bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Connectomic Atlas of the Human Cerebrum—Chapter 16: Tractographic Description of the Vertical Occipital Fasciculus
Authors: Briggs Robert G , Conner Andrew K , Sali Goksel , Rahimi Meherzad , Baker Cordell M , Burks Joshua D , Glenn Chad A , Battiste James D , Sughrue Michael E 
Published: September 2018

ABSTRACT
In this supplement, we show a comprehensive anatomic atlas of the human cerebrum demonstrating all 180 distinct regions comprising the cerebral cortex. The location, functional connectivity, and structural connectivity of these regions are outlined, and where possible a discussion is included of the functional significance of these areas. In this chapter, we specifically address regions integrating to form the vertical occipital fasciculus.
Interpersonal Partner Relationships, Bonds to Children, and Informal Social Control among Persistent Male Offenders
Authors: Valdez Avelardo , Nowotny Kathryn M , Zhao Qian-Wei , Cepeda Alice 
Published: September 2018

AbstractThis qualitative study applied a life course framework to characterize the nature of interpersonal partner relationships of Mexican American young adult men affiliated with street gangs during their adolescence. Data come from a 15-year longitudinal mixed-method cohort study conducted in San Antonio, Texas. We analyzed semi-structured interviews conducted with a subsample (n = 40) during the course of three face-to-face sessions to explore the men’s motivations, aspirations, and goals to lead conventional lives, despite their criminal justice involvement. Specifically, we focus on the complex nature of maintaining ties to children, the navigation of complicated family structures, the processes of seeking partners with economic resources, and on partnerships with criminal and delinquent partners. We document the complex interpersonal nature of these relationships as men contend with serial incarceration and their desires and motivations to desist from criminal behavior.
Impact of including distillers’ dried grains with solubles at expense of soybean meal on Boer-influenced goat growth performance
Authors: Paine J M , Jones C K , Lattimer J , Crane A R 
Published: September 2018

Abstract
The objective of this project was to evaluate the efficacy of distillers’ dried grains (DDGS) as a replacement for soybean meal (SBM) in a diet for Boer-influenced goats. Because diets were isonitrogenous and isocaloric, it was hypothesized that the replacement of SBM with DDGS would reduce diet costs without affecting growth performance. To test this hypothesis, forty-eight Boer-influenced goats (28.2 ± 0.96 kg BW; approximately 90 d of age) were allocated to four treatments in a completely random design in a climate-controlled (13°C) facility of the Kansas State University Sheep and Meat Goat Center. Goats were stratified by BW into 16 pens (four pens per treatment; three goats per pen) for a 42-d finishing study. The main effect concentration of DDGS (0%, 10%, 20%, or 30% DM basis) which resulted in dietary treatments of the following: 1) 0% SBM replaced by DDGS (0DDGS); 2) 33% SBM replaced by DDGS (10DDGS); 3) 66% SBM replaced by DDGS (20DDGS); and 4) 100% SBM replaced by DDGS (30DDGS). Goats remained on a self-feeder with continuous access to their respective pelleted, complete dietary treatments, and clean, fresh water. Two-day weights were taken at the beginning and end of the trial, with BW, ADG, ADFI, and G:F measured and calculated every 7 d. Beginning BW were similar across all treatments (P = 0.99). The inclusion of DDGS had no effect on BW or ADFI from days 0 to 42 (P ≥ 0.15). Both ADG (P = 0.04) and G:F (P = 0.001) increased linearly with increasing DDGS inclusion, with goats fed diets containing DDGS having 33% greater (P = 0.05) ADG than those fed diets without DDGS. Ultimately, these results confirm the hypothesis that DDGS can be used to replace SBM in the diet. At current commodity prices, this leads to a 17% savings in diet cost. This novel research shows similar improved performance measures to lambs and cattle when feeding DDGS.
Maternal influences on beef calf rumen microbiome in the first 4 wk of life
Authors: Powell S , Cunningham H C , Austin K J , Cammack K M 
Published: September 2018

