bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of Culter alburnus gonad tissues for discovery of sex-related genes
Authors: Zheng Jianbo , Jia Yongyi , Liu Shili , Jiang Wenping , Chi Meili , Cheng Shun , Gu Zhimin 
Published: June 2018

AbstractCulter alburnus is an important commercially fish species for freshwater breeding in China, and the females grow faster than the males. However, the molecular genetic mechanism of sex determination in C.alburnus is still poorly characterized. Here, we performed de novo assembly of a transcriptome from adult fish tissues of different gender using short read sequencing technology (Illumina). Our results showed that a total of 364,650 unigenes using Trinity software were obtained, giving rise to an average of 561.92 bp per read. Among them, 70,215 sequences matched known genes, including 5,892 male-biased unigenes and 942 female-biased unigenes. Many sex-related genes and pathways were identified based on annotation information. These results would provide new insights into the genetic mechanism of C.alburnus sex determination and also establish an important foundation for further research on aquaculture breeding.
In vitrotoxicity and efficacy of verdinexor, an exportin 1 inhibitor, on opportunistic viruses affecting immunocompromised individuals
Authors: Widman Douglas G. , Gornisiewicz Savanna , Shacham Sharon , Tamir Sharon 
Published: June 2018

AbstractInfection of immunocompromised individuals with normally benign opportunistic viruses is a major health burden globally. Infections with viruses such as Epstein-Barr virus (EBV), human cytomegalovirus (HCMV), Kaposi’s sarcoma virus (KSHV), adenoviruses (AdV), BK virus (BKPyV), John Cunningham virus (JCPyV), and human papillomavirus (HPV) are significant concerns for the immunocompromised, including when these viruses exist as a co-infection with human immunodeficiency virus (HIV). These viral infections are more complicated in patients with a weakened immune system, and often manifest as malignancies resulting in significant morbidity and mortality. Vaccination is not an attractive option for these immune compromised individuals due to defects in their adaptive immune response. Verdinexor is part of a novel class of small molecules known as SINE (Selective Inhibitor of Nuclear Export) compounds. These small molecules demonstrate specificity for the nuclear export protein XPO1, to which they bind and block function, resulting in sequestration of XPO1-dependent proteins in the nucleus of the cell. In antiviral screening, verdinexor demonstrated varying levels of efficacy against all of the aforementioned viruses including previously with HIV. Studies by other labs have discussed likely mechanisms of action for verdinexor (ie. XPO-1-dependence) against each virus. GLP toxicology studies suggest that anti-viral activity can be achieved at a tolerable dose range, based on the safety profile of a previous phase 1 clinical trial of verdinexor in healthy human volunteers. Taken together, these results indicate verdinexor has the potential to be a broad spectrum antiviral for immunocompromised subjects for which vaccination is a poor option.
Attenuation of obesity and related metabolic disorders by the individual or combination treatment with IL-2/anti-IL-2 complex and hyperbaric oxygen
Authors: Choi Eun-Jeong , Kim Hyung-Ran , Jeong-Hae Kie , Moon Byung-In , Seoh Ju-Young 
Published: June 2018

AbstractObesity is the disease accumulating excessive fat in the body. The prevalence of obesity and related metabolic disorders is increasing every year worldwide. Immunologically, obesity is a chronic low-grade inflammatory state with the increase of M1 macrophages and decrease of regulatory T cells (Tregs). IL-2/anti-IL-2 complex (IL-2C) and hyperbaric oxygen (HBO) are known to expand Tregsin vivoand suppress inflammation. Therefore, in this study, IL-2C and HBO were investigated for the preventive effect of obesity and related metabolic disorders. Male C57BL/6 mice were fed with a high-fat diet (HFD) for 16 weeks, and counterparts were fed with a low-fat diet (LFD). At the end of the experiment, the body weight gain and impaired glucose metabolism, elevated levels of insulin and total cholesterol induced by HFD were improved by the individual or combination treatment with Il-2C and HBO. Histological examination of the epididymal white adipose tissue showed adipocyte hypertrophy and many crown-like structures in the HFD control groups. In addition, the liver showed the progression of non-alcoholic fatty liver disease (NAFLD) in the HFD control groups, but it was significantly improved by the individual or combination treatment with IL-2C and HBO.As for the underlying mechanism, inflammation induced by obesity was decreased, and HIF-1α expression by adipocyte hypertrophy was also reduced by the individual or combination treatment with IL-2C and HBO. In addition, adipose tissue browning was activated in brown and inguinal adipose tissue, and the expression of UCP-1 involved in the thermogenesis was increased by the individual or combination treatment with IL-2C and HBO. Overall, these results suggested that IL-2C and HBO might be a new promising immunotherapy for the treatment of obesity and related metabolic disorders by regulation of inflammation and activation of adipose tissue browning.
High-performance biodegradable membrane for point of need paper-based micro-scale microbial fuel cell analytical devices
Authors: González-Pabón María Jesús , Figueredo Federico , Martínez-Casillas Diana C. , Cortón Eduardo 
Published: June 2018

