bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental test of microbiome protection across pathogen doses reveals importance of resident microbiome composition
Authors: Weitzman Chava L , Rostama Bahman , Thomason Courtney A , May Meghan , Belden Lisa K , Hawley Dana M 
Published: October 2021

ABSTRACT
The commensal microbes inhabiting a host tissue can interact with invading pathogens and host physiology in ways that alter pathogen growth and disease manifestation. Prior work in house finches (Haemorhous mexicanus) found that resident ocular microbiomes were protective against conjunctival infection and disease caused by a relatively high dose of Mycoplasma gallisepticum. Here, we used wild-caught house finches to experimentally examine whether protective effects of the resident ocular microbiome vary with the dose of invading pathogen. We hypothesized that commensal protection would be strongest at low M. gallisepticum inoculation doses because the resident microbiome would be less disrupted by invading pathogen. Our five M. gallisepticum dose treatments were fully factorial with an antibiotic treatment to perturb resident microbes just prior to M. gallisepticum inoculation. Unexpectedly, we found no indication of protective effects of the resident microbiome at any pathogen inoculation dose, which was inconsistent with the prior work. The ocular bacterial communities at the beginning of our experiment differed significantly from those previously reported in local wild-caught house finches, likely causing this discrepancy. These variable results underscore that microbiome-based protection in natural systems can be context dependent, and natural variation in community composition may alter the function of resident microbiomes in free-living animals.
A Neuroscience Primer for Integrating Geroscience With the Neurobiology of Aging
Authors: Hernandez Caesar M , Hernandez Abigail R , Hoffman Jessica M , King Peter H , McMahon Lori L , Buford Thomas W , Carter Christy , Bizon Jennifer L , Burke Sara N 
Published: October 2021

AbstractNeuroscience has a rich history of studies focusing on neurobiology of aging. However, much of the aging studies in neuroscience occur outside of the gerosciences. The goal of this primer is 2-fold: first, to briefly highlight some of the history of aging neurobiology and second, to introduce to geroscientists the broad spectrum of methodological approaches neuroscientists use to study the neurobiology of aging. This primer is accompanied by a corresponding geroscience primer, as well as a perspective on the current challenges and triumphs of the current divide across these 2 fields. This series of manuscripts is intended to foster enhanced collaborations between neuroscientists and geroscientists with the intent of strengthening the field of cognitive aging through inclusion of parameters from both areas of expertise.
Hospital Length of Stay After Hip Fracture and It’s Association With 4-Month Mortality—Exploring the Role of Patient Characteristics
Authors: Ek Stina , Meyer Anna C , Hedström Margareta , Modig Karin 
Published: October 2021

Abstract

Background
Hospital length of stay (LoS) is believed to be associated with higher mortality in hip fracture patients; however, previous research has shown conflicting results. We aimed to explore the association between LoS and 4-month mortality in different groups of hip fracture patients.

Methods
The study population in this Swedish register-based cohort study was 47 811 patients 65 years or older with a first hip fracture during 2012–2016, followed up for 4 months after discharge. LoS was categorized by cubic splines, and the association between LoS and mortality was analyzed with Cox regression models, adjusted for sociodemographic- and health-related factors.

Results
Mean LoS was 11.2 ± 5.9 days and 12.3% of the patients died within 4 months. Both a shorter and a longer LoS, compared to the reference 9–12 days, were associated with higher mortality (hazard ratio [95% confidence interval]): 2–4 days 2.15 (1.98–2.34), 5–8 days 1.58 (1.47–1.69), and 24+ days 1.29 (1.13–1.46). However, in fully adjusted models, only the association with a long LoS remained: 13–23 days 1.08 (1.00–1.17) and 24+ days 1.42 (1.25–1.61). Stratifying by living arrangement revealed that the increased risk for a short LoS was driven by the group living in care homes. For patients living at home, a short LoS was associated with lower risk: 0.65 (0.47–0.91) and 0.85 (0.74–0.98) for 2–4 and 5–8 days, respectively.

