MUC1, HER2 and cyclin B1. Although individual tumour‐associated autoantibodies showed low diagnostic sensitivity, combinations of autoantibodies offered relatively high sensitivity. Enzyme‐linked immunosorbent assay (ELISA) was the most common detection method, and nucleic acid programmable protein microarrays appeared preferable to common protein microarrays. As the most commonly studied autoantibody, anti‐p53 antibody was included in a meta‐analysis. When it had been detected using ELISA and cut‐off values were defined as the mean +2 or 3 standard deviations, the summary area under the receiver operating characteristic curve for the presence of BC was 0.78. Fagan's nomogram showed post‐test probabilities of 32% and 6% for positive and negative results, respectively. Mammography might be supplemented by the use of tumour‐associated autoantibodies as biomarkers for BC diagnosis in younger women with increased risks of BC. Even though several studies have investigated the diagnostic use of tumour‐associated autoantibodies as biomarkers for BC detection, a high‐quality prospective study is needed to validate their diagnostic value in practice.
Simultaneous Confidence Tubes in Multivariate Linear Regression
Authors: Liu Wei , Han Yang , Wan Fang , Bretz Frank , Hayter Anthony J. 
Published: March 2016

AbstractSimultaneous confidence bands have been shown in the statistical literature as powerful inferential tools in univariate linear regression. While the methodology of simultaneous confidence bands for univariate linear regression has been extensively researched and well developed, no published work seems available for multivariate linear regression. This paper fills this gap by studying one particular simultaneous confidence band for multivariate linear regression. Because of the shape of the band, the word ‘tube’ is more pertinent and so will be used to replace the word ‘band’. It is shown that the construction of the tube is related to the distribution of the largest eigenvalue. A simulation‐based method is proposed to compute the 1 − α quantile of this eigenvalue. With the computation power of modern computers, the simultaneous confidence tube can be computed fast and accurately. A real‐data example is used to illustrate the method, and many potential research problems have been pointed out.
Effect of Socioeconomic Status on the Linkage Between Suicidal Ideation and Suicide Attempts
Authors: Kim Jeong Lim , Kim Ji Man , Choi Young , Lee Tae‐Hoon , Park Eun‐Cheol 
Published: March 2016

Previous suicide attempts are a leading risk factor for completed suicide. To identify specific characteristics of those at high risk for attempts, we investigated associations with socioeconomic status (SES). Data from the 2013 Korean Community Health Survey (KCHS) included adults who reported suicidal ideation (N = 220,245). Attempts in the past 12 months were assessed. Associations of demographic, socioeconomic, and suicide‐related behavioral factors were analyzed using multiple logistic regression. Among those with suicidal ideation, 862 (3.9%) had attempted suicide. After stratification by age and gender, results showed that low education and unemployed young adult men and women had significantly higher rates of attempts. The lowest income level was associated with significantly higher rates of attempts in only young adult women. Among those with the lowest and highest income, the association between ideation and attempts was attenuated, whereas it was enhanced among other income groups.
Primary and secondary effects of real‐time feedback to reduce vertical loading rate during running
Authors: Baggaley M. , Willy R. W. , Meardon S. A. 
Published: March 2016

Gait modifications are often proposed to reduce average loading rate (AVLR) during running. While many modifications may reduce AVLR, little work has investigated secondary gait changes. Thirty‐two rearfoot runners [16M, 16F, 24.7 (3.3) years, 22.72 (3.01) kg/m2, >16 km/week] ran at a self‐selected speed (2.9 ± 0.3 m/s) on an instrumented treadmill, while 3D mechanics were calculated via real‐time data acquisition. Real‐time visual feedback was provided in a randomized order to cue a forefoot strike (FFS), a minimum 7.5% decrease in step length, or a minimum 15% reduction in AVLR. AVLR was reduced by FFS (mean difference = 26.4 BW/s; 95% CI = 20.1, 32.7; P < 0.001), shortened step length (8.4 BW/s; 95% CI = 2.9, 14.0; P = 0.004), and cues to reduce AVLR (14.9 BW/s; 95% CI = 10.2, 19.6; P < 0.001). FFS, shortened step length, and cues to reduce AVLR all reduced eccentric knee joint work per km [(−48.2 J/kg*m; 95% CI = −58.1, −38.3; P < 0.001), (−35.5 J/kg*m; 95% CI = −42.4, 28.6; P < 0.001), (−23.1 J/kg*m; 95% CI = −33.3, −12.9; P < 0.001)]. However, FFS and cues to reduce AVLR also increased eccentric ankle joint work per km [(54.49 J/kg*m; 95% CI = 45.3, 63.7; P < 0.001), (9.20 J/kg*m; 95% CI = 1.7, 16.7; P = 0.035)]. Potentially injurious secondary effects associated with FFS and cues to reduce AVLR may undermine their clinical utility. Alternatively, a shortened step length resulted in small reductions in AVLR, without any potentially injurious secondary effects.
Introducing dolomite seams: hybrid compaction–solution bands in dolomitic limestones
Authors: Tavani Stefano , Vitale Stefano , Grifa Celestino , Iannace Alessandro , Parente Mariano , Mazzoli Stefano 
Published: March 2016

