bluuebunny/crossref_metadata_2025_split huggingface dataset:
PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping
Authors: Sánchez Luis Francisco Hernández , Burger Bram , Horro Carlos , Fabregat Antonio , Johansson Stefan , Njølstad Pål Rasmus , Barsnes Harald , Hermjakob Henning , Vaudel Marc 
Published: July 2019

Abstract

Background
Mapping biomedical data to functional knowledge is an essential task in bioinformatics and can be achieved by querying identifiers (e.g., gene sets) in pathway knowledge bases. However, the isoform and posttranslational modification states of proteins are lost when converting input and pathways into gene-centric lists.

Findings
Based on the Reactome knowledge base, we built a network of protein-protein interactions accounting for the documented isoform and modification statuses of proteins. We then implemented a command line application called PathwayMatcher (github.com/PathwayAnalysisPlatform/PathwayMatcher) to query this network. PathwayMatcher supports multiple types of omics data as input and outputs the possibly affected biochemical reactions, subnetworks, and pathways.

Conclusions
PathwayMatcher enables refining the network representation of pathways by including proteoforms defined as protein isoforms with posttranslational modifications. The specificity of pathway analyses is hence adapted to different levels of granularity, and it becomes possible to distinguish interactions between different forms of the same protein.
To assemble or not to resemble—A validated Comparative Metatranscriptomics Workflow (CoMW)
Authors: Anwar Muhammad Zohaib , Lanzen Anders , Bang-Andreasen Toke , Jacobsen Carsten Suhr 
Published: July 2019

Abstract

Background
Metatranscriptomics has been used widely for investigation and quantification of microbial communities' activity in response to external stimuli. By assessing the genes expressed, metatranscriptomics provides an understanding of the interactions between different major functional guilds and the environment. Here, we present a de novo assembly-based Comparative Metatranscriptomics Workflow (CoMW) implemented in a modular, reproducible structure. Metatranscriptomics typically uses short sequence reads, which can either be directly aligned to external reference databases (“assembly-free approach”) or first assembled into contigs before alignment (“assembly-based approach”). We also compare CoMW (assembly-based implementation) with an assembly-free alternative workflow, using simulated and real-world metatranscriptomes from Arctic and temperate terrestrial environments. We evaluate their accuracy in precision and recall using generic and specialized hierarchical protein databases.

Results
CoMW provided significantly fewer false-positive results, resulting in more precise identification and quantification of functional genes in metatranscriptomes. Using the comprehensive database M5nr, the assembly-based approach identified genes with only 0.6% false-positive results at thresholds ranging from inclusive to stringent compared with the assembly-free approach, which yielded up to 15% false-positive results. Using specialized databases (carbohydrate-active enzyme and nitrogen cycle), the assembly-based approach identified and quantified genes with 3–5 times fewer false-positive results. We also evaluated the impact of both approaches on real-world datasets.

Conclusions
We present an open source de novo assembly-based CoMW. Our benchmarking findings support assembling short reads into contigs before alignment to a reference database because this provides higher precision and minimizes false-positive results.
Role-Play Simulations and Changing Perceptions of the Other: Model UN, Model Arab League, and Student Views of the Muslim World
Authors: Shannon Vaughn Parnell 
Published: July 2019

AbstractRole-play simulation can both enhance knowledge and favorably affect perceptions of others in global politics. This article tests these hypotheses in two quasi-experimental pretest/post-test surveys of student perceptions of Muslims, Arabs, and the countries of the Middle East. Students engaging in Model UN and Model Arab League simulations representing Arab and Muslim countries demonstrated improved knowledge of the countries they represented and, more importantly, positive changes in perceptions of Muslims and the Muslim countries they represented. A control group demonstrated no such change in images of the Muslims, Arabs, and countries of the Middle East. This preliminary study shows the potential importance of role-play simulations in fostering cross-national and cross-cultural understanding in the fraught relationship between the Middle East and the West.
58 A retrospective analysis of bull:cow ratio effects on pregnancy rates of beef cows previously enrolled in fixed-time artificial insemination protocols
Authors: Timlin Claire L , Hungerford Laura , Redifer Tracey , Currin John F , Mercadante Vitor R G 
Published: July 2019

