bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA sequencing of the in vivohuman herpesvirus 6B transcriptome to identify targets for clinical assays distinguishing between latent and active infections
Authors: Hill Joshua A. , Ikoma Minako , Zerr Danielle M. , Basom Ryan S. , Peddu Vikas , Huang Meei-Li , Sedlak Ruth Hall , Jerome Keith R. , Boeckh Michael , Barcy Serge 
Published: August 2018

ABSTRACTHuman herpesvirus 6B (HHV-6B) DNA is frequently detected in human samples, especially after hematopoietic cell transplantation (HCT). Diagnostic assays distinguishing HHV-6B reactivation from latency are limited, and this has contributed to confusion in research and made the design of clinical approaches to diagnose and treat HHV-6-associated diseases challenging. We used RNA sequencing to characterize and compare the HHV-6B transcriptome in multiplein vivoandin vitrosample types, including 1) whole blood from HCT recipients with and without HHV-6B plasma viremia; 2) tumor tissue samples from subjects with large B cell lymphoma infected with HHV-6B; 3) lymphoblastoid cell lines from subjects with inherited chromosomally integrated HHV-6B or latent infection with HHV-6B; and 4) HHV-6B Z29 infected SupT1 CD4+ T cells. We demonstrated substantial overlap in the HHV-6B transcriptome observed inin vivoandin vitrosamples, although there was variability in the breadth and quantity of gene expression across samples. No HHV-6B transcripts were detected in whole blood samples from subjects without plasma HHV-6B viremia. The HHV-6B viral polymerase gene U38 was the only HHV-6B transcript detected in all RNA-seq data sets and was one of the most highly expressed genes. Using a novel reverse transcription PCR assay targeting HHV-6B U38, we identified U38 messenger RNA in all tested whole blood samples from patients with concurrent HHV-6B viremia, indicating its utility as a diagnostic assay for HHV-6B replication. This study demonstrates the feasibility of pathogen transcriptome analyses in HCT recipients to identify better targets for diagnostic, and potentially therapeutic, applications.IMPORTANCEInfection with human herpesvirus 6B (HHV-6B), a DNA virus, occurs early in life, results in chronic viral latency in diverse cell types, and affects the population at large. Additionally, HHV- 6B can integrate into germline chromosomes, resulting in individuals with viral DNA in every nucleated cell. Given that PCR to detect viral DNA is the mainstay for diagnosing HHV-6B infection, the characteristics of HHV-6B infection complicate efforts to distinguish between latent and active viral infection, particularly in immunocompromised patients who have frequent HHV- 6B reactivation. In this study, we used RNA sequencing to characterize the HHV-6B gene expression profile in multiple sample types, and our findings identified evidence-based targets for diagnostic tests that distinguish between latent and active viral infection.
A novel function of Galactomyces candidum in highly efficient ammonia nitrogen removal from low C:N wastewater
Authors: Xiaochao Li , Hui Liu , Guihua Zeng , Hualin Li , Zhinan Chen , Wenbin Liu , Liping Yang 
Published: August 2018

AbstractA strain of bacteria that demonstrated efficient nitrogen removal potential under low C:N conditions was screened from landfill leachate. The strain was identified as Galactomyces candidum by ITS sequencing, and growth density and removal of ammonia nitrogen were assessed after 24 h of incubation. The results showed that the optimum ammonia nitrogen reduction conditions for G. candidum was at pH 8.0 and 30 °C, with a C:N ratio of 1.5:1; the highest rate of ammonia nitrogen removal was 93.1%. This novel function of G. candidum offers great potential in the removal of ammonia nitrogen from sewage, especially in low C:N wastewater. Our study provides a new theoretical basis for the industrial application of bacteria in the biochemical treatment of wastewater and reduces environmental pollution.A novel function and potential of Galamyces candidum in the removal of ammonia nitrogen from wastewater treatment was found, which provides a theoretical basis for the treatment of ammonia in wastewater.
Solitary bee larvae prioritize carbohydrate over protein in parentally provided pollen
Authors: Austin Alexander J. , Gilbert James D. J. 
Published: August 2018