AbstractBedding‐parallel dolomite seams occur in a clay‐poor carbonate succession of the Apennines. The seams are composed of a high concentration of dolomite crystals compared to the hosting dolomitic limestone. SEM images document microcracking, and in many cases even crushing and fragmentation, of dolomite crystals and accumulation of non‐carbonate insoluble material both along micro‐stylolites within the seams and around dolomite crystals of the seams. We interpret the seams as hybrid structures between pressure‐solution seams and compaction bands, which formed during burial. The euhedral dolomite crystals scattered in the micritic matrix represent the insoluble residue produced by the progressive dissolution of calcite. As calcite dissolution proceeds, the concentration of dolomite crystals increases, eventually resulting in a dolomite seam in which locally a dolomite crystal‐supported texture is attained. At this stage, the dolomite crystals within the seam start to collide, crush and fragment, so that the dolomite seam behaves like a compaction band.
The Formation and Sustainability of same Product Retail Store Clusters in A Modern Mega City
Authors: Mandhachitara Rujirutana , Shannon Randall 
Published: March 2016

AbstractCompared with manufacturing locational analysis, relatively few scholarly researchers have demonstrated serious interest in examining the forces responsible for same store retail clustering in large cities. The centrifugal and centripetal forces influencing retail locations were once the subject of serious intellectual debate. Same product retail store (SPRS) clusters, which were once common in the retail landscape of Manhattan and other Western primary cities, are now in severe decline. However, there remain modern megacities where similar retail store cluster phenomenon is resurgent. This paper attempts to examine the formation and sustainability of the SPRS clustering phenomenon illustrated by Bangkok, Thailand. The authors find 14,468 SPRS permanent retail outlets located in 299 clusters. The data were mapped and then classified according to the North American Industrial Classification System. Locational Gini coefficients were computed to permit an analysis of the city's retail clustering within and between its fifty administrative districts.
Children post liver transplantation hospitalized with fever are at a high risk for bacterial infections
Authors: Ashkenazi‐Hoffnung L. , Mozer‐Glassberg Y. , Bilavsky E. , Yassin R. , Shamir R. , Amir J. 
Published: March 2016

AbstractBackgroundAlthough infections post liver transplantation are a main cause of morbidity and mortality, data are limited on transplanted children. The objective of this study was to investigate the incidence, etiology, and predictors of infection in pediatric liver transplant recipients (LTR) in the specific practical clinical setting of hospitalization for fever in order to elucidate the appropriate management of these patients.MethodsClinical and laboratory data were retrospectively collected for all febrile pediatric LTR hospitalized from 2004 to 2012.ResultsWe analyzed 133 hospital admissions for fever among 44 pediatric LTR. Of these, 73 bacterial (54.8%) and 46 viral infections (34.5%) were diagnosed. No cases of protozoa or fungal infections were reported. Bacterial infections were most frequent during the first year post transplantation with ascending cholangitis being the most prevalent. Twenty‐six (36%) bacterial infections were microbiologically documented and 47 (64%) were clinically documented. Of the microbiologically confirmed cases, gram‐negative bacteria, namely Enterobacteriaceae, were most common (57.7%). Seven cases of bacteremia were observed including 1 case presenting with severe sepsis. Compared with the white blood cell count and absolute neutrophil count, C‐reactive protein level was found to be a more sensitive biomarker for bacterial disease. Older age on admission was a significant risk factor for bacterial infection.ConclusionFebrile hospitalized pediatric LTR are immunocompromised hosts at high risk for bacterial infections, and usually warrant prompt evaluation and empirical antibiotic treatment upon admission.
MOL1 is required for cambium homeostasis in Arabidopsis
Authors: Gursanscky Nial Rau , Jouannet Virginie , Grünwald Karin , Sanchez Pablo , Laaber‐Schwarz Martina , Greb Thomas 
Published: March 2016

SummaryPlants maintain pools of pluripotent stem cells which allow them to constantly produce new tissues and organs. Stem cell homeostasis in shoot and root tips depends on negative regulation by ligand–receptor pairs of the CLE peptide and leucine‐rich repeat receptor‐like kinase (LRR‐RLK) families. However, regulation of the cambium, the stem cell niche required for lateral growth of shoots and roots, is poorly characterized. Here we show that the LRR‐RLK MOL1 is necessary for cambium homeostasis in Arabidopsis thaliana. By employing promoter reporter lines, we reveal that MOL1 is active in a domain that is distinct from the domain of the positively acting CLE41/PXY signaling module. In particular, we show that MOL1 acts in an opposing manner to the CLE41/PXY module and that changing the domain or level of MOL1 expression both result in disturbed cambium organization. Underlining discrete roles of MOL1 and PXY, both LRR‐RLKs are not able to replace each other when their expression domains are interchanged. Furthermore, MOL1 but not PXY is able to rescue CLV1 deficiency in the shoot apical meristem. By identifying genes mis‐expressed in mol1 mutants, we demonstrate that MOL1 represses genes associated with stress‐related ethylene and jasmonic acid hormone signaling pathways which have known roles in coordinating lateral growth of the Arabidopsis stem. Our findings provide evidence that common regulatory mechanisms in different plant stem cell niches are adapted to specific niche anatomies and emphasize the importance of a complex spatial organization of intercellular signaling cascades for a strictly bidirectional tissue production.