bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structuring the Prison Life Index Through Value Focused Thinking Methodology
Authors: Martin‐Moro Lola , Öztürk Meltem , Laufer Florence 
Published: January 2025

ABSTRACTBuilding a composite index (CI) is a task that requiring a series of decisions, the consequences of which will determine the scope of the tool. This is especially true for the very first steps of this construction: the definition of the theoretical framework and the selection of relevant indicators, usually referred to as the construction of the structure. However, the literature seems to focus more on the other aspects, quite often eluding those first steps or considering it a self‐evident process. How to ensure the soundness of those tools when the values that they convey are not even clearly expressed? How to ensure the completeness of the structure according to the reality that it ought to synthesise when it is a highly complex or abstract one? Each of these steps involves hypotheses and presuppositions that must be explained and evaluated with care. In this article, we seek to identify a coherent method that will allow us to build the structure of CI answering those demands. The construction of a composite indicator can be conceptualised as a multi‐criteria decision aiding problem (MCDA), given that it entails the aggregation of evaluations pertaining to distinct attributes. The MCDA is rich in structuring methodologies, such as Ralph Keeney's Value Focused Thinking (VFT) approach. Using a real‐life application, the construction of the Prison Life Index (PLI), we try to show the relevance of those primary hypotheses by displaying the structure of the index and summarising the stage of its construction. This adapted methodology can guide index builders in the determination of a structure that comprehensively fits its intended purpose and that is not overly dependent on available data. Our article endeavours to underscore the importance of the structuring phase, arguing that it should take priority according to the ethical and moral values of the decision‐maker. It should not be solely reliant on data availability, as it is the case with most composite indices. We demonstrate, through the implementation of the PLI structure developed using VFT, that it can achieve a high degree of conformity with internationally established standards pertaining to human rights. This approach not only facilitates a comprehensive understanding of the interconnections among various normative texts but also provides jurists with a visual representation of these relationships.
Furry neighbours: Acceptability of feeding and managing free‐ranging dogs and cats in an urban area
Authors: Nayeri Danial , Sardari Pourya , Raisi Fateme Zahra , Ghorbanian Zahra , Glikman Jenny Anne 
Published: January 2025

Abstract

There is an increasing interest in researching urban invasion. When invasive species establish and spread in urban areas, their management becomes particularly challenging given the influence of public presence and perceptions. Cultural, religious, and moral values play a crucial role in shaping public perceptions toward management strategies for invasive species. Free‐ranging dogs (FRDs) and free‐ranging cats (FRCs) are among the urban invasive species that bring health, safety, and wildlife conservation concerns. However, given their close relationship with people controlling their populations is challenging.

We surveyed 500 residents of Karaj city in northern Iran to understand the behaviour of feeding FRDs and FRCs by people, as well as to uncover residents' acceptability of different control measures, focusing on culling FRDs and FRCs under different scenarios. We used generalized linear mixed models and cumulative link mixed models to address the issues of feeding FRDs and FRCs and acceptability of culling them respectively.

We found that more than half of the respondents fed FRDs and FRCs (63% and 59%, respectively), and among those who fed FRDs and FRCs, 74.8% and 78.2% respectively used food leftovers from home to feed these animals. Furthermore, around half and one‐third of respondents provided FRDs and FRCs outside their neighbourhoods, respectively. We also found that the religious belief of dogs being ritually impure (Najis) was a significant predictor for both feeding and culling FRDs. People who held the belief that dogs are Najis were more inclined toward culling and less willing to feed FRDs. Moreover, we found polarized and conflicting views concerning culling in higher‐intensity scenarios involving attacks on people and disease spread. On the contrary, in less‐intense scenarios such as attacks on wildlife and population control in urban areas, most respondents disagreed with culling.

In the end, we recommend (1) an improved waste management system for food residuals and leftovers that provide resources for FRDs and FRCs, (2) effective communication with pet‐owners to reduce feeding FRDs and FRCs and (3) bottom‐up de‐escalation of the conflict between polarized groups about culling FRDs and FRCs before it reaches to a destructive phase.

