bluuebunny/crossref_metadata_2025_split huggingface dataset:
GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering
Authors: Miladi Milad , Sokhoyan Eteri , Houwaart Torsten , Heyne Steffen , Costa Fabrizio , Grüning Björn , Backofen Rolf 
Published: December 2019

Abstract

Background
RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towards studying RNA function. With the advent of high-throughput sequencing techniques, experimental and genomic data are expanding to complement the predictive methods. However, the existing methods do not effectively utilize and cope with the immense amount of data becoming available.

Results
Hundreds of thousands of non-coding RNAs have been detected; however, their annotation is lagging behind. Here we present GraphClust2, a comprehensive approach for scalable clustering of RNAs based on sequence and structural similarities. GraphClust2 bridges the gap between high-throughput sequencing and structural RNA analysis and provides an integrative solution by incorporating diverse experimental and genomic data in an accessible manner via the Galaxy framework. GraphClust2 can efficiently cluster and annotate large datasets of RNAs and supports structure-probing data. We demonstrate that the annotation performance of clustering functional RNAs can be considerably improved. Furthermore, an off-the-shelf procedure is introduced for identifying locally conserved structure candidates in long RNAs. We suggest the presence and the sparseness of phylogenetically conserved local structures for a collection of long non-coding RNAs.

Conclusions
By clustering data from 2 cross-linking immunoprecipitation experiments, we demonstrate the benefits of GraphClust2 for motif discovery under the presence of biological and methodological biases. Finally, we uncover prominent targets of double-stranded RNA binding protein Roquin-1, such as BCOR's 3′ untranslated region that contains multiple binding stem-loops that are evolutionary conserved.
Rhodopsin signaling mediates light-induced photoreceptor cell death in rd10 mice through a transducin-independent mechanism
Authors: Sundar Jesse C , Munezero Daniella , Bryan-Haring Caitlyn , Saravanan Thamaraiselvi , Jacques Angelica , Ramamurthy Visvanathan 
Published: December 2019

AbstractRetinitis pigmentosa (RP) is a debilitating blinding disease affecting over 1.5 million people worldwide, but the mechanisms underlying this disease are not well understood. One of the common models used to study RP is the retinal degeneration-10 (rd10) mouse, which has a mutation in Phosphodiesterase-6b (Pde6b) that causes a phenotype mimicking the human disease. In rd10 mice, photoreceptor cell death occurs with exposure to normal light conditions, but as demonstrated in this study, rearing these mice in dark preserves their retinal function. We found that inactivating rhodopsin signaling protected photoreceptors from degeneration suggesting that the pathway activated by this G-protein-coupled receptor is causing light-induced photoreceptor cell death in rd10 mice. However, inhibition of transducin signaling did not prevent the loss of photoreceptors in rd10 mice reared under normal light conditions implying that the degeneration caused by rhodopsin signaling is not mediated through its canonical G-protein transducin. Inexplicably, loss of transducin in rd10 mice also led to photoreceptor cell death in darkness. Furthermore, we found that the rd10 mutation in Pde6b led to a reduction in the assembled PDE6αβγ2 complex, which was corroborated by our data showing mislocalization of the γ subunit. Based on our findings and previous studies, we propose a model where light activates a non-canonical pathway mediated by rhodopsin but independent of transducin that sensitizes cyclic nucleotide gated channels to cGMP and causes photoreceptor cell death. These results generate exciting possibilities for treatment of RP patients without affecting their vision or the canonical phototransduction cascade.
Association Between Side Effects and Blood microRNA Expression Levels and Their Targeted Pathways in Patients With Major Depressive Disorder Treated by a Selective Serotonin Reuptake Inhibitor, Escitalopram: A CAN-BIND-1 Report
Authors: Yrondi Antoine , Fiori Laura M , Frey Benicio N , Lam Raymond W , MacQueen Glenda M , Milev Roumen , Müller Daniel J , Foster Jane A , Kennedy Sidney H , Turecki Gustavo 
Published: December 2019