Abstract
This retrospective study analyzed the effect of bull:cow ratio on pregnancy rates of cows returning to estrus after enrollment in fixed-time artificial insemination (TAI). Data were compiled over the course of 6 breeding seasons between 2014 and 2017 from the Virginia Department of Corrections herd containing 15 farms and 141 groups of cows (average 44 cows/group). Multiparous cows aged 2 years and older (n = 6002) were exposed to estrus synchronization. Non-pregnant cows after TAI (n = 3079, average 21 cows/group) were exposed to natural service with bulls diagnosed as fertile by a breeding soundness exam. Percent data were given an arcsine transformation. A one-way ANOVA evaluated TAI rates by season and a linear regression was performed to compare conception rates to the bull:cow ratio. Pregnancy rate to TAI among groups averaged 53% and ranged from 11% to 83%. First bull pregnancy rate of cows returning to estrus was 47% overall, with fall seasons having greater conception rates than spring (51.1% vs. 44.5%, P = 0.03). The ratio of bulls to total number of cows ranged from 1:8 to 1:68 with an average ratio of 1:28. The ratio of bulls to the number of open cows ranged from 1:2 to 1:39 with an average ratio of 1:14. There was no correlation between the bull:cow ratio and return to estrus pregnancy rate (r = -0.12), and there was no correlation between the number of open cows per bull and return to estrus conception rates (r = -0.17). Thus, higher bull:cow ratios (between 1:8 and 1:68) did not effect return to estrus pregnancy rate; producers may consider a lower number of bulls needed for natural service breeding post TAI, decreasing bull related costs and increasing the economic feasibility of adopting TAI protocols
68 Arkansas Beef Industry Assessment: Educator results
Authors: Kimbrough Chelsey A , Gadberry Shane , Robinson Julie C , Looper Michael , Russell Mark R , Jennings John , Beck Paul A , Ward Heidi M 
Published: July 2019

Abstract
A two-phase study was conducted with educators to better understand the current state of the Arkansas beef industry. Educators are defined as individuals who directly work to educate both adults and youth. Ten educators participated in Phase 1 of the study. Nominal group research methods were utilized to identify current strengths, limitations, future opportunities, and future threats to the Arkansas beef industry. The items identified were then compiled for Phase 2 of the study. An online survey was emailed to 100 educators who were randomly selected from a larger list. Survey respondents were asked to rank the importance of items on a Likert-type scale where 1=not important and 5=highly important. Sixty-two surveys were completed of which 40% were adult educators, 34% were K-12 youth educators, 16% were youth educators, and 10% were post-secondary educators. When asked about the current strengths of educational support, participants indicated Educators stay current with knowledge (M = 4.58, SD = 0.64) as the top strength and State funding (M = 3.76, SD = 1.08) as the bottom strength. State, federal, and private investment funding for education, infrastructure, and technology (M = 4.44, SD = 0.73) was ranked with high importance when asked about current limitations whereas Education curriculum in classroom is outdated (M = 3.58, SD = 1.01) was ranked as somewhat important. The top future opportunity was Educating legislators about beef industry (M = 4.72, SD = 0.54) but Get beef cattle producers to increase check-off contribution by one cent (M = 3.26, SD = 1.10) was at the bottom. Lastly, educators ranked Entry costs to the industry (M = 4.51, SD = 0.71) as the most important future threat while Failure to lead or chase issues (M = 3.90, SD = 0.87) as the least important future threat.
140 Virginia Tech Graduate Extension Scholars program: Report of a scholar
Authors: Dias Nicholas , Scherer Hannah , Mercadante Vitor R G 
Published: July 2019

