bluuebunny/crossref_metadata_2025_split huggingface dataset:
A computational approach to investigate constitutive activation of NF‐κB
Authors: Mobeen Ahmed , Puniya Bhanwar Lal , Ramachandran Srinivasan 
Published: May 2022

AbstractNuclear factor kappa B (NF‐κB) signaling is the master regulator of inflammatory pathways; therefore, its regulation has been the subject of investigation since last two decades. Multiple models have been published that describes the dynamics of NF‐κB activity by stimulated activation and feedback loops. However, there is also paramount evidence of the critical role of posttranslational modifications (PTMs) in the regulation of NF‐κB pathway. With the premise that PTMs present alternate routes for activation or repression of the NF‐κB pathway, we have developed a model including all PTMs known so far describing the system behavior. We present a pathway network model consisting of 171 proteins forming 315 molecular species and consisting of 482 reactions that describe the NF‐κB activity regulation in totality. The overexpression or knockdown of interacting molecular partners that regulate NF‐κB transcriptional activity by PTMs is used to infer the dynamics of NF‐κB activity and offers qualitative agreement between model predictions and the experimental results heuristically. Finally, we have demonstrated an instance of NF‐κB constitutive activation through positive upregulation of cytokines (the stimuli) and IKK complex (NF‐κB activator), the characteristic features in several cancer types and metabolic disorders, and its reversal by employing combinatorial activation of PPARG, PIAS3, and P50‐homodimer. For the first time, we have presented a NF‐κB model that includes transcriptional regulation by PTMs and presented a theoretical strategy for the reversal of NF‐κB constitutive activation. The presented model would be important in understanding the NF‐κB system, and the described method can be used for other pathways as well.
Electrophysiological and behavioural responses ofStegobium paniceumto volatile compounds from Chinese medicinal plant materials
Authors: Cao Yu , Pistillo Onofrio Marco , Lou Yibin , D'Isita Ilaria , Maggi Filippo , Hu Qiqi , Germinara Giacinto Salvatore , Li Can 
Published: May 2022

AbstractBACKGROUNDStegobium paniceum(Coleoptera, Anobiidae) is an important pest of stored products causing severe damage to dried Chinese medicinal plant materials (CMPMs). Plant volatiles play an important role in host‐searching of insects. The olfactory responses ofS. paniceumto the most abundant volatile components of some drugstore attractant CMPMs such asPanax notoginseng,Angelica sinensis,Gastrodia elataandPeucedanum praeruptorum, namely falcarinol, 3‐n‐butylphthalide,p‐cresol and β‐pinene, respectively, were studied by electroantennography (EAG) and behavioural bioassays in six‐ and four‐arm olfactometers.RESULTSEAG recordings showed that male and female antennae are able to perceive the test compounds in a wide range of concentrations and in a dose‐dependent manner. Moreover, for each dose of different compounds tested, no significant differences were found between the mean male and female EAG responses. In six‐arm olfactometer bioassays,S. paniceumexhibited positive responses to falcarinol, 3‐n‐butylphthalide,p‐cresol and β‐pinene at doses of 1, 10, 100, 500 and 1000 μg. The most attractive dose was 500 μg for falcarinol, 100 μg for 3‐n‐butylphthalide, 500 μg forp‐cresol and 1000 μg for β‐pinene. Olfactory preferences ofS. paniceum, based on comparison of these four compounds at their optimally attractive concentrations in a four‐arm olfactometer, were 3‐n‐butylphthalide >p‐cresol > falcarinol > β‐pinene.CONCLUSIONThe results indicated that the four volatiles of CMPMs are perceived by the peripheral olfactory system ofS. paniceumadults and are able to individually elicit a positive chemotaxis inS. paniceumadults confirming the role of chemical cues in host‐plant detection and selection of this pest. Further field studies are needed to evaluate the potential of the attractive compounds identified in this study, particularly 3‐n‐butylphthalide, to be applied as a novel monitoring and control tool against this storage‐beetle pest. © 2022 The Authors.Pest Management Sciencepublished by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Residual‐based CUSUM beta regression control chart for monitoring double‐bounded processes
Authors: Rauber Cristine , Lima‐Filho Luiz M. A. , Bayer Fábio M. 
Published: May 2022