AbstractOne limiting aspect to make microbial fuel cells (MFCs) a viable technology is to obtain low cost and environmentally sound materials for their components. In this work we synthesized membranes by a simple procedure involving low price and biodegradable materials such as poly (vinyl alcohol) (PVA), chitosan (CS) and PVA:CS, all cross-linked with sulfuric acid; they were compared to Nafion®, as our reference/control membrane. PVA:CS show lower oxygen permeability in comparison to Nafion®membranes, a strong advantage in order to maintain anaerobic conditions in the anodic compartment of MFCs. Membranes were characterized in typical H-Type MFCs, and results show that PVA:CS membranes outperform Nafion®4 times (power production) while being 75 times more economic. Moreover, we design a paper-based micro-scale MFC, which was assayed as a toxicity biosensor; we obtained results in less than 20 min using 16 μL volume samples containing formaldehyde as a model toxicant. The PVA:CS membrane presented here can offer low environmental impact (materials, fabrication and disposal) and become a very interesting option for point of need single use disposable analytical devices.
Learned predictiveness acquired through experience prevails over the influence of conflicting verbal instructions in rapid selective attention
Authors: Cobos Pedro L. , Vadillo Miguel A. , Luque David , Le Pelley Mike E. 
Published: June 2018

AbstractPrevious studies have provided evidence that selective attention tends to prioritize the processing of stimuli that are good predictors of upcoming events over nonpredictive stimuli. In the present study we explored whether the mechanism responsible for this effect critically reflects the influence of prior experience of predictiveness (history of attentional selection of predictive stimuli), or whether it reflects a more flexible process that can be adapted to new verbally acquired knowledge. Our experiment manipulated participants’ experience of the predictiveness of different stimuli over the course of trial-by-trial training; we then provided explicit verbal instructions regarding stimulus predictiveness that were designed to be either consistent or inconsistent with the previously established learned predictiveness. The effects of training and instruction on attention to stimuli were measured using a dot probe task. Results revealed a rapid attentional bias towards stimuli experienced as predictive (versus those experienced as nonpredictive), that was completely unaffected by verbal instructions. This was not due to participants’ failure to recall or use instructions appropriately, as revealed by analyses of their learning about stimuli, and their memory for instructions. Overall, these findings suggest that stimuli experienced as predictive through trial-by-trial training produce a relatively inflexible attentional bias based on prior selection history, which is not (always) easily altered through instructions.
Potential PGPR properties of cellulolytic, nitrogen-fixing, and phosphate-solubilizing bacteria of a rehabilitated tropical forest soil
Authors: Tang Amelia , Haruna Ahmed Osumanu , Majid Nik Muhamad Ab. 
Published: June 2018