Conclusions
A long LoS after a hip fracture is associated with increased 4-month mortality risk even after considering patient characteristics. The association between mortality and a short LoS, however, is explained by individuals coming from care homes (with higher mortality risk), being discharged early.
There’s something about Brown: A reply to Emmett Macfarlane
Authors: Delaney Erin F , Schmidt Christopher W 
Published: October 2021

Abstract
Emmett Macfarlane’s theory of judicial constitutional amendment draws needed attention to the role of transformative court decisions in the process of constitutional development. We agree with Macfarlane that the analysis should include a controversial ruling’s reasoning and immediate reception. But in this response essay, we argue that expanding beyond Macfarlane’s focus allows us to better capture the full scope of what it means to amend a constitution. We use Brown v. Board of Education to illustrate the need for both ex ante and ex post analysis in constructing a theory of judicial constitutional amendment.
Genomic analysis of 600 vancomycin-resistant Enterococcus faecium reveals a high prevalence of ST80 and spread of similar vanA regions via IS1216E and plasmid transfer in diverse genetic lineages in Ireland
Authors: Egan Sarah A. , Kavanagh Nicole L. , Shore Anna C. , Mollerup Sarah , Samaniego Castruita José A. , O’Connell Brian , McManus Brenda A. , Brennan Grainne I. , Pinholt Mette , Westh Henrik , Coleman David C. 
Published: October 2021

Abstract

Background
Vancomycin-resistant Enterococcus faecium (VREfm) cause a wide range of hospital infections. Ireland has had one of the highest invasive VREfm infection rates in Europe over the last decade, yet little is known about Irish VREfm.

Objectives
To investigate the population structure of Irish VREfm, explore diversity by analysing the vanA transposon region and compare Irish, Danish and global isolates.

Methods
E. faecium (n = 648) from five Irish hospitals were investigated, including VREfm [547 rectal screening and 53 bloodstream infection (BSI)] isolates and 48 vancomycin-susceptible (VSEfm) BSI isolates recovered between June 2017 and December 2019. WGS and core-genome MLST (cgMLST) were used to assess population structure. Genetic environments surrounding vanA were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences.

Results
All isolates belonged to hospital-adapted clade A1 and the majority (435/648) belonged to MLST ST80. The population structure was highly polyclonal; cgMLST segregated 603/648 isolates into 51 clusters containing mixtures of screening and BSI isolates, isolates from different hospitals, and VREfm and VSEfm. Isolates within clusters were closely related (mean average ≤16 allelic differences). The majority (96.5%) of VREfm harboured highly similar vanA regions located on circular or linear plasmids with multiple IS1216E insertions, variable organization of vanA operon genes and 78.6% harboured a truncated tnpA transposase. Comparison of 648 Irish isolates with 846 global E. faecium from 30 countries using cgMLST revealed little overlap.

Conclusions
Irish VREfm are polyclonal, yet harbour a characteristic plasmid-located vanA region with multiple IS1216E insertions that may facilitate spread.
Dosing strategies of imipenem in neonates based on pharmacometric modelling and simulation
Authors: Dao Kim , Fuchs Aline , André Pascal , Giannoni Eric , Decosterd Laurent A. , Marchetti Oscar , Asner Sandra A. , Pfister Marc , Widmer Nicolas , Buclin Thierry , Csajka Chantal , Guidi Monia 
Published: October 2021

Abstract

Objectives
Imipenem is a broad-spectrum antibacterial agent used in critically ill neonates after failure of first-line treatments. Few studies have described imipenem disposition in this population. The objectives of our study were: (i) to characterize imipenem population pharmacokinetics (PK) in a cohort of neonates; and (ii) to conduct model-based simulations to evaluate the performance of six different dosing regimens aiming at optimizing PK target attainment.

Methods
A total of 173 plasma samples from 82 neonates were collected over 15 years at the Lausanne University Hospital, Switzerland. The majority of study subjects were preterm neonates with a median gestational age (GA) of 27 weeks (range: 24–41), a postnatal age (PNA) of 21 days (2–153) and a body weight (BW) of 1.16 kg (0.5–4.1). PK data were analysed using non-linear mixed-effect modelling (NONMEM).

