bluuebunny/crossref_metadata_2025_split huggingface dataset:
Olympus: a benchmarking framework for noisy optimization and experiment planning
Authors: Häse Florian , Aldeghi Matteo , Hickman Riley J , Roch Loïc M , Christensen Melodie , Liles Elena , Hein Jason E , Aspuru-Guzik Alán 
Published: March 2021

Abstract
Research challenges encountered across science, engineering, and economics can frequently be formulated as optimization tasks. In chemistry and materials science, recent growth in laboratory digitization and automation has sparked interest in optimization-guided autonomous discovery and closed-loop experimentation. Experiment planning strategies based on off-the-shelf optimization algorithms can be employed in fully autonomous research platforms to achieve desired experimentation goals with the minimum number of trials. However, the experiment planning strategy that is most suitable to a scientific discovery task is a priori unknown while rigorous comparisons of different strategies are highly time and resource demanding. As optimization algorithms are typically benchmarked on low-dimensional synthetic functions, it is unclear how their performance would translate to noisy, higher-dimensional experimental tasks encountered in chemistry and materials science. We introduce Olympus, a software package that provides a consistent and easy-to-use framework for benchmarking optimization algorithms against realistic experiments emulated via probabilistic deep-learning models. Olympus includes a collection of experimentally derived benchmark sets from chemistry and materials science and a suite of experiment planning strategies that can be easily accessed via a user-friendly Python interface. Furthermore, Olympus facilitates the integration, testing, and sharing of custom algorithms and user-defined datasets. In brief, Olympus mitigates the barriers associated with benchmarking optimization algorithms on realistic experimental scenarios, promoting data sharing and the creation of a standard framework for evaluating the performance of experiment planning strategies.
The Wentzel-Kramers-Brillouin approximation for light scattering by horizontally oriented prismatic particles
Authors: Tari E M , Bahaoui A , Lamsoudi R , Khouilid M , Ibnchaikh M 
Published: March 2021

Abstract
In this research, we propose a simple approximation technique based on the decomposition of particles and on the Wentzel-Kramers-Brillouin approximation (WKB). The latter allows us to express analytically the expression of the form factor of a particle of a regular prismatic ice crystal shape. Our focus will be on studying the light scattering by horizontally oriented prismatic particles which rotate about their principal axes. To illustrate our formalism, a few numerical examples will be analyzed.
Severe brachial plexopathy secondary to shingles (herpes zoster)
Authors: McFeely Aoife , Doyle Rachael , O’Riordan Sean , Connolly Sean , O’Dwyer Clodagh 
Published: March 2021

Abstract
Varicella zoster reactivation (“shingles” or “herpes zoster”) usually presents as a self-limiting, unilateral, dermatomal vesicular rash in older adults. We present the case of a 73 year-old woman with unilateral brachial plexopathy, an unusual but debilitating complication of shingles. Despite treatment with intravenous acyclovir and immunoglobulin she had a marked residual motor paresis that required an upper limb rehabilitation program after discharge.
Retroperitoneal Dedifferentiated Liposarcoma
Authors: Dehner Carina A , Hagemann Ian S , Chrisinger John S A 
Published: March 2021

Abstract

Objectives
We aimed to test the hypothesis that in retroperitoneal dedifferentiated liposarcoma (DDLS) the presence of the dedifferentiated (DD) component at the resection margin is associated with adverse outcome.

Methods
We retrospectively searched the archive for primary resections of retroperitoneal DDLS performed at our institution between 1990 and 2017. Slides were rereviewed for diagnosis, Fédération Nationale des Centres de Lutte Contre le Cancer grade, myogenic differentiation, and the presence of the well-differentiated (WD) or DD component at the resection margin. The medical records were reviewed for patient age, sex, tumor size, tumor focality, adjuvant/neoadjuvant therapy, local recurrence, distant metastases, local recurrence-free survival (LRFS), overall survival (OS), and follow-up duration.