AbstractIn the midst of major soil degradation and erosion faced by tropical ecosystems, rehabilitated forests are established to avoid further deterioration of forest land. In this context, cellulolytic, nitrogen-fixing (N-fixing), and phosphate-solubilizing bacteria are very important functional groups in regulating the elemental cycle and plant nutrition, hence replenishing the nutrient content in forest soil. As other potential plant growth-promoting (PGP) rhizobacteria, these functional bacteria could have cross-functional abilities or beneficial traits that are essential for plants and improve their growths. This study was conducted to isolate, identify, and characterize selected PGP properties of these 3 functional groups of bacteria from tropical rehabilitated forest soils at Universiti Putra Malaysia Bintulu Sarawak Campus, Malaysia. Isolated cellulolytic, N-fixing and phosphate-solubilizing bacteria were characterized for respective functional activities, biochemical properties, molecularly identified, and assessed for PGP assays based on seed germination and indole-3-acetic acid (IAA) production. Out of 15 identified bacterial isolates exhibiting beneficial phenotypic traits, a third belong to genusBurkholderiaand a fifth toStenotrophomonassp. with both genera consisting of members from two different functional groups. Among the tested bacterial strains, isolateSerratia nematodiphilaC46d,Burkholderia nodosaNB1, andBurkholderia cepaciaPC8 showed outstanding cellulase, N-fixing, and phosphate-solubilizing activities, respectively. The results of the experiments confirmed the multiple PGP traits of selected bacterial isolates based on respective high functional activities, root, shoot lengths, and seedling vigour improvements when bacterized on mung bean seeds, as well as presented some significant IAA productions. The results of this study indicated that these functional bacterial strains could potentially be included in future biotechnological screenings to produce beneficial synergistic effectsviatheir versatile properties on improving soil fertility and possible crop growth stimulation.
Antibiotic-driven Escape of Host in a Parasite-induced Red Queen Dynamics
Authors: Anzia Elizabeth L. , Rabajante Jomar F. 
Published: June 2018

AbstractWinnerless coevolution of hosts and parasites could exhibit Red Queen dynamics, which is characterized by parasite-driven cyclic switching of expressed host phenotypes. We hypothesize that the application of antibiotics to suppress the reproduction of parasites can provide opportunity for the hosts to escape such winnerless coevolution. Here, we formulate a minimal mathematical model of host-parasite interaction involving multiple host phenotypes that are targeted by adapting parasites. Our model predicts the levels of antibiotic effectiveness that can steer the parasite-driven cyclic switching of host phenotypes (heteroclinic oscillations) to a stable equilibrium of host survival. Our simulations show that uninterrupted application of antibiotic with high-level effectiveness (> 85%) is needed to escape the Red Queen dynamics. Intermittent and low level of antibiotic effectiveness are indeed useless to stop host-parasite coevolution. This study can be a guide in designing good practices and protocols to minimize risk of further progression of parasitic infections.
No evidence that predictions and attention modulate the first feedforward sweep of cortical information processing
Authors: Alilović Josipa , Timmermans Bart , Reteig Leon C. , van Gaal Simon , Slagter Heleen A. 
Published: June 2018

AbstractPredictive coding models propose that predictions (stimulus likelihood) reduce sensory signals as early as primary visual cortex (V1), and that attention (stimulus relevance) can modulate these effects. Indeed, both prediction and attention have been shown to modulate V1 activity, albeit with fMRI, which has low temporal resolution. This leaves it unclear whether these effects reflect a modulation of the first feedforward sweep of visual information processing and/or later, feedback-related activity. In two experiments, we used EEG and orthogonally manipulated spatial predictions and attention to address this issue. Although clear top-down biases were found, as reflected in pre-stimulus alpha-band activity, we found no evidence for top-down effects on the earliest visual cortical processing stage (<80ms post-stimulus), as indexed by the amplitude of the C1 ERP component and multivariate pattern analyses. These findings indicate that initial visual afferent activity may be impenetrable to top-down influences by spatial prediction and attention.
Biased signaling downstream of epidermal growth factor receptor regulates proliferative versus apoptotic response to ligand
Authors: Ali Remah , Brown Wells , Purdy Stephen Conner , Davisson V. Jo , Wendt Michael K. 
Published: June 2018