AbstractThis paper proposes a control chart useful for detecting small shifts in the mean of a double‐bounded process, such as fractions and proportions, in the presence of control variables. For this purpose, we consider the cumulative sum (CUSUM) control chart applied to different residuals of the beta regression model. We conduct an extensive Monte Carlo simulation study to evaluate and compare the performance of the proposed control chart with two other control charts in the literature in terms of run length analysis. The numerical results show that the proposed control chart is more sensitive to detect changes in the process than its competitors and that the quantile residual is the most suitable residual to be used in our proposal. Finally, based on the quantile residual, we present and discuss applications to real and simulated data to show the applicability of the proposed control chart.
Boosting the Electrocatalytic Oxygen Evolution of Perovskite LaCo1−xFexO3 by the Construction of Yolk‐Shell Nanostructures and Electronic Modulation
Authors: Bao Bian , Liu Yana , Sun Mingzi , Huang Bolong , Hu Yang , Da Pengfei , Ji Deguang , Xi Pinxian , Yan Chun‐Hua 
Published: May 2022

AbstractRealizing the rational design of perovskite oxides with controllable compositions and nanostructures remains a tremendous challenge for the development of efficient electrocatalysts. Herein, a ligand‐assisted synthetic strategy to fabricate perovskite oxides LaCo1−xFexO3 with yolk‐shell nanostructures is developed. Benefiting from the unique structural and compositional merits, LaCo0.75Fe0.25O3 exhibits an overpotential of 310 mV at a current density of 10 mA cm−2 and long‐term stability of 100 h for the oxygen evolution reaction. In situ Raman spectroscopy demonstrates that Fe substitution facilitates the pre‐oxidation of Co sites and induces the surface reconstruction into active Co oxyhydroxides at a relatively lower applied potential, guaranteeing excellent catalytic performances. Density functional theory calculations unravel that the appropriate introduction of Fe into perovskite LaCoO3 leads to the improved electroactivity and durability of the catalyst for the oxygen evolution reaction (OER). Fe‐3d orbitals show a pinning effect on Co‐3d orbitals to maintain the stable valence state of Co sites at the low overpotential of the OER. Furthermore, Zn–air batteries (ZABs) assembled with LaCo0.75Fe0.25O3 display a high open circuit potential of 1.47 V, superior energy density of 905 Wh kg−1 Zn, and excellent stability in a large temperature range. This work supplies novel insights into the future developments of perovskite‐based electrocatalysts.
A Top‐Down Templating Strategy toward Functional Porous Carbons
Authors: Zhang Le‐Le , Tong Lei , Lv Xue‐Hui , Yan Qiang‐Qiang , Ding Yan‐Wei , Wang Yu‐Cheng , Liang Hai‐Wei 
Published: May 2022

AbstractNanostructured carbon materials with high porosity and desired chemical functionalities are of immense interest because of their wide application potentials in catalysis, environment, and energy storage. Herein, a top‐down templating strategy is presented for the facile synthesis of functional porous carbons, based on the direct carbonization of diverse organic precursors with commercially available metal oxide powders. During the carbonization, the metal oxide powders can evolve into nanoparticles that serve as in situ templates to introduce nanopores in carbons. The porosity and heteroatom doping of the prepared carbon materials can be engineered by varying the organic precursors and/or the metal oxides. It is further demonstrated that the top‐down templating strategy is applicable to prepare carbon‐based single‐atom catalysts with iron‐nitrogen sites, which exhibit a high power density of 545 mW cm−2 in a H2–air proton exchange membrane fuel cell.
Automated evaluation of comments to aid software maintenance
Authors: Majumdar Srijoni , Bansal Ayush , Das Partha Pratim , Clough Paul D. , Datta Kausik , Ghosh Soumya Kanti 
Published: May 2022

