bluuebunny/crossref_metadata_2025_split huggingface dataset:
SDSS-IV MaNGA: the inner density slopes of nearby galaxies
Authors: Li Ran , Li Hongyu , Shao Shi , Lu Shengdong , Zhu Kai , Wang Chunxiang , Gao Liang , Mao Shude , Dutton Aaron A , Ge Junqiang , Wang Yunchong , Leauthaud Alexie , Zheng Zheng , Bundy Kevin , Brownstein Joel R 
Published: September 2019

ABSTRACT
We derive the mass-weighted total density slopes within the effective (half-light) radius, γ′, for more than 2000 nearby galaxies from the SDSS-IV (Sloan Digital Sky Survey IV) MaNGA survey using Jeans-anisotropic-models applied to integral field unit observations. Our galaxies span a wide range of the stellar mass (109 M⊙ &lt; M* &lt; 1012 M⊙) and the velocity dispersion (30 km s−1 &lt; σv &lt; 300 km s−1). We find that for galaxies with velocity dispersion σv &gt; 100 km s−1, the density slope has a mean value 〈γ′〉 = 2.24 and a dispersion σγ = 0.22, almost independent of velocity dispersion, consistent with previous lensing and stellar dynamical analysis. We also quantitatively confirm with high accuracy a turnover in the γ′–σv relation is present at σ ∼ 100 km s−1, below which the density slope decreases rapidly with σv, consistent with the results reported by previous analysis of ${\rm ATLAS^{\rm 3D}}$ survey. Our analysis shows that a large fraction of dwarf galaxies (below M* = 1010 M⊙) have total density slopes shallower than 1, which implies that they may reside in cold dark matter haloes with shallow density slopes. We compare our results with that of galaxies in hydrodynamical simulations of EAGLE, Illustris, and IllustrisTNG projects, and find all simulations predict shallower density slopes for massive galaxies with high σv. Finally, we explore the dependence of γ′ on the positions of galaxies in haloes, namely centrals versus satellites, and find that for the same velocity dispersion, the amplitude of γ′ is higher for satellite galaxies by about 0.1.
Signatures of cell death and proliferation in perturbation transcriptomics data—from confounding factor to effective prediction
Authors: Szalai Bence , Subramanian Vigneshwari , Holland Christian H , Alföldi Róbert , Puskás László G , Saez-Rodriguez Julio 
Published: September 2019

AbstractTranscriptional perturbation signatures are valuable data sources for functional genomics. Linking perturbation signatures to screenings opens the possibility to model cellular phenotypes from expression data and to identify efficacious drugs. We linked perturbation transcriptomics data from the LINCS-L1000 project with cell viability information upon genetic (Achilles project) and chemical (CTRP screen) perturbations yielding more than 90 000 signature–viability pairs. An integrated analysis showed that the cell viability signature is a major factor underlying perturbation signatures. The signature is linked to transcription factors regulating cell death, proliferation and division time. We used the cell viability–signature relationship to predict viability from transcriptomics signatures, and identified and validated compounds that induce cell death in tumor cell lines. We showed that cellular toxicity can lead to unexpected similarity of signatures, confounding mechanism of action discovery. Consensus compound signatures predicted cell-specific drug sensitivity, even if the signature is not measured in the same cell line, and outperformed conventional drug-specific features. Our results can help in understanding mechanisms behind cell death and removing confounding factors of transcriptomic perturbation screens. To interactively browse our results and predict cell viability in new gene expression samples, we developed CEVIChE (CEll VIability Calculator from gene Expression; https://saezlab.shinyapps.io/ceviche/).
Microsurgical Resection of Vestibular Schwannomas, Presentation of Cases in 3D: 3-Dimensional Operative Video
Authors: Campero Alvaro , Baldoncini Matias 
Published: September 2019

