bluuebunny/crossref_metadata_2025_split huggingface dataset:
DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction
Authors: Zhang Yu , Jia Cangzhi , Fullwood Melissa Jane , Kwoh Chee Keong 
Published: February 2020

Abstract
The development of deep sequencing technologies has led to the discovery of novel transcripts. Many in silico methods have been developed to assess the coding potential of these transcripts to further investigate their functions. Existing methods perform well on distinguishing majority long noncoding RNAs (lncRNAs) and coding RNAs (mRNAs) but poorly on RNAs with small open reading frames (sORFs). Here, we present DeepCPP (deep neural network for coding potential prediction), a deep learning method for RNA coding potential prediction. Extensive evaluations on four previous datasets and six new datasets constructed in different species show that DeepCPP outperforms other state-of-the-art methods, especially on sORF type data, which overcomes the bottleneck of sORF mRNA identification by improving more than 4.31, 37.24 and 5.89% on its accuracy for newly discovered human, vertebrate and insect data, respectively. Additionally, we also revealed that discontinuous k-mer, and our newly proposed nucleotide bias and minimal distribution similarity feature selection method play crucial roles in this classification problem. Taken together, DeepCPP is an effective method for RNA coding potential prediction.
LYPD4, mouse homolog of a human acrosome protein, is essential for sperm fertilizing ability and male fertility†
Authors: Wang Dan , Cheng Liping , Xia Wenjuan , Liu Xiaofei , Guo Yueshuai , Yang Xiaoyu , Guo Xuejiang , Xu Eugene Yujun 
Published: February 2020

Abstract
Fertilization is one of the fundamental biological processes, but so far, we still do not have a full understanding of the underlying molecular mechanism. We have identified a human acrosome protein, LY6/PLAUR domain containing 4 (LYPD4), expressed specifically in human testes and sperm, and conserved within mammals. Mouse Lypd4, also specific to the testis and sperm, is essential for male fertility. LYPD4 protein first appeared in round spermatids during acrosome biogenesis and became part of acrosomes during spermatogenesis and in mature sperm. Lypd4 knockout mice are infertile with normal sperm number and motility. Mutant sperm, however, failed to reach oviduct during sperm migration inside the female reproductive tract, leading to fertilization failure and infertility. In addition, Lypd4 mutant sperms were unable to fertilize denuded egg via IVF (in vitro fertilization) but could fertilize eggs within intact Cumulus-Oocyte Complex, supporting an additional role in sperm-zona interaction. Out of more than five thousand spermatozoa proteins identified by mass spectrometry analysis, only a small subset of proteins (26 proteins) was changed in the absence of LYPD4, revealing a whole proteome picture of mutant sperm defective in sperm migration and sperm-zona binding. ADAM3, a key component of fertilization complex, as well as other sperm ADAM proteins are significantly reduced. We hence propose that LYPD4 plays an essential role in mammalian fertilization, and further investigation of its function and its interaction with other sperm membrane complexes may yield insights into human fertilization and novel strategy to improve IVF success.
MRS Shows Regionally Increased Glutamate Levels among Patients with Exhaustion Syndrome Due to Occupational Stress
Authors: Savic Ivanka 
Published: February 2020

AbstractDespite the rapid increase of reports of exhaustion syndrome (ES) due to daily occupational stress, the mechanisms underlying ES are unknown. We used voxel-based 1H-MR spectroscopy to examine the potential role of glutamate in this condition. The levels of glutamate were found to be elevated among ES patients (n = 30, 16 females) compared with controls (n = 31, 15 females). Notably, this increase was detected only in the anterior cingulate and mesial prefrontal cortex (ACC/mPFC), and the glutamate levels were linearly correlated with the degree of perceived stress. Furthermore, there was a sex by group interaction, as the glutamate elevation was present only in female patients. Female but not male ES patients also showed an increase in N-acetyl aspartate (NAA) levels in the amygdala. No group differences were detected in glutamine concentration (also measured). These data show the key role of glutamate in stress-related neuronal signaling and the specific roles of the amygdala and ACC/mPFC. The data extend previous reports about the neurochemical basis of stress and identify a potential neural marker and mediator of ES due to occupational stress. The observation of specific sex differences provides a tentative explanation to the well-known female predominance in stress-related psychopathology.
Sweetness Enhancement by Aromas: Measured by Descriptive Sensory Analysis and Relative to Reference Scaling
Authors: Bertelsen Anne S , Mielby Line A , Alexi Niki , Byrne Derek V , Kidmose Ulla 
Published: February 2020

