bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows
Authors: Sun Hui-Zeng , Zhou Mi , Wang Ou , Chen Yanhong , Liu Jian-Xin , Guan Le Luo 
Published: December 2019

Abstract

Motivation
Enhancing the utilization of human-inedible crop by-products by ruminants to produce high-quality milk for human consumption is an emerging global task. We performed a multi-omics-based study to decipher the regulatory biological processes of milk production when cows fed low-quality crop by-products with the aim to improve their utilization.

Results
Seven types of different high-throughput omics data were generated across three central organs [rumen, liver and mammary gland (MG)] and biofluids (rumen fluid and blood) that involved in milk production. The integrated multi-omics analysis including metabolomics, metagenomics and transcriptomics showed altered microbiome at compositional and functional levels, microbial metabolites in the rumen, down-regulated genes and associated functions in liver and MG. These changes simultaneously contributed to down-regulated three key metabolic nodes (propionate, glucose and amino acid) across these organs and biofluids that led to lowered milk yield and quality when cows consumed corn stover (CS). Hippuric acid was identified as a biomarker that led to low milk production in CS-fed cows, suggesting a future evaluation parameter related to the metabolic mechanism of low-quality forage utilization. This study unveils the milk production-related biological mechanism across different biofluids and tissues under a low-quality forage diet, which provides a novel understanding and potential improvement strategies for future crop by-products utilization and sustainable ruminant production.

Availability and implementation
The raw files of metagenomics, metabolomics, and transcriptomics data can be accessed at NCBI SRA (No. SRR5028206), EMBI-EBI (No. MTBLS411), and GEO (NO. GSE78524) databases respectively.

Supplementary information
Supplementary data are available at Bioinformatics online.
Left hemisphere abnormalities in developmental prosopagnosia when looking at faces but not words
Authors: Gerlach Christian , Klargaard Solja K , Alnæs Dag , Kolskår Knut K , Karstoft Jens , Westlye Lars T , Starrfelt Randi 
Published: December 2019

AbstractDevelopmental prosopagnosia is a disorder characterized by profound and lifelong difficulties with face recognition in the absence of sensory or intellectual deficits or known brain injury. While there has been a surge in research on developmental prosopagnosia over the last decade and a half, the cognitive mechanisms behind the disorder and its neural underpinnings remain elusive. Most recently it has been proposed that developmental prosopagnosia may be a manifestation of widespread disturbance in neural migration which affects both face responsive brain regions as well as other category-sensitive visual areas. We present a combined behavioural and functional MRI study of face, object and word processing in a group of developmental prosopagnosics (N = 15). We show that developmental prosopagnosia is associated with reduced activation of core ventral face areas during perception of faces. The reductions were bilateral but tended to be more pronounced in the left hemisphere. As the first study to address category selectivity for word processing in developmental prosopagnosia, we do not, however, find evidence for reduced activation of the visual word form area during perception of orthographic material. We also find no evidence for reduced activation of the lateral occipital complex during perception of objects. These imaging findings correspond well with the behavioural performance of the developmental prosopagnosics, who show severe impairment for faces but normal reading and recognition of line drawings. Our findings suggest that a general deficit in neural migration across ventral occipito-temporal cortex is not a viable explanation for developmental prosopagnosia. The finding of left hemisphere involvement in our group of developmental prosopagnosics was at first surprising. However, a closer look at existing studies shows similar, but hitherto undiscussed, findings. These left hemisphere abnormalities seen in developmental prosopagnosia contrasts with lesion and imaging studies suggesting primarily right hemisphere involvement in acquired prosopagnosia, and this may reflect that the left hemisphere is important for the development of a normal face recognition network.
Is tau in the absence of amyloid on the Alzheimer’s continuum?: A study of discordant PET positivity
Authors: Weigand Alexandra J , Bangen Katherine J , Thomas Kelsey R , Delano-Wood Lisa , Gilbert Paul E , Brickman Adam M , Bondi Mark W ,   Alzheimer’s Disease Neuroimaging Initiative
Published: December 2019

