bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated IgM and abnormal free light chain ratio are increased in relatives from high-risk chronic lymphocytic leukemia pedigrees
Authors: Glenn Martha J. , Madsen Michael J. , Davis Ethan , Garner Cassandra D. , Curtin Karen , Jones Brandt , Williams Justin A. , Tomasson Michael H. , Camp Nicola J. 
Published: February 2019

AbstractAbnormal serum immunoglobulin (Ig) free light chains (FLC) are established biomarkers of early disease in multiple B-cell lymphoid malignancies, including chronic lymphocytic leukemia (CLL). Heavy chains have also been shown to be biomarkers in plasma cell disorders. An unanswered question is whether these Ig biomarkers are heritable, i.e., influenced by germline factors. CLL is heritable but highly heterogeneous. Heritable biomarkers could elucidate steps of disease pathogenesis that are affected by germline factors, and may help partition heterogeneity and identify genetic pleiotropies across malignancies. Relatives in CLL pedigrees present an opportunity to identify heritable biomarkers. We compared FLCs and heavy chains between relatives in 23 high-risk CLL pedigrees and population controls. Elevated IgM (eIgM) and abnormal FLC (aFLC) ratio was significantly increased in relatives, suggesting that these Ig biomarkers are heritable and could offer risk stratification in pedigree relatives. Within high-risk CLL pedigrees, B-cell lymphoid malignancies were five times more prevalent in close relatives of individuals with eIgM, prostate cancer was three times more prevalent in relatives of individuals with aFLC, and monoclonal B-cell lymphocytosis increased surrounding individuals with normal Ig levels. These different clustering patterns suggest Ig biomarkers have the potential to partition genetic heterogeneity in CLL and provide insight into distinct heritable pleiotropies associated with CLL.
Room temperature CO2 reduction to solid carbon species on liquid metals featuring atomically thin ceria interfaces
Authors: Esrafilzadeh Dorna , Zavabeti Ali , Jalili Rouhollah , Atkin Paul , Choi Jaecheol , Carey Benjamin J. , Brkljača Robert , O’Mullane Anthony P. , Dickey Michael D. , Officer David L. , MacFarlane Douglas R. , Daeneke Torben , Kalantar-Zadeh Kourosh 
Published: February 2019

AbstractNegative carbon emission technologies are critical for ensuring a future stable climate. However, the gaseous state of CO2 does render the indefinite storage of this greenhouse gas challenging. Herein, we created a liquid metal electrocatalyst that contains metallic elemental cerium nanoparticles, which facilitates the electrochemical reduction of CO2 to layered solid carbonaceous species, at a low onset potential of −310 mV vs CO2/C. We exploited the formation of a cerium oxide catalyst at the liquid metal/electrolyte interface, which together with cerium nanoparticles, promoted the room temperature reduction of CO2. Due to the inhibition of van der Waals adhesion at the liquid interface, the electrode was remarkably resistant to deactivation via coking caused by solid carbonaceous species. The as-produced solid carbonaceous materials could be utilised for the fabrication of high-performance capacitor electrodes. Overall, this liquid metal enabled electrocatalytic process at room temperature may result in a viable negative emission technology.
Impact of pre-existing dengue immunity on human antibody and memory B cell responses to Zika
Authors: Andrade Paulina , Gimblet-Ochieng Ciara , Modirian Faraz , Collins Matthew , Cárdenas Maritza , Katzelnick Leah C. , Montoya Magelda , Michlmayr Daniela , Kuan Guillermina , Balmaseda Angel , Coloma Josefina , de Silva Aravinda M. , Harris Eva 
Published: February 2019

AbstractLittle is known about enduring memory B cell (MBC) responses to Zika virus (ZIKV) and their relationship with circulating antibodies. Here we comprehensively assess MBC frequency and specificity alongside serum binding and neutralizing antibody responses to ZIKV ~2 weeks and ~8 months postinfection in 31 pediatric subjects with 0, 1 or >1 prior infections with the related dengue virus (DENV). ZIKV infection elicits a robust type-specific MBC response, and the majority of late convalescent anti-ZIKV serum neutralizing activity is attributable to ZIKV-specific antibodies. The number of prior DENV infections does not influence type-specific or cross-reactive MBC responses, although ZIKV has the highest cross-reactivity with DENV3. DENV cross-reactive MBCs expanded by ZIKV infection decline in number and proportion by late convalescence. Finally, ZIKV induces greater cross-reactivity in the MBC pool than in serum antibodies. Our data suggest immunity to DENV only modestly shapes breadth and magnitude of enduring ZIKV antibody responses.
Experimental crossbreeding reveals strain-specific variation in mortality, growth and personality in the brown trout (Salmo trutta)
Authors: Ågren Anni , Vainikka Anssi , Janhunen Matti , Hyvärinen Pekka , Piironen Jorma , Kortet Raine 
Published: February 2019