Abstract
Sweetness enhancement by aromas has been suggested as a strategy to mitigate sugar reduction in food products, but enhancement is dependent on type of aroma and sugar level. A careful screening of aromas across sugar levels is thus required. Screening results might, however, depend on the method employed. Both descriptive sensory analysis and relative to reference scaling were therefore used to screen 5 aromas across 3 sucrose concentrations for their sweetness-enhancing effects in aqueous solutions. In the descriptive analysis, samples with added vanilla, honey, and banana aroma were rated as significantly sweeter than samples with added elderflower or raspberry aroma at all sucrose concentrations. In relative to reference scaling, honey aroma significantly increased the sweet taste compared with samples with added elderflower or no aroma at low and medium sucrose concentrations. Banana and raspberry aromas also increased the sweet taste significantly compared with the sample with added elderflower aroma at medium sucrose concentration in the relative to reference scaling. This demonstrates that the cross-modal effects observed by the 2 methods were different. In terms of the methods applied, relative to reference scaling was generally found to result in a decrease in the measured sweetness enhancement by aromas. In the descriptive analysis, the cross-modal effect of aromas on sweet taste perception was found to be significantly higher at 2.5% and 5.0% w/w sucrose compared with 7.5% w/w sucrose. These results highlight the importance of considering how references are employed in sensory analysis and how they affect cross-modal interactions.
Zinc can counteract selection for ciprofloxacin resistance
Authors: Vos Michiel , Sibleyras Louise , Lo Lai Ka , Hesse Elze , Gaze William , Klümper Uli 
Published: February 2020

ABSTRACT
Antimicrobial resistance (AMR) has emerged as one of the most pressing threats to public health. AMR evolution occurs in the clinic but also in the environment, where antibiotics and heavy metals can select and co-select for AMR. While the selective potential of both antibiotics and metals is increasingly well-characterized, experimental studies exploring their combined effects on AMR evolution are rare. It has previously been demonstrated that fluoroquinolone antibiotics such as ciprofloxacin can chelate metal ions. To investigate how ciprofloxacin resistance is affected by the presence of metals, we quantified selection dynamics between a ciprofloxacin-susceptible and a ciprofloxacin-resistant Escherichia coli strain across a gradient of ciprofloxacin concentrations in presence and absence of zinc. The presence of zinc reduced growth of both strains, while ciprofloxacin inhibited exclusively the susceptible one. When present in combination zinc retained its inhibitory effect, while ciprofloxacin inhibition of the susceptible strain was reduced. Consequently, the minimal selective concentration for ciprofloxacin resistance increased up to five-fold in the presence of zinc. Environmental pollution usually comprises complex mixtures of antimicrobial agents. In addition to the usual focus on additive or synergistic interactions in complex selective mixtures, our findings highlight the importance of antagonistic selective interactions when considering resistance evolution.
Pentadecanal and pentadecanoic acid coatings reduce biofilm formation of Staphylococcus epidermidis on PDMS
Authors: Ricciardelli Annarita , Casillo Angela , Corsaro Maria Michela , Tutino Maria Luisa , Parrilli Ermenegilda , van der Mei Henny C 
Published: February 2020

ABSTRACT
Staphylococcus epidermidis is well known to be one of the major causes of infections related to medical devices, mostly due to its strong capacity to form device-associated biofilms. Nowadays, these infections represent a severe burden to the public health system and the necessity of novel antibacterial strategies for the treatment of these difficult-to-eradicate infections is urgent. The Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125 was found to be able to produce an anti-biofilm molecule, the pentadecanal, active against S. epidermidis. In this work, we modified one of the most widely used silicone-based polymers, polydimethylsiloxane (PDMS), by adsorption of pentadecanal and its most promising derivative, pentadecanoic acid, on the PDMS surface. The biofilm formation of S. epidermidis RP62A on both untreated and modified PDMS was performed in a parallel plate flow chamber system, demonstrating the capability of the proposed anti-biofilm coatings to strongly reduce the biofilm formation. Furthermore, drug-release capacity and long-term efficacy (21 days) were also proven for the pentadecanoic acid coating.
Sea surface network optimization for tsunami forecasting in the near field: application to the 2015 Illapel earthquake
Authors: Navarrete P , Cienfuegos R , Satake K , Wang Y , Urrutia A , Benavente R , Catalán P A , Crempien J , Mulia I 
Published: February 2020

SUMMARYWe propose a method for defining the optimal locations of a network of tsunameters in view of near real-time tsunami forecasting using sea surface data assimilation in the near and middle fields, just outside of the source region. The method requires first the application of the empirical orthogonal function analysis to identify the potential initial locations, followed by an optimization heuristic that minimizes a cost-benefit function to narrow down the number of stations. We apply the method to a synthetic case of the 2015 Mw8.4 Illapel Chile earthquake and show that it is possible to obtain an accurate tsunami forecast for wave heights at near coastal points, not too close to the source, from assimilating data from three tsunameters during 14 min, but with a minimum average time lag of nearly 5 min between simulated and forecasted waveforms. Additional tests show that the time lag is reduced for tsunami sources that are located just outside of the area covered by the tsunameter network. The latter suggests that sea surface data assimilation from a sparse network of stations could be a strong complement for the fastest tsunami early warning systems based on pre-modelled seismic scenarios.
Plasticity in dormancy behaviour of Calanoides acutus in Antarctic coastal waters
Authors: Biggs Tristan E G , Brussaard Corina P D , Evans Claire , Venables Hugh J , Pond David W 
Published: February 2020