Abstract
Vestibular schwannomas are the most common benign tumors of the pontocerebellar angle,
1,2
their microsurgical complexity is related to their size and neurovascular relationships. The purpose of this work is to analyze the clinical, anatomic characteristics, microsurgical treatment, and the postoperative results according to the Hannover gradual scale in 4 patients with vestibular schwannomas. The 4 patients gave their consent to the procedure and all consented to the use of their surgical videos, preoperative and postoperative studies, and postoperative pictures.
Case 1: A 39-yr-old woman, with left ear hearing loss. Magnetic resonance imaging (MRI) showed small Intracanalicular schwannoma (T1 classification by Hannover). Microsurgery was performed and resection through a retrosigmoid approach
2,3
with anatomic and functional preservation of the facial and cochlear nerve.
Case 2: A 40-yr-old woman, with left ear hypoacusia. MRI showed an extrameatal schwannoma reaching the brainstem (T3b Hannover classification). The complete re-section through retrosigmoid approach were performed.
Case 3: A 69-yr-old woman, without hearing in the right ear. RM: Medium schwannoma (T4a classification of Hannover). Microsurgery was performed with anatomic and functional preservation of the facial nerve.
4-6

Case 4: A 32-yr-old woman, without hearing in the left ear. In addition, cerebellar syndrome and headache. RM: Large schwannoma (T4b classification of Hannover). Sur-gery was performed, anatomic preservation of the facial nerve, with moderate paresis in the postoperative period.
Microsurgical resection with functional preservation of the facial and cochlear nerve is the main objective
7
when addressing this pathology.
Trabecular bone score improves fracture risk assessment in glucocorticoid-induced osteoporosis
Authors: Florez Helena , Hernández-Rodríguez José , Muxi Africa , Carrasco Josep Lluis , Prieto-González Sergio , Cid Maria C , Espinosa Gerard , Gómez-Puerta Jose A , Monegal Ana , Guañabens Núria , Peris Pilar 
Published: September 2019

Abstract

Objective
To analyse the clinical utility of trabecular bone score (TBS) evaluation for fracture risk assessment in glucocorticoid (GC)-treated patients compared with BMD assessment.

Methods
One hundred and twenty-seven patients on GC treatment were included [mean age 62 (18) years, 63% women] in this cross-sectional study. The medical history, anthropometric data, lumbar and femoral BMD (DXA) [considering osteoporosis (OP): T-score ⩽−2.5], TBS (considering degraded microarchitecture: &lt;1.230) and dorsolumbar X-ray [to assess vertebral fractures (VF)] were evaluated. BMD and TBS sensitivity, specificity, and positive and negative predictive values (PPV, NPV) were evaluated to determine the diagnostic accuracy of the two methods.

Results
All patients were receiving GC treatment for autoimmune diseases during 47.7 (68.9) months at a mean daily dose of 14.5 mg; 17% had VF, 28% any type of fragility fracture (VF + non-VF), 29% OP and 52% degraded microarchitecture. Degraded microarchitecture was significantly more frequent than densitometric OP in patients with VF (76% vs 38%) and with any fragility fracture (69% vs 36%). For VF, TBS and BMD sensitivity, specificity, PPV, and NPV were 0.76, 0.53, 0.25 and 0.92, and 0.38, 0.72, 0.22 and 0.85, respectively. Specificity increased to 0.89 for VF and 0.9 for any fragility fracture on combining BMD+TBS. TBS had better ability than BMD to discriminate between patients with fracture, especially VF (area under the curve = 0.73).