Read the free Plain Language Summary for this article on the Journal blog.
A functional helix shuffled variant of the B domain of Staphylococcus aureus
Authors: Bobolowski Hanna , Fiedler Erik , Haupts Ulrich , Lilie Hauke , Weininger Ulrich 
Published: January 2025

AbstractThe B domain of protein A is a biotechnologically important three‐helix bundle protein. It binds the Fc fragment of antibodies with helix 1/2 and the Fab region with helix 2/3. Here we designed a helix shuffled variant by changing the connectivity of the helices, in order to redesign the helix bundle, yielding altered helix–loop–helix properties. The new loops that generate the new connectivity were created in several protein libraries, and Fc binding variants were selected for a detailed biochemical characterization. We were able to create variants with Fc binding affinity at the same level as the wild type B but with significantly reduced thermal stability. The NMR structure proved that the overall three‐dimensional structure was maintained not only in the helix shuffled variant but also points to some potential local differences to wild‐type B, which could be the reason for the reduced thermal stability. Therefore, protein A is an example of an optimized structure being more important for stability than for function. Using the helix shuffled variant as a ligand on an affinity column facilitates a robust and straightforward purification of antibodies, but allows for a milder elution at less extreme pH. Therefore, the helix shuffled variant is a suitable ligand to purify more pH‐sensitive antibodies.
Methods for detecting, building, and improving tryptophan mannosylation in glycoprotein structures
Authors: Holland Lou , Pham Phuong Thao , Bagdonas Haroldas , Dialpuri Jordan S. , Schofield Lucy C. , Agirre Jon 
Published: January 2025

AbstractTryptophan mannosylation, the covalent addition of an α‐ᴅ‐mannose sugar to a tryptophan side chain, is a post‐translational modification (PTM) that can affect protein stability, folding, and interactions. Compared to other forms of protein glycosylation, it is relatively uncommon but is affected by conformational anomalies and modeling errors similar to those seen in N‐ and O‐glycans in the Protein Data Bank (PDB). In this work, we report methods for detecting, building, and improving mannose structures linked to tryptophans. These methods have been used to mine X‐ray crystallographic and cryo‐electron microscopy maps in the PDB looking for unmodeled mannosylation, resulting in a number of cases where the modification can be placed in the map with high confidence. Additionally, we address most conformational issues affecting this modification. Finally, the development of a structural template to recognize thrombospondin repeats (TSR) domains where tryptophan mannosylation occurs will allow for the mannosylation of candidate‐predicted models, for example, those predicted with AlphaFold.
Hijacking of plasminogen by dengue virus: The kringle‐4 and ‐5 domains of plasminogen binds synergistically to the domain I of envelope protein
Authors: Yuen Yee Jun , Sabitha Thekkoot , Li Lim Jian , Walvekar Varsha Ashok , Ramesh Karthik , Kini R. Manjunatha , Sivaraman J. , Mok Yu Keung 
Published: January 2025

AbstractDengue fever is a serious health issue, particularly in tropical countries like Singapore. We have previously found that dengue virus (DENV) recruits human plasmin in blood meal to enhance the permeability of the mosquito midgut for infection. Here, using biolayer interferometry, we found that neither kringle‐4 nor kringle‐5 plasmin domains alone binds well to dengue virus. However, the domains together lead to a synergistic effect, with both kringle‐4 and ‐5 domains required and sufficient for binding. Site‐directed mutagenesis experiments showed that the N‐terminal and C‐terminal aspartic acid residues in the “DXD” acidic motifs of the kringle‐4 and ‐5 domains likely have different roles when engaged with DENV. Hydrogen deuterium exchange mass spectrometry experiments on the plasmin:DENV complex led to the identification of two Lys‐containing regions on domain I of the E‐protein of DENV that are buried by plasmin and could be potential plasmin binding sites. These findings contradict with published literature that domain III of the DENV E‐protein interacts with the kringle‐1–3 domains of plasmin. We provide a plausible explanation for the observed discrepancies.
Synthesis, antifungal activity, and molecular simulation study of nootkatone‐based thiazole‐hydrazone compounds as novel succinate dehydrogenase inhibitor
Authors: Yang Maofang , Lin Guishan , Duan Wengui , Li Fangyao , Cui Yucheng , Man Yin , Lu Yuzhi , Meng Luqiong 
Published: January 2025

