bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responsive harvest control rules provide inherent resilience to adverse effects of climate change and scientific uncertainty
Authors: Kritzer J P , Costello C , Mangin T , Smith S L 
Published: March 2019

Abstract
Climate change is altering marine ecosystem and fish stock dynamics worldwide. These effects add to scientific uncertainties that compromise fisheries management. Among the strategies that can respond to climate change and scientific uncertainty, modifications to harvest control rules (HCRs) might be among the most direct and impactful. We used a bioeconomic model to compare alternative HCRs in terms of biomass, yield, and profits in response to potential effects of climate change and scientific uncertainty, specifically simulated retrospective patterns, for 14 stocks on the Northeast Shelf of the United States. Our results suggest that a responsive HCR in which fishing mortality changes with measured changes in biomass builds inherent resilience to adverse effects of both climate change and scientific uncertainty relative to an HCR in which fishing mortality is precautionary but fixed. This was despite that fact that the HCR algorithm did not account for the climate effects modelled. A fixed fishing mortality HCR was effective when climate effects were negligible or beneficial. Scientific uncertainty further reduced biomass, yield, and profits by about the same magnitude as climate change. Our results suggest that simple changes to HCRs can be a readily implementable strategy for responding to climate change and scientific uncertainty.
The Gromov Width of Generalized Bott Manifolds
Authors: Hwang Taekgyu , Lee Eunjeong , Suh Dong Youp 
Published: March 2019

Abstract
By Delzant’s theorem, closed symplectic toric manifolds are classified by the images of their moment maps. In the case of a generalized Bott manifold, this image is a polytope $P$ combinatorially equivalent to a product of simplices. We compute the Gromov width of generalized Bott manifolds in terms of the defining inequalities of $P$.
Canonical Heights on Hyper-Kähler Varieties and the Kawaguchi–Silverman Conjecture
Authors: Lesieutre John , Satriano Matthew 
Published: March 2019

AbstractThe Kawaguchi–Silverman conjecture predicts that if $f: X \dashrightarrow X$ is a dominant rational-self map of a projective variety over $\overline{{\mathbb{Q}}}$, and $P$ is a $\overline{{\mathbb{Q}}}$-point of $X$ with a Zariski dense orbit, then the dynamical and arithmetic degrees of $f$ coincide: $\lambda _1(f) = \alpha _f(P)$. We prove this conjecture in several higher-dimensional settings, including all endomorphisms of non-uniruled smooth projective threefolds with degree larger than $1$, and all endomorphisms of hyper-Kähler manifolds in any dimension. In the latter case, we construct a canonical height function associated with any automorphism $f: X \to X$ of a hyper-Kähler manifold defined over $\overline{{\mathbb{Q}}}$. We additionally obtain results on the periodic subvarieties of automorphisms for which the dynamical degrees are as large as possible subject to log concavity.
Nitric oxide deficiency decreases C-repeat binding factor-dependent and -independent induction of cold acclimation
Authors: Costa-Broseta Álvaro , Perea-Resa Carlos , Castillo Mari-Cruz , Ruíz M Fernanda , Salinas Julio , León José 
Published: March 2019

AbstractPlant tolerance to freezing temperatures is governed by endogenous components and environmental factors. Exposure to low non-freezing temperatures is a key factor in the induction of freezing tolerance in the process called cold acclimation. The role of nitric oxide (NO) in cold acclimation was explored in Arabidopsis using triple nia1nia2noa1-2 mutants that are impaired in the nitrate-dependent and nitrate-independent pathways of NO production, and are thus NO deficient. Here, we demonstrate that cold-induced NO accumulation is required to promote the full cold acclimation response through C-repeat Binding Factor (CBF)-dependent gene expression, as well as the CBF-independent expression of other cold-responsive genes such as Oxidation-Related Zinc Finger 2 (ZF/OZF2). NO deficiency also altered abscisic acid perception and signaling and the cold-induced production of anthocyanins, which are additional factors involved in cold acclimation.
The land snail fauna of a South American rainforest biodiversity hotspot: the Panguana conservation area in the Peruvian Amazon
Authors: Wendebourg Birte , Hausdorf Bernhard 
Published: March 2019