AbstractInhibition of EGFR signaling by small molecule kinase inhibitors and monocloncal antibodies has proven effective in the treatment of multiple cancers. In contrast, metastatic breast cancers (BC) derived from EGFR-expressing mammary tumors are inherently resistant to EGFR-targeted therapies. Mechanisms that contribute to this inherent resistance remain poorly defined. Here we show that in contrast to primary tumors, ligand-mediated activation of EGFR in metastatic BC is dominated by STAT1 signaling. This change in downstream signaling leads to apoptosis and growth inhibition in response to EGF in metastatic BC cells. Mechanistically, these changes in downstream signaling result from an increase in the internalized pool of EGFR in metastatic cells, increasing physical access to the nuclear pool of STAT1. Along these lines, an EGFR mutant that is defective in endocytosis is unable to elicit STAT1 phosphorylation and apoptosis. Additionally, inhibition of endosomal signaling using an EGFR inhibitor linked to a nuclear localization signal specifically prevents EGF-induced STAT1 phosphorylation and cell death, without affecting EGFR:ERK1/2 signaling. Pharmacologic blockade of ERK1/2 signaling through the use of the allosteric MEK1/2 inhibitor, trametinib, dramatically biases downstream EGFR signaling toward a STAT1 dominated event, resulting in enhanced EGF-induced apoptosis in metastatic BC cells. Importantly, combined administration of trametinib and EGF also facilitated an apoptotic switch in EGFR-transformed primary tumor cells, but not normal mammary epithelial cells. These studies reveal a fundamental distinction for EGFR function in metastatic BC. Furthermore, the data demonstrate that pharmacological biasing of EGFR signaling toward STAT1 activation is capable of revealing the apoptotic function of this critical pathway.
Role of clathrin-mediated endocytosis in the use of heme and hemoglobin by the fungal pathogen Cryptococcus neoformans
Authors: Bairwa Gaurav , Caza Mélissa , Horianopoulos Linda , Hu Guanggan , Kronstad James 
Published: June 2018

SummaryHeme is a major source of iron for pathogens of humans, and its use is critical in determining the outcome of infection and disease. Cryptococcus neoformans is an encapsulated fungal pathogen that causes life-threatening infections in immunocompromised individuals. C. neoformans effectively uses heme as an iron source but the underlying mechanisms are poorly defined. Non-iron metalloporphyrins (MPPs) are toxic analogues of heme and are thought to enter microbial cells via endogenous heme acquisition systems. We therefore carried out a mutant screen for susceptibility against manganese metalloporphyrin (Mn MPP) to identify new components for heme uptake in C. neoformans. We identified several genes involved in signaling, DNA repair, sugar metabolism and trafficking that play important roles in susceptibility to Mn MPP and in the use of heme as an iron source. We focused on investigating the role of clathrin-mediated endocytosis (CME) and found that several components of CME including Chc1, Las17, Rvs161 and Rvs167 are required for growth on heme and hemoglobin, and for endocytosis and intracellular trafficking of these molecules. We show that the hemoglobin uptake process in C. neoformans involves clathrin heavy chain, Chc1, which appears to co-localize with hemoglobin containing-vesicles and to potentially assist in proper delivery of hemoglobin to the vacuole. Additionally, C. neoformans strains lacking Chc1, Las17, Rvs161, or Rvs167 were defective in the elaboration of several key virulence factors and a las17 mutant was avirulent in a mouse model of cryptococcosis. Overall, this study unveils crucial functions of CME in the use of heme iron by C. neoformans and reveals a role for CME in fungal pathogenesis.
Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells
Authors: Ellis David A. , Mustonen Ville , Rodríguez-López María , Rallis Charalampos , Malecki Michał , Jeffares Daniel C. , Bähler Jürg 
Published: June 2018