Results
A one-compartment model best characterized imipenem disposition. Population PK parameters estimates of CL and volume of distribution were 0.21 L/h and 0.73 L, with an interpatient variability (CV%) of 20.1% on CL in a representative neonate (GA 27 weeks, PNA 21 days, BW 1.16 kg, serum creatinine, SCr 46.6 μmol/L). GA and PNA exhibited the greatest impact on PK parameters, followed by SCr. These covariates explained 36% and 15% of interindividual variability in CL, respectively.
Simulated regimens using a dose of 20–25 mg/kg every 6–12 h according to postnatal age led to the highest PTA (T&gt;MIC over 100% of time).

Conclusions
Dosing adjustment according to BW, GA and PNA optimizes imipenem exposure in neonates.
Simple, Precise, and Less Biased GMO Quantification by Multiplexed Genetic Element-Specific Digital PCR
Authors: Noma Satoshi , Kikuchi Yosuke , Satou Megumi , Tanaka Tomoki , Takiya Toshiyuki , Okusu Hideki , Futo Satoshi , Takabatake Reona , Kitta Kazumi , Mano Junichi 
Published: October 2021

Abstract

Background
To provide the consumer with choices of genetically modified organisms (GMO) or non-GMO, official food labeling systems were established in many countries. Because the threshold GMO content values were set to distinguish between “non-GMO” and “GMO” designations, GMO content quantification methods are required for ensuring the appropriateness of labeling.

Objective
As the number of GMOs is continuously increasing around the world, we set out to develop a low-cost, simple and less biased analytical strategy to cover all necessary detection targets.

Methods
Digital PCR methods are advantageous compared to the conventional quantitative real-time PCR methods. We developed a digital PCR-based GMO quantification method to evaluate the GMO content in maize grains. To minimize the analytical workload, we adopted multiplex digital PCR targeting the 35S promoter and the nopaline synthase terminator, which are genetic elements commonly introduced in many GMOs.

Results
Our method is significantly simpler and more precise than the conventional real-time PCR-based methods. Additionally, we found that this method enables quantification of the copy number of GMO DNA without double counting multiple elements (35S promoter and nopaline synthase terminator) tandemly placed in a recombinant DNA construct.

Conclusion
This is the first report on the development of a genetically modified maize quantification method using a multiplexed genetic element-specific digital PCR method. The tandem effect we report here is quite useful for reducing the bias in the analytical results.

Highlights
Multiplexed genetic element-specific digital PCR can simplify weight-based GMO quantification and thus should prove useful in light of the continuous increase in the number of GM events.
6 Does Bedding Influence Lying Behaviour of Cattle Unloaded for Rest During Long-distance Transportation?
Authors: Guzman Paula Olivares , Pearl David L , Schwartzkopf-Genswein Karen S , Widowski Tina M , Meléndez Suárez Daniela M , Marti Sonia , Haley Derek B 
Published: October 2021

Abstract
In Canada, cattle must be unloaded, fed, watered, and rested after 36 h of transport; however, little is known about what constitutes appropriate rest station conditions. The objective of this study was to determine the relationship between providing straw bedding (14-cm deep) and trip, load, and commercial rest station characteristics, on lying behaviour. Truckloads (n = 13) were split; half the animals were assigned to either bedded (n = 452 cattle) or non-bedded (n = 470 cattle) pens. Trip characteristics [time in motion (TIM), duration of stops en route (DUR_STOPS)], load characteristics (sex: heifers, steers, both; and load weight), and rest station characteristics [ambient temperature at unloading; rest pen space allowance (k_PEN); time in resting pen (TIP)] were recorded. Once unloaded we counted the number of cattle lying/pen, every 10 min for 8 h. A mixed logistic regression model with random intercepts for load and truck compartment was fitted to examine associations between the proportion of animals lying and the independent variables (i.e., treatment, trip, load, and rest station characteristics). Odds of lying increased with load weight (i.e., cattle weight class, P = 0.02) and with DUR_STOPS (P &lt; 0.03). There was an interaction (P &lt; 0.01) between treatment and TIM: as TIM increased, the odds of observing cattle lying showed a notable increase for cattle rested in bedded pens, whereas for those rested in non-bedded pens, the odds showed little change as TIM increased. An interaction (P &lt; 0.01) was also found between treatment and TIP: early in the observation period, the odds of cattle lying were greater in bedded pens. Both groups showed an increase in the probability of lying over time, plateauing at similar levels, near the end of the 8-h observation period. In conclusion, providing straw bedding at rest stations influenced cattle’s motivation to lie, particularly following longer transport durations.
1 Effect of Conditioning, Rest, and Post-rest Transport Duration on Welfare Indicators of Beef Cattle Transported by Road
Authors: Melendez Daniela M , Marti Sonia , Schwinghamer Timothy D , Haley Derek B , Schwartzkopf-Genswein Karen S 
Published: October 2021