Abstract
The Graduate Extension Scholar program has the purpose of providing graduate students a unique professional development opportunity to develop high quality outreach programs, where the students actively participate in youth and adult education. The graduate scholar is assigned to an extension agent and a high school teacher. The program director and the graduate assistants hold weekly seminars, where program development and engagement strategies are presented to prepare the scholar for the task. The program has existed since 2014, with 14 scholars participating. The present report is related to a single program during the fall of 2017. A beef cattle reproduction symposium of a total of 5 lectures were taught for juniors and seniors in the Holston High School’s (Damascus, VA) agricultural class. The lectures were planned to provide the students both theoretical and hands-on activities on the topic of beef cattle reproduction. The theoretical portion of the class consisted of PowerPoint presentations on anatomy and physiology, as well as applied topics, such as factors influencing fertility and discussion case studies. The hands-on portion of the class consisted of activities related to reproduction, such as bovine female reproductive tracts anatomy and artificial insemination, simulation of rectal palpation with a mannequin (Breed’n Betsy) and demonstration of materials and technologies used in the field (nitrogen tank for semen storing and ultrasound). In addition, student assessment of knowledge was conducted and scores were used for the agricultural class final grade. Final grade mean for the class was 95. Finally, a field trip was organized to a local farm where students were able to perform rectal palpation and ultrasound in cattle. At the completion of the program, a survey was performed and all students considered the program positive and claimed to have gained knowledge of the subject.
141 The Alliance for Grassland Renewal presents workshops to enhance the understanding and adoption of Novel Endophyte Tall Fescue
Authors: Poore Matthew H , Stratton Tony , Roberts Craig A , Smith S Ray , Andrae John G , Pent Gabe J , Shaeffer April D 
Published: July 2019

Abstract
The Alliance for Grassland Renewal (the Alliance) is a collaborative multi-state effort to enhance the understanding of fescue toxicosis and the adoption of Novel Endophyte Tall Fescue (NETF). The Alliance includes academic institutions, companies marketing NETF, allied companies, governmental agencies, and non-profits. The Alliance initially focused on the state of Missouri. After 2014, it expanded efforts with one-day workshops in MO, KY, OK, KS and UKY joined the board in 2017. In 2018, Clemson and NCSU joined the board, and workshops were expanded to the east coast, with five workshops in MO, KY, SC, NC and VA. In 2019, workshops will repeated in those states in addition GA. Key presentations included managing fescue toxicosis, establishment and first year management, second year management, and economics of conversion. Additionally the agenda included microscope viewing of the endophyte, quality control and endophyte testing, industry update, drill calibration, producer panel, and a tour of NETF plots. There were 214 paid attendees in 2018 (locations ranged 26 to 59; 75% farmers), and 146 evaluations were submitted. Attendees owned 9592 beef or dairy cows, 1997 stocker cattle, 121 horses, 545 sheep and goats, and 151 alpacas. Thirty percent of the audience had planted NETF in the past, while 55% intended to plant NETF in the future. Reasons given for not planting included: unclear cost/benefit (9%), limited financial resources (4%), lack of knowledge (5%), rented or unsuitable land (15%) and forage reserves lacking (5%). Registration fee was $60, and 45% of the audience said they would have paid $95, suggesting the registration fee was appropriate. The Alliance is a growing and successful partnership between academic institutions and industry. This approach is a model that could be applied to adoption of other new technologies.
143 Economics of cool-season annuals or reduced labor supplementation systems for wintering cowcalf pairs
Authors: Kelley William K , Runge Max , Mason Katie , Mullenix Kimberly , Elmore Joshua , Kelton Jessica 
Published: July 2019

