bluuebunny/crossref_metadata_2025_split huggingface dataset:
The gene structure and hypervariability of the complete Penaeus monodon Dscam gene
Authors: Apitanyasai Kantamas , Huang Shiao-Wei , Ng Tze Hann , He Shu-Ting , Huang Yu-Hsun , Chiu Shen-Po , Tseng Kuan-Chien , Lin Shih-Shun , Chang Wen-Chi , Baldwin-Brown James G. , Long Anthony D. , Lo Chu-Fang , Yu Hon-Tsen , Wang Han-Ching 
Published: November 2019

AbstractUsing two advanced sequencing approaches, Illumina and PacBio, we derive the entire Dscam gene from an M2 assembly of the complete Penaeus monodon genome. The P. monodon Dscam (PmDscam) gene is ~266 kbp, with a total of 44 exons, 5 of which are subject to alternative splicing. PmDscam has a conserved architectural structure consisting of an extracellular region with hypervariable Ig domains, a transmembrane domain, and a cytoplasmic tail. We show that, contrary to a previous report, there are in fact 26, 81 and 26 alternative exons in N-terminal Ig2, N-terminal Ig3 and the entirety of Ig7, respectively. We also identified two alternatively spliced exons in the cytoplasmic tail, with transmembrane domains in exon variants 32.1 and 32.2, and stop codons in exon variants 44.1 and 44.2. This means that alternative splicing is involved in the selection of the stop codon. There are also 7 non-constitutive cytoplasmic tail exons that can either be included or skipped. Alternative splicing and the non-constitutive exons together produce more than 21 million isoform combinations from one PmDscam locus in the P. monodon gene. A public-facing database that allows BLAST searches of all 175 exons in the PmDscam gene has been established at http://pmdscam.dbbs.ncku.edu.tw/.
Effects of combined d-fagomine and omega-3 PUFAs on gut microbiota subpopulations and diabetes risk factors in rats fed a high-fat diet
Authors: Hereu Mercè , Ramos-Romero Sara , Busquets Cristina , Atienza Lidia , Amézqueta Susana , Miralles-Pérez Bernat , Nogués Maria Rosa , Méndez Lucía , Medina Isabel , Torres Josep Lluís 
Published: November 2019

AbstractFood contains bioactive compounds that may prevent changes in gut microbiota associated with Westernized diets. The aim of this study is to explore the possible additive effects of d-fagomine and ω-3 PUFAs (EPA/DHA 1:1) on gut microbiota and related risk factors during early stages in the development of fat-induced pre-diabetes. Male Sprague Dawley (SD) rats were fed a standard diet, or a high-fat (HF) diet supplemented with d-fagomine, EPA/DHA 1:1, a combination of both, or neither, for 24 weeks. The variables measured were fasting glucose and glucose tolerance, plasma insulin, liver inflammation, fecal/cecal gut bacterial subgroups and short-chain fatty acids (SCFAs). The animals supplemented with d-fagomine alone and in combination with ω-3 PUFAs accumulated less fat than those in the non-supplemented HF group and those given only ω-3 PUFAs. The combined supplements attenuated the high-fat-induced incipient insulin resistance (IR), and liver inflammation, while increasing the cecal content, the Bacteroidetes:Firmicutes ratio and the populations of Bifidobacteriales. The functional effects of the combination of d-fagomine and EPA/DHA 1:1 against gut dysbiosis and the very early metabolic alterations induced by a high-fat diet are mainly those of d-fagomine complemented by the anti-inflammatory action of ω-3 PUFAs.
Effects of Eucalypt Plant Monoterpenes on Koala (Phascolarctos Cinereus) Cytokine Expression In Vitro
Authors: Marschner Caroline , Krockenberger Mark B. , Higgins Damien P. 
Published: November 2019

AbstractProtective immunity is crucial for survival of any species, though the koala as a specialist feeder adapted to an exclusive diet of eucalypts that contain plant secondary metabolites of varying toxicity and of immunomodulatory property. Being constantly exposed to such dietary chemicals it raises the question of their immune effects in a specialist eucalypt feeder. This study demonstrates that natural levels of circulating eucalypt plant secondary metabolites have dose dependent in vitro effects on cytokine expression of koala peripheral blood mononuclear cells, suggesting a potential trade-off of reduced function in multiple arms of the immune system associated with koala’s use of its specialized dietary niche.
Connecting Crop Productivity, Residue Fires, and Air Quality over Northern India
Authors: Jethva Hiren , Torres Omar , Field Robert D. , Lyapustin Alexei , Gautam Ritesh , Kayetha Vinay 
Published: November 2019