Abstract
The preruminant microbiome has the potential to set the stage for later life feed efficiency and is critical to proper development within the rumen. We hypothesized that the rumen microbiome is established at or near birth and is subject to maternal influences that can influence preruminant and postruminant microbial profiles. Our objective was to determine how mode of delivery and rearing affected the development of the rumen microbiome. Bred mature Charolais cows were randomly allocated to one of the three treatment groups: control (CON; n = 8), bottle reared (BOT; n = 8), and caesarian section (CSET; n = 8), where CON was vaginal birth and raised by their dam; BOT was vaginal birth, then removed 24-h post-parturition, and raised on commercial milk replacer; and CSET was born via caesarian section and raised by their respective dams. Calf rumen fluid was collected from calves at 1, 3, and 28 d of age via oral lavage and metagenomic shotgun sequencing was performed using the Illumina NextSeq 500 platform. Sequence data were analyzed utilizing Metataxa2 for taxonomic assignment followed by QIIME to determine α- and β-diversity differences. A total of 1,113 taxa had differential abundance when comparing day while 66 taxa had differential abundance across treatment groups. There were no differences across treatment group richness (P &gt; 0.05), but day 28 was significantly more rich (P = 0.003) compared with days 1 and 3 with no difference between days 1 and 3 (P = 0.58). No differences in β-diversity were detected across treatment group with the exception of greater variance in the BOT and CSET compared with the CON (P = 0.048). Microbial profiles of day 1 are more similar to each other than day 3 or 28 (P = 0.03); day 3 is more similar to each other than day 1 or 28 (P = 0.03); and day 28 is more similar to each other than day 1 or 3 (P = 0.03). These data suggest that while treatment group did not have a large impact on microbial diversity, several specific taxa were affected by treatment group. Day affects the microbial diversity both within and among samples. Understanding how these profiles shift with age is critical to understanding key intervention periods for optimal alteration of the microbiome.
Crude glycerin alters beef cow ruminal fluid degradability of nutrients in vitro
Authors: Pillmore S L , Catey M M , Mercier C M , Lopez F A , Klump L T , Muro B J , Carey R E , Oosthuysen E R , Scholljegerdes E J , Löest C A 
Published: September 2018

Abstract
Crude glycerin (GLY) is used as an energy supplement for cattle and has been shown to increase propionate and decrease acetate concentrations in the rumen. Glycerin also decreases ruminal NH3, and therefore, we hypothesized that GLY in rumen fluid would decrease protein degradability of feedstuffs. The objective was to evaluate the effect of GLY in bovine rumen fluid on extent of protein degradability of alfalfa hay (ALF), dried distiller’s grains (DDG), and soybean meal (SBM). The study was conducted using an in vitro incubator with four incubation jars. Each incubation jar contained 18 filter bags with 0.5 g of ground feed sample (six bags contained ALF, six contained DDG, and six contained SBM), six blank bags, 1,600 mL of buffer solution, 400-mL rumen fluid (collected from two ruminally cannulated cows), and one of the two treatments. Treatments were 12.7 g of deionized water (−GLY) or 12.7 g of GLY (+GLY) added to the 2-liter contents of each jar. Incubation jars were purged with CO2 and allowed to incubate at 39°C for 48 h. The 48-h incubation period was repeated for a total of three runs (the study was a randomized complete block design). Fluid samples from incubation jars were collected at 0 and 48 h into 25-mL vials for measurement of pH and analysis of VFA and NH3. At the end of the 48-h incubation period, filter bags containing feed samples were collected for determination of DM, NDF, and CP disappearance. The pH and NH3 concentrations of the contents of jars were lower (P ≤ 0.01) and total VFA concentrations were greater (P &lt; 0.01) for +GLY than −GLY after 48 h of incubation. Molar percentages of acetate, isobutyrate, and isovalerate were lower (P &lt; 0.01) and molar percentages of propionate and valerate were greater (P ≤ 0.02), resulting in a lower (P &lt; 0.01) acetate-to-propionate ratio for +GLY compared with −GLY after the 48-h incubation period. A GLY × feed interaction (P &lt; 0.01) occurred for DM and CP disappearance, where +GLY decreased DM and CP disappearance of SBM more than that of ALF and DDG. Disappearance of NDF from ALF, DDG, and SBM was lower for +GLY compared with −GLY (GLY; P &lt; 0.01). These results suggest that supplementing glycerin to ruminants may cause an increase in RUP fraction escaping to the small intestine for potential digestion and absorption.
Effects of Physical Exercise on Depressive Symptoms in Patients With Cognitive Impairment
Authors: Leng Minmin , Liang Bing , Zhou Haiyan , Zhang Ping , Hu Mingyue , Li Guichen , Li Feng , Chen Li 
Published: September 2018

