bluuebunny/crossref_metadata_2025 huggingface dataset:
Bio-filtration of Organic Pollutants: Simulation and Mathematical Modelling of Toluene and n-propanol
Authors: Tijani Yusuf Olatunji , Oloniiju Shina Daniel
Published: December 2024

Volatile organic compounds (VOCs) are chemical substances that evaporate quickly, releasing harmful fumes into the atmosphere. Among the various VOCs, toluene and n-propanol are particularly interesting due to their widespread occurrence and considerable industrial impact. This study uses a bio-reactor with microbial biofilm formation to present the bio-degradation of a composition of toluene (methylbenzol) and n-propanol (1-propanol). It predicts the coupled inhibition effect of n-propanol on the toluene removal efficiency. The bio-filtration process is modelled as a dynamical system using a set of deterministic nonlinear partial differential equations. The differential equation with its appropriate conditions describes the bio-filtration processes occurring in two distinct phases: the biofilm phase and the gaseous phase. The differential equation is solved using the Chebyshev pseudospectral method and the local linearization method to understand the physical dynamics of the mathematical model. The effectiveness of the spectral-based method was evaluated by comparing its accuracy to known results in the limiting cases of the current dynamical model. A parametric and partial rank correlation coefficient (PRCC) analysis of the dimensionless parameters is conducted. It was found that toluene removal is enhanced by the additional desorption rate constant, ζ
2. Increasing the air-biofilm coefficient for n-propanol supports the removal of n-propanol but not that of toluene. The findings of this study contribute to improvements in bio-degradation modelling and enhance our understanding of volatile organic compounds.
Analysing Battery Swapping of Battery Electric Load Haul Dump (LHD) Machines in Block Cave Mining Using Discrete Event Simulation (DES)
Authors: Hooli Jenni , Skawina Bartłomiej , Halim Adrianus , Sundqvist Fredrik
Published: December 2024

Diesel-powered load haul dump machines have been the backbone of underground mining loading and hauling operations for over six decades. However, as mines get deeper, and regulations become more rigorous, the adoption of battery electric vehicles (BEVs) has the potential to enhance energy efficiency and provide a healthier environment for miners. Electric engines have a significantly higher energy efficiency and produce no exhaust gases or diesel particulate matter. The use of BEVs in underground operations introduces additional factors to consider, such as battery swapping and the required number of batteries, swapping, and charging stations. This study conducted a discrete event simulation using Arena simulation software with a focus on queueing and its relationship to different numbers of machines, batteries, and swapping times in an underground block cave mine. The results suggest that when there are six, eight, or 12 LHDs and four swapping and charging stations with an unlimited number of batteries, the queueing time to swap the batteries remains minimal. In scenarios with eight LHDs and a limited number of batteries, depending on the battery swapping time, 2–2.5 batteries per machine are required to achieve maximum production with minimal queueing. However, when there are too few batteries, queueing becomes significant. Moreover, when the number of working groups (machines going for a battery swap around the same time) is less than the ratio between the battery operational time and the swapping time, the queueing remains low.
Husserl's Philosophy of Mathematical Practice
Authors: Hartimo Mirja
Published: December 2024

Husserl's Philosophy of Mathematical Practice explores the applicability of the phenomenological method to philosophy of mathematical practice. The first section elaborates on Husserl's own understanding of the method of radical sense-investigation (Besinnung), with which he thought the mathematics of his time should be approached. The second section shows how Husserl himself practiced it, tracking both constructive and platonistic features in mathematical practice. Finally, the third section situates Husserlian phenomenology within the contemporary philosophy of mathematical practice, where the examined styles are more diverse. Husserl's phenomenology is presented as a method, not a fixed doctrine, applicable to study and unify philosophy of mathematical practice and the metaphysics implied in it. In so doing, this Element develops Husserl's philosophy of mathematical practice as a species of Kantian critical philosophy and asks after the conditions of possibility of social and self-critical mathematical practices.
Advances in Efficient Design of Experiments in Economics
Authors: Krawczyk Michał Wiktor , Noble John Masson
Published: December 2024

Amidst concerns about replicability but also thanks to the professionalisation of labs, the rise of pre-registration, the switch to online experiments, and enhanced computational power, experimental economics is undergoing rapid changes. They all call for efficient designs and data analysis, that is, they require that, given the constraints on participants' time, experiments provide as rich information as possible. In this Element the authors explore some ways in which this goal may be reached.
State and Sub-State Nationalism in Southeast Asia
Authors: Bertrand Jacques
Published: December 2024

Nationalism is a political phenomenon with deep roots in Southeast Asia. Yet, state attempts to create homogenous nations met with resistance. This Element focuses on understanding the rise and subsequent ebbing of sub-state nationalist mobilization in response to state nationalism. Two factors allowed sub-state nationalist movements to be formed and persist: first, state nationalisms that were insufficiently inclusive; second, the state's use of authoritarian tools to implement its nationalist agenda. But Southeast Asian states were able to reduce sub-state nationalist mobilization when they changed their policies to meet two conditions: i) some degree of explicit recognition of the distinctiveness of groups; ii) institutional flexibility toward regional/local territorial units to accommodate a high degree of group self-governance. The Element focuses on four states in the region – namely Indonesia, the Philippines, Thailand, and Myanmar.
Challenges to mangroves of the Semiarid Equatorial Coast of Brazil in the Anthropocene
Authors: Lacerda Luiz Drude de , Ferreira Alexander Cesar , Borges Rebecca , Ward Raymond
Published: December 2024