AbstractMost organisms must regulate their nutritional intake in an environment full of complex food choices. While this process is well understood for self-sufficient organisms, dependent offspring, such as bee larvae, in practice have limited food choices because food is provided by parents. Nutrient balancing may therefore be achieved by offspring, by parents on offspring’s behalf, or by both, whether cooperatively or in conflict.We used the Geometric Framework to investigate the capacity of dependent larval mason bees (Osmia bicornis) to regulate their intake of protein and carbohydrate. FemaleOsmiaseal eggs individually inside cells they have provisioned with pollen, and have no contact with developing offspring, allowing offspring choices to be studied in isolation. Herbivorous insect larvae are typically expected to balance protein and carbohydrate to maximise growth and reproduction.Contrary to prediction, carbohydrate and not protein mediated both growth and survival to pupation. Accordingly, larvae prioritised maintaining a constant intake of carbohydrate and self-selected a relatively carbohydrate biased diet compared to other hymenopterans, while tolerating wide excesses and deficiencies of protein, rendering them potentially vulnerable to dietary change or manipulation. Reasons for prioritising carbohydrate may include (1) the relative abundance of protein in their normal pollen diet, (2) the relative paucity of nectar in parental provisions making carbohydrate a scarce resource, or (3) the requirement for diapause for allO. bicornislarvae. Larvae were intolerant of moderate dietary dilution, likely reflecting an evolutionary history of nutrient-dense food.Our results demonstrate that dependent offspring can remain active participants in balancing their own nutrients even when sedentary, and, moreover, even in mass provisioning systems where parents and offspring have no physical contact. Research should now focus on whether and how evolutionary interests of parent and dependent offspring coincide or conflict with respect to food composition, and the implications for species’ resilience to changing environments.
Significant antitumour effect of an antibody against TMEM180, a new cancer-specific molecule
Authors: Yasunaga Masahiro , Saijou Shinji , Hanaoka Shingo , Anzai Takahiro , Tsumura Ryo , Matsumura Yasuhiro 
Published: August 2018

AbstractThe present state of therapy for colorectal cancer (CRC) is far from satisfactory, highlighting the need for new targets for this disease. We identified a new colorectal cancer (CRC)-specific molecule, TMEM180, a predicted eleven-pass transmembrane protein that apparently functions as a cation symporter. Our anti-TMEM180 monoclonal antibody (mAb) eradicated SW480 CRC xenografts in mice. The TMEM180 promoter region contains ten hypoxia-responsive element consensus sequences; accordingly SW480 cells upregulated TMEM180 under low-oxygen conditions. TMEM180 expression in SW480 cells was positively correlated with anchorage-independent colony formation and tumourigenesis. TMEM180-positive SW480 cells resided at the tumour–stroma interface manifested by αSMA-positive fibroblasts, also known as the tumour niche. Some clusters of TMEM180-positive cells adjacent to the niche were integrin α6-positive. These data indicate that TMEM180 represents a possible cancer stem cell marker and that a mAb against this protein could be used as antibody-based therapeutic against CRC.
A draft reference genome sequence for Scutellaria baicalensis Georgi
Authors: Zhao Qing , Yang Jun , Liu Jie , Cui Meng-Ying , Fang Yuming , Qiu Wengqing , Shang Huiwen , Xu Zhicheng , Wei Yukun , Yang Lei , Hu Yonghong , Chen Xiao-Ya , Martin Cathie 
Published: August 2018

AbstractScutellaria baicalensis Georgi is an important medicinal plant used worldwide. Information about the genome of this species is important for scientists studying the metabolic pathways that synthesise the bioactive compounds in this plant. Here, we report a draft reference genome sequence for S. baicalensis obtained by a combination of Illumina and PacBio sequencing, which was assembled using 10 X Genomics and Hi-C technologies. We assembled 386.63 Mb of the 408.14 Mb genome, amounting to about 94.73% of the total genome size, and the sequences were anchored onto 9 pseudochromosomes with a super-N50 of 33.2 Mb. The reference genome sequence of S. baicalensis offers an important foundation for understanding the biosynthetic pathways for bioactive compounds in this medicinal plant and for its improvement through molecular breeding.
Validation of product quality through graphical interpretation of the Kano model
Authors: Madzík Peter , Pelantová Vera 
Published: August 2018

Purpose
Product verification and validation are integral to quality management. Product verification means verifying the conformity between a product’s actual and planned characteristics whereas validation means determining whether and to what extent it satisfies customers’ requirements. One of the key forms of product validation is testing with a group of customers. The purpose of this paper is to introduce a graphical method of product validation based on the Kano model.