AbstractBACKGROUNDPlant diseases cause huge losses in agriculture worldwide every year, but the prolonged use of current commercial fungicides has led to the development of resistance in plant pathogenic fungi. Therefore, there is an urgent need to develop new, efficient, and green fungicides.RESULTSTwenty‐three nootkatone‐based thiazole‐hydrazone compounds were designed, synthesized, and characterized by Fourier‐transform infrared (FTIR), proton (1H) nuclear magnetic resonance (NMR), carbon‐13 (13C) NMR, and high‐resolution mass spectrometry (HRMS). The antifungal activities results showed that all the target compounds displayed certain antifungal activity against eight tested fungi. Among them, target compounds 3a (88.7%), 3b (92.5%), 3d (88.7%), 3f (84.9%), 3j (88.7%), and 3l (92.5%) were comparable or superior to the positive control boscalid (88.7%) in their inhibitory activities against Physalospora piricola. Meanwhile, target compound 3l had half maximal effective concentration (EC50) values of 18.0172, 18.8236, 16.5914, 18.5044, and 16.5660 μg/mL against Fusarium oxysporum f. sp. cucumerinum, Alternaria solani, Gibberella zeae, Bipolaris maydis, and Colleterichum orbicalare, respectively, exhibiting outstanding and broad‐spectrum fungicidal activity. Moreover, a three‐dimensional quantitative structure–activity relationship (3D‐QSAR) study was carried out to investigate the relationship between the molecular structures of target compounds 3a–3w and their antifungal activity. Furthermore, the target compound 3l [half maximal inhibitory concentration (IC50) = 4.936 μmol/L] showed significantly better inhibitory activity against succinate dehydrogenase (SDH) than boscalid (IC50 = 6.631 μmol/L). The possible binding mode between target compound 3l and homology‐modeling built SDH, was also explored by molecular docking.CONCLUSIONTarget compound 3l deserved further study as the promising candidate for the development of novel SDH inhibitor. © 2025 Society of Chemical Industry.
Improved method for isotopic measurement of free‐living nitrogen fixation
Authors: Zhou Qianchen , Mulvaney Richard L. , Nunes Vander L. N. 
Published: January 2025

AbstractThe use of 15N‐labeled dinitrogen (15N2) affords the only direct means of measuring free‐living nitrogen fixation (FLNF); however, progress in utilizing this approach has been impeded by methodological limitations arising from the presence of nitrogenous contaminants, a lack of atmospheric uniformity, and incomplete description of procedural details. Such constraints are eliminated with an ex situ technique comprehensively described herein, which involves circulating 15N2 generated by hypobromite oxidation through a closed system that includes chemical (sulfuric acid–potassium permanganate) and cryogenic (isopentane–liquid N2) traps for atmospheric purification and an incubation chamber consisting of a desiccator equipped with a pressure gauge. Studies to evaluate the circulation system described showed that a uniform atmosphere was readily achieved with a 10‐L desiccator by pumping for 30 min, and that both chemical and cryogenic traps were necessary to ensure complete (98.8%–99.6%) removal of gaseous contaminants subject to physicochemical retention by sterilized soil samples. The method proposed was successfully demonstrated in detecting the stimulatory effect of organic carbon (C) on FLNF in active soils, and can be further utilized to improve the reliability of ex situ assessment of FLNF in relation to soil processing and storage, climatic conditions, microbial dynamics, and land management practices.
Informal networks and information environments
Authors: Lee Yonghoon G. , Choi Joon Nak 
Published: January 2025