The semiarid northeast coast of Brazil harbours just less than 44,300 ha of mangroves, 4% of Brazilian total. Notwithstanding this relatively small area, these forests have high ecological and economic importance, sustaining traditional fisheries and protecting biodiversity, including many threatened species. They present unique biogeochemical characteristics resulting in distinct ecosystem functioning compared to mangroves located in humid areas. Semiarid mangroves present lower aboveground biomass compared to humid region mangroves but show similar belowground biomass. Whereas mangrove soils in humid areas are strongly influenced by sulphate reduction, iron geochemistry is a primary driver of soil characteristics in semiarid mangrove soils, suggesting different responses to climate change drivers between them. Although legally protected, they have incurred continuous degradation due to regional drivers, mostly aquaculture and river damming, which differs from those in humid coast mangroves. Semiarid mangroves are also particularly sensitive to drivers associated with global climate change (high temperatures, reduced rainfall and sea level rise). These conditions occur at a global scale; however, the impacts are worsened by the natural conditions of semiarid coastlines, which already provide biologically stressful conditions for mangroves. This article compares the impacts of such drivers in semiarid mangroves with those of humid mangroves, focusing on their biogeochemical response and eventual rehabilitation.
Radical uncertainty and pragmatism: Threat perception and response
Authors: Stein Janice Gross
Published: December 2024

This article brings a pragmatic perspective to the analysis of threat perception in two important ways. First, as does the philosophical tradition of pragmatism, the article joins perception (or knowledge) together with response (action). Perception and response, knowledge and action, are inextricably linked as people learn through the creation of knowledge what is useful in the world. It is in this sense that pragmatists understand the perception and response to threats as evolved practices that are conjoined. Second, the paper explores threat perception and response under the condition of radical uncertainty. I explore the kinds of strategies leaders can use to respond to perceived threat in a context of radical uncertainty, the defining characteristic of contemporary world politics, and explore the advantages of pragmatic strategies that proceed to look for ‘what works in the world’ as provisional responses to perceived threats through iterative, ongoing experimental processes.
Under the shadow of occupation: cultural, archaeological, and military activities at Topkapı Palace during the armistice period, 1918–1923
Authors: Özlü Nilay
Published: December 2024

This article looks at Topkapı Palace as a showcase reflecting the changing cultural heritage policies of the Allies, as well as of the İstanbul and Ankara governments, during the occupation of İstanbul from 1918 to 1923. It analyzes the military, archaeological, and cultural facets of the occupation, focusing first on the military takeover of the Topkapı gardens, then on the French archaeological mission at the Seraglio, and finally on conflicts over the possession of the imperial treasures and sacred relics. Drawing on primary sources from Ottoman, Turkish, French, and British archives, memoirs, letters, newspapers, and visual material, this article explores the versatility of cultural heritage policies during the occupation and the entangled relations among various power groups, institutions, and actors. The military, strategic, cultural, and historical significance of the royal complex, together with its invaluable imperial collections, made the historic palace a place of rivalry and contestation, as well as deception and cooperation, among various agents and actors, including the Ottoman military and bureaucratic officials, local and foreign archaeologists, the dynastic family, the Interallied government, the occupation forces, and the Turkish resistance forces, ultimately reflecting the military and political empowerment of Ankara.
The role of processing goals in second language predictive processing
Authors: Kim Hyunwoo , Kim Kitaek , Kim Joonhee
Published: December 2024

This study investigates how second language (L2) learners engage in prediction based on their processing goals. While prediction is a prominent feature of human sentence comprehension in first–language speakers, it remains less understood when and how L2 learners engage in predictive processing. By conducting a visual–world eye–tracking experiment involving Chinese–speaking L2 learners of Korean, we tested the hypothesis that L2 learners determine whether to engage in prediction by evaluating the costs and benefits of anticipatory processing. The experiment specifically focused on the impact of a top–down comprehension goal for L2 learners’ predictive use of an honorific form in Korean by providing them with different types of task instruction. Our results indicated that all groups engaged in predictive processing in early and entire predictive regions. However, in the late predictive region, L2 learners presented with a prediction–oriented task, but not those with a simple comprehension task, actively generated expectations about the honorific status of an upcoming referent. These findings lend support to the utility account of L2 prediction, suggesting that L2 learners’ engagement in prediction depends on their current goals and strategies for processing efficiency.
Uterus Transplant: Bioethical and Biolegal Issues from Mexico
Authors: Calleja-Sordo Elisa Constanza , Medina-Arellano María de Jesús
Published: December 2024

Uterus transplants (UTx) provide women without a uterus the possibility of experiencing gestational motherhood. This paper delineates the complex bioethical landscape surrounding UTx, focusing on the critical aspects of informed consent, risk–benefit analysis, justice considerations, and the distinct challenges encountered by both donors and recipients. While not discussing UTx directly, John Harris’ seminal work, The Value of Life: An Introduction to Medical Ethics (1985) in its advocacy for reproductive freedom and informed consent provides an informative starting point for the discussion.