AbstractIntroductionAntidepressant drugs are effective therapies for major depressive disorder; however, they are frequently associated with side effects. Although there is some evidence for a relationship between genetic variation and side effects, little is known regarding the role of dynamic molecular factors as moderators of side effects. The aim of this study was to assess microRNA (miRNA) changes associated with side effects during escitalopram treatment and their downstream effects on target gene expression.MethodsA total 160 patients with major depressive disorder from the CAN-BIND-1 cohort were included. Side effects were assessed with the Toronto Side Effect Scale after 2 weeks of treatment with escitalopram. We assessed the relationship between side effects and changes in peripheral expression of miRNAs between baseline and week 2. For miRNA whose expression changed, we used target prediction algorithms to identify putative messenger RNA (mRNA) targets and assessed their expression.ResultsNausea was experienced by 42.5% of patients. We identified 45 miRNAs whose expression changed on initiation of escitalopram treatment, of which 10 displayed a negative association with intensity of nausea (miR15b-5p, miR17-5p, miR20a-5p, miR20b-5p, miR103a-3p, miR103b, miR106a-5p, miR182-5p, miR185-5p, and miR660-5p). Additionally, we found negative associations between 4 microRNAs (miR20a-5p, miR106a-5p, miR185-5p, miR660-5p) and mRNA targets. The expression of the miR185-5p target, CAMK2δ was significantly decreased [log 2 mean = −0.048 (0.233)] between weeks 0 and 2 (P = .01)].ConclusionsWe identified an overexpression of miR185-5p during escitalopram treatment of major depressive disorder, which was negatively associated with intensity of nausea, and identified a potential mRNA target that may mediate this effect.
Birkhoff and Lyapunov Spectra on Planar Self-affine Sets
Authors: Bárány Balázs , Jordan Thomas , Käenmäki Antti , Rams Michał 
Published: December 2019

Abstract
Working on strongly irreducible planar self-affine sets satisfying the strong open set condition, we calculate the Birkhoff spectrum of continuous potentials and the Lyapunov spectrum.
On classifying sepsis heterogeneity in the ICU: insight using machine learning
Authors: Ibrahim Zina M , Wu Honghan , Hamoud Ahmed , Stappen Lukas , Dobson Richard J B , Agarossi Andrea 
Published: December 2019

Abstract

Objectives
Current machine learning models aiming to predict sepsis from electronic health records (EHR) do not account 20 for the heterogeneity of the condition despite its emerging importance in prognosis and treatment. This work demonstrates the added value of stratifying the types of organ dysfunction observed in patients who develop sepsis in the intensive care unit (ICU) in improving the ability to recognize patients at risk of sepsis from their EHR data.

Materials and Methods
Using an ICU dataset of 13 728 records, we identify clinically significant sepsis subpopulations with distinct organ dysfunction patterns. We perform classification experiments with random forest, gradient boost trees, and support vector machines, using the identified subpopulations to distinguish patients who develop sepsis in the ICU from those who do not.

Results
The classification results show that features selected using sepsis subpopulations as background knowledge yield a superior performance in distinguishing septic from non-septic patients regardless of the classification model used. The improved performance is especially pronounced in specificity, which is a current bottleneck in sepsis prediction machine learning models.

Conclusion
Our findings can steer machine learning efforts toward more personalized models for complex conditions including sepsis.
195 Association of insulin, glucagon, and glucagon-like peptide-1 with production traits of growing and finishing beef heifers fed forage- and concentrate-based rations
Authors: Foote Andrew P , Freetly Harvey C 
Published: December 2019

