bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast excitation fluctuation transfer between two membranes based on transitionless quantum driving
Authors: Liu Wen-Wu , Zhang Chun-Ling 
Published: January 2022

Abstract
In this paper, we introduce a feasible scheme for implementing excitation fluctuation transfer between two membranes in a cavity optomechanical system. The transitionless tracking algorithm allows the system to evolve along a single path, and the process is sped up. Numerical simulations are shown to indicate that, compared with the schemes based on conventional adiabatic passage and Lewis–Riesenfeld invariants, the proposed scheme not only shortens the evolution time but also significantly decreases the negative effects of dissipation arising from membrane damping and cavity decay within specified bounds. This work provides a new idea for quantum state transfer between two membranes.
Eco-hydrological responses to recent droughts in tropical South America
Authors: Jiang Yelin , Yang Meijian , Liu Weiguang , Mohammadi Koushan , Wang Guiling 
Published: January 2022

Abstract
This study assesses the ecohydrological effects of recent meteorological droughts in tropical South America based on multiple sources of data, and investigates the possible mechanisms underlying the drought response and recovery of different ecohydrological systems. Soil drought response and recovery lag behind the meteorological drought, with delays longer in the dry region (Nordeste) than in the wet region (Amazonia), and longer in deep soil than in shallow soil. Evapotranspiration (ET) and vegetation in Nordeste are limited by water under normal conditions and decrease promptly in response to the onset of shallow soil drought. In most of the Amazon where water is normally abundant, ET and vegetation indices follow an increase-then-decrease pattern, increase at the drought onset due to increased sunshine and decrease when the drought is severe enough to cause a shift from an energy-limited regime to a water-limited regime. After the demise of meteorological droughts, ET and vegetation rapidly recover in Nordeste with the replenishment of shallow soil moisture (SM), but take longer to recover in southern Amazon due to their dependence on deep SM storage. Following severe droughts, the negative anomalies of ET and vegetation indices in southern Amazon tend to persist well beyond the end of soil drought, indicating drought-induced forest mortality that is slow to recover from. Findings from this study may have implications on the possibility of a future forest dieback as drought is projected to become more frequent and more severe in a warmer climate.
Bioinspired design proposal for a new external bone fixator device
Authors: Buso Carla , Zanini Plínio , Titotto Silvia 
Published: January 2022

Abstract
The article presents a new medical device through an authorial and interdisciplinary approach. It consists of a flexible external fixator, whose flexible property may bring advantages over rigid mechanisms. Its design was inspired by the DNA biological mechanism of condensation, while the modeling was based on the pseudo-rigid modeling technique. From the models obtained, this study conducted prototyping and computational tests to obtain a proof-of-concept of the bioinspired theory and dynamic functioning effectiveness. The prototyping relied on hot glue manufacturing and the computational simulations consisted of linear static analysis. The experimental analysis concluded that the prototype with fewer beams and thinner beams delivered better results in all three parameters: flexibility, height variation and rotation arc. In the computational analysis, among the design models with the variation of the number of beams, the model with 8 beams performed better. Concerning thickness variation, the one whose beams measured 8 mm in thickness showed better results. Among the models with length variation, the design made with 100 mm long beams better equilibrated the parameters.
FUNKI: interactive functional footprint-based analysis of omics data
Authors: Hernansaiz-Ballesteros Rosa , Holland Christian H , Dugourd Aurelien , Saez-Rodriguez Julio 
Published: January 2022

Abstract

Motivation
Omics data are broadly used to get a snapshot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription factors and kinases based on known regulated targets, that we call footprints. Then the molecular paths driving these activities can be estimated using causal reasoning on large signalling networks.

Results
We have developed FUNKI, a FUNctional toolKIt for footprint analysis. It provides a user-friendly interface for an easy and fast analysis of transcriptomics, phosphoproteomics and metabolomics data, either from bulk or single-cell experiments. FUNKI also features different options to visualize the results and run post-analyses, and is mirrored as a scripted version in R.