As an example, UTx is analyzed within the socio-political context of Mexico. The impact of the Mexican healthcare and legal systems on UTx procedures is discussed and the regulatory measures necessary to ensure that UTx is conducted ethically and equitably are outlined.
Beyond Virtuosity: Joachim, the Mendelssohn Circle, and the Illusion of Three Hands
Authors: Todd R. Larry
Published: December 2024

This article discusses illusions of ‘three hands’ in the circle of Joachim and the Mendelssohns, arguing that manifestations of ‘three hands’ at play created an aesthetic both in dialogue with the Golden Age of Virtuosity, and going beyond it. Though techniques alluding to three hands or multiple performing bodies diminished sharply in popularity after 1830–50, violin and piano music from the later nineteenth and twentieth centuries remained highly virtuosic and often ‘unplayable’ in other ways. The difference between before and after the half-century mark is that later examples tended not to celebrate so overtly such special effects, because doing so would revive the no-longer-tenable principle of ‘virtuosity as a reward in itself’. Rather, double-stop harmonics, left-hand pizzicato, three-hand techniques and their related sleights of hand were largely escorted off the stage into a pedagogical realm. As this article shows, Joachim helped to exorcise the spectre of Paganini, and to sweep effectively out the door the residual confetti of the Golden Age of Virtuosity. Following in the footsteps of Mendelssohn, Joachim did so with Clara Schumann, viewing himself, Clara Schumann (and, we might add, Brahms) as a cohort of artists seeking to reverse the tawdry display of virtuosity. It was precisely Joachim's acute historicist perception, solidified during the 1850s, that allowed his musical aesthetics to turn so sharply from his openness to, tolerance and acceptance of dazzling violinistic tricks in the 1840s, to their absolute rejection in his later career.
Psychosocial interventions for hoarding disorder: a systematic review
Authors: Twigger Daisy , Gregory James D. , Bowers Emma , Millar Josie F.A.
Published: December 2024

Introduction:

Hoarding disorder (HD) is primarily characterised by difficulties with discarding possessions. Evidence-based psychological interventions such as CBT have been found to be of benefit to people with HD. However, people with HD may receive a psychosocial intervention provided by other professions such as social workers or a multi-disciplinary team before receiving psychological therapy, if at all.

Objectives:

The aim of this systematic review is to evaluate psychosocial interventions for HD.

Method:

Searches were conducted on three databases (PsycInfo; MEDLINE; Embase) and grey literature, and the search strategy was designed to capture psychosocial interventions for adults with HD.

Results:

Studies (n=5) were included where the outcome was related to a psychosocial factors, such as fire safety, tenancy preservation and QoL. These psychosocial interventions show improvements in those with HD, with effect sizes ranging from d=0.86 to d=1.41.

Conclusions:

Despite the limited research on psychosocial interventions for HD, this systematic review suggests it is a promising area for further research in this area.

Key learning aims

(1)

To identify what psychosocial interventions are available for people experiencing hoarding difficulties.

(2)

To identify how available psychosocial interventions for hoarding difficulties are delivered and by whom.

(3)

To examine the effectiveness of psychosocial interventions for people experiencing hoarding difficulties.
Augmented und Virtual Reality in der Diagnostik und Therapie von Neglect nach Hirnschädigung
Authors: Stammler Britta , Karnath Hans-Otto
Published: December 2024

Zusammenfassung: In den letzten Jahren haben digitale Technologien in der Diagnostik sowie in der Therapie neurologischer Störungen an Bedeutung gewonnen. Dazu gehört auch der Neglect, eine der häufigsten kognitiven Störungen nach Schädigungen der rechten Hemisphäre. In der diagnostischen Anwendung ermöglicht der Einsatz von Virtual Reality (VR) und Augmented Reality (AR), das nach ipsiläsional verschobene Explorations- und Aufmerksamkeitsverhalten von Neglectpatienten in realitätsnahen, dreidimensionalen Umgebungen präzise zu erfassen und zu analysieren. Studien zeigen, dass diese Technologien herkömmliche Papier-und-Bleistift-Verfahren sinnvoll ergänzen und möglicherweise besser für die Detektion subtiler Neglectsymptomatik geeignet sind. Aufgaben, die in der Realität aufgrund des Gefahrenpotenzials nicht durchgeführt werden können, sind hier ein gutes Beispiel. Im therapeutischen Bereich bieten VR/AR-Anwendungen innovative Erweiterungen des aktiven Explorationstrainings von Neglectpatienten, was die Therapiemotivation und den Behandlungserfolg steigern kann. Studien belegen, dass immersive VR-Explorationstrainings und AR-basierte Anwendungen wirksam dazu beitragen, Neglectsymptome zu reduzieren und die Alltagskompetenzen der Patienten zu verbessern. AR-Anwendungen, die lediglich den Einsatz von im Alltag häufig schon vorhandenen Tablets oder Smartphones erfordern, bieten im Vergleich zu VR-Systemen eine kostengünstigere Alternative. Trotz positiver Ergebnisse bestehen für eine breite klinische Anwendung noch Herausforderungen hinsichtlich Standardisierung, Normierung und technischer Kompatibilität dieser Anwendungen. Zudem sind transparente Informationen zu apparativen Voraussetzungen, Verfügbarkeit und den Kosten der Anwendungen notwendig, um die Akzeptanz und Verbreitung dieser Technologien zu erhöhen. Weitere randomisierte, kontrollierte Studien werden benötigt, um auch die langfristige Wirksamkeit und Benutzerfreundlichkeit zu bestätigen. Zusammenfassend lässt sich sagen, dass die Nutzung digitaler VR/AR-Technologien in der Diagnostik und Therapie von Neglect großes Potenzial bietet.
New Generation Site and Estimated Propagation of Nonlinear Internal Waves Under Varying Background Stratification in the Northeastern East China Sea
Authors: Lee Seung‐Woo , Nam SungHyun , Noh Suyun
Published: December 2024