Results
The presence of the DD component at the resection margin was associated with worse LRFS compared with cases without the DD component at the margin (P = .002). However, OS was not significantly affected (P = .11).

Conclusions
LRFS is significantly shorter in cases with the DD component at the margin compared with cases without DD tumor at the margin, while there is no association with OS. We recommend reporting the presence or absence of DD tumor at the margin in retroperitoneal DDLS, as it adds meaningful prognostic information.
Associations of Binge Drinking With the Risks of Ischemic Heart Disease and Stroke: A Study of Pooled Norwegian Health Surveys
Authors: Degerud Eirik , Høiseth Gudrun , Mørland Jørg , Ariansen Inger , Graff-Iversen Sidsel , Ystrom Eivind , Zuccolo Luisa , Tell Grethe S , Næss Øyvind 
Published: March 2021

Abstract
Norwegian health survey data (1987–2003) were analyzed to determine if binge drinking increases the risk of incident major events from ischemic heart disease (IHD) and stroke. Among current drinkers reporting average alcohol intakes of 2.00–59.99 g/day (n = 44,476), frequent binge drinking (≥5 units at least once per month) was not associated with a greater risk of IHD (adjusted hazard ratio (HR) = 0.91, 95% confidence interval (CI): 0.76, 1.09) or stroke (adjusted HR = 0.98, 95% CI: 0.81, 1.19), in comparison with participants who reported that they never or only infrequently (less than once per month) had episodes of binge drinking. Participants with an average alcohol intake of 2.00–59.99 g/day had a lower risk of IHD in comparison with participants with very low intakes (&lt;2.00 g/day), both among frequent binge drinkers (adjusted HR = 0.67, 95% CI: 0.56, 0.80) and among never/infrequent binge drinkers (adjusted HR = 0.75, 95% CI: 0.67, 0.84). The findings suggest that frequent binge drinking, independent of average alcohol intake, does not increase the risk of incident IHD or stroke events. However, the findings should be interpreted in light of the limitations of the study design.
Synthesis of a plasmenylethanolamine
Authors: Maeda Satoshi , Mohri Tomoyo , Inoue Tsubasa , Asano Yoshio , Otoki Yurika , Enomoto Masaru , Nakagawa Kiyotaka , Kuwahara Shigefumi , Ogura Yusuke 
Published: March 2021

ABSTRACTA concise synthesis of a plasmenylethanolamine (PlsEtn-[16:0/18:1 n-9]), known as antioxidative phospholipids commonly found in cell membranes, has been achieved from an optically active known diol through 8 steps. The key transformations for the synthesis of PlsEtn-[16:0/18:1 n-9] are (1) regio- and Z-selective vinyl ether formation via the alkylation of a lithioalkoxy allyl intermediate with an alkyl iodide, and (2) a one-pot phosphite esterification–oxidation sequence to construct the ethanolamine phosphonate moiety in the presence of the vinyl ether functionality. The piperidine salt of synthetic PlsEtn-[16:0/18:1 n-9] was desalinated through reversed-phase high-performance liquid chromatography purification.
Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance
Authors: Chen Kexin , Xu Haoming , Lei Yiming , Lio Pietro , Li Yuan , Guo Hongyan , Ali Moni Mohammad 
Published: March 2021

Abstract
Although chemotherapy is the first-line treatment for ovarian cancer (OCa) patients, chemoresistance (CR) decreases their progression-free survival. This paper investigates the genetic interaction (GI) related to OCa-CR. To decrease the complexity of establishing gene networks, individual signature genes related to OCa-CR are identified using a gradient boosting decision tree algorithm. Additionally, the genetic interaction coefficient (GIC) is proposed to measure the correlation of two signature genes quantitatively and explain their joint influence on OCa-CR. Gene pair that possesses high GIC is identified as signature pair. A total of 24 signature gene pairs are selected that include 10 individual signature genes and the influence of signature gene pairs on OCa-CR is explored. Finally, a signature gene pair-based prediction of OCa-CR is identified. The area under curve (AUC) is a widely used performance measure for machine learning prediction. The AUC of signature gene pair reaches 0.9658, whereas the AUC of individual signature gene-based prediction is 0.6823 only. The identified signature gene pairs not only build an efficient GI network of OCa-CR but also provide an interesting way for OCa-CR prediction. This improvement shows that our proposed method is a useful tool to investigate GI related to OCa-CR.
Network-based modeling of herb combinations in traditional Chinese medicine
Authors: Wang Yinyin , Yang Hongbin , Chen Linxiao , Jafari Mohieddin , Tang Jing 
Published: March 2021