Abstract
Cattle producers typically feed hay and supplement for a 90 to 120 day window to maintain cows during the winter in Alabama. A 75-day trial evaluated the use of three systems (n = 3 replications per system): 1) rotationally grazed-winter annuals (GWA) on a 14-day rotation, 2) free-choice whole cottonseed (WCS) and bermudagrass hay, or 3) 50% soybean hulls and 50% corn gluten feed (SH:CGF) fed on alternate days at up to 1% BW daily and free-choice bermudagrass hay. GWA had the greatest Total Cost Per Pair Per Day (TCPD) for the 75 day grazing system at $6.58, followed by WCS at $4.73 and SH:CGF at $4.86. Initial and final cow BCS was not different among treatments (P = 0.1558). Cow ADG was greater (P = 0.0370) on GWA than SH:CGF and WCS (0.9, 0.2, and 0.2 kg, respectively), and calf ADG followed a similar pattern (1.5, 1.2, and 1.1 kg/day for GWA, WCS, and SH:CGF, respectively). WCS and SH:CGF were static across trial when only days of trial are considered, but TCPPD decreased linearly (R=.9723) as days on grazing increase. GWA becomes the low cost feed option (with WCS and SH:CGF inputs remaining constant) if trial days were extended to 119 days. This project demonstrates that GWA produces greater animal performance than other project diets, but requires additional grazing days (>119) to be the least cost feeding option.
12 Animal acceptability trail of olive pomace on Gallus gallus domesticus
Authors: Snokhous Payton W , Kelley Stanley , Beverly Marcy , Anderson Mark 
Published: July 2019

Abstract
In any livestock production system, feed is the most costly production input. The goal of any producer is to find a feed source or combination of sources that provide a balance of nutrients that meet the requirements for maintenance, growth, and performance while efficiently contributing to favorable carcass attributes at a low cost. Olive pomace is a by-product of the olive oil industry which can serve as a source of fat (14%), protein (3.6%), and fiber (44.5%). This by-product has potential as a supplemental source of energy and other essential nutrients to be blended into livestock rations. The objective of this study was to conduct an animal acceptability trial using a mixture of olive pomace and commercial poultry feed to determine which blend of feed and pomace would be most acceptable or most desired to broilers. Two pens, consisting of 20 broilers 34 days of age when put on trial, the broilers were provided three mixtures of feed in separate feeders. Feeders were filled with either a 1:3, 1:1, or 3:1 olive pomace to commercial broiler feed mixture (O:C). Daily consumption rates were used to determine ration preference. The troughs were rotated, twice daily, within each pen to eliminate location preference. The broilers found the 1:3 ratio to be the most preferred, (P < .001) while the 3:1, and 1:1 ratio of O:C. did not differentiate (P < .39) continuation of this study will be to feed a control group a commercial broiler feed, along with a 1:3, 1:1, and 3:1 O:C to determine the effect on performance and carcass attributes of each group.
11 Impact of weaning strategy on calf performance, behavior, and activity
Authors: Ott Grace C , Freeman Sharon R , Poore Matthew H , Pickworth Carrie L 
Published: July 2019

Abstract
Weaning is known to be the most stressful time in a beef calf’s post-natal life. Weaning stress may have long-term impacts on cattle performance. This study was conducted to determine differences in calf stress under three weaning strategies. Two hundred twenty-nine Angus or Angus-Simmental cross pairs at two locations were assigned to one of three weaning treatments: abrupt removal of the calf on d 0 (Abrupt, n = 77), fenceline contact for 7 d prior to removal of the calf on d 7 (Fence, n = 79), and abrupt removal of the calf on d 84 (Late, n = 73). Behavioral observations were conducted pre- and post-weaning and total activity was measured prior to and after weaning using accelerometers placed on collars on five calves per treatment. Calf weights, hip heights, and body condition scores (BCS) were collected to evaluate calf performance post-weaning. Data were analyzed using PROC MIXED of SAS. Statistical significance was determined at P < 0.05 and a tendency at 0.05<p<0.10. Skeletal growth via hip height was not affected by weaning treatment. During the first 28 d after initial weaning, the Abrupt calves lost while the Late weaned calves gained weight (-0.09 and 0.49 kg/d, respectively; P < 0.05). Fence were intermediate weight and tended to be different from both treatments (0.02 kg/d; P = 0.09). Overall ADG was not affected (P > 0.10) by timing or strategy of weaning. Total activity was greater (P < 0.05) in Abrupt than Fence on d 1 and d 2 post-wean (Abrupt 26772 and 22346 and Fence 22235 and 16691 relative activity units/hour, respectively). Calf activity was elevated (P < 0.05) on day of weaning until d 2 post-wean then returned to pre-wean level by d 3 for all treatments. Short-term differences in calf performance warrant further exploration of the possible long-term effects on heifer development and steer feedlot performance.
8 Environment enrichment reduces aggression and stereotypic behaviors in feedlot steers
Authors: Park Rachel M , Bova Rachel , Jennings Jenny S , Daigle Courtney L 
Published: July 2019