This study investigates the generation and propagation of nonlinear internal waves (NLIWs) in the northeastern East China Sea (ECS), focusing on the impact of time‐varying background stratification. Using satellite imagery and tide‐generating body force, 327 groups of NLIWs were identified from 93 MODIS images collected between 2015 and 2019 and classified into three distinct types based on their propagation directions—Type‐A (∼42%), Type‐B (∼38%), and Type‐C (∼20%)—each originating from different generation sites. Type‐B NLIWs were found to originate from a newly identified site near southwestern Fukue Island reported here for the first time, whereas Type‐A and Type‐C originated from the northern Okinawa Trough and southwestern Jeju Island, respectively. Seasonal variations in NLIW propagation speed using historical CTD data revealed an increase in the speed from winter to spring and fall, peaking in summer due to strong stratification. Although spatial distribution varied by season, propagation was generally faster in the eastern region than in the western region attributed to deeper thermoclines and higher density gradients. During field observation in May 2015, the observed NLIWs had an amplitude of 5–6 m, a characteristic width of 380–450 m, southwestward propagating directions, and a speed of ∼0.54 m s−1. An empirical model, used to track and predict these waves, confirmed their generation locations from southwestern Fukue Island (Type‐B) and indicated fast arrival speeds, influenced by time‐varying stratification conditions during the stratification period. These findings highlight the impacts of varying background conditions on NLIW propagation and would facilitate their prediction.
TIGAR coordinates senescence-associated secretory phenotype via lysosome repositioning and α-tubulin deacetylation
Authors: Nam Hae Yun , Park Seung-Ho , Lee Geun-Hee , Kim Eun-Young , Lee SangEun , Chang Hyo Won , Chang Eun-Ju , Choi Kyung-Chul , Kim Seong Who
Published: December 2024

TP53-induced glycolysis and apoptosis regulator (TIGAR) regulates redox homeostasis and provides the intermediates necessary for cell growth by reducing the glycolytic rate. During cellular senescence, cells undergo metabolic rewiring towards the glycolytic pathway, along with the development of the senescence-associated secretory phenotype (SASP), also known as the secretome. We observed that TIGAR expression increased during replicative senescence following the in vitro expansion of human mesenchymal stromal cells (MSCs) and that TIGAR knockout (KO) decreased SASP factors and triggered premature senescence with decelerated progression. Additionally, TIGAR KO impaired flexible lysosomal movement to the perinuclear region and decreased the autophagic flux of MSCs. Research on the mechanism of lysosomal movement revealed that, while native senescent MSCs presented low levels of Ac-α-tubulin (lysine 40) and increased sirtuin 2 (SIRT2) activity compared with those in growing cells, TIGAR KO-MSCs maintained Ac-α-tubulin levels and exhibited decreased SIRT2 activity despite being in a senescent state. The overexpression of SIRT2 reduced Ac-α-tubulin as a protein target of SIRT2 and induced the positioning of lysosomes at the perinuclear region, restoring the cytokine secretion of TIGAR KO-MSCs. Furthermore, TIGAR expression was positively correlated with SIRT2 activity, indicating that TIGAR affects SIRT2 activity partly by modulating the NAD+ level. Thus, our study demonstrated that TIGAR provides a foundation that translates the regulation of energy metabolism into lysosome positioning, affecting the secretome for senescence development. Considering the functional value of the cell-secretome in aging-related diseases, these findings suggest the feasibility of TIGAR for the regulation of secretory phenotypes.
Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application
Authors: Chen Yang , Liang Rui , Li Yong , Jiang Lingli , Ma Di , Luo Qing , Song Guanbin
Published: December 2024

The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.
Decoding the molecular, cellular, and functional heterogeneity of zebrafish intracardiac nervous system
Authors: Pedroni Andrea , Yilmaz Elanur , Del Vecchio Lisa , Bhattarai Prabesh , Vidal Inés Talaya , Dai Yu-Wen E. , Koutsogiannis Konstantinos , Kizil Caghan , Ampatzis Konstantinos
Published: December 2024