Conclusion
TBS seems to have greater discriminative power than BMD for fracture risk assessment in GC-treated patients, confirming the utility of this method as a complementary tool in the diagnosis of GC-induced OP.
DANSAC A/S v SALTS HEALTHCARE LTD
Authors:   Chancery Division
Published: September 2019

Abstract
H1 Trade marks – Infringement – Parallel imports – Medical devices – Ostomy bags – Strike out application – Sale in original unopened boxes – Some boxes re-labelled – Whether the BMS conditions applied – Whether any risk to guarantee of origin – “Legitimate reasons” for opposing further dealings – Whether breach of Medical Devices Regulations of itself sufficient – Whether likelihood of damage or serious damage necessary
Beneficiary disputes: Lines v Wilcox
Authors: Perselli Francesca 
Published: September 2019

Abstract
What is a trustee’s role when there is a dispute to be brought on behalf of the estate which is in the interests of one beneficiary at the expense of another? If the dispute is essentially one between the beneficiaries, can the trustee adopt a neutral position and leave the beneficiaries to litigate between themselves? Do the beneficiaries have standing to bring claims that properly belong to the estate? This article addresses these questions, which were recently considered by HHJ Paul Matthews (sitting as a Judge of the High Court) in Lines v Wilcox [2019] EWHC 1451 (Ch).
Association of Total Zinc Intake with Myopia in U.S. Children and Adolescents
Authors: Burke Niamh , Butler John S. , Flitcroft Ian , McCartney Daniel , Loughman James 
Published: September 2019

SIGNIFICANCE
This present study advances our knowledge on the role of lifestyle factors in myopia (short-sightedness), specifically dietary factors. It has been suggested in previous studies that lower zinc status is associated with myopia; however, this article shows no relationship between dietary zinc intake and myopia in U.S. adolescents.

PURPOSE
It has been suggested that low zinc levels may contribute to the development of myopia. The aim of the present study is to examine, for the first time in a Western population, the association of total dietary and supplement zinc intake with myopia.

METHODS
A total of 1095 children/adolescents aged 12 to 19 years who participated in the U.S. National Health and Nutrition Examination Survey from 2007 to 2008 were enrolled in this study. Multivariate logistic regression analysis was performed to examine the relationship between total zinc intake and myopia after adjustment for potential confounders. In addition, the association between total zinc intake and spherical equivalent refractive error was examined in the myopia group through multiple linear regression.

RESULTS
Among study participants, 30% were found to be myopic (≤−1.00 D). Although median total daily zinc intake was lower among myopes (10.8 [10.2] mg/d) than among nonmyopes (11.1 [10.8] mg/d), the difference was not statistically significant (P = .11). In multiple logistic regression analyses, zinc and copper intakes were not significantly associated with myopia after adjustment for age, sex, body mass index, ethnicity, family income, recreational activity, copper intake, and daily energy intake (in kilocalories per day). In multiple linear regression, spherical equivalent refractive error was not associated with total zinc intake in the myopic group after adjustment for confounding factors (P = .13).

CONCLUSIONS
In contrast to previous Asian studies, total zinc intake is not associated with the presence of myopia in U.S. adolescents/children.
Targeting the Id1-Kif11-Aurka axis in triple negative breast cancer using combination therapy
Authors: Murali Reshma , Varghese Binitha Anu , Karthikeyan Nitheesh , Archana PT , Teo Wee Siang , McFarland Andrea , Roden Daniel L , Holliday Holly , Konrad Christina , Cazet Aurelie , Dodson Eoin , George Jason T , Levine Herbert , Jolly Mohit Kumar , Swarbrick Alexander , Nair Radhika 
Published: September 2019