AbstractNorthwestern India is known as the “breadbasket” of the country producing two-thirds of food grains, with wheat and rice as the principal crops grown under the crop rotation system. Agricultural data from India indicates a 25% increase in the post-monsoon rice crop production in Punjab during 2002–2016. NASA’s A-train satellite sensors detect a consistent increase in the vegetation index (net 21%) and post-harvest agricultural fire activity (net ~60%) leading to nearly 43% increase in aerosol loading over the populous Indo-Gangetic Plain in northern India. The ground-level particulate matter (PM2.5) downwind over New Delhi shows a concurrent uptrend of net 60%. The effectiveness of a robust satellite-based relationship between vegetation index—a proxy for crop amounts, and post-harvest fires—a precursor of extreme air pollution events, has been further demonstrated in predicting the seasonal agricultural burning. An efficient crop residue management system is critically needed towards eliminating open field burning to mitigate episodic hazardous air quality over northern India.
Carbon isotopic evidence for rapid methane clathrate release recorded in coals at the terminus of the Late Palaeozoic Ice Age
Authors: Van de Wetering Nikola , Esterle Joan S. , Golding Suzanne D. , Rodrigues Sandra , Götz Annette E. 
Published: November 2019

AbstractThe end of the Late Palaeozoic Ice Age (LPIA) ushered in a period of significant change in Earth’s carbon cycle, demonstrated by the widespread occurrence of coals worldwide. In this study, we present stratigraphically constrained organic stable carbon isotope (δ13Corg) data for Early Permian coals (312 vitrain samples) from the Moatize Basin, Mozambique, which record the transition from global icehouse to greenhouse conditions. These coals exhibit a three-stage evolution in atmospheric δ13C from the Artinskian to the Kungurian. Early Kungurian coals effectively record the presence of the short-lived Kungurian Carbon Isotopic Excursion (KCIE), associated with the proposed rapid release of methane clathrates during deglaciation at the terminus of the Late Palaeozoic Ice Age (LPIA), with no observed disruption to peat-forming and terrestrial plant communities. δ13Corg variations in coals from the Moatize Basin are cyclic in nature on the order of 103–105 years and reflect changes in δ13Corg of ~±1‰ during periods of stable peat accumulation, supporting observations from Palaeozoic coals elsewhere. These cyclic variations express palaeoenvironmental factors constraining peat growth and deposition, associated with changes in base level. This study also demonstrates the effectiveness of vitrain in coal as a geochemical tool for recording global atmospheric change during the Late Palaeozoic.
CD56+CD57+ infiltrates as the most predominant subset of intragraft natural killer cells in renal transplant biopsies with antibody-mediated rejection
Authors: Jung Hey Rim , Kim Mi Joung , Wee Yu-Mee , Kim Jee Yeon , Choi Monica Young , Choi Ji Yoon , Kwon Hyunwook , Jung Joo Hee , Cho Yong Mee , Go Heounjeong , Kim Sang-Yeob , Ryu Yeon-Mi , Kim Yun Jae , Kim Young Hoon , Han Duck Jong , Shin Sung 
Published: November 2019

AbstractLittle is known about the characteristics and clinical implications of specific subsets of intragraft natural killer (NK) cells in kidney transplant recipients. We analyzed 39 for-cause renal transplant biopsies performed at our center from May 2015 to July 2017. According to histopathologic reports, 8 patients (20.5%) had no rejection (NR), 11 (28.2%) had T cell-mediated rejections (TCMR) only, and 20 (51.3%) had antibody-mediated rejection (ABMR). NK cells were defined as CD3–CD56+ lymphocytes that are positive for CD57, CD49b, NKG2A, or KIR. The density of NK cells was significantly higher in the ABMR group (2.57 ± 2.58/mm2) than in the NR (0.12 ± 0.22/mm2) or the TCMR (0.25 ± 0.34/mm2) group (P = 0.002). Notably, CD56+CD57+ infiltrates (2.16 ± 1.89) were the most frequently observed compared with CD56+CD49b+ (0.05 ± 0.13), CD56+NKG2A+ (0.21 ± 0.69), and CD56+KIR+ (0.15 ± 0.42) cells in the ABMR group (P < 0.001). Death-censored graft failure was significantly higher in patients with NK cell infiltration than those without (Log-rank test, P = 0.025). In conclusion, CD56+CD57+ infiltrates are a major subset of NK cells in kidney transplant recipients with ABMR and NK cell infiltration is significantly associated with graft failure post-transplant.
Logical measurement-based quantum computation in circuit-QED
Authors: Joo Jaewoo , Lee Chang-Woo , Kono Shingo , Kim Jaewan 
Published: November 2019