ABSTRACTQuantitative traits often show large variation caused by multiple genetic factors. One such trait is the chronological lifespan of non-dividing yeast cells, serving as a model for cellular aging. Screens for genetic factors involved in ageing typically assay mutants of protein-coding genes. To identify natural genetic variants contributing to cellular aging, we exploited two strains of the fission yeast,Schizosaccharomyces pombe, that differ in chronological lifespan. We generated segregant pools from these strains and subjected them to advanced intercrossing over multiple generations to break up linkage groups. We chronologically aged the intercrossed segregant pool, followed by genome sequencing at different times to detect genetic variants that became reproducibly enriched as a function of age. A region on Chromosome II showed strong positive selection during ageing. Based on expected functions, two candidate variants from this region in the long-lived strain were most promising to be causal: small insertions and deletions in the 5’-untranslated regions ofppk31andSPBC409.08. Ppk31 is an orthologue of Rim15, a conserved kinase controlling cell proliferation in response to nutrients, while SPBC409.08 is a predicted spermine transmembrane transporter. Both Rim15 and the spermine-precursor, spermidine, are implicated in ageing as they are involved in autophagy-dependent lifespan extension. Single and double allele replacement suggests that both variants, alone or combined, have subtle effects on cellular longevity. Furthermore, deletion mutants of bothppk31andSPBC409.08rescued growth defects caused by spermidine. We propose that Ppk31 and SPBC409.08 may function together to modulate lifespan, thus linking Rim15/Ppk31 with spermidine metabolism.
How is process mining technology used by organizations? A systematic literature review of empirical studies
Authors: Thiede Malte , Fuerstenau Daniel , Bezerra Barquet Ana Paula 
Published: June 2018

Purpose
The purpose of this paper is to review empirical studies on process mining in order to understand its use by organizations. The paper further aims to outline future research opportunities.

Design/methodology/approach
The authors propose a classification model that combines core conceptual elements of process mining with prior models from technology classification from the enterprise resource planning and business intelligence field. The model incorporates an organizational usage, a system-orientation and service nature, adding a focus on physical services. The application is based on a systematic literature review of 144 research papers.

Findings
The results show that, thus far, the literature has been chiefly concerned with realization of single business process management systems in single organizations. The authors conclude that cross-system or cross-organizational process mining is underrepresented in the ISR, as is the analysis of physical services.

Practical implications
Process mining researchers have paid little attention to utilizing complex use cases and mining mixed physical-digital services. Practitioners should work closely with academics to overcome these knowledge gaps. Only then will process mining be on the cusp of becoming a technology that allows new insights into customer processes by supplying business operations with valuable and detailed information.

Originality/value
Despite the scientific interest in process mining, particularly scant attention has been given by researchers to investigating its use in relatively complex scenarios, e.g., cross-system and cross-organizational process mining. Furthermore, coverage on the use of process mining from a service perspective is limited, which fails to reflect the marketing and business context of most contemporary organizations, wherein the importance of such scenarios is widely acknowledged. The small number of studies encountered may be due to a lack of knowledge about the potential of such scenarios as well as successful examples, a situation the authors seek to remedy with this study.
Determination of an additive time- and space-dependent coefficient in the heat equation
Authors: Huntul Mousa , Lesnic Daniel , Johansson Tomas 
Published: June 2018

Purpose
The purpose of this study is to provide an insight and to solve numerically the identification of an unknown coefficient of radiation/absorption/perfusion appearing in the heat equation from additional temperature measurements.

Design/methodology/approach
First, the uniqueness of solution of the inverse coefficient problem is briefly discussed in a particular case. However, the problem is still ill-posed as small errors in the input data cause large errors in the output solution. For numerical discretization, the finite difference method combined with a regularized nonlinear minimization is performed using the MATLAB toolbox routine lsqnonlin.

Findings
Numerical results presented for three examples show the efficiency of the computational method and the accuracy and stability of the numerical solution even in the presence of noise in the input data.

Research limitations/implications
The mathematical formulation is restricted to identify coefficients which separate additively in unknown components dependent individually on time and space, and this may be considered as a research limitation. However, there is no research implication to overcome this, as the known input data are also limited to single measurements of temperature at a particular time and space location.

Practical implications
As noisy data are inverted, the study models real situations in which practical measurements are inherently contaminated with noise.

Social implications
The identification of the additive time- and space-dependent perfusion coefficient will be of great interest to the bio-heat transfer community and applications.

Originality/value
The current investigation advances previous studies which assumed that the coefficient multiplying the lower-order temperature term depends on time or space separately. The knowledge of this physical property coefficient is very important in biomedical engineering for understanding the heat transfer in biological tissues. The originality lies in the insight gained by performing for the first time numerical simulations of inversion to find the coefficient additively dependent on time and space in the heat equation from noisy measurements.