bluuebunny/crossref_metadata_2025 huggingface dataset:
ENSO teleconnections and atmospheric mean state in idealised simulations
Authors: Di Carlo Emanuele , Ruggieri Paolo , Davini Paolo , Tibaldi Stefano , Corti Susanna
Published: April 2022

Understanding the natural and forced variability of the general circulation of the atmosphere and its drivers is one of the grand challenges in climate science. In particular, it is of paramount importance to understand to what extent the systematic error of global climate models affects the processes driving such variability. This is done by performing a set of simulations (ROCK experiments) with an intermediate complexity atmospheric model (SPEEDY), in which the Rocky Mountains orography is modified (increased or decreased) to influence the structure of the North Pacific jet stream. For each of these modified-orography experiments, the climatic response to idealized sea surface temperature (SST) anomalies of varying intensity in the El Niño Southern Oscillation (ENSO) region is studied. ROCK experiments are characterized by variations in the Pacific jet stream intensity whose extension encompasses the spread of the systematic error found in state-of-the-art climate models. When forced with ENSO-like idealised anomalies, they exhibit a non-negligible sensitivity in the response pattern over the Pacific North American region, indicating that a change/bias in the model mean state can affect the model response to ENSO. It is found that the classical Rossby wave train response generated by ENSO is more meridionally oriented when the Pacific jet stream is weaker, while it exhibits a more zonal structure when the jet is stronger. Rossby wave linear theory, used here to interpret the results, suggests that a stronger jet implies a stronger waveguide, which traps Rossby waves at a lower latitude, favouring a more zonally oriented propagation of the tropically induced Rossby waves. The shape of the dynamical response to ENSO, determined by changes in the intensity of the Pacific Jet, affects in turn the ENSO impacts on surface temperature and precipitation over Central and North America. Furthermore, a comparison of the SPEEDY results with CMIP6 models behaviour suggests a wider applicability of the results to more resources-demanding, complete climate GCMs, opening up to future works focusing on the relationship between Pacific jet misrepresentation and response to external forcing in fully-fledged GCMs.
Objective and Subjective Measurement of Cough in Asthma: A Systematic Review of the Literature
Authors: Holmes Joshua , Heaney Liam G. , McGarvey Lorcan P. A.
Published: April 2022

Background

The extent to which objective and subjective tools has been used to measure the characteristics and burden of cough in patients with asthma has not been reported.

Objective

To review the large and extensive body of literature in asthma with the specific hypothesis that the characteristics of cough and clinical impact in this disease has only occasionally been studied.

Methods

For this systematic review, we searched EMBASE and MEDLINE databases using a combination of MeSH terms for “cough” and “asthma” for studies published up to and including end of August 2021. Studies included for analysis were confined to those undertaken in adult patients (≥ 18 years) with asthma of any severity where any tool or method to specifically measure cough was employed.

Results

Of 12,090 citations identified after our initial search, 112 full-text articles met criteria for inclusion in our analysis. We found that a broad range of objective and subjective measures have been used albeit with a lack of consistency between studies. Clinically important levels of cough associated with impaired health status were identified in patients with asthma.

Conclusion

Although cough is a common symptom in asthma, the clinical features and accompanying healthcare burden have been studied infrequently. In studies where cough was measured, the methods employed varied considerably. A more consistent use of cough-specific measurement tools is required to better determine the nature and burden of cough in asthma.
Seeing others is believing – Analgetische Placeboeffekte durch Beobachtungslernen?
Authors: Schwartz Marie , Stuhlreyer J. , Klinger R.
Published: April 2022

Hintergrund

Es gibt viele Studien zur Placeboanalgesie und deren zugrundliegenden Wirkmechanismen, die eine Behandlung von Patient:innen mit chronischen Schmerzen signifikant verbessern können. Beobachtungslernen als ein Wirkmechanismus wurde hingegen noch wenig untersucht.

Fragestellung

Das Ziel der Arbeit ist es, einen Überblick über die aktuelle Forschungslage zu Placeboanalgesie durch Beobachtungslernen zu geben. Dabei soll geklärt werden, ob Beobachtungslernen überhaupt einen signifikanten Placeboeffekt auslösen kann und durch welche Faktoren dieses Lernen beeinflusst wird.

Material und Methoden

Dafür wurden die Forschungsdatenbanken nach Studien zur Placeboanalgesie durch Beobachtungslernen durchsucht.

Ergebnisse

Nach der Anwendung der Ein- und Ausschlusskriterien verblieben 12 Studien. Es gab nur eine Studie, die an Patient:innen mit chronischen Schmerzen durchgeführt wurde. Die geringe Anzahl an Studien lässt noch keine allgemeingültigen Aussagen zu, aber es gibt erste Hinweise für die folgenden Aussagen: Beobachtungslernen von Placeboeffekten ist unter Laborbedingungen möglich und eine Aufmerksamkeitslenkung ist wichtig. Die Effektstärken reichen von klein bis groß. Die Effekte von klassischer Konditionierung und Beobachtungslernen sind vergleichbar. Live-Modelle, Videoaufnahmen und Bilder lösen ähnliche Effekte aus. Beobachtungslernen führt zu einer Erwartungsänderung.