The proper functioning of the heart relies on the intricate interplay between the central nervous system and the local neuronal networks within the heart itself. While the central innervation of the heart has been extensively studied, the organization and functionality of the intracardiac nervous system (IcNS) remain largely unexplored. Here, we present a comprehensive taxonomy of the IcNS, utilizing single-cell RNA sequencing, anatomical studies, and electrophysiological techniques. Our findings reveal a diverse array of neuronal types within the IcNS, exceeding previous expectations. We identify a subset of neurons exhibiting characteristics akin to pacemaker/rhythmogenic neurons similar to those found in Central Pattern Generator networks of the central nervous system. Our results underscore the heterogeneity within the IcNS and its key role in regulating the heart’s rhythmic functionality. The classification and characterization of the IcNS presented here serve as a valuable resource for further exploration into the mechanisms underlying heart functionality and the pathophysiology of associated cardiac disorders.
Identification of rare disease genes as drivers of common diseases through tissue-specific gene regulatory networks
Authors: Bakker Olivier B. , Claringbould Annique , Westra Harm-Jan , Wiersma Henry , Boulogne Floranne , Võsa Urmo , Urzúa-Traslaviña Carlos G. , Mulcahy Symmons Sophie , Zidan Mahmoud M. M. , Sadler Marie C. , Kutalik Zoltán , Jonkers Iris H. , Franke Lude , Deelen Patrick
Published: December 2024

Genetic variants identified through genome-wide association studies (GWAS) are typically non-coding, exerting small regulatory effects on downstream genes. However, which downstream genes are ultimately impacted and how they confer risk remains mostly unclear. By contrast, variants that cause rare Mendelian diseases are often coding and have a more direct impact on disease development. Here we demonstrate that common and rare genetic diseases can be linked by studying how common disease-associated variants influence gene co-expression in 57 different tissues and cell types. We implemented this method in a framework called Downstreamer and applied it to 88 GWAS traits. We find that predicted downstream “genes” are enriched with Mendelian disease genes, e.g. key genes for height are enriched for genes that cause skeletal abnormalities and Ehlers–Danlos syndromes. 78% of these key genes are located outside of GWAS loci, suggesting that they result from complex trans regulation rather than being impacted by disease-associated variants in cis. Based on our findings, we discuss the challenges in reconstructing gene regulatory networks and provide a roadmap to improve the identification of these highly connected genes linked to common traits and diseases.
A fish-friendly axial flow pump turns out to be eel safe, roach unfriendly and bream unsafe
Authors: Bruneel Stijn , Pauwels Ine S. , Broos Sarah , Vandamme Lore , Van Wichelen Jeroen , Coeck Johan , Toming Gert , Tuhtan Jeffrey A. , Buysse David
Published: December 2024

Additional and refurbished pumping stations are required to mitigate the intensifying occurrence of droughts and floodings. These installations negatively impact threatened freshwater fish populations due to the increased risk of injury and mortality when fish pass through them. Fish-friendly pumping installations have been proposed as a potential solution to reduce these risks. However, published assessments of these new types of pumps remains lacking, and the few available studies do not enable a cross-comparison with conventional pump types. The promising, yet understudied, Fairbank Nijhuis ‘fish-friendly’ axial flow pump has been assessed in previous works, however the results remain ambiguous due to low recapture rates, unconsidered parameters, fixed operating conditions, and the inability to identify the likely sources of injury and mortality. In this study, we address the limitations of previous works by implementing a standardized protocol for live fish in conjunction with passive barotrauma detection sensors. The major finding of this work is that safe passage of eel (100% survival) is confirmed, but that bream and roach had a much lower survival probability (24% and 70% survival respectively) than expected, albeit higher than for a conventional axial flow pump (roach survival: 13%). Furthermore, roach and bream passing at higher rpm suffered significantly higher mortalities. The impact of the impeller was found to be the most common source of severe injury for both pumps. These results are significant because they conclusively show that fish-friendly pumps may be considered safe for eel, but not for other endemic European fish species such as roach and bream.
Potential energy landscape formalism for quantum molecular liquids
Authors: Eltareb Ali , Zhou Yang , Lopez Gustavo E. , Giovambattista Nicolas
Published: December 2024

The potential energy landscape (PEL) formalism is a powerful tool within statistical mechanics to study the thermodynamic properties of classical low-temperature liquids and glasses. Recently, the PEL formalism has been extended to liquids/glasses that obey quantum mechanics, but applications have been limited to atomistic model liquids. In this work, we extend the PEL formalism to liquid/glassy water using path-integral molecular dynamics (PIMD) simulations, where nuclear quantum effects (NQE) are included. Our PIMD simulations, based on the q-TIP4P/F water model, show that the PEL of quantum water is both Gaussian and anharmonic. Importantly, the ring-polymers associated to the O/H atoms in the PIMD simulations, collapse at the local minima of the PEL (inherent structures, IS) for both liquid and glassy states. This allows us to calculate, analytically, the IS vibrational density of states (IS-VDOS) of the ring-polymer system using the IS-VDOS of classical water (obtained from classical MD simulations). The role of NQE on the structural properties of liquid/glassy water at various pressures are discussed in detail. Overall, our results demonstrate that the PEL formalism can effectively describe the behavior of molecular liquids at low temperatures and in the glass states, regardless of whether the liquid/glass obeys classical or quantum mechanics.
Sensitivity of mesoscale modeling to urban morphological feature inputs and implications for characterizing urban sustainability
Authors: Allen-Dumas Melissa R. , Sweet-Breu Levi T. , Brelsford Christa M. , Wang Linying , New Joshua R. , Bass Brett C.
Published: December 2024