Abstract
The aim of this study was to assess the effects of conditioning, rest, and post-rest transport duration on welfare indicators of 6–7 mo old beef calves. Three hundred and twenty-eight weaned calves (237 ± 29.7 kg BW) were randomly assigned to a 2 × 2 × 2 nested factorial design: conditioning, conditioned (C) or non-conditioned (N); rest, 0 (R0) or 8 (R8) h, and post-rest transport, 4 (T4) or 15 (T15) h. Calves were sampled prior to the first loading (L1), after 20h of transport, prior to and after the additional 4 or 15-h transport, and at 1, 2, 3, 5, 14, and 28 d after transport ended. Data were analyzed using the GLIMMIX procedure of SAS. Fixed effects included conditioning, transport and time nested within rest period, while random effects included animal and pen. Greater shrink (P &lt; 0.01) was observed in C than N calves after the initial 20-h transport. The N calves had greater (P &lt; 0.01) ADG than C calves between L1 and d 5, while C had greater (P &lt; 0.01) ADG than N calves between 14 and 28 d. L-lactate concentrations and flight speed were greater (P ≤ 0.05) in C than N calves between L1 and d 5. The R8-T4 calves had greater (P &lt; 0.01) ADG than R8-T15 calves between L1 and d 5. The R0-T4 calves had greater (P = 0.02) L-lactate concentrations than R0-T15 and R8-T4 calves on d 1. The R0 calves had greater (P &lt; 0.01) ADG than R8 calves between 14 and 28 d. Preliminary results show physiological, behavioral, and performance differences across treatments, however, additional indicators are required to accurately assess the effect of conditioning, rest, and post-rest transport durations on calf welfare.
13 Innovative Strategies for Managing Swine Welfare During Natural Disasters
Authors: Johnson Anna K , Rademacher Christopher , Eggers Jamee , Gabler Nicholas K , Greiner Laura L , Kaisand Jeffery , Millman Suzanne , Patience John , Schulz Lee , Webb Sherrie , Ross Jason W 
Published: October 2021

Abstract
Coronavirus Disease 2019 (COVID-19) was declared a global pandemic on March 11, 2020, by the World Health Organization. By April 2020, COVID-19 resulted in the simultaneous closure or reduced operations of many processing plants in the upper Midwest, which quickly resulted in supply chain disruptions. Iowa is the leading pork production and processing state, and these disruptions caused producer uncertainty, confusion, and stress, including time-sensitive challenges for maintaining animal care. The Resource Coordination Center (RCC) was quickly created and launched from the Iowa Department of Agriculture and Land Stewardship. The RCC had strategic collaborations with public representation from the Iowa Pork Producers Association, Iowa Pork Industry Center, and Iowa State University Extension and Outreach, and private partners through producers, veterinarians, and technical specialists. The RCC’s mission was four-fold: (1) implement appropriate actions to ensure the health and safety of RCC members, stakeholders, and the public, (2) evaluate and reassess appropriate actions as needed for continuity of pork production operations, (3) provide information to pork producers during supply chain disruptions, and (4) maintain a safe and abundant pork supply for consumers. The command structure included Incident Commanders, Command Staff, and four Section Chiefs whom worked with their respective experts. Sections covered (1) operations, (2) planning, (3) logistics, and (4) finance and administration. As it related to animal welfare, the RCC provided information on management decisions, dietary alterations to slow pig growth, pig movement to increase living space, alternative markets, on-farm euthanasia and mass depopulation. Veterinary oversight was continually maintained. A manual was created to provide up-to-date information to inform producer decisions and aid. Although originally created for swine, the RCC also assisted poultry, cattle and sheep producers. In a crisis, Iowa created a model that reacted to producer’s pragmatic and emotional needs. This model could be replicated for any emergency by other states.
16 Identification of Structural Variants Associated with Mastitis in Holstein Dairy Cows Using Whole Genome Sequencing and RNA-sequencing
Authors: Asselstine Victoria , Medrano Juan F F , Muniz Malane M M , Cánovas Angela 
Published: October 2021