AbstractAlthough hybridization between populations with low genetic diversity may induce heterosis, it can also lead to reduced fitness of hybrid offspring through outbreeding depression and loss of local adaptations. Using a half-sib mating design, we studied on brown trout (Salmo trutta) how hybridization of migratory hatchery-strain females with males from various strains would affect early mortality, growth and personality in F1 offspring. No differences in mortality or alevin body length were found between the crossing groups by the end of the yolk-sac stage. At later developmental stages, higher mortality and slower growth in one of the geographically distant hybrid groups indicated potential outbreeding depression. The personality component indicating boldness and exploration tendency showed fairly low genetic variation and no phenotypic differences among the crossing groups while the personality component related to freezing behavior indicated stronger freezing responses in the purebred and local cross strain when compared to the two other strains. However, the purebred hatchery strain possessed stronger additive genetic tendency for boldness and explorative behavior, and weaker genetic tendency for freezing behavior, when compared to the wild × hatchery hybrid group. Our results add to the cumulating evidence of risks related to the stocking of fish strains from non-native origins.
Randomized controlled trial on the influence of dietary intervention on epigenetic mechanisms in children with cow’s milk allergy: the EPICMA study
Authors: Paparo Lorella , Nocerino Rita , Bruno Cristina , Di Scala Carmen , Cosenza Linda , Bedogni Giorgio , Di Costanzo Margherita , Mennini Maurizio , D’Argenio Valeria , Salvatore Francesco , Berni Canani Roberto 
Published: February 2019

AbstractEpigenetic mechanisms could drive the disease course of cow’s milk allergy (CMA) and formula choice could modulate these pathways. We compared the effect of two different dietary approaches on epigenetic mechanisms in CMA children. Randomized controlled trial on IgE-mediated CMA children receiving a 12-month treatment with extensively hydrolyzed casein formula containing the probiotic L.rhamnosus GG (EHCF + LGG) or with soy formula (SF). At the baseline, after 6 and 12 months of treatment FoxP3 methylation rate and its expression in CD4+ T cells were assessed. At same study points IL-4, IL-5, IL-10, and IFN-γ methylation rate, expression and serum concentration, miRNAs expression were also investigated. 20 children (10/group) were evaluated. Baseline demographic, clinical and epigenetic features were similar in the two study groups. At 6 and 12 months, EHCF + LGG group showed a significant increase in FoxP3 demethylation rate compared to SF group. At the same study points, EHCF + LGG group presented a higher increase in IL-4 and IL-5 and a higher reduction in IL-10 and IFN-γ DNA methylation rate compared to SF group. A different modulation of miR-155, -146a, -128 and -193a expression was observed in EHCF + LGG vs. SF. Dietary intervention could exert a different epigenetic modulation on the immune system in CMA children.
Single step fabrication of Silicon resistors on SOI substrate used as Thermistors
Authors: Rollo Serena , Rani Dipti , Olthuis Wouter , Pascual García César 
Published: February 2019

AbstractTemperature sensing is one of the important features of Micro Electro Mechanical Systems and a monolithic integration provides advantages for both fabrication simplicity and performance. The use of Silicon On Insulator substrates allows simple fabrication of integrated wires that can be used as thermistors. We fabricated rectangular and triangular silicon wires with different dimensions in a single step fabrication process based on the wet etching of a <110> Silicon On Insulator substrate. We determined the experimental resistivity of the two kinds of devices and tested their performance as thermistors in a temperature range between 24 and 100 °C. The accuracy and normalized sensitivities of our devices were 0.4 °C and 0.3–0.5%/°C, respectively. The potential of the proposed method resides in the possibility of having devices with different shapes in a single straightforward process.
Integrative analysis of postharvest chilling injury in cherry tomato fruit reveals contrapuntal spatio-temporal responses to ripening and cold stress
Authors: Albornoz Karin , Cantwell Marita I. , Zhang Lu , Beckles Diane M. 
Published: February 2019