Abstract
Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein–protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.
FrustratometeR: an R-package to compute local frustration in protein structures, point mutants and MD simulations
Authors: Rausch Atilio O , Freiberger Maria I , Leonetti Cesar O , Luna Diego M , Radusky Leandro G , Wolynes Peter G , Ferreiro Diego U , Parra R Gonzalo 
Published: March 2021

Abstract

Summary
Once folded, natural protein molecules have few energetic conflicts within their polypeptide chains. Many protein structures do however contain regions where energetic conflicts remain after folding, i.e. they are highly frustrated. These regions, kept in place over evolutionary and physiological timescales, are related to several functional aspects of natural proteins such as protein–protein interactions, small ligand recognition, catalytic sites and allostery. Here, we present FrustratometeR, an R package that easily computes local energetic frustration on a personal computer or a cluster. This package facilitates large scale analysis of local frustration, point mutants and molecular dynamics (MD) trajectories, allowing straightforward integration of local frustration analysis into pipelines for protein structural analysis.

Availability and implementation
https://github.com/proteinphysiologylab/frustratometeR.

Supplementary information
Supplementary data are available at Bioinformatics online.
Igf3: a novel player in fish reproduction
Authors: Li Jianzhen , Liu Zhiquan , Kang Tao , Li Minghui , Wang Deshou , Cheng Christopher H K 
Published: March 2021

AbstractAs in other vertebrates, fish reproduction is tightly controlled by gonadotropin signaling. One of the most perplexing aspects of gonadotropin action on germ cell biology is the restricted expression of gonadotropin receptors in somatic cells of the gonads. Therefore, the identification of factors conveying the action of gonadotropins on germ cells is particularly important for understanding the mechanism of reproduction. Insulin-like growth factors (Igfs) are recognized as key factors in regulating reproduction by triggering a series of physiological processes in vertebrates. Recently, a novel member of Igfs called Igf3 has been identified in teleost. Different from the conventional Igf1 and Igf2 that are ubiquitously expressed in a majority of tissues, Igf3 is solely or highly expressed in the fish gonads. The role of Igf3 in mediating the action of gonadotropin through Igf type 1 receptor on several aspects of oogenesis and spermatogenesis have been demonstrated in several fish species. In this review, we will summarize existing data on Igf3. This new information obtained from Igf3 provides insight into elucidating the molecular mechanism of fish reproduction, and also highlights the importance of Igf system in mediating the action of gonadotropin signaling on animal reproduction.
Anatomical and cellular heterogeneity in the mouse oviduct—its potential roles in reproduction and preimplantation development
Authors: Harwalkar Keerthana , Ford Matthew J , Teng Katie , Yamanaka Nobuko , Yang Brenna , Burtscher Ingo , Lickert Heiko , Yamanaka Yojiro 
Published: March 2021