Diskussion

Die vorliegende Evidenz liefert die Grundlage dafür, dass theoretisch und auch praktisch klinisch signifikante Effekte möglich sind. Weitere Studien sind nötig, um diese Aussagen verlässlich auch auf chronische Schmerzpatient:innen zu beziehen.
Evaluation of centers for information and support combining formal and informal care for patients with cancer: a systematic review of the literature
Authors: Driessen Helen P. A. , Kranenburg Leonieke W. , van der Rijt Karin C. D. , Bakker Evi M. , van Busschbach Jan J. , Jabbarian Lea J. , Bramer Wichor M. , Elfrink Erna J.
Published: April 2022

Purpose

Clear information and supportive care are necessary for patients with cancer to effectively manage their condition. Traditionally, healthcare professionals offer information and support via the so-called formal care route. In addition, research has found favorable effects of informal care provided by volunteer programs and informal “walk-in support centers.” Less research has been done on initiatives that combine formal and complementary informal supportive care for patients with cancer. This systematic literature study aimed to discover (1) which types of initiatives are described in the literature, (2) what type of care they offer, and (3). how they are evaluated in terms of outcome measures.

Methods

We performed a systematic literature search of MEDLINE, Embase, PsycINFO, and CINAHL. Studies were included if the collaboration between one type of formal care together with one type of informal care was explicitly mentioned in the article. The search was not restricted to a specific cancer type.

Results

A total of 4869 records were retrieved and 18 studies were included. In most studies, the care provided consisted of emotional support for, and/or providing information to, patients and their families. Initiatives were evaluated with interviews and questionnaires. Patients with cancer reported that they were satisfied with the care offered, including information, social and emotional support, help with activities of daily living, and family-related issues. Volunteers reported that visits they made were experienced positive and rewarding and the volunteers were confident about their contribution to general healthcare. Some negative experiences were reported by volunteers, e.g., interference of their own cancer diagnosis with volunteer work. The importance of proper training was stressed.

Conclusions

Initiatives combining formal and informal supportive care hold the potential of added value in terms of providing emotional support for, and providing information to, patients with cancer. Support and specific training for volunteers can be viewed as success factors in the involvement of volunteers in formal care practices.
Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags
Authors: Stadler Karina A. , Becker Walter , Darnhofer Barbara , Birner-Gruenberger Ruth , Zangger Klaus
Published: April 2022

Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of 1H-15N and 19F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive 19F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed 19F-NMR.
Identification of potent HDAC 2 inhibitors using E-pharmacophore modelling, structure-based virtual screening and molecular dynamic simulation
Authors: Pai Padmini , Kumar Avinash , Shetty Manasa Gangadhar , Kini Suvarna Ganesh , Krishna Manoj Bhat , Satyamoorthy Kapaettu , Babitha Kampa Sundara
Published: April 2022

Histone deacetylase 2 (HDAC 2) of class I HDACs plays a major role in embryonic and neural developments. However, HDAC 2 overexpression triggers cell proliferation by diverse mechanisms in cancer. Over the decades, many pan and class-specific inhibitors of HDAC were discovered. Limitations such as toxicity and differential cell localization of each isoform led researchers to hypothesize that isoform selective inhibitors may be relevant to bring about desired effects. In this study, we have employed the PHASE module to develop an e-pharmacophore model and virtually screened four focused libraries of around 300,000 compounds to identify isoform selective HDAC 2 inhibitors. The compounds with phase fitness score greater than or equal to 2.4 were subjected to structure-based virtual screening with HDAC 2. Ten molecules with docking score greater than  -12 kcal/mol were chosen for selectivity study, QikProp module (ADME prediction) and dG/bind energy identification. Compound 1A with the best dock score of  -13.3 kcal/mol and compound 1I with highest free binding energy,  -70.93 kcal/mol, were selected for molecular dynamic simulation studies (40 ns simulation). The results indicated that compound 1I may be a potent and selective HDAC 2 inhibitor. Further, in vitro and in vivo studies are necessary to validate the potency of selected lead molecule and its derivatives.