AbstractPostharvest chilling injury (PCI) reduces fruit quality and shelf-life in tomato (Solanum lycopersicum L.). PCI has been traditionally studied in the pericarp, however its development is likely heterogeneous in different fruit tissues. To gain insight into PCI’s spatio-temporal development, we used postharvest biomarkers e.g. respiration and ethylene rates, ion leakage etc., to confirm the occurrence of PCI, and compared these data with molecular (gene expression), biophysical (MRI data) and biochemical parameters (Malondialdehyde (MDA) and starch content) from the pericarp or columella. Tissues were stored at control (12.5 °C) or PCI-inducing temperatures (2.5 or 5 °C) followed by rewarming at 20 °C. MRI and ion leakage revealed that cold irreversibly impairs ripening-associated membrane liquefaction; MRI also showed that the internal and external fruit tissues responded differently to cold. MDA and especially starch contents, were affected by chilling in a tissue-specific manner. The expression of the six genes studied: ACO1 and ACS2 (ripening), CBF1 (cold response), DHN, AOX1a and LoxB (stress-related) showed non-overlapping temporal and spatially-specific responses. Overall, the data highlighted the interconnectedness of fruit cold response and ripening, and showed how cold stress reconfigures the latter. They further underscored that multidimensional spatial and temporal biological studies are needed to develop effective solutions to PCI.
Short-term and long-term effects of low serum bicarbonate level at admission in hospitalised patients
Authors: Lim Sung Yoon , Park Youngmi , Chin Ho Jun , Na Ki Young , Chae Dong-Wan , Kim Sejoong 
Published: February 2019

AbstractAlthough low serum bicarbonate level is known to be associated with adverse outcomes in patients with chronic kidney injury, it is unclear whether low serum bicarbonate level is associated with the development of acute kidney injury (AKI). The purpose of our study was to determine whether serum bicarbonate levels at admission could be a risk factor for AKI development and mortality in hospitalised patients. We retrospectively enrolled 17,320 adult patients who were admitted to the academic teaching hospital from January 2013 to December 2013. Patients were divided into 2 groups based on the first measurement of serum bicarbonate level at admission. The incidence of AKI was higher in patients with low serum bicarbonate level than in those with normal serum bicarbonate level (8.0% vs. 4.1%). Low serum bicarbonate levels at admission were significantly associated with the development of AKI. In addition, low serum bicarbonate levels also independently predicted the 90-day mortality. Pre-existing low bicarbonate levels and subsequent development of AKI increased in-hospital mortality by 15 times compared with that in patients with normal bicarbonate levels and no AKI. Low serum bicarbonate levels may be associated with the development of AKI and high mortality in hospitalised patients.
Early differentiation of long-standing persistent atrial fibrillation using the characteristics of fibrillatory waves in surface ECG multi-leads
Authors: Park Junbeom , Lee Chungkeun , Leshem Eran , Blau Ira , Kim Sungsoo , Lee Jung Myung , Hwang Jung-A , Choi Byung-il , Lee Moon-Hyoung , Hwang Hye Jin 
Published: February 2019

AbstractWe characterized the f-waves in atrial fibrillation (AF) in the surface ECG by quantifying the amplitude, irregularity, and dominant rate of the f-waves in leads II, aVL, and V1, and investigated whether those parameters of the f-waves could discriminate long-standing persistent AF (LPeAF) from non-LPeAF. A total of 224 AF patients were enrolled: 112 with PAF (87 males), 48 with PeAF (38 males), and 64 with LPeAF (47 males). The f-waves in surface ECG leads V1, aVL, and II, which reflect well electrical activity in the right atrium (RA), the left atrium (LA), and both atria, respectively, were analyzed. The f-waves for LPeAF had lower amplitudes in II and aVL, increased irregularity and a higher dominant rate in II and V1 compared to PAF and PeAF (all p < 0.02). In a multivariate analysis, a low amplitude in lead II (<34.6 uV) and high dominant rate in lead V1 (≧390/min) (p < 0.001) independently discriminated LPeAF from the other AF types. The f-waves combined with both a low amplitude in lead II and high dominant rate in lead V1 were significantly associated with LPeAF (OR 6.27, p < 0.001). Characteristics of the f-waves on the surface ECG could discriminate LPeAF from other types of AF.
Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress
Authors: Catacchio C. R. , Alagna F. , Perniola R. , Bergamini C. , Rotunno S. , Calabrese F. M. , Crupi P. , Antonacci D. , Ventura M. , Cardone M. F. 
Published: February 2019