AbstractWe investigated the land snail fauna of the Panguana conservation area on the western rim of the Amazonas basin in Peru. A total of 2,322 individuals assigned to 65 land snail species were collected in 32 plots. Ten additional species were found in collections made on previous expeditions to Panguana. On the basis of available data, Panguana is the most species rich locality for land snails in South America. The species density of 75 land snail species in c. 2 km2 of rather homogeneous rainforest is also high on a global scale. The land snail fauna of Panguana is characterized by a very high proportion of species belonging to the carnivorous family Scolodontidae, many of which are likely to be new to science. The fauna includes seven species that are new records for Peru, and the species Hirtudiscus sp., Xenodiscula venezuelensis, Geostilbia aperta, Guppya gundlachii and Thysanophora plagioptycha represent genera not previously recorded from the country. The synanthropic species Allopeas gracile, Opeas hannense, Subulina octona, Geostilbia aperta and Gastrocopta servilis form an ecologically distinct group that occurs mainly in sites strongly modified by humans. The presence of these species on the margin of the Amazon rainforest is evidence of the ongoing homogenization of the global fauna.
Thrombectomy for a Patient with Concomitant Acute Cervical Internal Carotid and Middle Cerebral Artery Occlusion: Video Case
Authors: Tian Fucheng , Abi-Aad Karl R , Bendok Bernard R , Krishna Chandan 
Published: March 2019

Abstract
We present the case of a 62-yr-old female who presented with ground-level fall and new onset of left-sided weakness of 30 min duration. CT angiogram revealed right ICA pseudo-occlusion and thrombus filling the right proximal M1 segment of the right MCA. On detailed neurological exam patient was noted to have NIHSS of 25. Patient was started on IV TPA infusion and was taken to interventional angiography suite after an informed consent was obtained. Diagnostic angiography was performed which demonstrated critical stenosis of the right proximal internal carotid artery. Right carotid artery stenting and balloon angioplasty of the carotid stent with distal embolic protection device was performed. Post carotid stent angiogram once again confirmed proximal right M1 pseudo-occlusion in the right MCA distribution. The clot was removed using a stent retriever, thus achieving complete recanalization (TICI 3) of the right cerebral hemisphere. The patient returned to baseline neurological status and a 1 mo follow-up diagnostic angiogram revealed patent carotid stent. Following the case presentation, we present the nuances of acute ischemic stroke management of large vessel occlusion with an emphasis on technical nuances, recent published guidelines
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and the literature.
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Probopyrinella latreuticola parasite infestation frequencies in pelagic Sargassum-associated shrimp, Latreutes fucorum
Authors: Martin Lindsay M , Schell Jeffrey M , Siuda Amy N S 
Published: March 2019

Abstract
Bopyrid isopod parasitic infestation of a variety of decapod definitive hosts is common worldwide. We report frequencies of a parasite infestation in the shrimp Latreutes fucorum associated with the pelagic macroalgae Sargassum in the Gulf of Mexico, Sargasso Sea and Eastern Caribbean. Average Probopyrinella latreuticola infestation frequency was 6.7% and did not significantly vary between regions. The presence of the ectoparasite appeared to impact fertility with only one infested individual found carrying eggs. In contrast, across all three regions, 13% (of n = 4001) of the non-infested shrimp were carrying eggs. With L. fucorum accounting for three quarters of lower trophic level biomass in the pelagic Sargassum-associated faunal community, parasite infestation may have negative consequences for ecologically and commercially important populations that rely directly or indirectly on the host as a food source.
COMPARISON OF RADIATION DOSE AND IMAGE QUALITY IN CTA OF THE PERIPHERAL ARTERIES
Authors: Georgiev Emil , Radeva Radina , Naseva Emilia , Kirova-Nedyalkova Galina 
Published: March 2019

Abstract
The aim of this study is to investigate the possibility of replacing the standard CTA protocol for peripheral arteries with a low dose CTA protocol without affecting the diagnostic image quality. Therefore a single centre retrospective study was conducted involving 200 exams of patients undergoing lower limb angiography. All exams were performed on a 64-row detector CT and the vascular density, muscle density, noise and radiation dose of each image were assessed. The subjective image quality was evaluated additionally by an experienced radiologist. Significant differences were observed in radiation dose and image quality between the standard CTA protocol and the lower dose CTA protocol. No differences were found between objective and subjective image quality. Using 80kVp instead of 120kVp as the tube voltage for lower limb CTA reduces the radiation dose without affecting the diagnostic image quality.
Size-Dependent Secretory Protein Reflux into the Cytosol in Association with Acute Endoplasmic Reticulum Stress
Authors: Lajoie Patrick , Snapp Erik L. 
Published: March 2019