AbstractThe amyloid cascade model of Alzheimer’s disease posits the primacy of amyloid beta deposition preceding tau-mediated neurofibrillary tangle formation. The amyloid-tau-neurodegeneration biomarker-only diagnostic framework similarly requires the presence of amyloid beta for a diagnosis on the Alzheimer’s continuum. However, medial temporal lobe tau pathology in the absence of amyloid beta is frequently observed at autopsy in cognitively normal individuals, a phenomenon that may reflect a consequence of aging and has been labelled ‘primary age-related tauopathy’. Alternatively, others argue that this tauopathy reflects an early stage of the developmental continuum leading to Alzheimer’s disease. We used positron emission tomography imaging to investigate amyloid beta and tau positivity and associations with cognition to better inform the conceptualization of biomarker changes in Alzheimer’s pathogenesis. Five hundred twenty-three individuals from the Alzheimer’s Disease Neuroimaging Initiative who had undergone flortaucipir positron emission tomography imaging were selected to derive positron emission tomography positivity thresholds using conditional inference decision tree regression. A subsample of 301 individuals without dementia (i.e. those with normal cognition or mild cognitive impairment) had also undergone florbetapir positron emission tomography imaging within 12 months and were categorized into one of the four groups based on cortical amyloid and Braak stage I/II tau positivity: A−/T−, A+/T−, A−/T+, or A+/T+. Tau positivity in the absence of amyloid beta positivity (i.e. A−/T+) comprised the largest group, representing 45% of the sample. In contrast, only 6% of the sample was identified as A+/T−, and the remainder of the sample fell into A−/T− (22%) or A+/T+ (27%) categories. A−/T− and A+/T− groups had the best cognitive performances across memory, language and executive function; the A−/T+ group showed small-to-moderate relative decreases in cognition; and the A+/T+ group had the worst cognitive performances. Furthermore, there were negative associations between Braak stage I/II tau values and all cognitive domains only in the A−/T+ and A+/T+ groups, with strongest associations for the A+/T+ group. Among our sample of older adults across the Alzheimer’s pathological spectrum, 7-fold fewer individuals have positron emission tomography evidence of amyloid beta pathology in the absence of tau pathology than the converse, challenging prevailing models of amyloid beta’s primacy in Alzheimer’s pathogenesis. Given that cognitive performance in the A−/T+ group was poorer than in individuals without either pathology, our results suggest that medial temporal lobe tau without cortical amyloid beta may reflect an early stage on the Alzheimer’s pathological continuum.
Consistency dynamics in accusation-endorsement networks with an external judge
Authors: Nishimura Joel , Goodloe Oscar 
Published: December 2019

AbstractPrevious network models have imagined that connections change to promote structural balance, or to reflect hierarchies. We propose a model where agents adjust their connections to appear credible to an external judge or observer. In particular, we envision a signed, directed network where positive edges represent endorsements or trust and negative edges represent accusations or doubt, and consider both the strategies an external judge might use to identify credible nodes and the strategies nodes might use to then appear credible by changing their outgoing edges. First, we establish that an external judge may be able to exactly identify a set of ‘honest’ nodes from an adversarial set of ‘cheater’ nodes regardless of the cheater nodes’ connections. However, while these results show that an external judge’s task is not hopeless, some of these theorems involve network structures that are NP-hard to find. Instead, we suggest a simple heuristic that an external judge might use to identify which nodes are not credible based upon their involvement with particular implicating edge motifs. Building on these notions, and analogously to some models of structural balance, we develop a discrete-time dynamical system where nodes engage in consistency dynamics, where inconsistent arrangements of edges that cause a node to look ‘suspicious’ exert pressure for that node to change edges. We demonstrate that these dynamics provide a new way to understand group fracture when nodes are worried about appearing consistent to an external judge or observer.
An expert opinion paper on statin adherence and implementation of new lipid-lowering medications by the ESC Working Group on Cardiovascular Pharmacotherapy: Barriers to be overcome
Authors: Drexel Heinz , Coats Andrew J S , Spoletini Ilaria , Bilato Claudio , Mollace Vincenzo , Perrone Filardi Pasquale , Rosano Giuseppe M C 
Published: December 2019