Abstract
The objective of this study was to determine the association of insulin, glucagon, and glucagon-like peptide (GLP-1) with production traits of growing and finishing beef heifers fed a forage- (FOR) and concentrate-based (CONC) ration. This experiment was conducted over 2 years. Shortly after weaning, heifers (n = 74 and 62, for year 1 and 2, respectively) were placed on a ration containing (DM basis) 69.8% corn silage, 30% alfalfa hay, and 0.2% salt. Feed intake was measured for 84 d using Calan gates and BW were measured at 7-time points to calculate ADG using a quadratic regression of BW on time. Cattle were then transitioned to a concentrate-based finishing ration containing (DM basis) 67.8% dry-rolled corn, 20% wet distillers grains with solubles, 8% alfalfa hay, and 4.2% vitamin/mineral supplement. Blood samples were collected on day 42 of each period. Data were analyzed as a mixed model with fixed effects of sire breed, period, and the random variable of year. Hormone concentration was included as an interaction with period to determine the association of the hormones with production traits. Dry matter intake (DMI), average daily body weight gain (ADG), gain:feed (G:F), and all three hormones were greater in the CONC period (P &lt; 0.01). Insulin was negatively associated with DMI only during the CONC period (P = 0.04) and positively associated with G:F (P = 0.01). GLP-1 was positively associated with CONC DMI (P &lt; 0.01), FOR ADG (P &lt; 0.01), and positively associated with FOR G:F and negatively associated with CONC G:F (P &lt; 0.01). Glucagon was positively associated with residual feed intake (P = 0.04). While these data do not infer causality, they do indicate that more in-depth understanding of the role of gut peptide and insulin signaling in feed efficiency needs to be evaluated.
230 Genome editing applications in plants: high-throughput CRISPR/Cas editing for crop improvement
Authors: Thomson Michael 
Published: December 2019

Abstract
The precision and ease of use of CRISPR nucleases, such as Cas9 and Cpf1, for plant genome editing has the potential to accelerate a wide range of applications for crop improvement. For upstream research on gene discovery and validation, rapid gene knock-outs can enable testing of single genes and multi-gene families for functional effects. Large chromosomal deletions can test the function of tandem gene arrays and assist with positional cloning of QTLs by helping to narrow down the target region. Nuclease-deactivated Cas9 fusion proteins with transcriptional activators and repressors can be used to up and down-regulate gene expression. Even more promising, gene insertions and allele replacements can provide the opportunity to rapidly test the effects of different alleles at key loci in the same genetic background, providing a more precise alternative to marker-assisted backcrossing. Recently, Texas A&M AgriLife Research has supported the development of a Crop Genome Editing Lab at Texas A&M working towards optimizing a high-throughput gene editing pipeline and providing an efficient and cost-effective gene editing service for research and breeding groups. The lab is using rice as a model to test and optimize new approaches aimed towards overcoming current bottlenecks. For example, a wealth of genomics data from the rice community enables the development of novel approaches to predict which genes and target modifications may be most beneficial for crop improvement, taking advantage of known major genes, high-resolution GWAS data, multiple high-quality reference genomes, transcriptomics data, and resequencing data from the 3,000 Rice Genomes Project. Current projects have now expanded to work across multiple crops to provide breeding and research groups with a rapid gene editing pipeline to test candidate genes in their programs, with the ultimate goal of developing nutritious, high-yielding, stress-tolerant crops for the future.
245 Effects of dietary macronutrient content on fecal microbiota populations and metabolite concentrations of healthy adult dogs
Authors: Lin Ching-Yen , Carroll Meredith , Yang Xiaojing , Do Sungho , Shi Wanting , Phungviwatnikul Thunyaporn , He Fei , Swanson Kelly S 
Published: December 2019

Abstract
Diet is one of the greatest influences on gut microbiota number and activity, and one that can rapidly alter conditions. However, limited information about the longitudinal effects of diet on canine fecal microbiota is available. The objective of this study was to determine the effects of dietary macronutrient content on fecal microbiota populations and metabolites of adult dogs. Twelve adult female beagles (age: 5.16±0.87 yr, BW: 13.37±0.68 kg) were used in a crossover design with two 27-d experimental periods. All dogs were fed a kibble diet (control) from d1–14, and then fed that diet supplemented with fiber (HFD) or changed to a canned diet (CD) from d15–27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for measurement of metabolites and microbiota populations. Microbial data were analyzed using QIIME 2. Other data were analyzed using Mixed Models procedure of SAS 9.4. Compared with controls, dogs fed HFD had greater (P &lt; 0.05) daily fiber intake, while dogs fed CD had greater (P &lt; 0.05) daily protein and fat intakes. Fecal acetate, propionate, and total SCFA increased (P &lt; 0.05) after the change to HFD (d16), with concentrations being maintained through d27. Fecal isobutyrate, isovalerate, total BCFA, phenol, and indole increased (P &lt; 0.05) after dogs consumed CD (d16), with concentrations being maintained through d27. When dogs consumed HFD (d16), microbial alpha-diversity increased (P &lt; 0.05) and was maintained through d27, while beta-diversity (weighted UniFrac distance measures) were altered (P &lt; 0.05) and stabilized from d20 to d27. Relative abundances of Firmicutes increased (P &lt; 0.05) by d24, while Fusobacteria decreased (P &lt; 0.05) by d16 and was stable from d20 to d27, in dogs fed HFD. In conclusion, diets affected fecal microbiota and metabolites. Although concentrations of fecal metabolites were stabilized after 2d, fecal microbial populations needed more time to stabilize after diet transition.
85 DNA parentage in multi-sire breeding groups and sire repeatability on replacement heifer performance
Authors: Mills Tess D , Larson Kathy A , Asai-Coakwell Mika , Fernandez Diego Moya , Campbell John R , Lardner Bart 
Published: December 2019