We examine the differences in meteorological output from the Weather Research and Forecasting (WRF) model run at 270 m horizontal resolution using 10 m, 100 m and 1 km resolution 3D neighborhood morphological inputs and with no morphological inputs. We find that the spatial variability in temperature, humidity, and other meteorological variables across the city can vary with the resolution and the coverage of the 3D urban morphological input, and that larger differences occur between simulations run without 3D morphological input and those run with some type of 3D morphology. We also find that the inclusion of input-building-defined roughness length calculations would improve simulation results further. We show that these inputs produce different patterns of heat wave spatial heterogeneity across the city of Washington, DC. These findings suggest that understanding neighborhood level urban sustainability under extreme heat waves, especially for vulnerable neighborhoods, requires attention to the representation of surface terrain in numerical weather models.
Photocontrol of ferroelectricity in multiferroic BiFeO3 via structural modification coupled with photocarrier
Authors: Takubo Kou , Ono Atsushi , Ueno Shunsuke , Banu Samiran , Yu Hongwu , En-ya Kaito , Nishimori Ryota , Kuwahara Makoto , Asaka Toru , Maeda Kei , Ono Daiki , Ozawa Keita , Itoh Takuma , Shigematsu Kei , Azuma Masaki , Ishikawa Tadahiko , Okimoto Yoichi , Hada Masaki , Koshihara Shin-ya
Published: December 2024

Ultrafast control of ferroelectricity and magnetism by light is essential for future development in multiple functioning devices. Here, we demonstrate that the intense and ultrafast photo-modulation of the electric dipole can be realized by photocarrier injection into a multiferroic BiFeO3 thin film using optical pump-probe and second harmonic generation measurements. Results of ultrafast electron diffraction with <100 fs time resolution and theoretical study reveal that the localized photocarrier strongly couples with the lattice structure and becomes the origin for the observed sudden change in the electric dipole. In addition, the subsequent structural dynamics involve a strong oscillation with a frequency of ~3.3 THz despite a poor structural symmetry change. Based on a theoretical calculation, this oscillation can be attributed to an unexpectedly softened new phonon mode generated by mixing essential two phonon modes governing the multiferroic (ferroelectric and antiferromagnetic) nature of BiFeO3 in the ground state due to strong coupling with a localized photocarrier. The comprehensive study shows that injection of the localized photocarrier strongly coupled with the lattice vibration mode can simultaneously realize the ultrafast switching of electric dipoles and magnetic interaction at once, even at room temperature, without modifying the long-range lattice structure.
Contribution of the infection ecosystem and biogeography to antibiotic failure in vivo
Authors: Nazeer Rahan Rudland , Askenasy Isabel , Swain Jemima E. V. , Welch Martin
Published: December 2024

The acquisition of antibiotic resistance in bacteria, though a deeply concerning international issue, is reasonably well-understood at a mechanistic level. Less well-understood is why bacteria that are sensitive in vitro to well-established and widely-used antibiotics sometimes fail to respond to these agents in vivo. This is a particularly common problem in chronic, polymicrobial infection scenarios. Here, we discuss this in vitro-in vivo disconnect from the perspective of the bacterium, focusing in particular on how infection micro/macro-environment, biogeography, and the presence of co-habiting species affect the response to antibiotics. Using selected exemplars, we also consider interventions that might improve treatment outcomes, as well as ecologically ‘eubiotic’ approaches that have less of an impact on the patient’s commensal microflora. In our view, the accrued data strongly suggest that we need a more comprehensive understanding of the in situ microbiology at infection sites.
Kinesin-like motor protein KIF23 maintains neural stem and progenitor cell pools in the developing cortex
Authors: Naher Sharmin , Iemura Kenji , Miyashita Satoshi , Hoshino Mikio , Tanaka Kozo , Niwa Shinsuke , Tsai Jin-Wu , Kikkawa Takako , Osumi Noriko
Published: December 2024

Accurate mitotic division of neural stem and progenitor cells (NSPCs) is crucial for the coordinated generation of progenitors and mature neurons, which determines cortical size and structure. While mutations in the kinesin-like motor protein KIF23 gene have been recently linked to microcephaly in humans, the underlying mechanisms remain elusive. Here, we explore the pivotal role of KIF23 in embryonic cortical development. We characterize the dynamic expression of KIF23 in the cortical NSPCs of mice, ferrets, and humans during embryonic neurogenesis. Knockdown of Kif23 in mice results in precocious neurogenesis and neuronal apoptosis, attributed to an accelerated cell cycle exit, likely resulting from disrupted mitotic spindle orientation and impaired cytokinesis. Additionally, KIF23 depletion perturbs the apical surface structure of NSPCs by affecting the localization of apical junction proteins. We further demonstrate that the phenotypes induced by Kif23 knockdown are rescued by introducing wild-type human KIF23, but not by a microcephaly-associated variant. Our findings unveil a previously unexplored role of KIF23 in neural stem and progenitor cell maintenance via regulating spindle orientation and apical structure in addition to cytokinesis, shedding light on microcephaly pathogenesis.
Transferable Skills and Reflection (the Career Building Transferable Skill)
Authors: Ziebell Angela
Published: December 2024