Availability and implementation
FUNKI is a free and open-source application built on R and Shiny, available at https://github.com/saezlab/ShinyFUNKI and https://saezlab.shinyapps.io/funki/.

Supplementary information
Supplementary data are available at Bioinformatics online.
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers
Authors: Roy Raj S , Quadir Farhan , Soltanikazemi Elham , Cheng Jianlin 
Published: January 2022

Abstract

Motivation
Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue–residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue–residue contacts in homodimers from residue–residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue–residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features.

Results
Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset and CASP-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.10% and 33.50% respectively at 6 Å contact threshold, which is substantially better than DeepHomo and DNCON2_inter and similar to Glinter. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs well, even though its accuracy is lower than using true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers.

Availability and implementation
The source code of DRCon is available at https://github.com/jianlin-cheng/DRCon. The datasets are available at https://zenodo.org/record/5998532#.YgF70vXMKsB.

Supplementary information
Supplementary data are available at Bioinformatics online.
A decrease in cluster of differentiation 2 expression on natural killer cells is associated with polycystic ovary syndrome but not influenced by metformin in a mouse model
Authors: Czika Armin , Yang Yin , Yang Jun-Pu , Adu-Gyamfi Enoch Appiah , Ullah Amin , Ruan Ling-Ling , Chen Xue-Mei , Wang Ying-Xiong , Wang Mei-Jiao , Ding Yu-Bin 
Published: January 2022

Abstract

Problem
Natural killer (NK) cells from the peripheral blood and spleen represent the source from which various tissues replenish their immune cell populations. Hyperandrogenism and high interleukin-2 (IL-2) levels are factors present in polycystic ovary syndrome (PCOS). These factors and metformin, one of the commonest medications used in treating PCOS, may have an impact on NK cells. However, this is presently unknown. Here, we aimed to assess the distribution of peripheral blood and splenic NK cells and their CD2 and CD94 expression patterns in a PCOS mouse model and test whether metformin could reverse these effects.

Method of study
Four mouse groups were designed as follows (n = 15/group): control, PCOS, PCOS plus vehicle, PCOS plus metformin. Dehydroepiandrosterone and a high-fat diet were administered to induce the PCOS mouse model. Flow cytometry was used to analyze the expressions of CD2 and CD94 on peripheral blood and splenic NK cells.

Results
PCOS mice had a low surface-density of CD2 on peripheral blood NK cells and a decreased percentage of CD2+ splenic NK cells. Metformin administration did not significantly influence these changes; however, it reduced the splenic NK cell counts.

Conclusions
Our findings proved the association of PCOS with an altered expression of CD2 on peripheral blood and splenic NK cells and that of metformin with a lowered splenic NK cell reserve in PCOS conditions. These findings could further unlock key mechanisms in PCOS pathophysiology and in the mechanism of action of metformin, towards improving PCOS management.
Efficient semiparametric estimation of network treatment effects under partial interference
Authors: Park C , Kang H 
Published: January 2022

Summary
Although many estimators for network treatment effects have been proposed, their optimality properties, in terms of semiparametric efficiency, have yet to be resolved. We present a simple yet flexible asymptotic framework for deriving the efficient influence function and the semiparametric efficiency lower bound for a family of network causal effects under partial interference. An important corollary of our results is that one existing estimator, that proposed by Liu et al. (2019), is locally efficient. We also present other estimators that are efficient and discuss results on adaptive estimation. We illustrate application of the efficient estimators in a study of the direct and spillover effects of conditional cash transfer programmes in Colombia.
Two-stage linked component analysis for joint decomposition of multiple biologically related data sets
Authors: Chen Huan , Caffo Brian , Stein-O’Brien Genevieve , Liu Jinrui , Langmead Ben , Colantuoni Carlo , Xiao Luo 
Published: January 2022