Abstract
The objective of this study was to apply DNA parentage testing in multi-sire breeding groups to assess repeatability of a sire’s impact on replacement females and terminal animals. Parentage testing was performed on DNA from 37 bulls and 1578 calves from a commercial ranch using natural breeding in four multi-sire breeding pastures over a four-year period (2015–2018). Parentage data was analyzed using Chi-square procedures. In 2016 and 2018, all bulls in the four breeding groups sired significantly different (P &lt; 0.01) numbers of calves than expected. In 2015 and 2017, bulls in 2 of 4 and 3 of 4 breeding groups, respectively, sired significantly different (P &lt; 0.01) numbers of calves than expected. For the 2015 and 2016 calf crops, three of 24 bulls used sired 30% of the calves and 33% of the selected replacement heifers. In 2017 and 2018, the calves born to the daughters of these three most prolific sires, averaged 4.5kg lower weaning weights than the average wean weights of the remaining calves. In 2018, all calves were tested for breed composition and vigour score using the EnvigourHX test from Neogen (Neogen Canada Inc., Edmonton Alberta, Canada). The average herd vigour score was 70%; the average vigour score for 2018 calves born to daughters of the top three prolific sires was 56%. Coupling production measures (weaning weights, birth dates, calving intervals) with sire parentage and vigour score data provides beef cattle producers with additional information to guide breeding choices to improve production in their operations.
256 Rye with or without purple top turnips for stocker calf grazing as part of a Southeastern U.S. integrated crop-livestock system
Authors: Cox - O’Neill Jordan L , Ott Grace C , Harmon Deidre D , Poore Matt H , Eisemann Joan H , Pickworth Carrie L 
Published: December 2019

Abstract
The objective was to evaluate stocker calf performance and grazing potential of double-crop annual forages during the winter as a diversified crop-livestock system. Angus crossbred steers (n = 56) were stratified by BW (275 ± 1.3 kg) and hip-height (118.3 ± 0.66 cm) into 12 groups (n = 4 to 6/group) and randomly assigned to graze either monoculture rye (RYE) or rye and turnip mixture (MIX). The study was conducted at two locations in eastern North Carolina. Each treatment had 3 replicate pastures (6 to 9 ha) per location with a stocking rate of 0.6 ha/steer. Winter annual treatments were planted following corn grain harvest in early October, with the MIX producing 64% ± 2.9% rye and 36% ± 2.0% turnip (leaf and root) on a DM basis. Two-day consecutive weights of steers were taken at initiation and completion of the grazing period. Mineral and water were available ad libitum. Data were analyzed using Mixed Procedure of SAS and differences were declared at P &lt; 0.05, with tendencies declared between P = 0.05 and 0.10. Initial forage mass was greater (P &lt; 0.05) for MIX (1889 kg DM/ha; 9.4% turnip root) than RYE (1568 kg DM/ha). All steers at a location were removed from grazing when forage mass was estimated at 1200 kg DM/ha. The grazing period was 45 days for location 1 and 77 days for location 2. Values for steers grazing RYE and MIX, respectively, for the following variables did not differ (P &gt; 0.10): free choice mineral intake, 201 g/d and 216 g/d; ADG 0.99 kg/d and 1.05 kg/d; gain per hectare 104 kg/ha and 110 kg/ha; and hip-height growth 8.9 cm and 8.1 cm. The increased forage availability for the MIX did not result in greater ADG or gain per hectare when stocking rate and grazing period remained constant.
127 Dietary supplementation with glycine improves the post-weaning growth of low-birth-weight pigs
Authors: He Wenliang , Posey Erin A , Wu Guoyao 
Published: December 2019