AbstractGrapevine (Vitis vinifera L.) is importantly cultivated worldwide for table grape and wine production. Its cultivation requires irrigation supply, especially in arid and semiarid areas. Water deficiency can affect berry and wine quality mostly depending on the extent of plant perceived stress, which is a cultivar-specific trait. We tested the physiological and molecular responses to water deficiency of two table grape cultivars, Italia and Autumn royal, and we highlighted their different adaptation. Microarray analyses revealed that Autumn royal reacts involving only 29 genes, related to plant stress response and ABA/hormone signal transduction, to modulate the response to water deficit. Instead, cultivar Italia orchestrates a very broad response (we found 1037 differentially expressed genes) that modifies the cell wall organization, carbohydrate metabolism, response to reactive oxygen species, hormones and osmotic stress. For the first time, we integrated transcriptomic data with cultivar-specific genomics and found that ABA-perception and –signalling are key factors mediating the varietal-specific behaviour of the early response to drought. We were thus able to isolate candidate genes for the genotype-dependent response to drought. These insights will allow the identification of reliable plant stress indicators and the definition of sustainable cultivar-specific protocols for water management.
Serum biomarkers identification by iTRAQ and verification by MRM: S100A8/S100A9 levels predict tumor-stroma involvement and prognosis in Glioblastoma
Authors: Arora Anjali , Patil Vikas , Kundu Paramita , Kondaiah Paturu , Hegde A. S. , Arivazhagan A. , Santosh Vani , Pal Debnath , Somasundaram Kumaravel 
Published: February 2019

AbstractDespite advances in biology and treatment modalities, the prognosis of glioblastoma (GBM) remains poor. Serum reflects disease macroenvironment and thus provides a less invasive means to diagnose and monitor a diseased condition. By employing 4-plex iTRAQ methodology, we identified 40 proteins with differential abundance in GBM sera. The high abundance of serum S100A8/S100A9 was verified by multiple reaction monitoring (MRM). ELISA and MRM-based quantitation showed a significant positive correlation. Further, an integrated investigation using stromal, tumor purity and cell type scores demonstrated an enrichment of myeloid cell lineage in the GBM tumor microenvironment. Transcript levels of S100A8/S100A9 were found to be independent poor prognostic indicators in GBM. Medium levels of pre-operative and three-month post-operative follow-up serum S100A8 levels predicted poor prognosis in GBM patients who lived beyond median survival. In vitro experiments showed that recombinant S100A8/S100A9 proteins promoted integrin signalling dependent glioma cell migration and invasion up to a threshold level of concentrations. Thus, we have discovered GBM serum marker by iTRAQ and verified by MRM. We also demonstrate interplay between tumor micro and macroenvironment and identified S100A8 as a potential marker with diagnostic and prognostic value in GBM.
Very High Refractive Index Transition Metal Dichalcogenide Photonic Conformal Coatings by Conversion of ALD Metal Oxides
Authors: Chen Christopher T. , Pedrini Jacopo , Gaulding E. Ashley , Kastl Christoph , Calafiore Giuseppe , Dhuey Scott , Kuykendall Tevye R. , Cabrini Stefano , Toma Francesca M. , Aloni Shaul , Schwartzberg Adam M. 
Published: February 2019

AbstractMaterials for nanophotonic devices ideally combine ease of deposition, very high refractive index, and facile pattern formation through lithographic templating and/or etching. In this work, we present a scalable method for producing high refractive index WS2 layers by chemical conversion of WO3 synthesized via atomic layer deposition (ALD). These conformal nanocrystalline thin films demonstrate a surprisingly high index of refraction (n > 3.9), and structural fidelity compatible with lithographically defined features down to ~10 nm. Although this process yields highly polycrystalline films, the optical constants are in agreement with those reported for single crystal bulk WS2. Subsequently, we demonstrate three photonic structures - first, a two-dimensional hole array made possible by patterning and etching an ALD WO3 thin film before conversion, second, an analogue of the 2D hole array first patterned into fused silica before conformal coating and conversion, and third, a three-dimensional inverse opal photonic crystal made by conformal coating of a self-assembled polystyrene bead template. These results can be trivially extended to other transition metal dichalcogenides, thus opening new opportunities for photonic devices based on high refractive index materials.
Glyoxylate cycle gene ICL1 is essential for the metabolic flexibility and virulence of Candida glabrata
Authors: Chew Shu Yih , Ho Kok Lian , Cheah Yoke Kqueen , Ng Tzu Shan , Sandai Doblin , Brown Alistair J. P. , Than Leslie Thian Lung 
Published: February 2019