AbstractThe oviduct/fallopian tube is a tube-like structure that extends from the uterus to the ovary. It is an essential reproductive organ that provides an environment for internal fertilization and preimplantation development. However, our knowledge of its regional and cellular heterogeneity is still limited. Here, we examined the anatomical complexity of mouse oviducts using modern imaging techniques and fluorescence reporter lines. We found that there are consistent coiling patterns and turning points in the coiled mouse oviduct that serve as reliable landmarks for luminal morphological regionalities. We also found previously unrecognized anatomical structures in the isthmus and uterotubal junction, which likely play roles in reproduction. Furthermore, we demarcated the ampulla–isthmus junction as a distinct region. Taken together, the oviduct mucosal epithelium has highly diverse structures with distinct epithelial cell populations, reflecting its complex functions in reproduction.
GABAergic cortical network physiology in frontotemporal lobar degeneration
Authors: Adams Natalie E , Hughes Laura E , Rouse Matthew A , Phillips Holly N , Shaw Alexander D , Murley Alexander G , Cope Thomas E , Bevan-Jones W Richard , Passamonti Luca , Street Duncan , Holland Negin , Nesbitt David , Friston Karl , Rowe James B 
Published: March 2021

Abstract
The clinical syndromes caused by frontotemporal lobar degeneration are heterogeneous, including the behavioural variant frontotemporal dementia (bvFTD) and progressive supranuclear palsy. Although pathologically distinct, they share many behavioural, cognitive and physiological features, which may in part arise from common deficits of major neurotransmitters such as γ-aminobutyric acid (GABA). Here, we quantify the GABAergic impairment and its restoration with dynamic causal modelling of a double-blind placebo-controlled crossover pharmaco-magnetoencephalography study. We analysed 17 patients with bvFTD, 15 patients with progressive supranuclear palsy, and 20 healthy age- and gender-matched controls. In addition to neuropsychological assessment and structural MRI, participants undertook two magnetoencephalography sessions using a roving auditory oddball paradigm: once on placebo and once on 10 mg of the oral GABA reuptake inhibitor tiagabine. A subgroup underwent ultrahigh-field magnetic resonance spectroscopy measurement of GABA concentration, which was reduced among patients. We identified deficits in frontotemporal processing using conductance-based biophysical models of local and global neuronal networks. The clinical relevance of this physiological deficit is indicated by the correlation between top-down connectivity from frontal to temporal cortex and clinical measures of cognitive and behavioural change. A critical validation of the biophysical modelling approach was evidence from parametric empirical Bayes analysis that GABA levels in patients, measured by spectroscopy, were related to posterior estimates of patients’ GABAergic synaptic connectivity. Further evidence for the role of GABA in frontotemporal lobar degeneration came from confirmation that the effects of tiagabine on local circuits depended not only on participant group, but also on individual baseline GABA levels. Specifically, the phasic inhibition of deep cortico-cortical pyramidal neurons following tiagabine, but not placebo, was a function of GABA concentration. The study provides proof-of-concept for the potential of dynamic causal modelling to elucidate mechanisms of human neurodegenerative disease, and explains the variation in response to candidate therapies among patients. The laminar- and neurotransmitter-specific features of the modelling framework, can be used to study other treatment approaches and disorders. In the context of frontotemporal lobar degeneration, we suggest that neurophysiological restoration in selected patients, by targeting neurotransmitter deficits, could be used to bridge between clinical and preclinical models of disease, and inform the personalized selection of drugs and stratification of patients for future clinical trials.
The role of noradrenaline in cognition and cognitive disorders
Authors: Holland Negin , Robbins Trevor W , Rowe James B 
Published: March 2021

Abstract
Many aspects of cognition and behaviour are regulated by noradrenergic projections to the forebrain originating from the locus coeruleus, acting through alpha and beta adrenoreceptors. Loss of these projections is common in neurodegenerative diseases and contributes to their cognitive and behavioural deficits. We review the evidence for a noradrenergic modulation of cognition in its contribution to Alzheimer’s disease, Parkinson’s disease and other cognitive disorders. We discuss the advances in human imaging and computational methods that quantify the locus coeruleus and its function in humans, and highlight the potential for new noradrenergic treatment strategies.
Conventional generation emulation for power grids with a high penetration of wind power
Authors: El-Azab Rasha , Wazeer Eslam M , Daowd Mohamed , Abdel Ghany A M 
Published: March 2021