Abstract
Pigs with intrauterine growth restriction (IUGR) represent 20–25% of all pigs born and are culled on farm, resulting in enormous losses. This study tested the hypothesis that dietary supplementation with glycine enhanced the growth of IUGR pigs after weaning. Healthy pigs [14 IUGR pigs (birth weight = 0.98±0.03 kg, mean ± SEM) and 20 NBW pigs (birth weight = 1.44±0.02 kg, mean ± SEM)] were used for the trial. At weaning (21 d of age), pigs within each birth weight group were assigned randomly into corn- and soybean meal-based diets supplemented with 1% glycine plus 0.19% corn starch or 1.19% alanine (isonitrogenous control). There were 7 IUGR pigs and 10 NBW pigs per subgroup. Crude protein content in basal diets was 20% between d 21 and 64, 18% between d 65 and 108, and 16% between d 109 and 120 of age. During the 100-d period of feeding, feed intake per kg body weight did not differ (P &gt; 0.05) between IUGR and NBW pigs or between control and glycine groups. Growth rates of NBW pigs supplemented with 1% glycine did not differ (P &gt; 0.05) from those for NBW pigs without glycine supplementation. In contrast, growth rates of IUGR pigs supplemented with 1% glycine were 28%, 15%, and 10% greater (P &gt; 0.05) than those for IUGR pigs without glycine supplementation during d 21–35, d 35–64, and d 65–120 of age, respectively. Growth rates of NBW pigs were greater (P &gt; 0.05) than those for IUGR pigs without glycine supplementation during any experimental period. By d 120 of age, the body weight of IUGR pigs with glycine supplementation did not differ (P &gt; 0.05) from that of NBW pigs. Collectively, our results indicate that dietary supplementation with 1% glycine (a low-cost supplement) beneficially improves their growth rate and economic returns. Supported by a USDA/NIFA grant.
PSIII-3 The effects of feeding milk from a nipple or a bucket on performance, blood metabolism, rumen fermentation and behavior of dairy calves during preweaning period
Authors: Liu Shuai , Bayindaoerji Saiergelin , Wang Jingjun , Li Shengli 
Published: December 2019

Abstract
The aim of this study was to evaluate the effects of two milk feeding methods on performance, blood metabolism, rumen fermentation and behavior of preweaning dairy calves. Forty newborn Holstein female calves were assigned to one of two treatments equally: nipple feeding (NF) and bucket feeding (BF). Gradual weaning commenced on d 35 and weaning occurred on d 56. Starter intake, fecal scoring, body weight and structural measurements (withers height, heart girth, abdominal girth, body length) were collected. Blood samples and Rumen fluid samples were collected on day 28 and 56, respectively. Ten calves from each treatment were selected randomly and instantaneous scan-sampling with 3 min intervals was used to collect the behavior data (licking nipple or bucket, manipulating objects, self-grooming, lying, standing). Observation were conducted twice per week (1 h session duration) and were centered around morning (0900 h), afternoon (1500 h), and evening (1700 h) milk feeding period. Data were analyzed by mixed effect model with treatment, time, and the interaction between them as fixed effects, and animal within treatment as a random effect. Results showed that body weight, average daily gain, starter intake and structural measurements were similar between two treatments. NF group had higher diarrhea frequency than BF group during week 6 (P = 0.03). NF group had higher concentration of insulin (P = 0.01), IGF-1 (P = 0.03) and β-hydroxybutyric acid (P = 0.04) than BF group on d 56. Rumen pH and volatile fatty acids were similar between two treatments. No differences between two treatments for behavior observation were found, except that NF group spent more time licking nipple than BF group (P = 0.001). In conclusion, nipple or bucket feeding had no effects on performance, starter intake and rumen fermentation, yet nipple feeding increased licking time and different feeding methods influenced blood metabolism.