AbstractEvidence points to breast cancer following a hierarchical model, with Cancer Stem Cells (CSCs) driving critical phenotypes of the bulk tumor. Chemoresistant CSCs are not an abstract concept but have clinical consequences as they drive relapse and ultimately lead to mortality in patients, making it imperative to understand how these subpopulations of cells survive. Our previous work (1-2) has demonstrated that the bHLH transcription factor, Inhibitor of Differentiation 1 (Id1) and it’s closely related family member Id3, have an important role in maintaining the CSC phenotype in the Triple Negative breast cancer (TNBC) subtype. A genetic screen conducted to further elucidate the molecular mechanism underlying the Id (Id1/3) mediated CSC phenotypes in TNBC revealed critical cell cycle genes such as Kif11 and Aurka as putative Id targets. We take this work forward by investigating how alteration in Kif11 and Aurka via Id proteins promotes the CSC phenotype in TNBC. Cells lacking Id are poised in a state of G0/G1 arrest from which they can re-enter the cell cycle. Intriguingly, depletion of Kif11 and Aurka independently did not phenocopy the G0/G1 arrest observed in Id knockdown (Id KD) cells. We have further explored the hypothesis that we can deplete the chemo resistant Id expressing CSC population by combining chemotherapy with targeted therapy using existing small molecule inhibitors (against Id target Kif11) to more effectively debulk the entire tumor. This work opens up exciting new possibilities of targeting Id targets like Kif11, in the TNBC subtype which is currently refractory to chemotherapy.
Accumulation of genetic variants associated with immunity in the selective breeding of broilers
Authors: Zou Angela , Nadeau Kerry , Wang Pauline W. , Lee Jee Yeon , Guttman David S. , Sharif Shayan , Korver Doug , Brumell John H. , Parkinson John 
Published: September 2019

ABSTRACTTo satisfy an increasing demand for dietary protein, the poultry industry has employed genetic selection to increase the growth rate of broilers by over 400% in the past 50 years. Although modern broilers reach a marketable weight of ∼2 kg in a short span of 35 days, a speed twice as fast as a broiler 50 years ago, the expedited growth has been associated with several negative detrimental consequences. Aside from heart and musculoskeletal problems, which are direct consequences of additional weight, the immune response is also thought to be altered in modern broilers. Given that identifying the underlying genetic basis responsible for a less sensitive innate immune response would be economically beneficial for poultry breeding, we decided to compare the genomes of two unselected meat control strains that are representative of broilers from 1957 and 1978, and a current commercial broiler line. Through analysis of genetic variants, we developed a custom prioritization strategy to identify genes and pathways that have accumulated genetic changes and are biologically relevant to immune response and growth performance. Our results highlight two genes, TLR3 and PLIN3, with genetic variants that are predicted to enhance growth performance at the expense of immune function. Placing these new genomes in the context of other chicken lines, reveal genetic changes that have specifically arisen in selective breeding programs that were implemented in the last 50 years.
Short Neuropeptide F regulates the starvation mediated enhanced locomotor Activity in Drosophila
Authors: Geo Anna , Pathak Himani , Kujur Anamika Elizabeth , Sudhakar Sreesha R , Kannan Nisha N 
Published: September 2019

AbstractThe circadian clock regulates various behavioral, metabolic and physiological processes to occur at the most suitable time of the day. Internal energy stores and nutrient availability modulates the most apparent circadian clock mediated locmotor activity rhythm in Drosophila. Although previous studies unraveled the role of circadian clock in metabolism and activity rest rhythm, the precise pathway through which the circadian neuropeptidergic signaling regulates internal energy storage and the starvation-mediated increase in activity resembling foraging remains largely unclear. This study was aimed to elucidate the role of circadian neuropeptide, short neuropeptide F (sNPF) in triglyceride metabolism, starvation resistance and starvation-mediated increased locomotor activity in Drosophila. The results showed that snpf transcripts exhibits significant rhythmicity in wild type flies under 12:12 hour light-dark cycles (LD) and constant darkness (DD) whereas snpf transcript level in period null flies did not exhibit any significant rhythmicity under LD. Knockdown of sNPF in circadian clock neurons reduced the triglyceride level, starvation resistance and increased the starvation-mediated hyperactivity response after 24 hour of starvation. Further studies showed that knock down of sNPF receptors (sNPFR) expressed in insulin producing cells (IPC) increased the starvation resistance and reduced starvation-induced hyperactivity response after 24 hour of starvation. Collectively, our results suggest that transcriptional oscillation of snpf mRNA is endogenously controlled by the circadian clock and elucidate the role of sNPF in modulating locomotor activity in accordance with the nutrient availability in Drosophila.
Evolutionary insights into PtdIns3P signaling through FYVE and PHOX effector proteins from the moss Physcomitrella patens
Authors: Agudelo-Romero Patricia , Fortes Ana Margarida , Suárez Trinidad , Lascano Hernán Ramiro , Saavedra Laura 
Published: September 2019