Abstract
We aimed to evaluate the efficacy of physical exercise in ameliorating depressive symptoms in patients with cognitive impairment. The databases of PubMed, EMBASE, Web of Science, the Cochrane Library, PsycINFO, China National Knowledge Infrastructure, WanFang, and WeiPu (VIP) were searched to identify randomized controlled trials (RCTs) that involved physical exercise for patients with cognitive impairment. A random effects model and a fixed effects model were used to calculate the pooled effect size. Twenty-one studies were identified. The meta-analysis showed that physical exercise significantly ameliorated depressive symptoms (standardized mean difference [SMD] = −0.23; 95% confidence interval [CI], −0.39 to −0.07; p = 0.004). In addition, beneficial improvements in neuropsychiatric symptoms (mean difference, −4.62; 95% CI, −9.07 to −0.16, p = 0.04), quality of life (SMD = 0.23; 95% CI, 0.01–0.46; p = 0.04), and activities of daily living (SMD = 0.27; 95% CI, 0.12–0.43; p = 0.0005) were observed in our study. No significant improvements were found in anxiety or apathy. Nevertheless, further high-quality, multicenter RCTs are needed to identify the clinical value of our results.
Exploring Resilience at Work Among First-Line Nurse Managers
Authors: Carpio Ron C. , Castro Laura P. , Huerto Heinrich M. , Highfield Martha E.F. , Mendelson Sherri 
Published: September 2018

OBJECTIVES
This study explored the assessment of resilience at work among 1st-line nurse managers (NMs).

BACKGROUND
Resilience is the ability to cope with stress. NMs have stressful roles and may ultimately withdraw from management if they lack resilient behaviors. Having a measurement of resilience at work in NMs and other healthcare workers may facilitate resilience development approaches.

METHODS
In a descriptive, cross-sectional design, an electronic survey of 25-item, 7-subscale Resilience at Work (RAW) self-report assessment was distributed to 77 NMs.

RESULTS
The highest reported subscale was living authentically; lowest was maintaining perspective. Total years as NM was related to overall RAW mean, maintaining perspective, staying healthy.

CONCLUSION
The application of an instrument to determine resilience may focus support for NMs on maintaining perspective, for example. Further study exploring the application of the RAW assessment to healthcare workers is indicated.
Evaluation of Outcomes From an Online Nurse Residency Program
Authors: Wilson Thad , Weathers Nicole , Forneris Lori 
Published: September 2018

OBJECTIVE
This retrospective study examined the nurse outcomes from new-graduate nurse residents completing an online nurse residency program (NRP).

BACKGROUND
Studies have shown that hospital-based NRPs help new graduates transition from beginners to competent nurses. However, NRPs can tax the resources of smaller institutions, making such a program unrealistic. Little is published exploring the efficacy of online programs for nursing residents.

METHODS
Surveys assessing the impact of the online program were completed by residents in an online NRP at initiation, 6 months, and at completion.

RESULTS
There were statistically significant improvements in organizational and prioritizing skills; confidence in communication with other healthcare providers, patients, and families; and improved leadership ability. The percentage of residents reporting negative safety practices and patient errors decreased over time.

CONCLUSIONS
An NRP using online educational modules results in nurse outcomes comparable to those reported from traditional models.
Detection and Mitigation of Spurious Antisense Reads with RoSA
Authors: Mourão Kira , Schurch Nicholas J. , Lucoszek Radoslaw , Froussios Kimon , MacKinnon Katarzyna , Duc Céline , Simpson Gordon , Barton Geoffrey J. 
Published: September 2018

AbstractMotivationAntisense transcription is known to have a range of impacts on sense gene expression, including (but not limited to) impeding transcription initiation, disrupting post-transcriptional processes, and enhancing, slowing, or even preventing transcription of the sense gene. Strand-specific RNA-Seq protocols preserve the strand information of the original RNA in the data, and so can be used to identify where antisense transcription may be implicated in regulating gene expression. However, our analysis of 199 strand-specific RNA-Seq experiments reveals that spurious antisense reads are often present in these datasets at levels greater than 1% of sense gene expression levels. Furthermore, these levels can vary substantially even between replicates in the same experiment, potentially disrupting any downstream analysis, if the incorrectly assigned antisense counts dominate the set of genes with high antisense transcription levels. Currently, no tools exist to detect or correct for this spurious antisense signal.ResultsOur tool, RoSA (Removal of Spurious Antisense), detects the presence of high levels of spurious antisense read alignments in strand-specific RNA-Seq datasets. It uses incorrectly spliced reads on the antisense strand and/or ERCC spike-ins (if present in the data) to calculate both global and gene-specific antisense correction factors. We demonstrate the utility of our tool to filter out spurious antisense transcript counts in an Arabidopsis thaliana RNA-Seq experiment.AvailabilityRoSA is open source software available under the GPL licence via the Barton Group GitHub page https://github.com/bartongroup.Contactg.j.barton@dundee.ac.uk, g.g.simpson@dundee.ac.uk
FLASH: A next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences
Authors: Quan Jenai , Langelier Charles , Kuchta Alison , Batson Joshua , Teyssier Noam , Lyden Amy , Caldera Saharai , McGeever Aaron , Dimitrov Boris , King Ryan , Wilheim Jordan , Murphy Maxwell , Ares Lara Pesce , Travisano Katherine A. , Sit Rene , Amato Roberto , Mumbengegwi Davis R. , Smith Jennifer L. , Bennett Adam , Gosling Roly , Mourani Peter M. , Calfee Carolyn S. , Neff Norma F. , Chow Eric D. , Kim Peter S. , Greenhouse Bryan , DeRisi Joseph L. , Crawford Emily D. 
Published: September 2018