ABSTRACTOnce secretory proteins have been targeted to the endoplasmic reticulum (ER), the proteins typically remain partitioned from the cytosol. If the secretory proteins misfold, they can be unfolded and retrotranslocated into the cytosol for destruction by the proteasome by ER-associated protein Degradation (ERAD). Here, we report that correctly folded and targeted luminal ER fluorescent protein reporters accumulate in the cytosol during acute misfolded secretory protein stress in yeast. Photoactivation fluorescence microscopy experiments reveal that luminal reporters already localized to the ER relocalize to the cytosol, even in the absence of essential ERAD machinery. We named this process “ER reflux.” Reflux appears to be regulated in a size-dependent manner for reporters. Interestingly, prior heat shock stress also prevents ER stress-induced reflux. Together, our findings establish a new ER stress-regulated pathway for relocalization of small luminal secretory proteins into the cytosol, distinct from the ERAD and pre-emptive quality control pathways.
Effects of dietary replacement of broiler litter withMelia azedarachfoliage on productive performance, fatty acid composition and health-related fatty acid indices in beef fats from Nguni x Brahman steers fed sugarcane tops based diets
Authors: Mthiyane D.M.N. , Dlamini B.J. , Hugo A. , Nsahlai I.V. 
Published: March 2019

AbstractThe study investigated the nutritional value ofM. azedarachLinn. (umsilinga;Meliaceaefamily) leaf meal (MALM) as an alternative protein source for beef cattle. In a completely randomised design (CRD), 18 Nguni x Brahman 18–20 months old steers were randomly offered 3 iso-energetic and iso-nitrogenous dietary treatments with, respectively, 0% (Control), 15% and 30% MALM replacing broiler litter, each with 6 replicate animals, for 90 days. Feed intake (FI), water intake (WI), slaughter weight, body weight gain (BWG), feed conversion efficiency (FCE) and kidney fat depot fatty acid (FA) composition as well as health-related FA totals, ratios and other indices were measured. Results showed MALM contained rather high CP (290.0 g/kg DM), CF (170 g/kg DM), EE (78.1 g/kg DM) and ash (77.5 g/kg DM) contents. Also, dietary supplementation with MALM increased BWG and FCE (P < 0.01) but had no effect on FI, WI and slaughter weight of steers (P > 0.05). Also, it increased kidney fat margaric acid (P < 0.05) whilst it decreased arachidic acid (P < 0.01) content. There was no effect of diet on the content of all other saturated fatty acids (SFAs) (P > 0.05) in kidney fat. Further, dietary MALM supplementation increased kidney fat α-linolenic (P < 0.001) and conjugated linoleic acid (CLA) (P = 0.01) but had no effect on the content of all other unsaturated fatty acid (UFA) components (P > 0.05). Furthermore, it increased kidney fat total polyunsaturated fatty acids (PUFAs) (P < 0.01), total omega-3 (n-3) PUFAs (P < 0.001) and the CLA/vaccenic acid index but decreased the omega-6/omega-3 (n-6 PUFA/n-3 PUFA) ratio (P = 0.001). Otherwise, dietary MALM supplementation had no effect on all other FA totals, ratios and health-related indices (P > 0.05). In conclusion, dietary MALM supplementation improved productive performance of beef steers and enhanced their desirable meat fat FA profiles.ImplicationsBroiler litter is widely used as an alternative cheap protein and mineral rich feedstuffs for supplementing poor quality forage based diets for ruminants in Southern Africa and elsewhere. However, its use is limited by the presence of human pathogens, pesticides, drug residues and heavy metals, which pose health hazards to livestock and human consumers. Our study demonstrated MALM as a better and safer alternative source of protein, the use of which in beef cattle diets would improve animal productivity and the desirable FA profile of meat which would potentially enhance the health status of consumers. By improving beef productivity, dietary MALM supplementation thus promises to enhance food and nutrition security and to contribute to poverty alleviation in Eswatini, Africa and beyond.
Cross-disorder genetic analyses implicate dopaminergic signaling as a biological link between Attention-Deficit/Hyperactivity Disorder and obesity measures
Authors: Mota Nina Roth , Poelmans Geert , Klein Marieke , Torrico Bàrbara , Fernàndez-Castillo Noèlia , Cormand Bru , Reif Andreas , Franke Barbara , Arias Vásquez Alejandro 
Published: March 2019