Abstract
Integrating large-scale wind plants with the electricity grids has many challenges for grid operators. Besides the variability and uncertainty of wind power, coordinating between different technologies of generation in the same grid can be considered the main problem, specifically for short-term frequency stability. Therefore, a large penetration of wind power generation in modern power grids has a risky influence on the power-system frequency. Wind-generation plants have contradictory behaviour compared to classic thermal plants, especially in active generated power-shortage events due to the variable nature of wind power. Existing experience in wind plants keeps part of the available wind power unloaded, using what are known as deloading techniques. Different deloading techniques are usually applied to emulate the thermal-plant-governor function and confirm a proper spinning reserve for any active-power shortages. These techniques decrease the generated power from wind plants continuously from maximum point tracking ones. Consequently, the practical capacity, annual generated energy and economical income of wind plants are reduced. In addition, grid-protection and control sub-schemes are set and designed according to the well-known conventional responses of thermal plants, which increase the need for thermal-plant-behaviour emulation. In this paper, instead of the usual deloading methods, a supercapacitors scheme is proposed with wind turbines to emulate the response of conventional power plants. The study discusses the technical and economic benefits of the proposed addition of supercapacitors in the wind-plant-planning phase. Restricted frequency grid-code indices are selected to evaluate studied behaviours. Simulation results of the IEEE four-generation two-area system determines the effectiveness of suggested schemes technically. The System Advisor Model (SAM) program estimates the economic benefits of a typical US study case compared with the existing wind-deloading technique.
New aspects of endocrine control of atrial fibrillation and possibilities for clinical translation
Authors: Aguilar Martin , Rose Robert A , Takawale Abhijit , Nattel Stanley , Reilly Svetlana 
Published: March 2021

AbstractHormones are potent endo-, para-, and autocrine endogenous regulators of the function of multiple organs, including the heart. Endocrine dysfunction promotes a number of cardiovascular diseases, including atrial fibrillation (AF). While the heart is a target for endocrine regulation, it is also an active endocrine organ itself, secreting a number of important bioactive hormones that convey significant endocrine effects, but also through para-/autocrine actions, actively participate in cardiac self-regulation. The hormones regulating heart-function work in concert to support myocardial performance. AF is a serious clinical problem associated with increased morbidity and mortality, mainly due to stroke and heart failure. Current therapies for AF remain inadequate. AF is characterized by altered atrial function and structure, including electrical and profibrotic remodelling in the atria and ventricles, which facilitates AF progression and hampers its treatment. Although features of this remodelling are well-established and its mechanisms are partly understood, important pathways pertinent to AF arrhythmogenesis are still unidentified. The discovery of these missing pathways has the potential to lead to therapeutic breakthroughs. Endocrine dysfunction is well-recognized to lead to AF. In this review, we discuss endocrine and cardiocrine signalling systems that directly, or as a consequence of an underlying cardiac pathology, contribute to AF pathogenesis. More specifically, we consider the roles of products from the hypothalamic-pituitary axis, the adrenal glands, adipose tissue, the renin–angiotensin system, atrial cardiomyocytes, and the thyroid gland in controlling atrial electrical and structural properties. The influence of endocrine/paracrine dysfunction on AF risk and mechanisms is evaluated and discussed. We focus on the most recent findings and reflect on the potential of translating them into clinical application.
Quantifying the mortality impact of the 1935 old-age assistance
Authors: Galofré-Vilà Gregori , McKee Martin , Stuckler David 
Published: March 2021

Abstract
In 1935, the United States introduced the old-age assistance (OAA) program, a means-tested program to help the elderly poor. The OAA improved retirement conditions and aimed to enable older persons to live independently. We use the transition from early elderly plans to OAA and the large differences in payments and eligibility across states to show that OAA reduced mortality by between 30 and 39 percent among those older than 65 years. This finding, based on an event study design, is robust to a range of specifications, a range of fixed effects, placebo tests, and a border-pair policy discontinuity design using county-level data. The largest mortality reductions came from drops in communicable and infectious diseases, such as influenza and nephritis, and mostly affected white citizens.