AbstractWe propose a new scheme of measurement-based quantum computation (MBQC) using an error-correcting code against photon-loss in circuit quantum electrodynamics. We describe a specific protocol of logical single-qubit gates given by sequential cavity measurements for logical MBQC and a generalised Schrödinger cat state is used for a continuous-variable (CV) logical qubit captured in a microwave cavity. To apply an error-correcting scheme on the logical qubit, we utilise a d-dimensional quantum system called a qudit. It is assumed that a three CV-qudit entangled state is initially prepared in three jointed cavities and the microwave qudit states are individually controlled, operated, and measured through a readout resonator coupled with an ancillary superconducting qubit. We then examine a practical approach of how to create the CV-qudit cluster state via a cross-Kerr interaction induced by intermediary superconducting qubits between neighbouring cavities under the Jaynes-Cummings Hamiltonian. This approach could be scalable for building 2D logical cluster states and therefore will pave a new pathway of logical MBQC in superconducting circuits toward fault-tolerant quantum computing.
Hepcidin mediates hypoferremia and reduces the growth potential of bacteria in the immediate post-natal period in human neonates
Authors: Prentice Sarah , Jallow Amadou T. , Sinjanka Edrissa , Jallow Momodou W. , Sise Ebrima A. , Kessler Noah J. , Wegmuller Rita , Cerami Carla , Prentice Andrew M. 
Published: November 2019

AbstractSepticemia is a leading cause of death among neonates in low-income settings, a situation that is deteriorating due to high levels of antimicrobial resistance. Novel interventions are urgently needed. Iron stimulates the growth of most bacteria and hypoferremia induced by the acute phase response is a key element of innate immunity. Cord blood, which has high levels of hemoglobin, iron and transferrin saturation, has hitherto been used as a proxy for the iron status of neonates. We investigated hepcidin-mediated redistribution of iron in the immediate post-natal period and tested the effect of the observed hypoferremia on the growth of pathogens frequently associated with neonatal sepsis. Healthy, vaginally delivered neonates were enrolled in a cohort study at a single center in rural Gambia (N = 120). Cord blood and two further blood samples up to 96 hours of age were analyzed for markers of iron metabolism. Samples pooled by transferrin saturation were used to conductex-vivogrowth assays withStaphylococcus aureus, Streptococcus agalactiae, Escherichia coliandKlebsiella pneumonia. A profound reduction in transferrin saturation occurred within the first 12 h of life, from high mean levels in cord blood (47.6% (95% CI 43.7–51.5%)) to levels at the lower end of the normal reference range by 24 h of age (24.4% (21.2–27.6%)). These levels remained suppressed to 48 h of age with some recovery by 96 h. Reductions in serum iron were associated with high hepcidin and IL-6 levels.Ex-vivogrowth of all sentinel pathogens was strongly associated with serum transferrin saturation. These results suggest the possibility that the hypoferremia could be augmented (e.g. by mini-hepcidins) as a novel therapeutic option that would not be vulnerable to antimicrobial resistance. Trial registration: The original trial in which this study was nested is registered at ISRCTN, number 93854442.
Takotsubo syndrome and cardiac implantable electronic device therapy
Authors: El-Battrawy Ibrahim , Erath Julia W. , Lang Siegfried , Ansari Uzair , Behnes Michael , Gietzen Thorsten , Zhou Xiaobo , Borggrefe Martin , Akin Ibrahim 
Published: November 2019