Abstract
For the dairy industry, animal welfare and economic viability are key factors in determining the long-term sustainability of the industry. One challenge in lactating dairy cows is mastitis, as there are significant costs associated with each mastitis case due to treatment, milk loss, and potential cow culling. Differentially expressed (DE) genes, DE mRNA isoforms and DE long non-coding RNA (lncRNA) candidates were previously identified by our group between healthy and mastitic samples from six Holstein dairy cows. In total, 7 candidate genes, 5 mRNA isoforms and 4 lncRNA were targeted as they play an important role due to their association with mastitis or the immune system. The aim of the current research is to identify new structural variants in the transcriptome of these previously identified potential candidates using RNA-Sequencing. These structural variants could occur in both coding and intergenic regions of the genome and potentially impact the amino acid that is transcribed, creating a new functional or non-functional protein. In addition, whole genome sequencing (WGS) analysis was performed using hair samples collected from ten Holstein dairy cows (first lactation). Five of these animals had no previous reports of mastitis and five animals had at least one report of mastitis in her lifespan. The WGS results will be used to identify additional structural variants, especially within introns, of the previously identified candidates that could cause a genetic variation in individuals and an association to their susceptibility to mastitis disease.
23 Exploring the Role of Gut Microbiota in Host Feeding Behavior Among Breeds in Swine
Authors: He Yuqing , Tiezzi Francesco , Howard Jeremy T , Huang Yijian , Gray Kent A , Maltecca Christian 
Published: October 2021

Abstract
The present study aimed to explore gut microbiota’s overall influence on feeding behavior and identify specific microbes associated with the traits in three commercial swine breeds at different growth stages. Feeding behavior measures were obtained from 651 pigs of three breeds (Duroc, Landrace, and Large White) from 67 to 175 days of age. Seven feeding behavior traits cover the information of feed intake, feeder occupation time, feeding rate, and the number of visits to the feeder. Rectal swabs were collected from each pig at 73 ± 3, 123 ± 4, and 158 ± 4 days of age. DNA was extracted and subjected to 16S rRNA gene sequencing. Sequences were analyzed using the QIIME2. The amplicon sequence variant table was constructed using the DADA2. Mixed linear models were used to perform statistical analyses. Differences in feeding behavior traits among breeds and across time periods were found. The proportion of phenotypic variances explained by the microbiome ranged from 0.10 to 0.26, 0.14 to 0.25, and 0.12 to 0.28 in Duroc pigs, from 0.09 to 0.20, 0.10 to 0.23, and 0.12 to 0.23 in Landrace pigs, from 0.10 to 0.17, 0.11 to 0.19, and 0.10 to 0.31 in Large White pigs at three time points, respectively. A total of 21, 10, and 35 amplicon sequence variants were found to be significantly (q-value &lt; 0.05) associated with feeding behavior traits for Duroc, Landrace, and Large White across three time points. This study demonstrated the importance of the gut microbiome composition in influencing the host feeding behavior and identified multiple microbes associated with the feeding behavior of pigs from either Duroc, Landrace, or Large White breeds at three growth stages. Our study provides insight into the interaction between gut microbiota and feeding behavior and highlights the breed effects in swine microbial studies.