Abstract
Copepods that enter dormancy, such as Calanoides acutus, are key primary consumers in Southern Ocean food webs where they convert a portion of the seasonal phytoplankton biomass into a longer-term energetic and physiological resource as wax ester (WE) reserves. We studied the seasonal abundance and lipid profiles of pre-adult and adult C. acutus in relation to phytoplankton dynamics on the Western Antarctic Peninsula. Initiation of dormancy occurred when WE unsaturation was relatively high, and chlorophyll a (Chl a) concentrations, predominantly attributable to diatoms, were reducing. Declines in WE unsaturation during the winter may act as a dormancy timing mechanism with increased Chl a concentrations likely to promote sedimentation that results in a teleconnection between the surface and deep water inducing ascent. A late summer diatom bloom was linked to early dormancy termination of females and a second spawning event. The frequency and duration of high biomass phytoplankton blooms may have consequences for the lifespan of the iteroparous C. acutus females (either 1 or 2 years) if limited by a total of two main spawning events. Late summer recruits, generated by a second spawning event, likely benefitted from lower predation and high phytoplankton food availability. The flexibility of copepods to modulate their life-cycle strategy in response to bottom-up and top-down conditions enables individuals to optimize their probability of reproductive success in the very variable environment prevalent in the Southern Ocean.
Resources
Authors: Gregoline Brenda 
Published: February 2020

Abstract
The Resources chapter of the 11th edition of the AMA Manual of Style includes updated information on general dictionaries, medical and scientific dictionaries, general style and usage guides, guides to medical/scientific style and usage, and resources on writing, as well as helpful sources for addressing ethical and legal concerns and questions related to peer review and illustrations/display of data. Also included are useful websites, guidelines developed by professional organizations, and current contact information for professional scientific writing, editing, and communications organizations and groups.
A17 ASSOCIATION BETWEEN HOST INFLAMMATION-RELATED PROTEOMICS AND GUT MICROBIOME IN HEALTHY FIRST-DEGREE RELATIVES OF CROHN’S DISEASE PATIENTS
Authors: Raygoza Garay J , Turpin W , Smith M , Goethel A , Guttman D S , Croitoru K 
Published: February 2020

Abstract

Background
Crohn’s disease (CD) is a chronic inflammatory condition of the gastrointestinal tract. It has been suggested that the cause of CD is due to microbial and environmental factors that induce an imbalance of the immune system in genetically susceptible individuals. The Genetic Environmental Microbial (GEM) Project is a prospective study of asymptomatic first-degree relatives (FDR) of CD patients, recruited to understand the biological and environmental determinants of disease development.

Aims
Here, we aim to define the relationships between the host inflammation-related proteomics and gut microbiome composition in a cohort of 320 healthy CD FDRs at the time of recruitment.

Methods
We measured 92 inflammation-related serum proteins using the Olink® ’Inflammation’ proteomics panel. Stool microbial composition was determined by sequencing the V4 region of the 16S rRNA. To assess the relationship between serum protein levels and the relative abundance of microbial taxa, we used a zero-inflated two-part regression model corrected for multiple-comparisons (significant association at p&lt; 2.75 × 10–4).

Results
We found fifteen serum proteins that were each significantly associated with the relative abundances of one to five genera or families, depending on the analyte. Of particular interest to CD, the relative abundance of both TNF-β and LIGHT (TNFSF14) were negatively associated with the relative abundance of bacteria in the Parabacteroides genus. Both TNF-β and LIGHT are members of the Tumor Necrosis Factor (TNF) family of cytokines with roles in mucosal healing, IgA production, and in control of innate lymphoid cells (ILCs). These processes have been hypothesized to have critical roles in CD pathology. Interestingly, prior work also demonstrates that Parabacteroides distasonis enhanced colitis in a mouse model and was isolated from a gut wall-cavitating microlesion in a patient with severe CD. Other inflammation-related proteins with significant taxa associations include IL-2, IL-33, OSM, 4E_BP1, IL-1α, ARTN, AXIN1, and CDCP1.

Conclusions
This study highlights the associations between inflammation associated proteomics and gut microbial taxa in asymptomatic FDRs of CD patients. The mechanisms explaining this association will require further analysis.