Graphical abstract
Age-Restriction of a Validated Risk Scoring Tool Better Predicts HIV Acquisition in South African Women: CAPRISA 004
Authors: Castor Delivette , Burgess Emma K. , Yende-Zuma Nonhlanhla , Heck Craig J. , Abdool Karim Quarraisha
Published: April 2022

We examined the predictive ability of the VOICE risk screening tool among adolescent girls and young women at heightened HIV risk in urban and peri-urban Kwa-Zulu-Natal, South Africa. Using participant data from CAPRISA 004’s control arm (N = 444), we applied the initial VOICE risk screening score (IRS), a modified risk score (MRS) based on predictive and non-predictive variables in our data, and age-restricted (AIRS and AMRS, respectively). We estimated incidence rates, 95% confidence bounds, sensitivity, specificity, negative and positive predictive values and area under the curve (AUC). The sample’s HIV incidence rate was 9.1/100 Person-Years [95% CI 6.9–11.7], resulting from 60 seroconversions (60/660.7 Person-Years). The IRS’ ≥ 8 cutpoint produced moderate discrimination [AUC = 0.66 (0.54–0.74), sensitivity = 63%, specificity = 57%]. Restricting to age < 25 years improved the score’s predictive ability (AIRS: AUC = 0.69, AMRS: AUC = 0.70), owing mainly to male partner having other partners and HSV-2. The risk tool predicted HIV acquisition at a higher cutpoint in this sample than in the initial VOICE analysis. After age-stratification, fewer variables were needed for maintaining score’s predictiveness. In this high incidence setting, risk screening may still improve the efficiency or effectiveness of prevention counseling services. However, PrEP should be offered to all prevention-seeking individuals, regardless of risk ascertainment.
Measuring players’ importance in basketball using the generalized Shapley value
Authors: Metulini Rodolfo , Gnecco Giorgio
Published: April 2022

Measuring players’ importance in team sports to help coaches and staff with the aim of winning the game is gaining relevance, mainly because of the advent of new data and advanced technologies. In this paper we evaluate each player’s importance - for the first time in basketball - as his/her average marginal contribution to the utility of an ordered subset of players, through a generalized version of the Shapley value, where the value assumed by the generalized characteristic function of the generalized coalitional game is expressed in terms of the probability a certain lineup has to win the game. In turn, such probability is estimated by applying a logistic regression model in which the response is represented by the game outcome and the Dean’s factors are used as explanatory features. Then, we estimate the generalized Shapley values of the players, with associated bootstrap confidence intervals. A novelty, allowed by explicitly considering single lineups, is represented by the possibility of forming best lineups based on players’ estimated generalized Shapley values conditional on specific constraints, such as an injury or an “a-priori” coach’s decision. A comparison of our proposed approach with industry-standard counterparts shows a strong linear relation. We show the application of our proposed method to seventeen full NBA seasons (from 2004/2005 to 2020/21). We eventually estimate generalized Shapley values for Utah Jazz players and we show how our method is allowed to be used to form best lineups.
Stochastic dominance spanning and augmenting the human development index with institutional quality
Authors: Pinar Mehmet , Stengos Thanasis , Topaloglou Nikolas
Published: April 2022

The well-known Human Development Index (HDI) goes beyond a single measure of well-being as it is constructed as a composite index of achievements in education, income, and health dimensions. However, it is argued that the above dimensions do not reflect the overall well-being, and new indicators should be included in its construction. This paper uses stochastic dominance spanning to test the inclusion of additional institutional quality (governance) dimensions to the HDI, and we examine whether the augmentation of the original set of welfare dimensions by an additional component leads to distributional welfare gains or losses or neither. We find that differently constructed indicators of the same institutional quality measure produce different distributions of well-being.
Optimising small-scale electronic commerce supply chain operations: a dynamic cost-sharing contract approach
Authors: Rathnasiri Sahani , Ray Pritee , Vega-Mejía Carlos A. , Islam Sardar M. N. , Rana Nripendra P. , Dwivedi Yogesh K.
Published: April 2022

For small-scale electronic commerce supply chains, designing effective strategies to improve operational effectiveness, market share and long-term survival are essential aspects. However, researchers have given less attention in addressing these issues. This study proposes a dynamic cost-sharing contract for an e-tailer supply chain to address the issues of asymmetric information, long-term integration, and ineffective costs. We include consistency constraints to obtain stable incentives over time and eliminate the need for re-negotiation. The findings emphasise that the dynamic contract significantly reduces the overall supply chain costs. The consistency constraints guarantee high incentives, thus assuring the players remain in the total contract period and enable long-term integration.
Anticipatory scheduling of synchromodal transport using approximate dynamic programming
Authors: Rivera Arturo E. Pérez , Mes Martijn R. K.
Published: April 2022