Transferrable skills are all those non-technical skills that allow us to do the technical part of our role well. They are highly valued by employers and managers. This chapter introduces what transferrable skills are and how important it is to both have transferrable skills and be able to articulate what your transferrable skills are. One particularly important transferable skill is reflection. This chapter also looks at the skill of reflection in detail, helping the reader understand reflection and improve their reflective skills so they can use these skills to develop all aspects of their career.
Portfolio Building
Authors: Mckenzie Sophie
Published: December 2024

Portfolios can be an important part of developing your professional self, beginning from when you are a student (although it is never too late to start). Portfolios have the triple purpose of giving you a mechanism to collect records of your achievements for future reference so they do not get forgotten. It is a place to reflect on your progress, aims, strengths and weaknesses. Lastly, a portfolio is a place where you can construct and, if you want, display your finest achievements. This chapter takes you through the ins and outs of constructing a portfolio and how they can help you.
Developing Your STEM Career: What Next?
Authors: Ziebell Angela
Published: December 2024

This chapter can help you make plans for what is next on your career building journey. It is likely that your plan will include returning to the book as you work on particular skills or gain particular experiences that you have determined will help you progress. We understand that everyone’s next steps look different. To help you move forward, sections of this chapter specifically address different cohorts, for example, final year students vs. those trying to redirect their career. We finish the chapter by hearing insights from each of the five authors who hope their words have helped you on your way to Building Your Career in STEM.
A Cu/β-cyclodextrin/reduced graphene oxide nanocomposite for efficient and multi-aflatoxin detection in rice, ginger and bean samples
Authors: Shahryari Behnaz , Khani Rouhollah , Feizy Javad
Published: December 2024

Aflatoxins (AFs) are some of the most important mycotoxins or fungal toxins that cause contamination of food products and are considered a threat to human and animal health.
Expression of concern: An ‘on-demand’ photothermal antibiotic release cryogel patch: evaluation of efficacy on an ex vivo model for skin wound infection
Authors: Rosselle Léa , Cantelmo Anna Rita , Barras Alexandre , Skandrani Nadia , Pastore Michael , Aydin Duygu , Chambre Laura , Sanyal Rana , Sanyal Amitav , Boukherroub Rabah , Szunerits Sabine
Published: December 2024

Expression of concern for ‘An ‘on-demand’ photothermal antibiotic release cryogel patch: evaluation of efficacy on an ex vivo model for skin wound infection’ by Léa Rosselle, et al., Biomater. Sci., 2020, 8, 5911–5919, https://doi.org/10.1039/D0BM01535K.
Implications of non-native metal substitution in carbonic anhydrase – engineered enzymes and models
Authors: Bhandary Dyuti , de Visser Sam P. , Mukherjee Gourab
Published: December 2024

The effect of non-native metal ions on the carbonic anhydrase activity of CO2 hydration has been studied by substituting the native zinc with non-native metal ions in engineered enzymes and biomimetic models.
Relationship between Lewis acid sites and carbohydrate reactivity over Sn-β catalysts
Authors: Boudjema Yacine , Brunel Antoine , Del Cerro Raphaël , Pirngruber Gerhard , Chizallet Céline , Larmier Kim
Published: December 2024

Sn-β is a promising Lewis acid zeolite for carbohydrate conversion.
Visualizing high entropy alloy spaces: methods and best practices
Authors: Vela Brent , Hastings Trevor , Allen Marshall , Arróyave Raymundo
Published: December 2024

Multi-Principal Element Alloys (MPEAs) have emerged as an exciting area of research in materials science in the 2020s, owing to the vast potential for discovering alloys with unique and tailored properties enabled by the combinations of elements.
Photocurable epoxy-based composite for rapid orthopedic soft casting
Authors: Tosetto Beatrice , Mo Roberto , Pirri Candido Fabrizio , Roppolo Ignazio
Published: December 2024

A soft cast based on a photocurable composite is investigated to produce breathable and easily applicable medical devices. Two main innovations are introduced: the use of market-ready epoxy resins and the use of a stretchable tubular medical net.
Unravelling the oxygen exchange mechanism on La2Ce2O7
Authors: Shen Yizhou , Thoréton Vincent , Haugsrud Reidar
Published: December 2024

Electronic defects enhance oxygen exchange kinetics in Pr-doped La2Ce2O7. Humidity reduces the exchange rate and increases activation energy below 800 °C due to the adsorption of hydroxide species.
Solvation structure regulation of zinc ions with nitrogen-heterocyclic additives for advanced batteries
Authors: Shang Junhao , Wang Yanxu , Chen Song , Zhang Jintao
Published: December 2024

The coordination and electrode–electrolyte interface microenvironment of zinc ions have been effectively regulated using poly-nitrogen heterocyclic compounds as electrolyte additives, achieving long reversible cycling of zinc batteries.
Helical magnetism in poly(aniline-co-ferrocene): structure and magnetism
Authors: Miyashita Ryo , Kawakami Ryo , Kumai Reiji , Tomita Takashi , Goto Hiromasa
Published: December 2024

This study reports the synthesis and characterisation of a ferrocene-based conjugated polymer and a chiral composite.
Se–S dynamic exchange reaction: a strategy of highly efficient S–S bond cleavage for synthesizing benzothiazole derivatives
Authors: Zhang Tian-Xing , Zhang Er-Wei , Zhang Wen-Yue , Zhao Zihao , Guo Qingxiang , Zhu Ning
Published: December 2024