AbstractThe human fungal pathogen Candida glabrata appears to utilise unique stealth, evasion and persistence strategies in subverting the onslaught of host immune response during systemic infection. However, macrophages actively deprive the intracellular fungal pathogen of glucose, and therefore alternative carbon sources probably support the growth and survival of engulfed C. glabrata. The present study aimed to investigate the role of the glyoxylate cycle gene ICL1 in alternative carbon utilisation and its importance for the virulence of C. glabrata. The data showed that disruption of ICL1 rendered C. glabrata unable to utilise acetate, ethanol or oleic acid. In addition, C. glabrata icl1∆ cells displayed significantly reduced biofilm growth in the presence of several alternative carbon sources. It was also found that ICL1 is crucial for the survival of C. glabrata in response to macrophage engulfment. Disruption of ICL1 also conferred a severe attenuation in the virulence of C. glabrata in the mouse model of invasive candidiasis. In conclusion, a functional glyoxylate cycle is essential for C. glabrata to utilise certain alternative carbon sources in vitro and to display full virulence in vivo. This reinforces the view that antifungal drugs that target fungal Icl1 have potential for future therapeutic intervention.
Early postoperative hypoalbuminaemia is associated with pleural effusion after donor hepatectomy: A propensity score analysis of 2316 donors
Authors: Jeong Hye-Won , Kim Jung-Won , Shin Won-Jung , Kim Seon-Ok , Moon Young-Jin , Kwon Hye-Mee , Jung Kyeo-Woon , Jun In-Gu , Song Jun-Gol , Hwang Gyu-Sam 
Published: February 2019

AbstractPleural effusion and hypoalbuminaemia frequently occur after hepatectomy. Despite the emphasis on the safety of donors, little is known about the impact of postoperative albumin level on pleural effusion in liver donors. We retrospectively assessed 2316 consecutive liver donors from 2004 to 2014. The analysis of donors from 2004 to 2012 showed that postoperative pleural effusion occurred in 47.4% (970/2046), and serum albumin levels decreased until postoperative day 2 (POD2) and increased thereafter. In multivariable analysis, the lowest albumin level within POD2 (POD2ALB) was inversely associated with pleural effusion (OR 0.28, 95% CI 0.20–0.38; P < 0.001). POD2ALB ≤3.0 g/dL, the cutoff value at the 75th percentile, was associated with increased incidence of pleural effusion after propensity score (PS) matching (431 pairs; OR 1.69, 95% CI 1.30–2.21; P < 0.001). When we further analysed data from 2010 to 2014, intraoperative albumin infusion was associated with higher POD2ALB (P < 0.001) and lower incidence of pleural effusion (P = 0.024), compared with synthetic colloid infusion after PS matching (193 pairs). In conclusion, our data showed that POD2ALB is inversely associated with pleural effusion, and that intraoperative albumin infusion is associated with a lower incidence of pleural effusion when compared to synthetic colloid infusion in liver donors.
Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning
Authors: O’Brien Aidan R. , Wilson Laurence O. W. , Burgio Gaetan , Bauer Denis C. 
Published: February 2019

AbstractEditing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated “base editing” being limited to certain nucleotide changes, and only achievable within a small window around CRISPR-Cas target sites. The more versatile alternative, HDR (homology directed repair), has a 3-fold lower efficiency with known optimization factors being largely immutable in experiments. Here, we investigated the variable efficiency-governing factors on a novel mouse dataset using machine learning. We found the sequence composition of the single-stranded oligodeoxynucleotide (ssODN), i.e. the repair template, to be a governing factor. Furthermore, different regions of the ssODN have variable influence, which reflects the underlying mechanism of the repair process. Our model improves HDR efficiency by 83% compared to traditionally chosen targets. Using our findings, we developed CUNE (Computational Universal Nucleotide Editor), which enables users to identify and design the optimal targeting strategy using traditional base editing or – for-the-first-time – HDR-mediated nucleotide changes.