Abstract
Benefits and safety on statins have been well-established over 20 years of research. Despite this, the vast majority of patients are not adequately treated and do not achieve the low-density lipoprotein cholesterol target levels. This is mainly due to poor adherence, which is associated with dangerous and sometimes fatal outcomes. To increase adherence and prevent worse outcomes, a combination therapy with lower dosage of statins and new lipid-lowering drugs may be used. However, the implementation of new lipid-lowering drugs in European countries is still at the beginning. For these reasons, the aim of this position paper is to give an up-to-date indication from the ESC Working Group on Cardiovascular Pharmacotherapy in order to discuss the barriers towards statins adherence and new lipid-lowering drugs implementation in Europe.
Functional convergence in the decomposition of fungal necromass in soil and wood
Authors: Maillard François , Schilling Jonathan , Andrews Erin , Schreiner Kathryn M , Kennedy Peter 
Published: December 2019

ABSTRACT
Understanding the post-senescent fate of fungal mycelium is critical to accurately quantifying forest carbon and nutrient cycling, but how this organic matter source decomposes in wood remains poorly studied. In this study, we compared the decomposition of dead fungal biomass (a.k.a. necromass) of two species, Mortierella elongata and Meliniomyces bicolor, in paired wood and soil plots in a boreal forest in northern Minnesota, USA. Mass loss was quantified at four time points over an 8-week incubation and the richness and composition of the fungal communities colonizing fungal necromass were characterized using high-throughput sequencing. We found that the structure of fungal decomposer communities in wood and soil differed, but, in both habitats, there was relatively rapid decay (∼30% remaining after 56 days). Mass loss was significantly faster in soil and for high-quality (i.e. high nitrogen and low melanin) fungal necromass. In both habitats, there was a clear trajectory of early colonization by opportunistic fungal taxa followed by colonization of fungi with greater enzymatic capacities to degrade more recalcitrant compounds, including white-rot and ectomycorrhizal fungi. Collectively, our results indicate that patterns emerging regarding substrate quality effects on fungal necromass decomposition in soil and leaf litter can be largely extended to fungal necromass decomposition in wood.
EFSA guidelines for emerald ash borer survey in the EU
Authors: Schrader Gritta , Ciubotaru Ramona Mihaela , Diakaki Makrina , Vos Sybren 
Published: December 2019

Abstract
The European Food Safety Authority (EFSA), by request of the European Commission, develops pest survey cards for pests of relevance for the European Union (EU) member states, summarizing key biological, epidemiological and diagnostic information relevant for the detection and identification of these pests by inspectors and laboratory technicians in the EU member states. For three pilot pests, including emerald ash borer (Agrilus planipennis), detailed guidelines are being prepared for the survey planners in the EU member states. Interaction with experts on the relevant organisms and the member states is needed before and after implementation of the surveys to ensure they are fit for purpose and can be harmonized across the EU. An important feature of the survey cards is the identification of risk factors, to focus the surveys on the most likely areas to find the pest if it is present and thus being able to apply a risk-based surveillance. Since 2014, ash wood and bark (from countries where A. planipennis is known to occur) are subjected to specific requirements laid down in Council Directive 2000/29/EC, the beetle is unlikely to enter the EU via this pathway. However, it cannot fully be excluded that introductions have happened before these requirements came into force, without being detected until now. In addition, the beetle could already be present in new third countries without being noticed yet and thus not regulated. Furthermore, firewood from countries adjacent to Russia (Belarus, Ukraine) is not restricted. The beetle could also hitch-hike to the EU by various means of transport, in particular via highways and railroads. Given the above, surveys should focus on these areas.
The prognostic role of c-MYC amplification in schistosomiasis-associated colorectal cancer
Authors: Pan Weiyu , Wang Weixia , Huang Jie , Lu Kui , Huang Sinian , Jiang Dongxian , Bu Dacheng , Liu Jing , Jing Hongyan , Yao Junxia , Hou Yingyong 
Published: December 2019

AbstractObjectiveThe purpose of this study was to explore the prognostic role of c-MYC amplification in colorectal cancer, particularly in schistosomiasis-associated colorectal cancer.MethodsThree hundred and fifty four cases of colorectal cancer, which were from Qingpu Branch of Zhongshan Hospital affiliated to Fudan University, were retrospectively analyzed in a tissue microarray (TMA) format, with fluorescence in situ hybridization (FISH) assay and immunohistochemistry (IHC).Resultsc-MYC gene amplification was found in 14.1% (50 out of 354) of patients with colorectal cancer and was correlated with old age (P = 0.028), positive lymph node metastasis (P = 0.004) and advanced stage tumors (P = 0.002). The overexpression of c-MYC was closely associated with the amplification status (P = 0.023). Kaplan–Meier survival curves for overall survival (OS) showed a statistically significant difference for patients with c-MYC amplification in full cohort of colorectal cancer, stage III-IV set and patients with lymph node metastasis (P = 0.002, 0.034, 0.012, respectively). Further analysis found c-MYC amplification associated with poorer survival in the subgroup of colorectal cancer with schistosomiasis (CRC-S, P &lt; 0.001), but not in colorectal cancer without schistosomiasis (CRC-NS, P = 0.155). By multivariate analysis, c-MYC amplification was an independent poor-prognostic factor in CRC-S set (P = 0.046).ConclusionsOur study firstly found c-MYC amplification could predict poor prognosis in schistosomiasis-associated colorectal cancer, but not in colorectal cancer without schistosomiasis.
Assessing the use of rivers as migratory corridors for temperate bats
Authors: Cortes Kevin M , Gillam Erin H 
Published: December 2019

AbstractInvestigating landscape-level movement patterns of migratory animals can be challenging, but this is a major component of some animal’s life history and behavior. In particular, bat migration has been difficult to characterize, yet recent research on bat migratory ecology has made major advances. It has been largely accepted that rivers and other linear landscape features may be important migratory corridors for bats during both long- and short-distance migrations. We assessed the migratory behavior of multiple temperate bat species along the Missouri River, a major river corridor in North Dakota, during March through October of 2016–2017. Bat detectors with paired microphones were deployed and oriented parallel to the riverbank. This configuration permitted detection of directional passes of bats, approximately 10–20 m above the microphones and 40 m into the river, which were used as an estimate of migratory behavior. We found the effects of season and species explained less than 2% of the variation of directional passes, indicating an absence of season-specific movement patterns along the studied river corridor. Although our study only assessed a portion of a major river corridor, the results suggest that migratory movements of bats along rivers may not be as straightforward as once thought, highlighting the need for future studies investigating the fine-scaled movement patterns of bats during migration.
An Evaluation of the Utility of Big Data to Supplement Cancer Treatment Information: Linkage Between IQVIA Pharmacy Database and the Surveillance, Epidemiology, and End Results Program
Authors: Tran Quyen , Warren Joan L , Barrett Michael J , Annett Dave , Marth Melissa , Cress Rosemary D , Deapen Dennis , Glaser Sally L , Gomez Scarlett L , Schwartz Stephen M , Li Christopher I , Wu Xiao-Cheng , Enewold Lindsey , Harlan Linda C , Rivera Donna R , Winn Deborah M , Penberthy Lynne , Cronin Kathleen A 
Published: December 2019

Abstract
Oral anticancer medications (OAMs) are increasingly utilized. We evaluated the representativeness and completeness of IQVIA, a large aggregator of pharmacy data, for breast cancer, colon cancer, chronic myeloid leukemia, and myeloma cases diagnosed in six Surveillance, Epidemiology, and End Results Program (SEER) registries between 2007 and 2011. Patient’s SEER and SEER-Medicare data were linked and compared with IQVIA pharmacy data from 2006 to 2012 for specific OAMs. Overall, 67.6% of SEER cases had a pharmacy claim in IQVIA during the treatment assessment window. This varied by location, race and ethnicity, and insurance status. IQVIA consistently identified fewer cases who received an OAM of interest than SEER-Medicare. The difference was least pronounced for breast cancer agents and most pronounced for myeloma agents. The IQVIA pharmacy database included a large portion of persons in the SEER areas. Future studies should assess receipt of OAMs for other cancer sites and in different SEER registries.
Earliness per se×temperature interaction: consequences on leaf, spikelet, and floret development in wheat
Authors: Prieto Paula , Ochagavía Helga , Griffiths Simon , Slafer Gustavo A 
Published: December 2019