AbstractApproaches to evaluate comments based on whether they increase code comprehensibility for software maintenance tasks are important, but largely missing. We proposeCommentfor automated classification and quality evaluation of code comments of C codebases based on how they can help to understand existing code. We conduct surveys and document developers' perceptions on the type of comments that prove useful to maintaining software in the form of comment categories. A total of 20,206 comments have been collected from open‐sourceGithubprojects and annotated with assistance from industry experts. We develop features to semantically analyze comments to locate concepts related to categories of usefulness. Additionally, features based on code and comment correlation are designed to infer whether the comment is also consistent and not superfluous. Using neural networks, comments are classified asuseful,partially useful, andnot usefulwith precision and recall scores of 86.27% and 86.42%, respectively. The proposed framework for comment quality evaluation incorporates industry practices and adds significant value to companies wanting to formulate better code commenting strategies. Furthermore, large codebases can be de‐cluttered by removing comments not helpful in maintaining code.
Comprehensive investigation on isolation, quantification, and activity evaluation of salvianolic acids for injection based on improved dry load injection technology
Authors: Gao Jian , Zhou Lin , Zhang Lele , Luo Xi , Fu Zhifei , Pan Guixiang , Xu Qiang , Han Lifeng 
Published: May 2022

AbstractIn this work, an effective method for simultaneous isolation of eight compounds from Salvianolic Acids for Injection was developed by preparative high‐performance liquid chromatography based on improved dry load injection. Firstly, the chemical structures of the obtained compounds were identified by mass spectrometry and nuclear magnetic resonance spectra. Subsequently, a sensitive liquid chromatography‐tandem mass spectrometry method was established to precisely quantify the eight isolated target analytes. The quantitative results show salvianolic acid B as the most abundant component (460.06–514.68‰) and protocatechualdehyde (0.03–0.08‰) as the least. Finally, the antioxidant activities of the isolated compounds were further investigated. The 2,2‐diphenyl‐1‐picrylhydrazyl‐scavenging assay indicated that (7′R, 8′S, 8″R, 8′′′R)‐epi‐salvianolic acid B had the lowest half‐maximal inhibitory concentration (5.05 μg/ml). This study reports on the development of an effective and rapid method for simultaneous isolation of multiple compounds from traditional Chinese medicine preparation, which could be used as reference compounds for further quality control and activities screening.
Current State and Future Perspectives of Starch Derivatives and Their Blends as Antimicrobial Materials
Authors: Kanth Shreya , Puttaiahgowda Yashoda Malgar 
Published: May 2022

AbstractAntimicrobial resistance is increasingly recognized as a serious worldwide threat, jeopardizing medical progress, and the ability to treat infectious illness. Antimicrobial polymers have sparked the interest of researchers because of the increased demand for enhancing human health by lowering illness caused by different bacteria. Polysaccharides are ideal starting materials for the synthesis of antimicrobial polymers due to their bio renewability and broad availability. Starch is one such polysaccharide which has many advantages such as low‐cost, nontoxicicity, and renewable sourcing and thus can be used for the synthesis of antimicrobial polymers. Here, the most recent research on starch‐based antimicrobial polymers in the context of microbial infections is given in this article. The possibility of employing starch based films to alleviate environmental waste and prevent food spoiling is discussed in this paper. The goal of this study is to show the barrier and mechanical properties of starch containing antimicrobial agents, as well as their antimicrobial activity, in order to improve product storability. This study aims to advance knowledge in this area and urges additional research into the synthesis of starch‐based antibacterial materials.
The Advent of Precision Immunology: Immunogenetics at the Center of Immune Cell Analysis in Health and Disease
Authors: Langerak Anton W. 
Published: May 2022