SUMMARYIntegrative analysis of multiple data sets has the potential of fully leveraging the vast amount of high throughput biological data being generated. In particular such analysis will be powerful in making inference from publicly available collections of genetic, transcriptomic and epigenetic data sets which are designed to study shared biological processes, but which vary in their target measurements, biological variation, unwanted noise, and batch variation. Thus, methods that enable the joint analysis of multiple data sets are needed to gain insights into shared biological processes that would otherwise be hidden by unwanted intra-data set variation. Here, we propose a method called two-stage linked component analysis (2s-LCA) to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition. The consistency of the proposed method is established and its empirical performance is evaluated via simulation studies. We apply 2s-LCA to jointly analyze four data sets focused on human brain development and identify meaningful patterns of gene expression in human neurogenesis that have shared structure across these data sets.
Biomarkers and Clinical Laboratory Detection of Acute and Chronic Ethanol Use
Authors: Tawiah Kwaku D , Riley Sarah B , Budelier Melissa M 
Published: January 2022

Abstract

Background
Ethanol use can lead to many health and socio-economic problems. Early identification of risky drinking behaviors helps provide timely clinical and social interventions. Laboratory testing of biomarkers of ethanol use supports the timely identification of individuals with risky drinking behaviors. This review provides an overview of the utility and limitations of ethanol biomarkers in the clinical laboratory.

Content
Direct assessment of ethanol in tissues and body fluids has limited utility due to the pharmacokinetics of ethanol. Therefore, the evaluation of ethanol use relies on nonvolatile metabolites of ethanol (direct biomarkers) and measurement of the physiological response to the toxic metabolites of ethanol (indirect biomarkers). Ethanol biomarkers help monitor both chronic and acute ethanol use. The points discussed here include the clinical utility of ethanol biomarkers, testing modalities used for laboratory assessment, the specimens of choice, limitations, and clinical interpretation of results. Finally, we discuss the ethical principles that should guide physicians and laboratorians when using these tests to evaluate alcohol use.

Summary
Indirect biomarkers such as carbohydrate-deficient transferrin, mean corpuscular volume, and liver enzymes activities may suggest heavy ethanol use. They lack sensitivity and specificity for timely detection of risky drinking behavior and have limited utility for acute ethanol use. Direct biomarkers such as ethyl glucuronide, ethyl sulfate, and phosphatidylethanol are considered sensitive and specific for detecting acute and chronic ethanol use. However, laboratory assessment and result interpretation lack standardization, limiting clinical utility. Ethical principles including respect for persons, beneficence, and justice should guide testing.
Survival of patients undergoing cardiac resynchronization therapy with or without defibrillator: the RESET-CRT project
Authors: Hadwiger Moritz , Dagres Nikolaos , Haug Janina , Wolf Michael , Marschall Ursula , Tijssen Jan , Katalinic Alexander , Frielitz Fabian Simon , Hindricks Gerhard 
Published: January 2022

Abstract

Aims
Cardiac resynchronization therapy (CRT) is an established treatment for heart failure. There is contradictory evidence whether defibrillator capability improves prognosis in patients receiving CRT. We compared the survival of patients undergoing de novo implantation of a CRT with defibrillator (CRT-D) option and CRT with pacemaker (CRT-P) in a large health claims database.

Methods and results
Using health claims data of a major German statutory health insurance, we analysed patients with de novo CRT implantation from 2014 to 2019 without indication for defibrillator implantation for secondary prevention of sudden cardiac death. We performed age-adjusted Cox proportional hazard regression and entropy balancing to calculate weights to control for baseline imbalances. The analysis comprised 847 CRT-P and 2722 CRT-D patients. Overall, 714 deaths were recorded during a median follow-up of 2.35 years. A higher cumulative incidence of all-cause death was observed in the initial unadjusted Kaplan–Meier time-to-event analysis [hazard ratio (HR): 1.63, 95% confidence interval (CI): 1.38–1.92]. After adjustment for age, HR was 1.13 (95% CI: 0.95–1.35) and after entropy balancing 0.99 (95% CI: 0.81–1.20). No survival differences were found in different age groups. The results were robust in sensitivity analyses.