We report a Se–S dynamic exchange reaction as a methodology involving highly efficient S–S bond cleavage for the preparation of benzothiazole derivatives.
Structure–property relationships to direct the dynamic properties of acylsemicarbazide-based materials
Authors: Maessen Stefan J. D. , Lekanne Deprez Siebe , Vermeeren Pascal , van den Bersselaar Bart W. L. , Lutz Martin , Heuts Johan P. A. , Fonseca Guerra Célia , Palmans Anja R. A.
Published: December 2024

We demonstrate that tuning both the dissociation rate and the strength and cooperativity of hydrogen bonds by molecular design is important for controlling thermal stability and creep resistance in dynamic covalent materials.
Acid-responsive singlet oxygen nanodepots
Authors: Ran Zengwei , Wang Maolin , Yuan Zhu , Zhang Yan , Liu Guhuan , Yang Ronghua
Published: December 2024

The aSOND releases 1O2 slowly at neutral pH for blood stability, but rapidly in acidic tumor environments. This controlled, tumor-specific ROS release offers high selectivity and independence from oxygen/light, promising targeted cancer therapy.
3DSMILES-GPT: 3D molecular pocket-based generation with token-only large language model
Authors: Wang Jike , Luo Hao , Qin Rui , Wang Mingyang , Wan Xiaozhe , Fang Meijing , Zhang Odin , Gou Qiaolin , Su Qun , Shen Chao , You Ziyi , Liu Liwei , Hsieh Chang-Yu , Hou Tingjun , Kang Yu
Published: December 2024

We introduce 3DSMILES-GPT, a token-based large language model for 3D molecular generation that integrates 2D and 3D molecular data.
Fast synthesis of DNA origami single crystals at room temperature
Authors: Yu Yifan , Ji Min , Wang Yong , Yan Xuehui , Dai Lizhi , Ma Ningning , Zhou Zhaoyu , Xing Hang , Tian Ye
Published: December 2024

Urea makes the fast and ordered assembly of DNA origami building blocks into user-defined microstructures at room temperature feasible.
Correction: Ion pair extractant selective for LiCl and LiBr
Authors: Heo Nam Jung , Oh Ju Hyun , Li Aimin , Lee Kyounghoon , He Qing , Sessler Jonathan L. , Kim Sung Kuk
Published: December 2024

Correction for ‘Ion pair extractant selective for LiCl and LiBr’ by Nam Jung Heo et al., Chem. Sci., 2024, 15, 13958–13965, https://doi.org/10.1039/D4SC03760J.
Role of SiO2 in enhancing CO yield by using silica-supported La0.5Ba0.5FeO3 in reverse water–gas shift chemical looping
Authors: Shi Hanzhong , Guo Jiawei , Singh Prabhsimran , Bhethanabotla Venkat R. , Kuhn John N.
Published: December 2024

Perovskite oxides facilitate CO2 conversion by reverse water–gas shift chemical looping at moderate conditions by employing an oxygen vacancy at the surface to aid CO2 adsorption and then to scavenge an oxygen atom from it to fill the vacancy.
Mechanistic study on moisture exposure of Ti-based layered oxides for sodium storage applications
Authors: Campéon Benoît D. L. , Ishikawa Tetsuya , Tomohiro Kuriyama , Yabuuchi Naoaki
Published: December 2024

The air stability and moisture sensitivity of titanium-based layered negative electrode materials for sodium storage play a critical role in their practical applications for advanced energy storage systems.
A bifunctional Na-deficient strategy induced pure phase Na4−xFe3(PO4)2P2O7 cathode with high capacity for sodium-ion batteries
Authors: Ma Rongze , Meng Jiaqi , Su Xuping , Wang Qidi , Li Ze , Zeng Qihang , Jing Yawei , Li Long , Ding. Shujiang
Published: December 2024

This study proposes a Na-deficient strategy for the structural modulation of NFPP, successfully synthesizing pure-phase Na4−xFe3(PO4)2(P2O7) with a near-theoretical specific capacity of 127.2 mA h g−1 at 0.1C.
One-step synthesis of hollow spherical Co/Ni hydroxides as multifunctional polysulfide mediators to steer sulfur redox kinetics for high performance lithium–sulfur batteries
Authors: Li Zhen , Yang Man , Li Qing , Cheng Xianghan , Geng Fengting , Wang Yuye , Wang Xiaoli , Zhang Dashuai , Zhang Yongzheng , Zhang Xiuling , Liu Zhongmin , Pang Xuliang , Geng Longlong
Published: December 2024

A series of hollow bimetallic hydroxides with controllable composition and modulated electronic structure have been readily constructed, and exhibit stronger affinity and a synergistic catalysis effect for LiPS intermediates.
Centimeter-level double perovskite single crystals with strong interlaminar hydrogen bonds for high-performance X-ray detection
Authors: Wei Linjie , Liu Yi , Ma Yu , Fan Qingshun , Tang Liwei , Zhang Jingtian , Luo Junhua , Sun Zhihua
Published: December 2024

Strong interlaminar O–H⋯O hydrogen bonds are created to eliminate the van der Waals gap in 2D double perovskites, which facilitates the growth of large crystals toward high performance X-ray detection.