AbstractAdaptive immune cells (i.e., lymphocytes of the B and T lineage) are equipped with unique antigen receptors, which collectively form a highly diverse repertoire. Within the lymphocytes, the antigen receptor diversity is created at the DNA level through recombination processes in the immunoglobulin (IG) and T cell receptor (TR) genes that encode these receptors. This gives rise to an enormous immune repertoire (a.k.a. the “immunome”) that can be studied in health and disease, both in a scientific and clinical context. In fact, the inherent distinctiveness of the IG/TR rearrangements on a per cell basis allows their usage as unique DNA fingerprints, which enables precision medicine, or for that matter “precision immunology.” The field of (fundamental and translational) research on IG/TR repertoire diversity is the topic of the Immunogenetics volume in the Methods in Molecular Biology series.
Single-Cell Analysis and Tracking of Antigen-Specific T Cells: Integrating Paired Chain AIRR-Seq and Transcriptome Sequencing: A Method by the AIRR Community
Authors: Gupta Nidhi , Lindeman Ida , Reinhardt Susanne , Mariotti-Ferrandiz Encarnita , Mujangi-Ebeka Kevin , Martins-Taylor Kristen , Eugster Anne 
Published: May 2022

AbstractSingle-cell adaptive immune receptor repertoire sequencing (scAIRR-seq) offers the possibility to access the nucleotide sequences of paired receptor chains from T-cell receptors (TCR) or B-cell receptors (BCR). Here we describe two protocols and the downstream bioinformatic approaches that facilitate the integrated analysis of paired T-cell receptor (TR) alpha/beta (TRA/TRB) AIRR-seq, RNA sequencing (RNAseq), immunophenotyping, and antigen-binding information. To illustrate the methodologies with a use case, we describe how to identify, characterize, and track SARS-CoV-2-specific T cells over multiple time points following infection with the virus. The first method allows the analysis of pools of memory CD8+cells, identifying expansions and contractions of clones of interest. The second method allows the study of rare or antigen-specific cells and allows studying their changes over time.
Quality Control: Chain Pairing Precision and Monitoring of Cross-Sample Contamination: A Method by the AIRR Community
Authors: Chung Cheng-Yu , Gutiérrez-González Matías , López Acevedo Sheila N. , Fahad Ahmed S. , DeKosky Brandon J. ,   on behalf of the AIRR Community
Published: May 2022

AbstractNew approaches in high-throughput analysis of immune receptor repertoires are enabling major advances in immunology and for the discovery of precision immunotherapeutics. Commensurate with growth of the field, there has been an increased need for the establishment of techniques for quality control of immune receptor data. Our laboratory has standardized the use of multiple quality control techniques in immunoglobulin (IG) and T-cell receptor (TR) sequencing experiments to ensure quality control throughout diverse experimental conditions. These quality control methods can also validate the development of new technological approaches and accelerate the training of laboratory personnel. This chapter describes multiple quality control techniques, including split-replicate cell preparations that enable repeat analyses and bioinformatic methods to quantify and ensure high sample quality. We hope that these quality control approaches can accelerate the technical adoption and validated use of unpaired and natively paired immune receptor data.
Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq
Authors: van der Velden Vincent H. J. , Bastian Lorenz , Brüggemann Monika , Hartmann Alina M. , Darzentas Nikos 
Published: May 2022

AbstractIdentification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation are crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. Here we describe how RNA-Seq data can be generated and subsequently analyzed with ARResT/Interrogate to identify possible MRD markers. In addition to the procedures, possible pitfalls will be discussed. Similar strategies can be employed for other lymphoid malignancies, such as lymphoma and myeloma.
Energy and the Economy in the Middle East and North Africa
Authors: Sedaoui Radia 
Published: May 2022

AbstractThe Arab region consists of a diverse set of countries with different national contexts, including in the case of energy. However, most countries remain exceptionally reliant on fossil fuels with a highly limited role played by clean energy alternatives; while the region also lags behind other region’s progress in energy efficiency. In the Arab LDCs, energy access remains incomplete, severely obstructing socio-economic progress.Arab countries need to better integrate sustainable energy as a fundamental element of national development policies by directly linking policy goals across sectors such as energy, transport and urban planning; as well as elevating topics such as natural resource management, air and environmental protection along with more inclusive ways to ensure energy is used and produced sustainably to matters of explicit national interest.
S-foldings of 5d SCFTs
Authors: Kim Hee-Cheol , Kim Sung-Soo , Lee Kimyeong 
Published: May 2022