Conclusion
In a large health claims database of CRT implantations performed in a contemporary setting, CRT-P treatment was not associated with inferior survival compared with CRT-D. Age differences accounted for the greatest part of the survival difference that was observed in the initial unadjusted analysis.
Estimation of recurrent atherosclerotic cardiovascular event risk in patients with established cardiovascular disease: the updated SMART2 algorithm
Authors: Hageman Steven H J , McKay Ailsa J , Ueda Peter , Gunn Laura H , Jernberg Tomas , Hagström Emil , Bhatt Deepak L , Steg Ph. Gabriel , Läll Kristi , Mägi Reedik , Gynnild Mari Nordbø , Ellekjær Hanne , Saltvedt Ingvild , Tuñón José , Mahíllo Ignacio , Aceña Álvaro , Kaminski Karol , Chlabicz Malgorzata , Sawicka Emilia , Tillman Taavi , McEvoy John W , Di Angelantonio Emanuele , Graham Ian , De Bacquer Dirk , Ray Kausik K , Dorresteijn Jannick A N , Visseren Frank L J 
Published: January 2022

Abstract

Aims
The 10-year risk of recurrent atherosclerotic cardiovascular disease (ASCVD) events in patients with established ASCVD can be estimated with the Secondary Manifestations of ARTerial disease (SMART) risk score, and may help refine clinical management. To broaden generalizability across regions, we updated the existing tool (SMART2 risk score) and recalibrated it with regional incidence rates and assessed its performance in external populations.

Methods and results
Individuals with coronary artery disease, cerebrovascular disease, peripheral artery disease, or abdominal aortic aneurysms were included from the Utrecht Cardiovascular Cohort-SMART cohort [n = 8355; 1706 ASCVD events during a median follow-up of 8.2 years (interquartile range 4.2–12.5)] to derive a 10-year risk prediction model for recurrent ASCVD events (non-fatal myocardial infarction, non-fatal stroke, or cardiovascular mortality) using a Fine and Gray competing risk-adjusted model. The model was recalibrated to four regions across Europe, and to Asia (excluding Japan), Japan, Australia, North America, and Latin America using contemporary cohort data from each target region. External validation used data from seven cohorts [Clinical Practice Research Datalink, SWEDEHEART, the international REduction of Atherothrombosis for Continued Health (REACH) Registry, Estonian Biobank, Spanish Biomarkers in Acute Coronary Syndrome and Biomarkers in Acute Myocardial Infarction (BACS/BAMI), the Norwegian COgnitive Impairment After STroke, and Bialystok PLUS/Polaspire] and included 369 044 individuals with established ASCVD of whom 62 807 experienced an ASCVD event. C-statistics ranged from 0.605 [95% confidence interval (CI) 0.547–0.664] in BACS/BAMI to 0.772 (95% CI 0.659–0.886) in REACH Europe high-risk region. The clinical utility of the model was demonstrated across a range of clinically relevant treatment thresholds for intensified treatment options.

Conclusion
The SMART2 risk score provides an updated, validated tool for the prediction of recurrent ASCVD events in patients with established ASCVD across European and non-European populations. The use of this tool could allow for a more personalized approach to secondary prevention based upon quantitative rather than qualitative estimates of residual risk.
Religious Regulation Meets International Trade Law: Halal Measures, a Trade Obstacle? Evidence from the SPS and TBT Committees
Authors: Johan Eva , Schebesta Hanna 
Published: January 2022