We study the problem of scheduling container transport in synchromodal networks considering stochastic demand. In synchromodal networks, the transportation modes can be selected dynamically given the actual circumstances and performance is measured over the entire network and over time. We model this problem as a Markov Decision Process and propose a heuristic solution based on Approximate Dynamic Programming (ADP). Due to the multi-period nature of the problem, the one-step look-ahead perspective of the traditional approximate value-iteration approach can make the heuristic flounder and end in a local-optimum. To tackle this, we study the inclusion of Bayesian exploration using the Value of Perfect Information (VPI). In a series of numerical experiments, we show how VPI significantly improves a traditional ADP algorithm. Furthermore, we show how our proposed ADP–VPI combination achieves significant gains over common practice heuristics.
Inner-imaging 3D attention module for residual network
Authors: Liu Wenjie , Wu Guoqing , Ren Fuji , Shi Quan
Published: April 2022

We propose an Inner-Imaging three-dimensional (3D) attentional feature fusion module for a residual network, which is a simple yet effective approach for residual networks. In our attention module, we constructed a 3D soft attention feature map to refine the input feature. The map fuses the attentional features from different dimensions, including channel and spatial axes, to create a 3D attention map. Then, we implemented a feature fusion module to further fuse the attentional features. Lastly, the attention module outputs a 3D soft attention map that is applied to the residual branch. The attention module can also model the relationship between attentional features from different dimensions and achieve the interaction between attentional features. This function allows our attention module to acquire more attentional features. To demonstrate the effectiveness of our method, extensive experiments were conducted on several computer vision benchmark datasets, including ImageNet 2012 and Microsoft COCO (MS COCO) 2017 datasets. The experimental results show that our method performed better than the baseline methods in the tasks of image classification, object detection, and instance segmentation tasks.
Explaining predictions and attacks in federated learning via random forests
Authors: Haffar Rami , Sánchez David , Domingo-Ferrer Josep
Published: April 2022

Artificial intelligence (AI) is used for various purposes that are critical to human life. However, most state-of-the-art AI algorithms are black-box models, which means that humans cannot understand how such models make decisions. To forestall an algorithm-based authoritarian society, decisions based on machine learning ought to inspire trust by being explainable. For AI explainability to be practical, it must be feasible to obtain explanations systematically and automatically. A usual methodology to explain predictions made by a (black-box) deep learning model is to build a surrogate model based on a less difficult, more understandable decision algorithm. In this work, we focus on explaining by means of model surrogates the (mis)behavior of black-box models trained via federated learning. Federated learning is a decentralized machine learning technique that aggregates partial models trained by a set of peers on their own private data to obtain a global model. Due to its decentralized nature, federated learning offers some privacy protection to the participating peers. Nonetheless, it remains vulnerable to a variety of security attacks and even to sophisticated privacy attacks. To mitigate the effects of such attacks, we turn to the causes underlying misclassification by the federated model, which may indicate manipulations of the model. Our approach is to use random forests containing decision trees of restricted depth as surrogates of the federated black-box model. Then, we leverage decision trees in the forest to compute the importance of the features involved in the wrong predictions. We have applied our method to detect security and privacy attacks that malicious peers or the model manager may orchestrate in federated learning scenarios. Empirical results show that our method can detect attacks with high accuracy and, unlike other attack detection mechanisms, it can also explain the operation of such attacks at the peers’ side.
Method validation and risk assessment for sulfonamides and tetracyclines in bees’ honey from Egypt, Libya and Saudi Arabia
Authors: Ahmed Mohamed Bedair M. , Taha Amro Ahmed , Mehaya Fathy Mohamed Saber
Published: April 2022

Several studies worldwide have reported contamination of bees’ honey by antibiotics, which may pose a hazard to consumers’ health. The present study was thus established to: (1) introduce a validated multi-residue method for determining sulfonamides (SAs) and tetracyclines (TCs) in honey; and (2) characterize the potential risk due to the exposure to SAs and TCs in honey samples from Egypt, Libya, and Saudi Arabia. SAs and TCs were simultaneously extracted using solid-phase extraction and matrix solid phase dispersion methods. SAs and TCs were screened using HPLC–MS/MS and HPLC–DAD. The results confirmed detection limits for SAs and TCs by HPLC–MS/MS of 0.01 and 0.02–0.04 (ng g−1), respectively. The limits were 2.5–5.6 and 12.0–21.0 (ng g−1) for SAs and TCs by HPLC–DAD, respectively. The obtained accuracy rates were in the ranges of 83.07–86.93% and 86.90–91.19%, respectively, for SAs and TCs, with precision rates lower than 9.54%. Concerning the occurrence of antibiotics, the positive samples constituted 57.6%, 75%, and 77.7% of the Egyptian, Saudi Arabian, and Libyan samples, respectively. Notably, SAs antibiotics were the most prevalent in the Egyptian and Saudi Arabian samples; in contrast, TCs were the most dominant in Libya. Calculated parameters of risk assessment, concerning the aggregated exposure to SAs and TCs, showed no potential adverse effects from the exposure to contaminated honey in studied countries.
Last minute only bidding is implausible in eBay sealed bid type-of-auctions
Authors: Dimitri Nicola
Published: April 2022