Design/methodology/approach
The approach is based on a proposed method for categorising requirements based on a Kano questionnaire and then applies this method for the validation of a product – a website. The proposed method is based on three steps: graphical determination of requirements in a Kano model; determination of requirement fulfilment degree and prioritisation of corrective measures and improvements.

Findings
The study opens space for discussion of the potential for improving a product and methods for identifying critical faults in products. The proposed method also permits an assessment of the potential effectiveness of an improvement because it is able to quantify the effect of the product on the consumer resulting from a given quantity of effort. A case study demonstrated that the resulting priority of corrective measures and improvements was affected not only by the level of fulfilment of the requirements but also by the type, the most critical being non-fulfilment of must-be requirements.

Research limitations/implications
The requirement curves are based on a verbal assessment of satisfaction in two states – if the requirement were fulfilled and if it were not fulfilled. The values of the start and end points may not be precise and could be affected by the natural character of subjective variables.

Practical implications
The proposed method is particularly suited to the initial testing of a product that is intended to lead to measures to eliminate customer dissatisfaction or increase their satisfaction – that is, to improve the product. The method also permits an assessment of the extent to which customers feel that their expectations have been satisfied and the effect that will be felt if the organisation decides to increase fulfilment.

Originality/value
The Kano model has not yet been applied to product validation, although it contains all the information necessary for this task. Knowing how satisfied customers are is an important part of product validation. At the same time, knowing a mechanism for “creating” this satisfaction is also very valuable information.
Exploration of Iron ore deposits in Patagonia. Insights from gravity, magnetic and SP modelling
Authors: Christiansen Rodolfo , Kostadinoff José , Bouhier Julia , Martinez Patricia 
Published: August 2018

ABSTRACTThe Sierra Grande region in northern Patagonia is considered the largest iron ore reserve in Argentina; however, the extension of the non‐outcropping deposits as well as the depth of the basins that contain them remains unknown. Utilizing 3D litho‐constrained inversion of gravity and magnetic data, we delimited an area with good prospects for iron ore deposits. In this region, high‐resolution magnetic and self‐potential profiles were acquired over the most important anomalies. Correlating both methodologies, it was possible to specify the possible existence of iron oxides (martite–hematite) in the form of 2D inclined sheets.
3D multi‐fractal analysis of porous media using 3D digital images: considerations for heterogeneity evaluation
Authors: Karimpouli Sadegh , Tahmasebi Pejman 
Published: August 2018

ABSTRACTPore structure heterogeneity is a critical parameter controlling mechanical, electrical and flow transport behaviour of rock. Multi‐fractal analysis method was used for a heterogeneity comparison of three‐dimensional rock samples with different lithology. Six real digital samples, containing three sandstones and three carbonates, were used. Based on the mercury injection capillary pressure test on these samples, we found that the carbonate samples are more heterogeneous than sandstones, but primary results of multi‐fractal behaviours for all samples were similar. We show that if multi‐fractal is used to evaluate and compare heterogeneity of different samples, one needs to follow some considerations such as (1) all samples must have the same size in pixel, (2) samples volume must be bigger than representative volume element, (3) multi‐fractal dimensions should be firstly normalized to a determined porosity value and (4) multi‐fractal results should be interpreted based on resolution of the imaging tool (effects of fine scale sub‐resolution pores are missed). Results revealed that using normalized fractal dimensions, the real samples were divided to less and high heterogeneous groups. Moreover, the study of scale effect also showed that porous structures of these samples are scale invariant in a wide range of scales (from one to eight times bigger).
Rock physics modelling based on depositional and burial history of Barents Sea sandstones
Authors: Bredesen Kenneth , Avseth Per , Johansen Tor Arne , Olstad Richard 
Published: August 2018

ABSTRACTUnderstanding how physical properties and seismic signatures of present day rocks are related to ancient geological processes is important for enhanced reservoir characterization. In this paper, we have studied this relationship for the Kobbe Formation sandstone in the Barents Sea. These rocks show anomalous low shear velocities and high VP/VS ratios, which does not agree well with conventional rock physics models for moderately to well consolidated sandstones. These sandstones have been buried relatively deeply and subsequently uplifted 1–2 km. We compared well log data of the Kobbe sandstone with velocity–depth trends modelled by integrating basin modelling principles and rock physics. We found that more accurate velocity predictions were obtained when first honouring mechanical and chemical compaction during burial, followed by generation of micro‐cracks during uplift. We suspect that these micro‐cracks are formed as overburden is eroded, leading to changes in the subsurface stress‐field. Moreover, the Kobbe Formation is typically heterogeneous and characterized by structural clays and mica that can reduce the rigidity of grain contacts. By accounting for depositional and burial history, our velocity predictions become more consistent with geophysical observables. Our approach yields more robust velocity predictions, which are important in prospect risking and net erosion estimates.
Pneumococcal sepsis requiring mechanical ventilation: Cohort study in 38 patients with rapid progression to septic shock
Authors: Ursin Rein Pernille , Jacobsen Dag , Ormaasen Vidar , Dunlop Oona 
Published: August 2018