Abstract
We explore the ℤ2,3,4,6 S-foldings of some 5d superconformal field theories from the (p, q) 5-brane web perspective. The S-folding involves both a spatial quotient and an SL(2, ℤ) transformation on 5-branes simultaneously. The ℤ2,3,4,6 S-foldings are achieved by the insertion of the D4, E6, E7, E8 7-branes, respectively. The deficit angles and monodromies of these 7-branes are exactly those necessary for the S-foldings. We explore the details of the S-folding process, especially the enhancement of global flavor symmetry in various simple cases. The characteristic of the S-folding depends sharply on whether the fixed point of the discrete symmetry is at the center of a compact face (or surface), at a 5-brane, or at a crossing point of 5 branes. The analysis of the prepotential greatly supports this view of the discrete gauging.
Boundary values of zero solutions of hypoelliptic differential operators in ultradistribution spaces
Authors: Debrouwere Andreas , Kalmes Thomas 
Published: May 2022

AbstractWe study ultradistributional boundary values of zero solutions of a hypoelliptic constant coefficient partial differential operator $$P(D) = P(D_x, D_t)$$

P

(
D
)

=
P

(

D
x

,

D
t

)

on $${\mathbb {R}}^{d+1}$$

R

d
+
1

. Our work unifies and considerably extends various classical results of Komatsu and Matsuzawa about boundary values of holomorphic functions, harmonic functions and zero solutions of the heat equation in ultradistribution spaces. We also give new proofs of several results of Langenbruch (Manuscripta Math. 26:17–35, 1978/79) about distributional boundary values of zero solutions of P(D).
High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance
Authors: Vázquez Víctor , León Pablo , Gordillo Francisco J. L. , Jiménez Carlos , Concepción Iñiguez , Mackenzie Kevin , Bresnan Eileen , Segovia María 
Published: May 2022

AbstractThe coccolithophoreEmiliania huxleyishows a variety of responses to ocean acidification (OA) and to high-CO2concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2or H+, and how it impacted cell growth performance, calcification, and physiological stress management.Emiliania huxleyiresponded differently to each acidification method. CO2-enriched aeration (1200 µatm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2than by low pH without CO2enrichment with respect to the control (400 µatm, pH 8.1). High CO2also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2enrichment. These results highlight the capacity of CO2rather than acidification itself to generate metabolic stress, not reducing calcification.
Long-term field studies in bat research: importance for basic and applied research questions in animal behavior
Authors: Kerth Gerald 
Published: May 2022

AbstractAnimal species differ considerably in longevity. Among mammals, short-lived species such as shrews have a maximum lifespan of about a year, whereas long-lived species such as whales can live for more than two centuries. Because of their slow pace of life, long-lived species are typically of high conservation concern and of special scientific interest. This applies not only to large mammals such as whales, but also to small-sized bats and mole-rats. To understand the typically complex social behavior of long-lived mammals and protect their threatened populations, field studies that cover substantial parts of a species’ maximum lifespan are required. However, long-term field studies on mammals are an exception because the collection of individualized data requires considerable resources over long time periods in species where individuals can live for decades. Field studies that span decades do not fit well in the current career and funding regime in science. This is unfortunate, as the existing long-term studies on mammals yielded exciting insights into animal behavior and contributed data important for protecting their populations. Here, I present results of long-term field studies on the behavior, demography, and life history of bats, with a particular focus on my long-term studies on wild Bechstein’s bats. I show that long-term studies on individually marked populations are invaluable to understand the social system of bats, investigate the causes and consequences of their extraordinary longevity, and assess their responses to changing environments with the aim to efficiently protect these unique mammals in the face of anthropogenic global change.