In recent years internet auctions have attracted much attention. This paper discusses the "last minute bidding" (sniping) phenomenon, first investigated by Roth and Ockenfels (American Economic Review 92, 1093-1103) in eBay, fixed-end, auctions. Unlike standard auctions where each offer is processed by the auctioneer due to system traffic, and connection time, in eBay auctions very late bids may be left unprocessed. In the paper we consider a simple two-players, two-periods sealed-bid auction model, inspired by eBay auctions, with private values and complete information. The main difference with respect to e-Bay auctions is given by the first period. Indeed, players can submit at most one bid per period. In the first stage bids are processed with certainty by the system while in the second stage, with positive probability, bids may not be processed due to system congestion. Unlike eBay we show how in this model last minute, that is second stage only, bidding may have low plausibility, as it can be a Nash equilibrium only under very specific circumstances and is never a unique best reply. Intuitively this is because the first stage is sealed-bid, with at most one offer per bidder, and players have no guarantee that they could outbid the opponent in the second period, once after the first round they realise that their bid is not the best.
US National Banks and Local Economic Fragility
Authors: Calice Giovanni , Gam Yong Kyu
Published: April 2022

We examine the relationship between US national banks’ local market shares and the economic fragility of the counties in which they operate. We find that counties with national banks that have large local market shares experience a greater fluctuation in their income growth in the subsequent year. Further, an increase in income growth is more pronounced during normal times but declines significantly in a distressed market. We further find that the national banks create greater liquidity during normal times and lower liquidity in distressed times. Overall, our results indicate that national banks may expose local economies to macro-level distress.
The market for foreign cinema in contemporary Italy: a geography of film consumption
Authors: Avezzù Giorgio
Published: April 2022

The article aims at studying the geographical variability of theatrical consumption and popularity of contemporary films imported in Italy since the beginning of the XXI century. It relies on the data about regional admissions and theatrical distribution of more than 4100 titles, namely all the films with more than 15,000 admissions that had been projected in Italy from January 2000 to the pandemic outbreak in mid-February 2020, which forced the closure of all cinemas nationwide. While the regional patterns of distribution of both domestic and foreign films are always rather homogeneous and do not undergo major regional variations, Italian and non-Italian films are consumed in very different ways, geographically. When it comes to foreign cinema, a Regional Popularity Index shows how different regions and primarily wider trans-regional areas have different preferences linked to particular themes and genres. Different films are more or less popular in different areas, even regardless of any disparities in their distribution, precisely because they meet (or fail to meet) the specific tastes of macro-regional audiences. Specifically, the data consistently show a divide in taste between the northern-central audiences and their southern counterparts, which replicates the great distance that still divides the North from the South of Italy, from an economic, social and cultural point of view.
Catheter ablation of atrial fibrillation using 2nd-generation cryoballoon in congenital heart disease patients — significance of RF ablation of additional atrial macro-reentrant tachycardia
Authors: Krause Ulrich , Müller Matthias J. , Schneider Heike E. , Paul Thomas
Published: April 2022

Background

Prevalence of atrial fibrillation (AF) is increasing in adult patients with congenital heart disease (CHD). Experience using the cryoballoon to achieve pulmonary vein isolation (PVI) in adult CHD patients is limited. The aim of the present study was to assess the value of PVI by cryoballoon in adult CHD patients and to evaluate the significance of additional radiofrequency (RF) ablation of atrial tachycardia (AT).

Patients and methods

Prospective data analysis; all patients with CHD and AF and PVI using the cryoballoon from January 2017 through November 2021 were included.

Results

Nineteen patients with various types of CHD were included. Median age was 58 (IQR 47–63) years. A total of 12/19 (63%) patients had had RF ablation of right atrial AT before. Median procedure duration was 225 (IQR 196–261) min. Median fluoroscopy time was 12.3 (IQR 5.2–19.5) min and median freeze time was 32 (IQR 28–36.3) min. Procedural success was achieved in all patients. Additional RF catheter ablation of intraatrial reentrant tachycardia within the left atrium was performed in 3/19 (16%) subjects and within the right atrium in 6/19 (32%) patients. Median follow-up was 26 (IQR 9–49) months. Excluding a 90-day blanking period, recurrence of AF was observed in 6/19 subjects (32%). After one redo procedure deploying RF energy only, 84% of all patients remained free from recurrence. Phrenic nerve palsy was observed in 1 subject.