BackgroundThe aim was to study the course of severe pneumococcal sepsis in patients who rapidly developed septic shock with multiorgan failure.MethodsCombined retrospective and prospective cohort study of all patients with pneumococcal sepsis requiring mechanical ventilation admitted to our Medical Intensive Care Unit at Oslo University Hospital Ullevaal, during an 8‐year period (01 January 2006 to 31 December 2013). The inclusion criteria were growth of Streptococcus pneumoniae in blood culture and respiratory failure treated with invasive mechanical ventilation.ResultsThirty‐eight patients were included. Median age was 57 years (interquartile range 49‐68, range 22‐79). For 84% (32/38), it took <24 hours from the first medical evaluation until they were in septic shock. Initial clinical features were variable; none were treated with antibiotics before hospital admission. Median Sequential Organ Failure Assessment (SOFA) score at admission was 11 (range 1‐15) and maximum 15 (range 5‐22), all patients developed multiorgan failure. Mutilating complications were seen in 47% (18/38) of the patients: six with amputations, 11 had adverse neurological complications and one patient both. In‐hospital mortality was 40% (15/38), 20% (8/38) survived with sequelae and 40% (15/38) returned to their habitual state. Poor outcome was associated with meningitis, disseminated intravascular coagulation, and gastrointestinal symptoms.ConclusionIn this patient cohort with pneumococcal sepsis and respiratory failure rapid development of septic shock was seen in all cases, even in young healthy individuals. Initial clinical features were variable; none were treated with antibiotics before admission. Mortality was high (40%), as was morbidity with limb amputations and neurological complications.
Erythropoietin in traumatic brain injury associated acute kidney injury: A randomized controlled trial
Authors: Skrifvars Markus B. , Moore Elizabeth , Mårtensson Johan , Bailey Michael , French Craig , Presneill Jeffrey , Nichol Alistair , Little Lorraine , Duranteau Jacques , Huet Olivier , Haddad Samir , Arabi Yaseen , McArthur Colin , Cooper David J. , Bellomo Rinaldo ,   The EPO‐TBI Investigators and the ANZICS Clinical Trials Group
Published: August 2018

BackgroundAcute kidney injury (AKI) in traumatic brain injury (TBI) is poorly understood and it is unknown if it can be attenuated using erythropoietin (EPO).MethodsPre‐planned analysis of patients included in the EPO‐TBI (ClinicalTrials.gov NCT00987454) trial who were randomized to weekly EPO (40 000 units) or placebo (0.9% sodium chloride) subcutaneously up to three doses or until intensive care unit (ICU) discharge. Creatinine levels and urinary output (up to 7 days) were categorized according to the Kidney Disease Improving Global Outcome (KDIGO) classification. Severity of TBI was categorized with the International Mission for Prognosis and Analysis of Clinical Trials in TBI.ResultsOf 3348 screened patients, 606 were randomized and 603 were analyzed. Of these, 82 (14%) patients developed AKI according to KDIGO (60 [10%] with KDIGO 1, 11 [2%] patients with KDIGO 2, and 11 [2%] patients with KDIGO 3). Male gender (hazard ratio [HR] 4.0 95% confidence interval [CI] 1.4‐11.2, P = 0.008) and severity of TBI (HR 1.3 95% CI 1.1‐1.4, P < 0.001 for each 10% increase in risk of poor 6 month outcome) predicted time to AKI. KDIGO stage 1 (HR 8.8 95% CI 4.5‐17, P < 0.001), KDIGO stage 2 (HR 13.2 95% CI 3.9‐45.2, P < 0.001) and KDIGO stage 3 (HR 11.7 95% CI 3.5‐39.7, P < 0.005) predicted time to mortality. EPO did not influence time to AKI (HR 1.08 95% CI 0.7‐1.67, P = 0.73) or creatinine levels during ICU stay (P = 0.09).ConclusionsAcute kidney injury is more common in male patients and those with severe compared to moderate TBI and appears associated with worse outcome. EPO does not prevent AKI after TBI.
Ultrasound‐assisted Lumbar Punctures: A Systematic Review and Meta‐Analysis
Authors: Gottlieb Michael , Holladay Dallas , Peksa Gary D. 
Published: August 2018