AbstractRecent studies have reported that takotsubo syndrome (TTS) patients are suffering from life-threatening arrhythmias. The aim of our study was to understand the short and long-term usefulness of cardiac implantable electronic devices in TTS patients.We constituted a collective of 142 patients in a bi-centric study diagnosed with TTS between 2003 and 2017. The patient groups, divided according to the treatment with (n = 9, 6.3%) or without cardiac devices (n = 133, 93.7%), were followed-up to determine the importance of devices and its complications. One patient was treated with a permanent pacemaker, five patients with a wearable cardioverter defibrillator, two patients with a subcutaneous defibrillator and one patient with a transvenous defibrillator. Regular device check-up was documented in all patients, presenting an ongoing high-degree AV-block. Neither device complications nor life-threatening tachyarrhythmias were documented after acute TTS event. However, patients comprising the device group suffered significantly more often from a highly reduced EF (30 ± 7.7% versus 39.1 ± 9.7%; p < 0.05), cardiogenic shock with use of inotropic agents (66.6% versus 16.6%; p < 0.05) and cardiopulmonary resuscitation (44.4% versus 5.3%; p < 0.05). Our data confirm the usefulness of pacemaker in TTS patients. However, the cardioverter defibrillator including wearable cardioverter defibrillator may not be recommended.
A plant biostimulant from the seaweed Ascophyllum nodosum (Sealicit) reduces podshatter and yield loss in oilseed rape through modulation of IND expression
Authors: Łangowski Łukasz , Goñi Oscar , Quille Patrick , Stephenson Pauline , Carmody Nicholas , Feeney Ewan , Barton David , Østergaard Lars , O’Connell Shane 
Published: November 2019

AbstractThe yield of podded crops such as oilseed rape (OSR) is limited by evolutionary adaptations of the plants for more efficient and successful seed dispersal for survival. These plants have evolved dehiscent dry fruits that shatter along a specifically developed junction at carpel margins. A number of strategies such as pod sealants, GMOs and hybrids have been developed to mitigate the impact of pod shatter on crop yield with limited success. Plant biostimulants have been shown to influence plant development. A challenge in plant biostimulant research is elucidating the mechanisms of action. Here we have focused on understanding the effect of an Ascophyllum nodosum based biostimulant (Sealicit) on fruit development and seed dispersal trait in Arabidopsis and OSR at genetic and physiological level. The results indicate that Sealicit is affecting the expression of the major regulator of pod shattering, INDEHISCENT, as well as disrupting the auxin minimum. Both factors influence the formation of the dehiscence zone and consequently reduce pod shattering. Unravelling the mode of action of this unique biostimulant provides data to support its effectiveness in reducing pod shatter and highlights its potential for growers to increase seed yield in a number of OSR varieties.
Identifying sex-linked markers in Litoria aurea: a novel approach to understanding sex chromosome evolution in an amphibian
Authors: Sopniewski Jarrod , Shams Foyez , Scheele Benjamin C. , Kefford Ben J. , Ezaz Tariq 
Published: November 2019

AbstractFew taxa exhibit the variability of sex-determining modes as amphibians. However, due to the presence of homomorphic sex chromosomes in many species, this phenomenon has been difficult to study. The Australian frog, Litoria aurea, has been relatively well studied over the past 20 years due to widespread declines largely attributable to chytrid fungus. However, it has been subject to few molecular studies and its mode of sex determination remained unknown. We applied DArTseq™ to develop sex-linked single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 44 phenotypically sexed L. aurea individuals from the Molonglo River in NSW, Australia. We conclusively identified a male heterogametic (XX-XY) sex determination mode in this species, identifying 11 perfectly sex-linked SNP and six strongly sex-linked PA markers. We identified a further 47 moderately sex-linked SNP loci, likely serving as evidence indicative of XY recombination. Furthermore, within these 47 loci, a group of nine males were found to have a feminised Y chromosome that significantly differed to all other males. We postulate ancestral sex-reversal as a means for the evolution of this now pseudoautosomal region on the Y chromosome. Our findings present new evidence for the ‘fountain of youth’ hypothesis for the retention of homomorphic sex chromosomes in amphibians and describe a novel approach for the study of sex chromosome evolution in amphibia.
Total adiponectin is associated with incident cardiovascular and renal events in treated hypertensive patients: subanalysis of the ATTEMPT-CVD randomized trial
Authors: Kim-Mitsuyama Shokei , Soejima Hirofumi , Yasuda Osamu , Node Koichi , Jinnouchi Hideaki , Yamamoto Eiichiro , Sekigami Taiji , Ogawa Hisao , Matsui Kunihiko 
Published: November 2019