Conclusion

Results after PVI using the cryoballoon plus additional RF ablation of AT were promising (84% success including one redo procedure). Success of AF ablation was unsatisfactory in all patients who had no additional AT ablation. Ablation of any AT in these patients should therefore be considered in addition to PVI.
Modulation of free energy landscapes as a strategy for the design of antimicrobial peptides
Authors: Hassan Sergio A. , Steinbach Peter J.
Published: April 2022

Computational design of antimicrobial peptides (AMPs) is a promising area of research for developing novel agents against drug-resistant bacteria. AMPs are present naturally in many organisms, from bacteria to humans, a time-tested mechanism that makes them attractive as effective antibiotics. Depending on the environment, AMPs can exhibit α-helical or β-sheet conformations, a mix of both, or lack secondary structure; they can be linear or cyclic. Prediction of their structures is challenging but critical for rational design. Promising AMP leads can be developed using essentially two approaches: traditional modeling of the physicochemical mechanisms that determine peptide behavior in aqueous and membrane environments and knowledge-based, e.g., machine learning (ML) techniques, that exploit ever-growing AMP databases. Here, we explore the conformational landscapes of two recently ML-designed AMPs, characterize the dependence of these landscapes on the medium conditions, and identify features in peptide and membrane landscapes that mediate protein-membrane association. For both peptides, we observe greater conformational diversity in an aqueous solvent than in a less polar solvent, and one peptide is seen to alter its conformation more dramatically than the other upon the change of solvent. Our results support the view that structural rearrangement in response to environmental changes is central to the mechanism of membrane-structure disruption by linear peptides. We expect that the design of AMPs by ML will benefit from the incorporation of peptide conformational substates as quantified here with molecular simulations.
The projected polar proximal point algorithm converges globally
Authors: Lindstrom Scott B.
Published: April 2022

Friedlander, Macêdo, and Pong recently introduced the projected polar proximal point algorithm (P4A) for solving optimization problems by using the closed perspective transforms of convex objectives. We analyse a generalization (GP4A) which replaces the closed perspective transform with a more general closed gauge. We decompose GP4A into the iterative application of two separate operators, and analyse it as a splitting method. By showing that GP4A and its under-relaxations exhibit global convergence whenever a fixed point exists, we obtain convergence guarantees for P4A by letting the gauge specify to the closed perspective transform for a convex function. We then provide easy-to-verify sufficient conditions for the existence of fixed points for the GP4A, using the Minkowski function representation of the gauge. Conveniently, the approach reveals that global minimizers of the objective function for P4A form an exposed face of the dilated fundamental set of the closed perspective transform.
En route from metal alkoxides to metal oxides: metal oxo/alkoxo clusters
Authors: Schubert Ulrich
Published: April 2022

Molecular metal oxo or oxo/alkoxo clusters, MwOx(OH/OR)y(L/X)z (L or X = organic ligands), can often be isolated upon (partial) hydrolysis of metal alkoxides. Investigation of such clusters leads to a better understanding of the basic processes of sol–gel chemistry. The ligands not only stabilize the cluster core but also influence to some extent the cluster structures. They can easily change their position on the cluster surface, thus adapting to changing cluster geometries, and can be exchanged under certain conditions. A close inspection of titanium oxo/alkoxo cluster structures, taken as an informative example, shows that Ti3O units (with or without organic ligands) are the basic building blocks. Clusters with higher nuclearities appear to be predominantly formed by cluster–cluster or by cluster–monomer condensations. Ligand substitution or condensation reactions within a cluster unit are also possible.
Scrutinizing XAI using linear ground-truth data with suppressor variables
Authors: Wilming Rick , Budding Céline , Müller Klaus-Robert , Haufe Stefan
Published: April 2022

Machine learning (ML) is increasingly often used to inform high-stakes decisions. As complex ML models (e.g., deep neural networks) are often considered black boxes, a wealth of procedures has been developed to shed light on their inner workings and the ways in which their predictions come about, defining the field of ‘explainable AI’ (XAI). Saliency methods rank input features according to some measure of ‘importance’. Such methods are difficult to validate since a formal definition of feature importance is, thus far, lacking. It has been demonstrated that some saliency methods can highlight features that have no statistical association with the prediction target (suppressor variables). To avoid misinterpretations due to such behavior, we propose the actual presence of such an association as a necessary condition and objective preliminary definition for feature importance. We carefully crafted a ground-truth dataset in which all statistical dependencies are well-defined and linear, serving as a benchmark to study the problem of suppressor variables. We evaluate common explanation methods including LRP, DTD, PatternNet, PatternAttribution, LIME, Anchors, SHAP, and permutation-based methods with respect to our objective definition. We show that most of these methods are unable to distinguish important features from suppressors in this setting.
DFC-D: A dynamic weight-based multiple features combination for real-time moving object detection
Authors: Hossain Md Alamgir , Hossain Md Imtiaz , Hossain Md Delowar , Huh Eui-Nam
Published: April 2022