AbstractBackgroundLumbar punctures (LPs) are a common procedure in emergency medicine. However, studies have found that failed procedure rates can be as high as 50%. Ultrasound has been suggested to improve success rates by visually identifying the location and trajectory for the LP procedure. This systematic review and meta‐analysis was performed to determine whether the use of ultrasound improved the rate of successful LP performance.MethodsPubMed, CINAHL, Scopus, LILACS, the Cochrane Database of Systematic Reviews, the Cochrane Central Register of Controlled Trials, and bibliographies of selected articles were assessed for all randomized controlled trials comparing the success rates of ultrasound‐assisted LP with landmark‐based LP. Secondary outcomes included the rate of traumatic LPs, time to procedural success, number of needle passes, and patient pain score. Data were dual extracted into a predefined worksheet, and quality analysis was performed using the Cochrane Risk of Bias tool. Data were summarized and a meta‐analysis was performed with subgroup analyses by pediatric versus adult patients and by operator training level.ResultsTwelve studies (n = 957 total patients) were identified. Ultrasound‐assisted LP was successful in 90.0% of patients and landmark‐based LP was successful in 81.4% of patients. The calculated risk difference (RD) was 8.9% (95% confidence interval [CI] = 1.2% to 16.7%) with an odds ratio (OR) of 2.22 (95% CI = 1.03 to 4.77) in favor of the ultrasound‐assisted group. There were fewer traumatic LPs in the ultrasound‐assisted group (10.7% vs. 26.5%; RD = –16.4%, 95% CI = –27.6% to –5.2%; OR = 0.28, 95% CI = 0.18 to 0.45). Ultrasound‐assisted LP was also associated with a shorter time to successful LP (6.87 minutes vs. 7.97 minutes), fewer mean needle passes (2.07 vs. 2.66), and lower patient pain scores (3.75 vs. 6.31).ConclusionsUltrasound‐assisted LPs were associated with higher success rates, fewer traumatic LPs, shorter time to successful LP, fewer needle passes, and lower patient pain scores. Ultrasound should be considered prior to performing all LPs, especially in patients with difficult anatomy. Further studies are recommended to determine whether this effect is consistent in both adult and pediatric subgroups, as well as the impact of transducer type and body habitus on this technique.
Increased number of monocytes and plasma levels ofMCP‐1 andYKL‐40 in first‐episode psychosis
Authors: Orhan F. , Schwieler L. , Fatouros‐Bergman H. , Malmqvist A. , Cervenka S. , Collste K. , Flyckt L. , Farde L. , Sellgren C. M. , Piehl F. ,   Karolinska Schizophrenia Project (KaSP) Consortium, Engberg G. , Erhardt S. 
Published: August 2018

ObjectiveAccumulating evidence implicates immune activation in the development of schizophrenia. Here, monocyte numbers, monocyte chemoattractant protein‐1 (MCP‐1) and chitinase‐3‐like protein 1 (YKL‐40) were investigated in plasma and cerebrospinal fluid (CSF) in first‐episode psychosis (FEP) patients.MethodCSFand blood were sampled from 42 first‐episode psychosis (FEP) patients and 22 healthy controls. The levels ofYKL‐40 andMCP‐1 were measured using electrochemiluminescence assay, and blood monocytes were counted using anXN‐9000‐hematology analyzer.ResultsWe found higher plasma levels ofMCP‐1 andYKL‐40 inFEPpatients compared with healthy controls, a condition that was unrelated to antipsychotic and/or anxiolytic medication. This was combined with an increased number of blood monocytes and a borderline significant increase inYKL‐40 levels in theCSFof tobacco‐freeFEPpatients. Plasma orCSFchemokines or blood monocytes did not correlate with the severity of symptoms or the level of functioning.ConclusionThese data demonstrate activation of monocytes inFEPand strengthens the idea of an immune dysfunction of psychotic disorders. Further studies are required to perceive a role ofYKL‐40 andMCP‐1 in the initiation and progression of schizophrenia.