AbstractThe predictive value of serum adiponectin for hypertensive cardiovascular outcomes is unknown. This study was performed to investigate the association of adiponectin with incident cardiovascular and renal events (CV events) in hypertensive patients. We performed post-hoc analysis on 1,228 hypertensive patients enrolled in the ATTEMPT-CVD study, a prospective randomized study comparing the effects of two antihypertensive therapies. The participants were divided into quartiles of baseline serum total adiponectin or high molecular weight (HMW) adiponectin. Multivariable Cox proportional hazards analysis was performed to determine the prognostic factors associated with CV events. Kaplan-Meier analysis for CV events by quartiles of baseline total adiponectin showed that patients in the highest total adiponectin quartile (Q4) had more CV events (P = 0.0135). On the other hand, no significant difference was noted regarding the incidence of CV events among patients stratified by HMW adiponectin quartile (P = 0.2551). Even after adjustment for potential confounders, the highest total adiponectin quartile (Q4) remained independently associated with incident CV events in hypertensive patients (HR = 1.949: 95%CI 1.051–3.612; P = 0.0341). These results showed that total adiponectin, but not HMW adiponectin, was independently associated with the incidence of CV events in treated hypertensive patients, thereby highlighting total adiponectin as a valuable predictor for hypertensive cardiovascular outcomes.
Predicting need for intensive care unit admission in adult emphysematous pyelonephritis patients at emergency departments: comparison of five scoring systems
Authors: Yap Xiao-Han , Ng Chip-Jin , Hsu Kuang-Hung , Chien Cheng-Yu , Goh Zhong Ning Leonard , Li Chih-Huang , Weng Yi-Ming , Hsieh Ming-Shun , Chen Hsien-Yi , Chen-Yeen Seak Joanna , Seak Chen-Ken , Seak Chen-June 
Published: November 2019

AbstractThis study assesses the performance of National Early Warning Score (NEWS), Quick Sepsis-related Organ Failure Assessment (qSOFA), Modified Early Warning Score (MEWS), Rapid Emergency Medicine Score (REMS), and Rapid Acute Physiology Score (RAPS) in predicting emphysematous pyelonephritis (EPN) patients’ need for intensive care unit (ICU) admission. A retrospective analysis was conducted at four training and research hospitals’ emergency departments (EDs) on all EPN adult patients from January 2007 to August 2017. Data extracted were used to calculate raw scores for five physiologic scoring systems. Mann-Whitney U tests and χ2 tests were done for numerical and categorical variables respectively to examine differences between characteristics of ICU and non-ICU patient populations. Predictability of ICU admission was evaluated with AUROC analysis. ICU patients had lower GCS scores, SpO2, platelet counts, and estimated glomerular filtration rate; and higher bands, blood urea nitrogen, creatinine, and incidences of septic shock and nephrectomy. NEWS performed best, with 73.85% accuracy at optimal cut-off of 3. In this multicentre ED EPN series, we recommend using NEWS in early identification of critical EPN patients and advance planning for ICU admission. This would reduce delays in ICU transfer and ultimately improve patient outcomes.
Demographic characteristics of free-roaming dogs (FRD) in rural and urban India following a photographic sight-resight survey
Authors: Tiwari Harish Kumar , Robertson Ian D. , O’Dea Mark , Vanak Abi Tamim 
Published: November 2019

AbstractAn understanding of the core demographic characteristics of the sub-populations of FRD is essential to effectively implement both rabies control interventions through mass vaccination of FRD, and dog population control programmes. This study compares the data obtained following photographic sight-resight surveys in rural (Shirsuphal village in west India) and urban (Municipal Corporation Panchkula in north India) locations . A total of 263 and 1408 FRD were seen at least once through 617 and 3465 sightings in the rural and urban sites, respectively. The rural location had a lower proportion of females (OR 0.5, 95% CI 0.4–0.7) and a higher proportion of poor and fair conditioned dogs (OR 1.8, 95% CI 1.3–2.3) compared to the urban setting. The rural site also had fewer active FRD (OR 0.6, 95% CI 0.5–0.7) and FRD were less likely to be sighted within 20 m of garbage points (OR 0.3, 95% CI 0.2–0.3) compared to the urban site. The demographic composition of the FRD population was found to vary within the urban location, with the odds of sighting a de-sexed dog being significantly higher in residential areas compared to other areas. The study underlines the importance of knowing the demographic composition of FRD for implementation of effective interventions against rabies. Fewer female dogs in the rural location indicate that spaying could be an effective tool for dog population management in this setting, while presence of dogs within 20 m of garbage points in urban settings highlights that an improved garbage management may reduce the carrying capacity of the urban locality resulting in smaller FRD population. It is concluded that quick and low cost surveys can generate useful demographic data for FRD in urban and rural settings which can be useful to understand the epidemiology of rabies and its control.