Real-time moving object detection is an emerging method in Industry 5.0, that is applied in video surveillance, video coding, human-computer interaction, IoT, robotics, smart home, smart environment, edge and fog computing, cloud computing, and so on. One of the main issues is accurate moving object detection in real-time in a video with challenging background scenes. Numerous existing approaches used multiple features simultaneously to address the problem but did not consider any adaptive/dynamic weight factor to combine these feature spaces. Being inspired by these observations, we propose a background subtraction-based real-time moving object detection method, called DFC-D. This proposal determines an adaptive/dynamic weight factor to provide a weighted fusion of non-smoothing color/gray intensity and non-smoothing gradient magnitude. Moreover, the color-gradient background difference and segmentation noise are employed to modify thresholds and background samples. Our proposed solution achieves the best trade-off between detection accuracy and algorithmic complexity on the benchmark datasets while comparing with the state-of-the-art approaches.
Asymmetrical copper root pruning may improve root traits for reforesting steep and/or windy sites
Authors: Montagnoli Antonio , Dumroese R. Kasten , Negri Giulia , Scippa Gabriella Stefania , Chiatante Donato , Terzaghi Mattia
Published: April 2022

Our research demonstrates that plant material can be produced in the nursery with asymmetrical root systems, which may have utility for reforestation of difficult planting sites characterized by steep slopes and/or windy conditions. Such a root system can be generated using chemical root pruning by applying cupric carbonate (Cu) that can arrest the development of, or cause mortality to, root apical meristems resulting in the formation of new lateral roots with an overall increase in the biomass, length, and volume of the root system. Our objective was to investigate the effect of chemical root pruning on the morphological and architectural traits of adventitious roots produced by poplar cuttings (Populus nigra L.) grown in containers coated with Cu in various symmetrical (Side, Bottom, Side + Bottom) and asymmetrical (half side + half bottom) patterns. After six weeks, roots of the cuttings were extracted from different container depths (Top, Middle, and Bottom) and portions (non-coated, Cu-coated), and analyzed. The root systems reacted to all coating patterns by increasing length, biomass, volume, and average diameters, but magnitude of increase was further affected by depth. In particular, root growth was unaffected at the Top of the container, and length was the highest at the Bottom depth. The Middle depth had a significant increment in both biomass and volume. Also, the root population increased in diameter as a possible response to Cu exposure. Interestingly, in the asymmetrically coated containers this depth response in the non-coated portions was of higher magnitude than in the Cu-coated portions.
Cocoercivity, smoothness and bias in variance-reduced stochastic gradient methods
Authors: Morin Martin , Giselsson Pontus
Published: April 2022

With the purpose of examining biased updates in variance-reduced stochastic gradient methods, we introduce SVAG, a SAG/SAGA-like method with adjustable bias. SVAG is analyzed in a cocoercive root-finding setting, a setting which yields the same results as in the usual smooth convex optimization setting for the ordinary proximal-gradient method. We show that the same is not true for SVAG when biased updates are used. The step-size requirements for when the operators are gradients are significantly less restrictive compared to when they are not. This highlights the need to not rely solely on cocoercivity when analyzing variance-reduced methods meant for optimization. Our analysis either match or improve on previously known convergence conditions for SAG and SAGA. However, in the biased cases they still do not correspond well with practical experiences and we therefore examine the effect of bias numerically on a set of classification problems. The choice of bias seem to primarily affect the early stages of convergence and in most cases the differences vanish in the later stages of convergence. However, the effect of the bias choice is still significant in a couple of cases.
Interstellar Neutrals, Pickup Ions, and Energetic Neutral Atoms Throughout the Heliosphere: Present Theory and Modeling Overview
Authors: Sokół Justyna M. , Kucharek Harald , Baliukin Igor I. , Fahr Hans , Izmodenov Vladislav V. , Kornbleuth Marc , Mostafavi Parisa , Opher Merav , Park Jeewoo , Pogorelov Nikolai V. , Quinn Philip R. , Smith Charles W. , Zank Gary P. , Zhang Ming
Published: April 2022

Interstellar neutrals (ISNs), pick-up ions (PUIs), and energetic neutral atoms (ENAs) are fundamental constituents of the heliosphere and its interaction with the neighboring interstellar medium. Here, we focus on selected aspects of present-day theory and modeling of these particles. In the last decades, progress in the understanding of the role of PUIs and ENAs for the global heliosphere and its interaction with very local interstellar medium is impressive and still growing. The increasing number of measurements allows for verification and continuing development of the theories and model attempts. We present an overview of various model descriptions of the heliosphere and the processes throughout it including the kinetic, fluid, and hybrid solutions. We also discuss topics in which interplay between theory, models, and interpretation of measurements reveals the complexity of the heliosphere and its understanding. They include model-based interpretation of the ISN, PUI, and ENA measurements conducted from the Earth’s vicinity. In addition, we describe selected processes beyond the Earth’s orbit up to the heliosphere boundary regions, where PUIs significantly contribute to the complex system of the global heliosphere and its interaction with the VLISM.
Reducing implicit prejudice towards migrants in fifth grade pupils: efficacy of a multi-faceted school-based program
Authors: Gabrielli Sara , Catalano Maria Gaetana , Maricchiolo Fridanna , Paolini Daniele , Perucchini Paola
Published: April 2022