ABSTRACTPhosphatidylinositol 3-phosphate (PtdIns3P) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through PtdIns3P-binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest diverging group of terrestrial flora.In this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution.
Functional divergence and potential mechanisms of the duplicaterecAgenes inMyxococcus xanthus
Authors: Sheng Duo-hong , Wang Yi-xue , Qiu Miao , Zhao Jin-yi , Yue Xin-jing , Li Yue-zhong 
Published: September 2019

AbstractRecA is a ubiquitous multifunctional protein for bacterial homologous recombination and SOS response activation.Myxococcus xanthusDK1622 possesses tworecAgenes, and their functions and mechanisms are almost unclear. Here, we showed that the transcription ofrecA1(MXAN_1441) was less than one-tenth ofrecA2(MXAN_1388). Expressions of the tworecAgenes were both induced by ultraviolet (UV) irradiation, but in different periods. Deletion ofrecA1did not affect the growth, but significantly decreased the UV-irradiation survival, the homologous recombination ability, and the induction of the LexA-dependent SOS genes. Comparably, the deletion ofrecA2markedly prolonged the lag phase for cellular growth and antioxidation of hydrogen peroxide, but did not change the UV-irradiation resistance and the SOS-gene inducibility. The two RecA proteins are both DNA-dependent ATPase enzymes. We demonstrated that RecA1, but not RecA2, hadin vitroDNA recombination capacity and LexA-autolysis promotion activity. Transcriptomic analysis indicated that the duplicate RecA2 has evolved to mainly regulate the gene expressions for cellular transportation and antioxidation. We discuss the potential mechanisms for the functional divergence. This is the first time to clearly determine the divergent functions of duplicatedrecAgenes in bacterial cells. The present results highlight that the functional divergence of RecA duplicates facilitates the exertion of multiple RecA functions.Author summaryMyxobacteria has a large-size genome, contains many DNA repeats that are rare in the prokaryotic genome. It encodes bacterial RecA that could promote recombination between homologous DNA sequences. How myxobacteria avoid the undesired recombination between DNA repeats in its genome is an interesting question.M. xanthusencodes two RecA proteins, RecA1 (MXAN_1441) and RecA2 (MXAN_1388). Both RecA1 and RecA2 shows more than 60% sequence consistency withE. coliRecA (EcRecA) and can partly restore the UV resistance ofE. coli recAmutant. Here, our results proved their divergent functions of the two RecAs. RecA1 retains the ability to catalyze DNA recombination, but its basal expression level is very low. RecA2 basal expression level is high, but no recombination activity is detected in vitro. This may be a strategy forM. xanthusto adapt to more repetitive sequences in its genome and avoid incorrect recombination.HighlightsM. xanthushas tworecAs, which are expressed with significantly different levels. BothrecAs are inducible by UV irradiation, but in different stages.The absence ofrecA1reduces bacterial UV-irradiation resistance, while the absence ofrecA2delays bacterial growth and antioxidant capacity.RecA1 retains the DNA recombination and SOS induction abilities, while RecA2 has evolved to regulate the expression of genes for cellular transport and antioxidation.
WormQTL2: an interactive platform for systems genetics inCaenorhabditis elegans
Authors: Snoek Basten L. , Sterken Mark G. , Hartanto Margi , van Zuilichem Albert-Jan , Kammenga Jan E. , de Ridder Dick , Nijveen Harm 
Published: September 2019

AbstractQuantitative genetics provides the tools for linking polymorphic loci (QTLs) to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here we present WormQTL2 (www.bioinformatics.nl/WormQTL2/), a database and platform for comparative investigations and meta-analyses of published (e)QTL datasets in the model nematode wormC. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as-well-as over 1000 traits from 32 studies and allows experimental results to be compared, reused, and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression.