bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strong error analysis for stochastic gradient descent optimization algorithms
Authors: Jentzen Arnulf , Kuckuck Benno , Neufeld Ariel , von Wurstemberger Philippe 
Published: December 2019

AbstractStochastic gradient descent (SGD) optimization algorithms are key ingredients in a series of machine learning applications. In this article we perform a rigorous strong error analysis for SGD optimization algorithms. In particular, we prove for every arbitrarily small $\varepsilon \in (0,\infty )$ and every arbitrarily large $p{\,\in\,} (0,\infty )$ that the considered SGD optimization algorithm converges in the strong $L^p$-sense with order $1/2-\varepsilon $ to the global minimum of the objective function of the considered stochastic optimization problem under standard convexity-type assumptions on the objective function and relaxed assumptions on the moments of the stochastic errors appearing in the employed SGD optimization algorithm. The key ideas in our convergence proof are, first, to employ techniques from the theory of Lyapunov-type functions for dynamical systems to develop a general convergence machinery for SGD optimization algorithms based on such functions, then, to apply this general machinery to concrete Lyapunov-type functions with polynomial structures and, thereafter, to perform an induction argument along the powers appearing in the Lyapunov-type functions in order to achieve for every arbitrarily large $ p \in (0,\infty ) $ strong $ L^p $-convergence rates.
Bridging the hybrid high-order and virtual element methods
Authors: Lemaire Simon 
Published: December 2019

Abstract
We present a unifying viewpoint on hybrid high-order and virtual element methods on general polytopal meshes in dimension $2$ or $3$, in terms of both formulation and analysis. We focus on a model Poisson problem. To build our bridge (i) we transcribe the (conforming) virtual element method into the hybrid high-order framework and (ii) we prove $H^m$ approximation properties for the local polynomial projector in terms of which the local virtual element discrete bilinear form is defined. This allows us to perform a unified analysis of virtual element/hybrid high-order methods, that differs from standard virtual element analyses by the fact that the approximation properties of the underlying virtual space are not explicitly used. As a complement to our unified analysis we also study interpolation in local virtual spaces, shedding light on the differences between the conforming and nonconforming cases.
A novel multiresistance gene cluster located on a plasmid-borne transposon in Listeria monocytogenes
Authors: Yan He , Yu Runhao , Li Dexi , Shi Lei , Schwarz Stefan , Yao Hong , Li Xin-Sheng , Du Xiang-Dang 
Published: December 2019

Abstract

Objectives
To identify the genetic context and the transferability of the multiresistance gene lsa(E) in Listeria monocytogenes.

Methods
MICs were determined by broth microdilution. Transferability of lsa(E) was investigated by conjugation, electrotransformation and natural transformation. The lsa(E)-carrying plasmid was sequenced using the Illumina MiSeq and PacBio RSII platforms. The presence of translocatable units (TUs) was examined by PCR.

Results
The 85 555 bp non-conjugative multiresistance plasmid pNH1 from L. monocytogenes harboured nine antimicrobial resistance genes including a multiresistance gene cluster, consisting of the genes aphA3, erm(B), aadE, spw, lsa(E) and lnu(B), and in addition the genes dfrG, tet(S) and catA8 were also located on plasmid pNH1 The multiresistance gene cluster, and each of the genes tet(S), catA8 and cadA were flanked by IS1216 elements. PCR identified four types of TUs, consisting of either the multiresistance gene cluster and one copy of IS1216, the catA8 gene and one copy of IS1216, or both, but also the tet(S) gene and one copy of IS1216, respectively. Natural transformation into Streptococcus mutans UA159 yielded transformants that harboured a novel 13 208 bp transposon, designated Tn6659. This transposon consisted of the multiresistance gene cluster bounded by IS1216 copies. All transformants displayed elevated MICs of the respective antimicrobial agents. At the integration site in the transformants, 8 bp direct target duplications (5′-ATTCAAAC-3′) were found immediately up- and downstream of Tn6659.

Conclusions
To the best of our knowledge, this is the first report of this novel multiresistance gene cluster and the gene catA8, flanked by IS1216 elements located on a plasmid of L. monocytogenes. Moreover, a novel functionally active multiresistance transposon was identified.
Local habitat specialization as an evolutionary response to interspecific competition between two sympatric shrews
Authors: Biedma Luis , Calzada Javier , Godoy José A , Román Jacinto 
Published: December 2019

AbstractInterspecific competition affects population dynamics, distributional ranges, and evolution of competing species. The competitive exclusion principle states that ecologically similar species cannot coexist unless they exhibit niche segregation. Herein, we assess whether niche segregation allows the coexistence of Crocidura russula and C. suaveolens in southwestern Iberia and whether segregation is the result of current (ecological effect) or past (evolutionary effect) competition. We performed an annual live-trapping cycle in the two main habitats of the Odiel Marshes Natural Reserve (OMNR), the tidal marsh and the Mediterranean forest, both in syntopic (i.e., where both species co-occur) and allotopic (where only one of the two species occurs) sites within this Reserve. We modeled the presence–absence of each species in both habitats and sites by generalized linear mixed models. The coexistence of both species was favored by spatial and temporal niche segregation. Crocidura suaveolens was restricted to tidal marsh and did not occupy Mediterranean forest, even when C. russula was absent. We interpret this to be the result of competition in the past triggering an evolutionary response in C. suaveolens towards its specialization in tidal marsh. Moreover, the specialist C. suaveolens currently is outcompeting C. russula in tidal marshes, reversing the dominance pattern observed elsewhere. The degree of co-occurrence between both species in syntopic sites was low, as they showed inverse dynamics of seasonal abundances. Interspecific competition leading to habitat specialization favors the coexistence of these ecologically similar species.
CDH1 on Multigene Panel Testing: Look Before You Leap
Authors: Katona Bryson W , Clark Dana Farengo , Domchek Susan M 
Published: December 2019

Abstract
Multigene panel testing (MGPT) has become a critical component of cancer risk assessment in clinical practice. As technology and access improve and costs decrease, more individuals than ever are undergoing MGPT for genetic evaluation. One gene that deserves special consideration when included on MGPT is CDH1, which codes for the cell-cell adhesion protein E-cadherin. Pathogenic and likely pathogenic germline variants in CDH1 have been associated with hereditary diffuse gastric cancer syndrome, and in highly penetrant families, testing for these variants is critical for proper risk management. However, recent data demonstrated that gastric cancer penetrance in unselected CDH1 carriers may be lower than expected. Further complicating matters are the lack of effective screening strategies for gastric cancer and recommendation for risk-reducing total gastrectomy in CDH1 carriers. Therefore, the discovery of an unexpected pathogenic or likely pathogenic CDH1 variant on multigene panel testing, when testing for CDH1 would not normally be considered based on personal or family history alone, creates dilemmas for both patients and providers. In this commentary, we highlight the potential for unexpected CDH1 variants on MGPT, outline the uncertainties associated with these variants, and emphasize the importance of pretest counseling regarding the potential for an unexpected CDH1 variant. Although CDH1 testing is often important for clinical decision-making, individuals and providers need to be aware of the potential for an unexpected CDH1 variant when CDH1 is included on MGPT for cancer risk assessment.
Conflict Environments and Civil War Onset
Authors: Reid Lindsay , Myrick Rachel , Kadera Kelly M , Crescenzi Mark J C 
Published: December 2019

AbstractThe spread of civil war poses serious risks and costs. We argue that conflict environments, which vary across time and space, systematically exacerbate the spread of civil war. As conflict in a state’s neighborhood becomes more spatially proximate and as lingering effects of conflict accumulate over time, that state’s risk of civil war onset increases. To theorize and test this argument, we construct the conflict environment (CE) score, a concept that taps into spatial and temporal dimensions of violence in a state’s neighborhood. Using the CE score in established empirical models of civil war onset, we demonstrate that a dangerous conflict environment consistently elevates the risk of civil war, outperforming traditional measures of nearby violence, even when domestic factors are taken into account.
Concentration ratios of 238U and 226Ra for insects and amphibians living in the vicinity of the closed uranium mine at Ningyo-toge, Japan
Authors: Sakoda Akihiro , Murakami Shoichi , Ishimori Yuu , Horai Sawako 
Published: December 2019

Abstract
There is still a scarcity of data on the transfer of naturally occurring radionuclides to wildlife in various ecosystems. In the present study, concentration ratios (CRwo-media) of 238U and 226Ra were obtained for grasshoppers, frogs and newts in terrestrial and freshwater ecosystems. Soil, water and animal samples were collected for 2 years in the vicinity of the closed uranium mine at Ningyo-toge, Japan. Three sites with different 238U and 226Ra levels were of interest: (i) pond and its shore (PO); (ii) low-level stream and its shore near overburden dump (OD); and (iii) uranium mill tailings pond and its shore (MP). The activity concentrations in both soil and water were PO ≈ OD &lt; MP for 238U, and PO &lt; OD &lt; MP for 226Ra. Regarding the wildlife, 238U was able to be determined for all samples, but the detection of 226Ra was observed only for part of the samples. The means and standard deviations of CRwo-soil or CRwo-water were then calculated and may indicate the insignificant dependence of CRwo-media on environmental conditions characterized by the tested sites. The present data on CRwo-media were compared to the corresponding data or surrogate data from the IAEA’s database, showing both agreement and discrepancy. Our data contribute to enhancing the available data for those radionuclides and animals. In particular, the transfer to amphibians, one of the main links in common food webs, is reported here for the first time.
Forming early-type galaxies without AGN feedback: a combination of merger-driven outflows and inefficient star formation
Authors: Kretschmer Michael , Teyssier Romain 
Published: December 2019

ABSTRACT
Regulating the available gas mass inside galaxies proceeds through a delicate balance between inflows and outflows, but also through the internal depletion of gas due to star formation. At the same time, stellar feedback is the internal engine that powers the strong outflows. Since star formation and stellar feedback are both small-scale phenomena, we need a realistic and predictive subgrid model for both. We describe the implementation of supernova momentum feedback and star formation based on the turbulence of the gas in the ramses code. For star formation, we adopt the so-called multifreefall model. The resulting star formation efficiencies can be significantly smaller or bigger than the traditionally chosen value of $1\, {\rm per\, cent}$. We apply these new numerical models to a prototype cosmological simulation of a massive halo that features a major merger which results in the formation of an early-type galaxy without using AGN feedback. We find that the feedback model provides the first-order mechanism for regulating the stellar and baryonic content in our simulated galaxy. At high redshift, the merger event pushes gas to large densities and large turbulent velocity dispersions, such that efficiencies come close to $10\, {\rm per\, cent}$, resulting in large star formation rate (SFR). We find small molecular gas depletion time during the starburst, in perfect agreement with observations. Furthermore, at late times, the galaxy becomes quiescent with efficiencies significantly smaller than $1\, {\rm per\, cent}$, resulting in small SFR and long molecular gas depletion time.
Ionization correction factors for sodium, potassium, and calcium in planetary nebulae
Authors: Amayo A , Delgado-Inglada G , García-Rojas J 
Published: December 2019

ABSTRACT
We use a large grid of photoionization models that are representative of observed planetary nebulae (PNe) to derive ionization correction factors (ICFs) for sodium, potassium, and calcium. In addition to the analytical expressions of the ICFs, we provide the range of validity where the ICFs can be safely used and an estimate of the typical uncertainties associated with the ICFs. We improved the previous ICFs for calcium and potassium in the literature and suggest for the first time an ICF for sodium. We tested our ICFs with a sample of 39 PNe with emission lines of some ion of these elements. No obvious trend is found between the derived abundances and the degree of ionization, suggesting that our ICFs do not seem to be introducing an artificial bias in the results. The abundances found in the studied PNe range from $-2.88_{-0.22}^{+0.21}$ to −2.09 ± 0.21 in log (Na/O), from $-4.20_{-0.45}^{+0.31}$ to $-3.05_{-0.47}^{+0.26}$ in log (K/O), and from $-3.71_{-0.34}^{+0.41}$ to $-1.57_{-0.47}^{+0.33}$ in log (Ca/O). These numbers imply that some of the studied PNe have up to ∼65 per cent, 75 per cent, or 95 per cent of their Na, K, and/or Ca atoms condensed into dust grains, respectively. As expected, the highest depletions are found for calcium which is the element with the highest condensation temperature.
Activation of endoplasmic reticulum stress mediates oxidative stress–induced apoptosis of granulosa cells in ovaries affected by endometrioma
Authors: Kunitomi Chisato , Harada Miyuki , Takahashi Nozomi , Azhary Jerilee M K , Kusamoto Akari , Nose Emi , Oi Nagisa , Takeuchi Arisa , Wada-Hiraike Osamu , Hirata Tetsuya , Hirota Yasushi , Koga Kaori , Fujii Tomoyuki , Osuga Yutaka 
Published: December 2019

AbstractEndometriosis exerts detrimental effects on ovarian physiology and compromises follicular health. Granulosa cells from patients with endometriosis are characterized by increased apoptosis, as well as high oxidative stress. Endoplasmic reticulum (ER) stress, a local factor closely associated with oxidative stress, has emerged as a critical regulator of ovarian function. We hypothesized that ER stress is activated by high oxidative stress in granulosa cells in ovaries with endometrioma and that this mediates oxidative stress–induced apoptosis. Human granulosa-lutein cells (GLCs) from patients with endometrioma expressed high levels of mRNAs associated with the unfolded protein response (UPR). In addition, the levels of phosphorylated ER stress sensor proteins, inositol-requiring enzyme 1 (IRE1) and double-stranded RNA-activated protein kinase-like ER kinase (PERK), were elevated in granulosa cells from patients with endometrioma. Given that ER stress results in phosphorylation of ER stress sensor proteins and induces UPR factors, these findings indicate that these cells were under ER stress. H2O2, an inducer of oxidative stress, increased expression of UPR-associated mRNAs in cultured human GLCs, and this effect was abrogated by pretreatment with tauroursodeoxycholic acid (TUDCA), an ER stress inhibitor in clinical use. Treatment with H2O2 increased apoptosis and the activity of the pro-apoptotic factors caspase-8 and caspase-3, both of which were attenuated by TUDCA. Our findings suggest that activated ER stress induced by high oxidative stress in granulosa cells in ovaries with endometrioma mediates apoptosis of these cells, leading to ovarian dysfunction in patients with endometriosis.
Burnout and career satisfaction in neuro-oncology: a survey of the Society for Neuro-Oncology and the European Association of Neuro-Oncology memberships
Authors: Yust-Katz Shlomit , O’Brien Barbara , Vera Elizabeth , Acquaye Alvina , Weller Michael , Armstrong Terri 
Published: December 2019

Abstract

Background
Professional burnout is a syndrome characterized by emotional exhaustion, depersonalization, and loss of personal achievement. Burnout is a significant issue among health care providers, and neuro-oncology providers may be at high risk. We conducted a survey to evaluate burnout and career satisfaction among those caring for patients with brain tumors, and to identify risk factors for burnout.

Methods
We distributed an anonymous online survey to Society for Neuro-Oncology (SNO) members in 2016 and to European Association of Neuro-Oncology (EANO) members in 2017. The survey comprised questions about personal and professional characteristics and the validated Maslach Burnout Inventory–Human Services Survey (MBI-HSS) questionnaire. Statistical analysis included descriptive statistics, univariate and multivariate analyses, and incorporation of recently defined burnout profiles.

Results
Sixty-three percent of SNO and 61% of EANO participants were identified as having high burnout according to MBI-HSS. Among SNO participants, physicians had a lower rate of high burnout (61%) compared with allied health professionals (68%, P &lt; 0.01) and basic scientists (83%, P &lt; 0.01). Regarding the factors most commonly contributing to high burnout, SNO participants most commonly experienced high emotional exhaustion (48% of SNO participants vs 34% of EANO participants), whereas EANO participants most commonly experienced low personal achievement (40% vs 28%). Among both SNO and EANO participants, increasing job satisfaction reduced the likelihood of high burnout.

Conclusions
The prevalence of burnout among neuro-oncology professionals is high and personal risk factors were identified. Burnout profiles recognize a continuum of well-being and warrant further research.
Radiosurgery for Unruptured Intervention-Naïve Pediatric Brain Arteriovenous Malformations
Authors: Chen Ching-Jen , Lee Cheng-Chia , Kano Hideyuki , Kearns Kathryn N , Ding Dale , Tzeng Shih-Wei , Atik Ahmet Fatih , Joshi Krishna , Huang Paul P , Kondziolka Douglas , Ironside Natasha , Mathieu David , Iorio-Morin Christian , Grills Inga S , Quinn Thomas J , Siddiqui Zaid A , Marvin Kim , Feliciano Caleb , Starke Robert M , Faramand Andrew , Barnett Gene , Lunsford L Dade , Sheehan Jason P ,   on behalf of the International Radiosurgery Research Foundation
Published: December 2019

Abstract

BACKGROUND
Long-term data regarding stereotactic radiosurgery (SRS) as a standalone therapy for unruptured pediatric brain arteriovenous malformations (AVMs) are incompletely defined.

OBJECTIVE
To evaluate, in a multicenter, retrospective cohort study, the outcomes after SRS for unruptured, intervention-naïve pediatric AVMs.

METHODS
To retrospectively analyze the International Radiosurgery Research Foundation pediatric AVM database from 1987 to 2018. Pediatric patients with unruptured, previously untreated AVMs who underwent SRS were included. The primary endpoint was a composite of hemorrhagic stroke, death, or permanently symptomatic radiation-induced changes.

RESULTS
The study cohort comprised 101 patients (mean follow-up 80.8 mo). The primary endpoint occurred in 14%, comprising hemorrhagic stroke, death, and permanent radiation-induced changes in 6%, 3%, and 8%, respectively. Estimated probabilities of the primary endpoint were 5.2%, 10.8%, and 23.0% at 2, 5, and 10 yr, respectively. Estimated probabilities of AVM obliteration at 5 and 10 yr were 64% and 82%, respectively. Single SRS treatment (P = .007) and higher margin dose (P = .005) were predictors of obliteration. Subgroup analysis of Spetzler-Martin grade I-III AVMs estimated primary endpoint probabilities of 3.7%, 8.4%, and 18.7% at 2, 5, and 10 yr, respectively.

CONCLUSION
Treatment of unruptured, intervention-naïve AVMs in the pediatric population with SRS carries an approximately 2% annual risk of morbidity and mortality, which appears to plateau after 10 yr. The poorly described natural history of pediatric AVMs renders any comparison of SRS vs conservative management imperfect.
Biomarkers of Exposure for Dual Use of Electronic Cigarettes and Combustible Cigarettes: Nicotelline, NNAL, and Total Nicotine Equivalents
Authors: Jacob Peyton , St. Helen Gideon , Yu Lisa , Nardone Natalie , Havel Christopher , Cheung Polly , Benowitz Neal L 
Published: December 2019

Abstract

Introduction
Dual use of electronic cigarettes (e-cigarettes) and combustible cigarettes is a major public health issue. It is generally accepted that exclusive e-cigarette use is less harmful than exclusive combustible cigarette use, but most e-cigarette users continue to smoke combustible cigarettes as well. To what extent the use of e-cigarettes reduces harm in people who continue to smoke combustible cigarettes has been debated. The aim of this study was to explore the utility of biomarkers as measures of dual use.

Methods
In two human studies of participants who used e-cigarettes only or both combustible cigarettes and e-cigarettes, we measured urine concentrations of the metabolites of nicotine (total nicotine equivalents) as well as two biomarkers of tobacco exposure: 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), a tobacco-specific carcinogen metabolite, and nicotelline, a tobacco alkaloid not found in significant concentrations in e-cigarette products.

Results
The presence of nicotine metabolites indicates either e-cigarette or combustible cigarette use. Nicotelline (half-life of 2–3 hours) indicates recent combustible cigarette use and NNAL (half-life of 10 days or more), indicates combustible cigarette use occurring within several weeks prior to sample collection.

Conclusions
Nicotelline and NNAL are useful biomarkers for combustible tobacco use in users e-cigarettes. The application of these biomarkers provides a tool to help assess whether, or to what extent, dual use of e-cigarettes and combustible cigarettes reduces harm compared to sole use of combustible cigarettes. These biomarkers can also verify exclusive use of e-cigarettes over short (24 hour) or long (several week) time periods.

Implications:
To what extent dual use of e-cigarettes and combustible cigarettes reduce harm compared to smoking combustible cigarettes only is of considerable public health interest. We show that the levels of the minor tobacco alkaloid nicotelline and the nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) are extremely low in electronic cigarette fluids. The urine biomarkers nicotelline and the NNK metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) are indicative of cigarette smoking and can be used to assess recent and past smoking in dual users.