ABSTRACTThe growing prevalence of deadly microbes with resistance to previously life-saving drug therapies is a dire threat to human health. Detection of low abundance pathogen sequences remains a challenge for metagenomic Next Generation Sequencing (NGS). We introduce FLASH (Finding Low Abundance Sequences by Hybridization), a next-generation CRISPR/Cas9 diagnostic method that takes advantage of the efficiency, specificity and flexibility of Cas9 to enrich for a programmed set of sequences. FLASH-NGS achieves up to 5 orders of magnitude of enrichment and sub-attomolar gene detection with minimal background. We provide an open-source software tool (FLASHit) for guide RNA design. Here we applied it to detection of antimicrobial resistance genes in respiratory fluid and dried blood spots, but FLASH-NGS is applicable to all areas that rely on multiplex PCR.
An introduction to MPEG-G, the new ISO standard for genomic information representation
Authors: Albert Claudio , Paridaens Tom , Voges Jan , Naro Daniel , Ahmad Junaid J. , Ravasi Massimo , Renzi Daniele , Zoia Giorgio , Ribeca Paolo , Ochoa Idoia , Mattavelli Marco , Delgado Jaime , Hernaez Mikel 
Published: September 2018

AbstractThe MPEG-G standardization initiative is a coordinated international effort to specify a compressed data format that enables large scale genomic data to be processed, transported and shared. The standard consists of a set of specifications (i.e., a book) describing: i) a nor-mative format syntax, and ii) a normative decoding process to retrieve the information coded in a compliant file or bitstream. Such decoding process enables the use of leading-edge com-pression technologies that have exhibited significant compression gains over currently used formats for storage of unaligned and aligned sequencing reads. Additionally, the standard provides a wealth of much needed functionality, such as selective access, data aggregation, ap-plication programming interfaces to the compressed data, standard interfaces to support data protection mechanisms, support for streaming and a procedure to assess the conformance of implementations. ISO/IEC is engaged in supporting the maintenance and availability of the standard specification, which guarantees the perenniality of applications using MPEG-G. Fi-nally, the standard ensures interoperability and integration with existing genomic information processing pipelines by providing support for conversion from the FASTQ/SAM/BAM file formats.In this paper we provide an overview of the MPEG-G specification, with particular focus on the main advantages and novel functionality it offers. As the standard only specifies the decoding process, encoding performance, both in terms of speed and compression ratio, can vary depending on specific encoder implementations, and will likely improve during the lifetime of MPEG-G. Hence, the performance statistics provided here are only indicative baseline examples of the technologies included in the standard.
FlashPack: Fast and simple preparation of ultra-high performance capillary columns for LC-MS
Authors: Kovalchuk Sergey , Jensen Ole N. , Rogowska-Wrzesinska Adelina 
Published: September 2018

AbstractCapillary ultra-high-pressure liquid chromatography (cUHPLC) is essential for in-depth characterization of complex biomolecule mixtures by LC-MS. We developed a simple and fast method called FlashPack for custom packing of capillary columns of 50-100 cm length with sub-2-μm sorbent particles. FlashPack uses high sorbent concentrations of 500-1000 mg/ml for packing at relatively low pressure of 100 bar. Column blocking by sorbent aggregation is avoided during the packing of sorbent particles by gentle mechanical tapping of the capillary proximal end by a slowly rotating magnet bar. Utilizing a standard 100 bar pressure bomb, Flashpack allows for production of 15-25 cm cUHPLC columns within a few minutes and of 50 cm cUHPLC columns in less than an hour. Columns exhibit excellent reproducibility of back-pressure, retention time and resolution (CV 8,7 %). FlashPack cUHPLC columns are inexpensive, robust and deliver performance comparable to commercially available cUHPLC columns. The FlashPack method is versatile and enables production of cUHPLC columns using a variety of sorbent materials.
BitterSweet: Building machine learning models for predicting the bitter and sweet taste of small molecules
Authors: Tuwani Rudraksh , Wadhwa Somin , Bagler Ganesh 
Published: September 2018