AbstractResearch SummaryManagers draw on their informal networks of peers outside of their firm to better understand uncertain markets and help their firms adapt. This helps firms enhance their performance in information environments characterized by idiosyncratic and difficult‐to‐standardize soft information. However, in information environments characterized by standardized hard information, joint discussions facilitated by informal networks can make managers and their firms maladaptive towards uncertain markets. Based on the performance of two different categories of hedge funds during the 2008 financial crisis, we find that long–short funds, which heavily draw on soft information, performed better when embedded into networks of closely connected managers. In contrast, relative value funds, which heavily draw on hard information, performed better when their managers were more disconnected.Managerial SummaryWhen are managers’ professional networks with peers in the industry valuable to the firm? We examined how hedge fund managers performed during the 2008 financial crisis to find out. When fund managers worked primarily with idiosyncratic and difficult‐to‐standardized soft information, we found that their networks helped them make sense of such information. In contrast, when fund managers worked primarily with quantified and codified hard information (e.g., financial statements and ratings), we found that their networks became echo chambers reinforcing similar opinions, which caused managers to fail to adapt quickly to the market crisis. Our findings counterintuitively suggest that funds using hard information may better off hiring relatively isolated managers who are not deeply tied to the industry.
Real‐Time Unsupervised Learning and Image Recognition via Memristive Neural Integrated Chip Based on Negative Differential Resistance of Electrochemical Metallization Cell Neuron Device
Authors: Woo Dae‐Seong , Kim Jae‐Kyeong , Park Gwang‐Ho , Lee Woo‐Guk , Han Min‐Jong , Jin Soo‐Min , Shim Tae‐Hun , Kim Jae‐Joon , Park Jinsub , Park Jea‐Gun 
Published: January 2025

AbstractSpiking neurons are essential for building energy‐efficient biomimetic spatiotemporal systems because they communicate with other neurons using sparse and binary signals. However, the achievable high density of artificial neurons having a capacitor for emulating the integrate function of biological neurons has a limit. Furthermore, a low‐voltage operation (<1.0 V) is essential for connecting with modern complementary metal‐oxide‐semiconductor‐field‐effect‐transistor‐based (C‐MOSFET—based) integrated circuits. Here, a capacitorless memristive‐neural integrated chip (MnIC) based on the negative differential resistance of the electrochemical metallization cell designed using a 28‐nm C‐MOSFET process in a foundry is reported. The fabricated MnIC exhibits extremely low‐voltage operation (<0.7 V) via the rupture dynamics of Ag filaments formed in the GeS2 chalcogenide layer, with a nonlinear increase in the action potential in a manner similar to a human sensory system. Moreover, to construct a fully‐structured spiking neural network (SNN), an oxygenated amorphous carbon‐based (α‐COx‐based) synaptic device having 32 multi‐level conductance states is designed. The designed MnIC and α‐COx‐based synaptic device demonstrate real‐time unsupervised learning via a spike‐timing‐dependent plasticity learning rule with an SNN. Using the trained SNN, the real‐time hand‐written digit image of a cell phone obtained from a live webcam is successfully classified, which suggests practical applications for brain‐like neuromorphic chips.
Concentration and Model Selection Consistency of the Group Lasso for α$$ \alpha $$‐Mixing Errors
Authors: Martens Robin , Steland Ansgar 
Published: January 2025

ABSTRACTThe group lasso in linear regression models is studied for ‐mixing subexponential errors. Nonasymptotic guarantees are provided for the estimation error of the sparse coefficient vector and the associated predictions for the high‐dimensional regime where the number of regressors can grow much faster than the sample size. Further, the group lasso is model selection consistent; that is, it picks the right variables with arbitrarily high probability. The results are applied to the index tracking problem in finance and illustrated by analysing stock data from the United States and Asia.
Guiding Aquatic Reptile (Chelonian and Crocodylian) Conservation in the Face of Growing Light Pollution: Lessons From Experience
Authors: Khanduri Megha , Hölker Franz , Sah Ruchika , Hussain Syed Ainul , Badola Ruchi , Candolin Ulrika 
Published: January 2025