Abstract
Wheat adaptation can be fine-tuned by earliness per se (Eps) genes. Although the effects of Eps genes are often assumed to act independently of the environment, previous studies have shown that they exhibit temperature sensitivity. The number of leaves and phyllochron are considered determinants of flowering time and the numerical components of yield include spikelets per spike and fertile floret number within spikelets. We studied the dynamics of leaf, spikelet, and floret development in near isogenic lines with either late or early alleles of Eps-D1 under seven temperature regimes. Leaf appearance dynamics were modulated by temperature, and Eps alleles had a greater effect on the period from flag leaf to heading than phyllochron. In addition, the effects of the Eps alleles on spikelets per spike were minor, and more related to spikelet plastochron than the duration of the early reproductive phase. However, fertile floret number was affected by the interaction between Eps alleles and temperature. So, at 9 °C, Eps-early alleles had more fertile florets than Eps-late alleles, at intermediate temperatures there was no significant difference, and at 18 °C (the highest temperature) the effect was reversed, with lines carrying the late allele producing more fertile florets. These effects were mediated through changes in floret survival; there were no clear effects on the maximum number of floret primordia.
Outpatient parenteral antifungal therapy (OPAT) for invasive fungal infections with intermittent dosing of liposomal amphotericin B
Authors: van de Peppel Robert J , Schauwvlieghe Alexander , Van Daele Ruth , Spriet Isabel , van't Wout Jan W , Brüggemann Roger J , Rijnders Bart J A , Hendriks Bart J C , de Boer Mark G J 
Published: December 2019

Abstract
Triazole resistant A. fumigatus has been documented in many parts of the world. In the Netherlands, incidence is now above 10% and results in the need for long-term parenteral therapy with liposomal amphotericin B (LAmB). The long terminal half-life of LAmB suggests that intermittent dosing could be effective, making the application of outpatient antifungal therapy (OPAT) possible. Here, we report our experience with the use of OPAT for Invasive Fungal Infections (IFI). All adult patients treated with LAmB with a 2 or 3 times weekly administration via the outpatient departments in four academic tertiary care centers in the Netherlands and Belgium since January 2010 were included in our analysis. Patient characteristics were collected, as well as information about diagnostics, therapy dose and duration, toxicity, treatment history and outcome of the IFI. In total, 18 patients were included. The most frequently used regimen (67%) was 5 mg/kg 3 times weekly. A partial response to the daily treatment prior to discharge was confirmed by CT-scan in 17 (94%) of patients. A favorable outcome was achieved in 13 (72%) patients. Decrease in renal function occurred in 10 (56%) cases but was reversible in all and was treatment limiting in one patient only. The 100-day mortality and 1-year mortality after initiation of OPAT were 0% and 6%, respectively. In a selected population, and after confirmation of initial response to treatment, our data support the use of OPAT with LAmB for treatment of IFI in an intermittent dosing regimen.
Radio haloes of star-forming galaxies
Authors: Vijayan Aditi , Nath Biman B , Sharma Prateek , Shchekinov Yuri 
Published: December 2019

ABSTRACT
We study the synchrotron radio emission from extra-planar regions of star-forming galaxies. We use ideal magnetohydrodynamic simulations of a rotating Milky Way-type disc galaxy with distributed star formation sites for three star formation rates (0.3, 3, 30 M⊙ yr−1). From our simulations, we see emergence of galactic-scale magnetized outflows, carrying gas from the disc. We compare the morphology of the outflowing gas with hydrodynamic simulations. We look at the spatial distribution of magnetic field in the outflows. Assuming that a certain fraction of gas energy density is converted into cosmic ray energy density, and using information about the magnetic field, we obtain synchrotron emissivity throughout the simulation domain. We generate the surface brightness maps at 1.4 GHz. The outflows are more extended in the vertical direction than radial and hence have an oblate shape. We further find that the matter right behind the outer shock shines brighter in these maps than that above or below. To understand whether this feature can be observed, we produce vertical intensity profiles. We convolve the vertical intensity profile with the typical beam sizes of radio telescopes, for a galaxy located at 10 Mpc to estimate the radio scale height and compare with observations. The radio scale height is ∼300–1200 pc, depending on the resolution of the telescope. We relate the advection speed of the outer shock with the surface density of star formation as ${\rm v}_{\rm adv} \propto \Sigma _{\rm SFR}^{0.3}$, which is consistent with earlier observations and analytical estimates.