ABSTRACTThe dichotomy of sweet and bitter tastes is a salient evolutionary feature of human gustatory system with an innate attraction to sweet taste and aversion to bitterness. A better understanding of molecular correlates of bitter-sweet taste gradient is crucial for identification of natural as well as synthetic compounds of desirable taste on this axis. While previous studies have advanced our understanding of the molecular basis of bitter-sweet taste and contributed models for their identification, there is ample scope to enhance these models by meticulous compilation of bitter-sweet molecules and utilization of a wide spectrum of molecular descriptors. Towards these goals, based on structured data compilation our study provides an integrative framework with state-of-the-art machine learning models for bitter-sweet taste prediction (BitterSweet). We compare different sets of molecular descriptors for their predictive performance and further identify important features as well as feature blocks. The utility of BitterSweet models is demonstrated by taste prediction on large specialized chemical sets such as FlavorDB, FooDB, SuperSweet, Super Natural II, DSSTox, and DrugBank. To facilitate future research in this direction, we make all datasets and BitterSweet models publicly available, and also present an end-to-end software for bitter-sweet taste prediction based on freely available chemical descriptors.
Dnmt1has an essential function despite the absence of CpG DNA methylation in the red flour beetleTribolium castaneum
Authors: Schulz Nora KE , Wagner C Isabel , Ebeling Julia , Raddatz Günter , Buhr Maike F Diddens-de , Lyko Frank , Kurtz Joachim 
Published: September 2018

AbstractEpigenetic mechanisms, such as CpG DNA methylation enable phenotypic plasticity and rapid adaptation to changing environments. CpG DNA methylation is established by DNA methyltransferases (DNMTs), which are well conserved across vertebrates and invertebrates. There are insects with functional DNA methylation despite lacking a complete set ofDnmts.But at least one of the enzymes, DNMT1, appears to be required to maintain an active DNA methylation system. The red flour beetle,Tribolium castaneum,lacksDnmt3but possessesDnmt1and it has been controversial whether it has a functional DNA methylation system.Using whole genome bisulfite sequencing, we did not find any defined patterns of CpG DNA methylation in embryos. Nevertheless, we foundDnmt1expressed throughout the entire life cycle of the beetle, with mRNA transcripts significantly more abundant in eggs and ovaries. A maternal knockdown ofDnmt1caused a developmental arrest in offspring embryos.We show thatDnmt1plays an essential role inT. castaneumembryos and that its downregulation leads to an early developmental arrest. This function appears to be unrelated to DNA methylation, since we did not find any evidence for this modification. This strongly suggests an alternative role of this protein.
Characterization of the role of several COPI complex isoforms during the early acceptance of compatible pollen grains inArabidopsis thaliana
Authors: Gomez Daniel A. Cabada , Chavez M. Isabella , Indriolo Emily 
Published: September 2018

AbstractCOPI is a seven subunit coatomer complex, consisting of α, β, β′, γ, δ, ε, and ξ; inA. thaliana, COPI is necessary for retrograde transport from the Golgi to the Endoplasmic Reticulum, Golgi maintenance, and cell-plate formation in plant cells. Vesicle recruitment to the pollen contact point is required for pollen hydration and pollen tube penetration. To determine what other aspects of trafficking may be involved in the stigmatic papillae acceptance of compatible pollen, knock-out lines of several isoforms of the COPI complex were characterized in their roles during compatible pollination. Isoforms that were studied included α1-COPI, β-COPI, β′-COPI, γ-COPI and ε-COPI. Each mutant line was characterized in regards to pollen grain adherence, pollen tube penetration, and seed set. Of the mutant lines examined,α1-copihad the strongest phenotype with issues with compatible pollen grain adherence, tube germination and reduction in seed set while other lines had milder but visible retardation in compatible pollen acceptance. The data presented here are the first study of the role of the COPI complex in compatible pollinations and that certain subunit isoforms are required for compatible pollen acceptance.