ABSTRACT
The article studies the intersection of religious regulation and trade law. Specifically, it provides evidence about whether, when, and how domestic Halal measures are regarded as trade obstacles under World Trade Organization law. We conduct a systematic content analysis of Halal measures as a trade concern in the work of the Sanitary and Phytosanitary Measures and the Technical Barriers to Trade Committees, by analysing notifications of domestic Halal measures and Specific Trade Concerns raised. On this basis, we identify the five most pressing trade concerns relating to Halal measures in International Economic Law.
Naturalism, Disease, and Levels of Functional Description
Authors: Varga Somogy , Gray David Miguel 
Published: January 2022

AbstractThe paper engages Christopher Boorse’s Bio-Statistical Theory (BST). In its current form, BST runs into a significant challenge. For BST to account for its central tenet—that lower-level part-dysfunction is sufficient for higher-level pathology—it must provide criteria for how to decide which lower-level parts are the ones to be analyzed for health or pathology. As BST is a naturalistic theory, such choices must be based solely on naturalistic considerations. An argument is provided to show that, if BST is to be preserved, such parthood choices are based on non-naturalistic considerations. We demonstrate that even when parthood choices are based on the best way to preserve BST, there are counterintuitive results which bring the central tenet of BST into question.
Marketing Communications and the Digital Single Market
Authors: Goanta Catalina , Louisse Marije , Ortolani Pietro 
Published: January 2022

Abstract
This chapter studies marketing communications and the Digital Single Market. The regulation of online crowdfunding advertisement is particularly challenging for two interrelated reasons. First, it plays a key role in the protection of weaker parties (such as non-professional investors), both at the national and EU level. Second, this phenomenon highlights the rising regulatory role of web platforms (such as social media networks) which enable and moderate advertisement. The chapter analyses these challenges and the relevance of Articles 27 and 28 of the Crowdfunding Regulation. Articles 27 and 28 are applicable not only to the crowdfunding service providers’ advertisement aimed at investors, but also to communications of CSPs towards project owners.
Declarations of War and Neutrality
Authors: Clapham Andrew 
Published: January 2022

Abstract
This chapter looks at the institution of a Declaration of War and the rights and obligations associated with neutrality. Declarations of War, and the question of who is entitled to make them, remain significant in some circumstances. In particular they create expectations that other states may choose to declare their Neutral Status. The chapter separates out formal Neutral Status from non-belligerency and the rights and obligations that attach to such non-participating states. It is argued that while some rights and obligations apply to all non-participating states, the older rights and obligations applicable to Neutral Status only apply where a state expressing an explicit intention to acquire Neutral Status under international law. Switzerland’s particular permanent neutrality is examined and explained in the context of conflicts such as the conflicts in the Gulf in 1991 and 2003 and with regard to UN authorized use of force. The rights of a belligerent towards neutral shipping on the high seas and in the context of blockade are touched on but dealt with in more detail in Chapter 8. It is suggested that there should no longer be any international law Belligerent Right to attack or seize neutral shipping or goods in the context of breach of blockade.
Outlawing War
Authors: Clapham Andrew 
Published: January 2022

Abstract
This Chapter looks at justifications for war that were given to right wrongs and recover debts, restore honour, dignity or equilibrium, or simply as part of a right of self-preservation. It details how Germany and Great Britain, joined by Italy, decided to take coercive measures against Venezuela for unpaid debts in 1902. The chapter covers the attempt to outlaw the use of force through a multilateral treaty: the Kellogg-Briand Pact or Pact of Paris 1928. There is also a detailed look at the discussions at the League of Nations over whether the military action by Italy and Japan were Wars or something else. The emergence of the rule that territory cannot be seized by force is examined and related to the parallel rule that prohibits recognition of any such claimed acquisition of territory.
Triggering the International Law of Armed Conflict
Authors: Clapham Andrew 
Published: January 2022

Abstract
This chapter deals with thresholds which must be met before the law of armed conflict applies. This law of armed conflict (also known as international humanitarian law) is often known as the jus in bello. It applies whether or not the conflict is accepted as having given rise to a State of War. The chapter highlights the different situations where the international law of armed conflict applies and how this affects the regimes which can be used to prosecute war crimes.