Abstract
Feedlots provide limited environmental complexity to cattle – a highly curious and social species. In the absence of adequate stimulation, cattle may engage in aggressive or abnormal behaviors. Implementation of biologically appropriate and species specific environmental enrichment (EE) has the potential to enhance welfare of feedlot steers. The objective of this study was to identify behavioral differences between cattle exposed to EE compared to those without. Composite steers (n = 54) were assigned to one of two treatments: 1) No enrichment (CON; n = 3 at 9 head/pen) and 2) BRUSH (cattle brush; n = 3 at 9 head/pen). Video recordings were decoded utilizing continuous observation for the frequency and duration of headbutting, mounting, kicking, bar licking, tongue rolling, allogrooming, and brush usage from 0800 to 1730 on d -2, -1, 0, 1, 2, 4, 8, 16, 32, and 64 relative to brush implementation. Impact of day, treatment and their interaction on cattle behavior was evaluated using a Generalized Linear Mixed Model (PROC MIXED) in SAS. (BRUSH) steers spent less time bar licking (P = 0.023) and engaged in bar licking less frequency (P = 0.005) than CON throughout the duration of the study. Compared to CON, BRUSH steers performed fewer headbutts across the duration of the study (P = 0.004). Brush usage frequency (P = 0.0002) and duration (P = 0.008) were greatest on d 0 compared to all other research days. The frequency (P = 0.0006) and duration (P = 0.0002) of tongue rolling increased with research day. Similarly, the frequency (P = 0.0001) and duration (P = 0.002) of allogrooming increased over time; however, there was a decrease in allogrooming on d 64. Mounting frequency was impacted by research day and peaked at d 8 (P = 0.002). BRUSH cattle performed less stereotypic and aggressive behaviors suggesting that EE is beneficial for feedlot cattle welfare
18 Weaning weight trends in the U.S. beef cattle industry
Authors: Lalman David , Andresen Claire , Goad Carla , Kriese-Anderson Lisa , Odde Kenneth , King Mike E 
Published: July 2019

Abstract
The objective of this study was to characterize the trend over time for weaning BW in commercial cow/ calf operations in the U.S. beef cattle industry. The first data set contained weaning BW data from four enterprise analysis programs from 1991 to 2015. The second data set included mean forecasted delivery BW of sale lots of beef calves sold through Superior Livestock Auction (SLA) from 1995 to 2016. The SLA data were evaluated for two regions, North Central/Rocky Mountain region (NC) and South Central region (SC) and were restricted to sale dates and projected delivery dates approximating those associated with spring-calving operations. The third data set included mean actual and adjusted weaning BW of commercial cow/calf operations participating in the Alabama Beef Cattle Improvement Association (BCIA) from 1983 to 2017. Adjusted annual weaning BW reported from the American Angus Association and American International Charolais Association were used to evaluate trend over time for bull calves from 1995 to 2016. There was a significant linear increase (0.5 kg per yr; P = 0.01) for weaning BW reported by the Kansas Farm Management Association. Projected delivery BW for NC implanted and non-implanted calves increased (P < 0.01) and plateaued in 2006 and 2007, respectively. In contrast, projected delivery BW for non-weaned SC implanted and non-implanted calves increased (P < 0.01) linearly over time. Adjusted and unadjusted weaning BW reported to the Alabama BCIA increased until 1998 and 1995, respectively. The phenotypic trend for Angus and Charolais bulls was a polynomial regression equation (P < 0.01) with declining rate of change in weaning BW. Substantial variation in the trend over time for weaning BW in commercial cow/ calf operations exists within region and record program. Furthermore, weaning BW is substantially more variable in Southern states. Environmental limitations to continued progress in this trait are evident