This study evaluated the impact of a school-based program designed to reduce implicit prejudice towards migrants in fifth-grade school children. The program used empathy and perspective taking and direct and indirect contact as strategies to reduce ethnic prejudice. Multiple activities were used, including drawings by migrant children as instruments to promote inclusive behaviors. One hundred and five students were divided into two groups (control, experimental), and the children in each completed the Child-IAT (Implicit Association Test) before and after the program, to measure their implicit prejudice. Only the experimental group participated in the program. The results showed a significant reduction in the implicit prejudice in the experimental group after the educational program, but not in the control group. The results are discussed considering the practical implications of such a school program.
Development of a facile genetic transformation system for the Spanish elite rice paella genotype Bomba
Authors: Saba-Mayoral Andrea , Bassie Ludovic , Christou Paul , Capell Teresa
Published: April 2022

We report the development of an efficient and reproducible genetic transformation system for the recalcitrant Spanish elite rice paella genotype, Bomba. Preconditioned embryos derived from dry seeds were bombarded with gold particles carrying a plasmid containing a screenable and a selectable marker. We confirmed integration and expression of hpt and gusA in the rice genome. Transformation frequency was ca: 10% in several independent experiments. We show Mendelian inheritance of the input transgenes and zygosity determination of the transgenic lines in the T1 generation. A unique and critical step for the regeneration of plants from transformed tissue was shading during the early stages of regeneration, combined with a specific cytokinin:auxin ration at the onset of shifting callus to regeneration media.
Evaluation of biotransformation capacity of transplastomic plants and hairy roots of Nicotiana tabacum expressing human cytochrome P450 2D6
Authors: Sheludko Y. V. , Gerasymenko I. M. , Herrmann F. J. , Warzecha H.
Published: April 2022

Cytochrome P450 monooxygenases (CYPs) are important tools for regio- and stereoselective oxidation of target molecules or engineering of metabolic pathways. Functional heterologous expression of eukaryotic CYPs is often problematic due to their dependency on the specific redox partner and the necessity of correct association with the membranes for displaying enzymatic activity. Plant hosts offer advantages of accessibility of reducing partners and a choice of membranes to insert heterologous CYPs. For the evaluation of plant systems for efficient CYP expression, we established transplastomic plants and hairy root cultures of Nicotiana tabacum carrying the gene encoding human CYP2D6 with broad substrate specificity. The levels of CYP2D6 transcript accumulation and enzymatic activity were estimated and compared with the data of CYP2D6 transient expression in N. benthamiana. The relative level of CYP2D6 transcripts in transplastomic plants was 2–3 orders of magnitude higher of that observed after constitutive or transient expression from the nucleus. CYP2D6 expressed in chloroplasts converted exogenous synthetic substrate loratadine without the need for co-expression of the cognate CYP reductase. The loratadine conversion rate in transplastomic plants was comparable to that in N. benthamiana plants transiently expressing a chloroplast targeted CYP2D6 from the nucleus, but was lower than the value reported for transiently expressed CYP2D6 with the native endoplasmic reticulum signal-anchor sequence. Hairy roots showed the lowest substrate conversion rate, but demonstrated the ability to release the product into the culture medium. The obtained results illustrate the potential of plant-based expression systems for exploiting the enzymatic activities of eukaryotic CYPs with broad substrate specificities.
N-type calcium channel and renal injury
Authors: Bai Lei , Sun Shichao , Sun Yao , Wang Fujun , Nishiyama Akira
Published: April 2022

Accumulating evidences indicated that voltage-gated calcium channels (VDCC), including L-, T-, N-, and P/Q-type, are present in kidney and contribute to renal injury during various chronic diseases trough different mechanisms. As a voltage-gated calcium channel, N-type calcium channel was firstly been founded predominately distributed on nerve endings which control neurotransmitter releases. Since sympathetic nerve is distributed along renal afferent and efferent arterioles, N-type calcium channel blockade on sympathetic nerve terminals would bring renal dynamic improvement by dilating both arterioles and reducing glomerular pressure. In addition, large body of scientific research indicated that neurotransmitters, such as norepinephrine, releases by activating N-type calcium channel can trigger inflammatory and fibrotic signaling pathways in kidney. Interestingly, we recently demonstrated that N-type calcium channel is also expressed on podocytes and may directly contribute to podocyte injury in denervated animal models. In this paper, we will summarize our current knowledge regarding renal N-type calcium channels, and discuss how they might contribute to the river that terminates in renal injury.