ABSTRACTAttention-Deficit/Hyperactivity Disorder (ADHD) and obesity are frequently comorbid, genetically correlated, and share brain substrates. The biological mechanisms driving this association are unclear, but candidate systems, like dopaminergic neurotransmission and circadian rhythm, have been suggested. Our aim was to identify the biological mechanisms underpinning the genetic link between ADHD and obesity measures and investigate associations of overlapping genes with brain volumes. We tested the association of dopaminergic and circadian rhythm gene sets with ADHD, body mass index (BMI), and obesity (using GWAS data of N=53,293, N=681,275, and N=98,697, respectively). We then conducted genome-wide ADHD-BMI and ADHD-obesity gene-based meta-analyses, followed by pathway enrichment analyses. Finally, we tested the association of ADHD-BMI overlapping genes with brain volumes (primary GWAS data N=10,720–10,928; replication data N=9,428). The dopaminergic gene set was associated with both ADHD (P=5.81×10−3) and BMI (P=1.63×10−5), the circadian rhythm was associated with BMI (P=1.28×10−3). The genome-wide approach also implicated the dopaminergic system, as the Dopamine-DARPP32 Feedback in cAMP Signaling pathway was enriched in both ADHD-BMI and ADHD-obesity results. The ADHD-BMI overlapping genes were associated with putamen volume (P=7.7×10−3; replication data P=3.9×10−2) – a brain region with volumetric reductions in ADHD and BMI and linked to inhibitory control. Our findings suggest that dopaminergic neurotransmission, partially through DARPP-32-dependent signaling and involving the putamen, is a key player underlying the genetic overlap between ADHD and obesity measures. Uncovering shared etiological factors underlying the frequently observed ADHD-obesity comorbidity may have important implications in terms of prevention and/or efficient treatment of these conditions.
iEDGE: integration of Epi-DNA and Gene Expression and applications to the discovery of somatic copy number-associated drivers in cancer
Authors: Li Amy , Chapuy Bjoern , Varelas Xaralabos , Sebastiani Paola , Monti Stefano 
Published: March 2019

AbstractThe emergence of large-scale multi-omics data warrants method development for data integration. Genomic studies from cancer patients have identified epigenetic and genetic regulators – such as methylation marks, somatic mutations, and somatic copy number alterations (SCNAs), among others – as predictive features of cancer outcome. However, identification of “driver genes” associated with a given alteration remains a challenge. To this end, we developed a computational tool, iEDGE, to model cis and trans effects of (epi-)DNA alterations and identify potential cis driver genes, where cis and trans genes denote those genes falling within and outside the genomic boundaries of a given (epi-)genetic alteration, respectively.First, iEDGE identifies the cis and trans genes associated with the presence/absence of a particular epi-DNA alteration across samples. Tests of statistical mediation are then performed to determine the cis genes predictive of the trans gene expression. Finally, cis and trans effects are annotated by pathway enrichment analysis to gain insights into the underlying regulatory networks.We used iEDGE to perform integrative analysis of SCNAs and gene expression data from breast cancer and 18 additional cancer types included in The Cancer Genome Atlas (TCGA). Notably, cis gene drivers identified by iEDGE were found to be significantly enriched for known driver genes from multiple compendia of validated oncogenes and tumor suppressors, suggesting that the remainder are of equal importance. Furthermore, predicted drivers were enriched for functionally relevant cancer genes with amplification-driven dependencies, which are of potential prognostic and therapeutic value. All the analyses results are accessible athttps://montilab.bu.edu/iEDGE.
Computational Inference Software for Tetrad Assembly from Randomly Arrayed Yeast Colonies
Authors: Sakhanenko Nikita A. , Cromie Gareth A. , Dudley Aimée M. , Galas David J. 
Published: March 2019

AbstractHere, we describe an information-theory-based method and associated software for computationally identifying sister spores derived from the same meiotic tetrad. The method exploits specific DNA sequence features of tetrads that result from meiotic centromere and allele segregation patterns. Because the method uses only the genomic sequence, it alleviates the need for tetrad-specific barcodes or other genetic modifications to the strains. Using this method, strains derived from randomly arrayed spores can be efficiently grouped back into tetrads.
Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia
Authors: Tam Oliver H. , Rozhkov Nikolay V. , Shaw Regina , Kim Duyang , Hubbard Isabel , Fennessey Samantha , Propp Nadia ,   The NYGC ALS Consortium, Fagegaltier Delphine , Ostrow Lyle W. , Phatnani Hemali , Ravits John , Dubnau Josh , Hammell Molly Gale 
Published: March 2019

SummaryAmyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons. While several inherited pathogenic mutations have been identified as causative, the vast majority of cases are sporadic with no family history of disease. Thus, for the majority of ALS cases, a specific causal abnormality is not known and the disease may be a product of multiple inter-related pathways contributing to varying degrees in different ALS patients. Using unsupervised machine learning algorithms, we stratified the transcriptomes of 148 ALS decedent cortex tissue samples into three distinct and robust molecular subtypes. The largest cluster, identified in 61% of patient samples, displayed hallmarks of oxidative and proteotoxic stress. Another 20% of the ALS patient samples exhibited high levels of retrotransposon expression and other signatures of TDP-43 dysfunction. Finally, a third group showed predominant signatures of glial activation (19%). Together these results demonstrate that at least three distinct molecular signatures contribute to ALS disease. While multiple dysregulated components and pathways comprising these clusters have previously been implicated in ALS pathogenesis, unbiased analysis of this large survey demonstrated that sporadic ALS patient tissues can be segregated into distinct molecular subsets.
Feature Selection and Dimension Reduction for Single Cell RNA-Seq based on a Multinomial Model
Authors: Townes F. William , Hicks Stephanie C. , Aryee Martin J. , Irizarry Rafael A. 
Published: March 2019

AbstractSingle cell RNA-Seq (scRNA-Seq) profiles gene expression of individual cells. Recent scRNA-Seq datasets have incorporated unique molecular identifiers (UMIs). Using negative controls, we show UMI counts follow multinomial sampling with no zero-inflation. Current normalization pro-cedures such as log of counts per million and feature selection by highly variable genes produce false variability in dimension reduction. We pro-pose simple multinomial methods, including generalized principal component analysis (GLM-PCA) for non-normal distributions, and feature selection using deviance. These methods outperform current practice in a downstream clustering assessment using ground-truth datasets.
Transcriptional profiling reveals running promotes cerebrovascular remodeling in young but not aged mice
Authors: Foley Kate E. , Yang Stanley , Graham Leah C. , Howell Gareth R. 
Published: March 2019

AbstractBackgroundThe incidence of dementia and cognitive decline is increasing with no therapy or cure. One of the reasons treatment remains elusive is because there are various pathologies that contribute to age-related cognitive decline. Specifically, with Alzheimer’s disease, targeting to reduce amyloid beta plaques and phosphorylated tau aggregates in clinical trials has not yielded results to slow symptomology, suggesting a new approach is needed. Interestingly, exercise has been proposed as a potential therapeutic intervention to improve brain health and reduce the risk for dementia, however the benefits throughout aging are not well understood.ResultsTo better understand the effects of exercise, we preformed transcriptional profiling on young (1-2 months) and midlife (12 months) C57BL/6J (B6) male mice after 12 weeks of voluntary running. Data was compared to age-matched sedentary controls. Interestingly, the midlife running group naturally broke into two cohorts based on distance ran - either running a lot and more intensely (high runners) or running less and less intensely (low runners). Midlife high runners had lower LDL cholesterol as well as lower adiposity (%fat) compared to sedentary, than midlife low runners compared to sedentary suggesting more intense running lowered systemic markers of risk for age-related diseases including dementias. Differential gene analysis of transcriptional profiles generated from the cortex and hippocampus showed thousands of differentially expressed (DE) genes when comparing young runners to sedentary controls. However, only a few hundred genes were DE comparing either midlife high runners or midlife low runners to midlife sedentary controls. This indicates that, in our study, the effects of running are reduced through aging. Gene set enrichment analyses identified enrichment of genes involved in extracellular matrix (ECM), vascular remodeling and angiogenesis in young runners but not midlife runners. These genes are known to be expressed in multiple vascular-related cell types including astrocytes, endothelial cells, pericytes and smooth muscle cells.ConclusionsTaken together these results suggest running may best serve as a preventative measure to reduce risk for cerebrovascular decline. Ultimately, this work shows that exercise may be more effective to prevent dementia if introduced at younger ages.