Funding Agencies
CCC The Leona M. and Harry B. Helmsley Charitable Trust
A24 RATE OF GASTROINTESTINAL ENDOSCOPY USE AND CONCOMITTANT ANESHESIOLOGY ASSISTANCE AND PREDICTORS OF ANESTHESIOLOGY ASSISTANCE: A POPULATION-BASED ANALYSIS
Authors: Singh H , Derksen S , Sirski M , McCulloch S , Lix L M 
Published: February 2020

Abstract

Background
There are limited Canadian data on time trends of gastrointestinal endoscopy (GIE) use and concomitant anesthesiology assistance.

Aims
To test the time trends and variations in concomitant anesthesiology assistance during GIE in the central Canadian province of Manitoba.

Methods
Physicians claims reimbursement data from the provincial health ministry were used to ascertain upper & lower GIE procedures and anesthesiology assistance annually from 1984 to 2016. The annual provincial population was determined from health insurance registration files. Generalized linear models with generalized estimating equations were used to test the linear trend over time and differences amongst age groups, health regions and income quintiles. Logistic regression analysis with generalized estimating equations was used to assess predictors of anesthesiology use.

Results
410, 685 individuals had at least one procedure in the observation period. Approximately half of the procedures were performed outside the recommended CRC screening age group of 50–74 years, with 38% among those less than 50 years. The average annual rate of increase was 4.6% (95% CI 4.4–4.8%). The rate of increase stabilized among the &gt; 75 years group over the last 5 years of the study. There were marked regional variation in GIE procedures, with the smallest increase in Winnipeg region (the largest urban region):2.9% (95%CI: 2.5–3.3) vs. 5.2% (95%CI: 4.8–5.6) in Southern Health; RR: 2.2(figure 1 A). There were no differences in GIE rates by income quintile. Similar patterns were seen in analysis stratified by upper and lower GIE. Concomitant anesthesiology use ranged from 1% in Winnipeg region to 80% in the southern rural region (figure 1B). In the logistic regression analysis, independent predictors of concomitant anesthesiology use in rural regions included younger age, female sex, lower income quintile, and higher comorbidities of patients, GP endoscopist, region of physician practice, and lower volume endoscopy physician.

Conclusions
Marked regional variations in GIE use and concomitant anesthesiology use were observed in a universal health care system. Efforts to standardize care are needed to reduce variations.

Funding Agencies
Manitoba Health
A27 INCREASING INCIDENCE OF COLORECTAL CANCER IN ADULTS UNDER AGE OF 50 IN ALBERTA
Authors: Liu E Y , Wong C 
Published: February 2020

Abstract

Background
Overall colorectal cancer (CRC) incidence has been decreasing in Canada since the early 2000s, most likely due to increased use of colorectal cancer screening for adults over the age of 50. However, the incidence of CRC may be rising in adults younger than age 50 both in Canada and the USA. The American Cancer Society in 2018 issued a qualified recommendation that people with an average risk of CRC should start screening at age 45. The burden of CRC in adults under the age of 50 is not well-characterized in Alberta.

Aims
The aim of this study is to determine the incidence trends in colorectal cancer in adults under the age of 50 compared to those over the age of 50 in Alberta.

Methods
This cohort study determined the incidence of colorectal cancer in patients under the age of 50 compared to those over the age of 50 reported to the Alberta Cancer Registry (ACR) from 2010 to 2017. Annualized percentage changes (APCs) in incidence rate were estimated using the Joinpoint Regression Program 4.7.0.0 (Nation Cancer Institute). APCs in relative risk of CRC in different age groups compared to the 50–74 age group were also estimated in the same methodology.

Results
From 2010 to 2017 there were 17167 incident cases of colorectal cancer. Of these, 92% were in adults over the age of 50 while 8% were in those under the age of 50. For adults under the age of 50, incidence of CRC increased from 6 to 7.2 per 100,000 with a mean annual percentage change of 2.58% between 2010 and 2017. This is in contrast to adults over the age of 50, where the incidence of CRC decreased from 170 to 128 per 100,000 with a mean annual percentage change of -1.64% from 2010 to 2015 and -9.42% from 2015 to 2017. Compared to the 50–74 age group, the average relative risk of CRC in the 46–49 age group is 0.26 with an annual increase of 0.55%; while in the 40–45 age group the average relative risk of CRC is 0.15 with an annual increase of 2.61%.

Conclusions
Similar to national incidence trends, the incidence of CRC in adults under the age of 50 is increasing in Alberta. Although the overall incidence in this population is relatively low, suspicion of CRC in adults under age 50 can help prevent delays in diagnosis.

Incidence of colorectal cancer in Alberta for adults under the age of 50 increased from 6 to 7.2 per 100,000 with a mean annual percentage change of 2.58% between 2010 and 2017.

Funding Agencies
None