ABSTRACTLife on earth has evolved in response to the spatial, temporal, and spectral properties of natural light. However, with the advent of electricity and artificial lighting, the planet's nocturnal light environment has changed dramatically. This changing light environment is accompanied by altered behaviors in wild organisms, often resulting in drastic impacts on their fitness and population dynamics. Such effects have been demonstrated in a wide range of organisms, from plants to animals. However, there is a gap in our knowledge regarding freshwater reptiles. While extensive studies on sea turtles show alarming impacts of light pollution on their survival and recruitment, little is known about the effects on their freshwater counterparts and other aquatic reptiles, particularly crocodylians. Yet, these species face high extinction risk from anthropogenic stressors. The current lack of knowledge of their responses to the growing global pervasiveness of light pollution is a barrier to their effective conservation. Moreover, their responses could translate into ecosystem‐level alterations through top‐down effects, as have been observed for other species. Here, we synthesize the existing knowledge of the responses of aquatic reptiles, particularly freshwater crocodiles and turtles, to light pollution and discuss existing mitigation strategies to safeguard these species against the new threat. Knowledge gaps and existing mitigation strategies need to be addressed to promote species conservation in the face of the novel stressor, including in developing countries.
Analytical approach to control the irreversibilities in a chemically reactive nanofluid flow over a Darcy–Forchheimer medium with nonuniform heat source/sink
Authors: Devi A A , Chakraborty Tanmoy 
Published: January 2025

AbstractIn real‐world processes, such as heat transfer, fluid flow, and chemical reactions, irreversibility occurs frequently, which induces an augment in entropy. The optimization of the entropy generation in a mechanical system is one of the fundamental areas of research to channel the energy of the system for utilization. This research exhibits an entropy generation in a nanofluid flow drenched in a fluid‐saturated non‐Darcy porous medium toward a stagnation point. The flow line also experiences the existence of nonuniform heat generation/absorption following the first‐order chemical reaction, which enhances the applicability of this model in different domains of science and engineering. A special form of the Lie group approach is applied to revert the governing partial differential system into its self‐similar ordinary differential form. The solutions of the transformed nonlinear ODEs are acquired analytically through the DTM ‐Padé as well as numerically by the Runge–Kutta–Fehlberg (RKF‐45) method coupled with the shooting process. The fallouts are vividly sketched graphically. One of the upshots reveals that the escalation of space and temperature‐reliant heat absorption parameters can optimize the thermal irreversibility of the system and so as the total entropy generation. Meanwhile, by incrementing the Darcy parameter from 0 to 0.8, the wall shear stress decays by 23.7%, whereas with the same hike in the Forchheimer resistance factor, declines the rate of heat and mass transfer approximately by 2.6% and 3.6%, respectively. Another upshot reveals that with the escalation of the space‐dependent heat source parameter from 0.1 to 0.5, the Nusselt number significantly decreased by 23.9%. Meanwhile boosting the temperature‐reliant heat sink parameter from ‐0.1 to ‐0.5 causes an inclination in the rate of heat transportation by 10.5%. Moreover, it is found that mass transport irreversibility can be controlled by enhancing the constructive chemical reaction rate. We hope that this study will be beneficial for many engineering and industrial processes, particularly in geothermal energy extraction, nuclear waste disposal management, groundwater filtration machinery and food processing equipment.
Numerical investigation of nanofluid flow over a bidirectional stretching surface in porous media
Authors: Ullah Waseef , Ahmed Zahid , Naeem Khowllah 
Published: January 2025

AbstractFlow‐induced by bidirectional stretching surfaces has significant applications in various engineering processes. This study aims to address the research gap in understanding the three‐dimensional flow of nanofluid over a flat bidirectional stretching surface in a porous medium considering both axisymmetric and non‐axisymmetric scenarios. The analysis incorporates the effects of radiation, internal heat sources, viscous dissipation, and Joule heating. A single‐phase approach is utilized to model the problem. The governing nonlinear PDEs are non‐dimensionalized and transformed into a set of ordinary differential equations using appropriate proportional similarity transformations. A numerical solution is obtained using an implicit finite difference scheme. Using graphical representations, the influence of the Eckert and Prandtl numbers, along with parameters such as permeability, stretching, radiation, and heat sources, is inspected. The study reveals that porosity and magnetic parameters reduce fluid velocity while enhancing the temperature distribution. Conversely, the Eckert number, radiation, and heat source parameters increase the nanofluid temperature. Furthermore, the dimensionless friction coefficient and Nusselt numbers at the boundary are illustrated and computed. These findings offer valuable insights into the fluid dynamics and heat transfer characteristics of the system, enhancing the comprehension of these complex phenomena.