bluuebunny/crossref_metadata_2025 huggingface dataset:
Vietnam, A War, Not a Country
Authors: Eyerman Ron , Madigan Todd , Ring Magnus
Published: November 2023

Vietnam, A War, Not a Country explores the conflicting ways in which the American-Vietnamese War has been collectively remembered and represented from the perspective of the war's three primary belligerents: the Vietnamese communists, the South Vietnamese, and the Americans. The book examines how the three different collectives memorialize this traumatizing historical event. Within each of these three groups there exists a number of competing narratives, generating not only a sense of shared meaning and community, but also impassioned social conflict. In order to trace these narratives within each collectivity, the authors develop the concept of arenas of memory, distinct discourses that are tied to specific individuals, organizations, and institutions that advocate specific narratives through specific forms of media. Their analysis leads them to make the case as to whether each of these societies experienced a cultural trauma as a result of the way in which the war is remembered.
Development of a handheld integrating sphere snow grain sizer (HISSGraS)
Authors: Aoki Teruo , Hachikubo Akihiro , Nishimura Motoshi , Hori Masahiro , Niwano Masashi , Tanikawa Tomonori , Sugiura Konosuke , Inoue Ryo , Yamaguchi Satoru , Matoba Sumito , Shimada Rigen , Ishimoto Hiroshi , Gallet Jean-Charles
Published: November 2023

We developed a Handheld Integrating Sphere Snow Grain Sizer (HISSGraS) for field use to measure the specific surface area (SSA) of snow. In addition to snow samples, HISSGraS can directly measure snow surfaces and snow pit walls. The basic measurement principle is the same as that of the IceCube SSA instrument. The retrieval algorithm for SSA from reflectance employs two conversion equations formulated using spherical and nonspherical grain shape models. We observed SSAs using HISSGraS, IceCube and the gas adsorption method in a snowfield in Hokkaido, Japan. Intercomparison of the results confirmed that with HISSGraS direct measurement, SSA profile observations can be completed in just ~1/10 the time required for measurement of snow samples. Our results also suggest that HISSGraS and IceCube have similar accuracy when the same snow samples are measured using the same grain shape model. However, SSAs of near-surface snow layers measured using the three techniques exhibited some biases, possibly due to rapid snow metamorphism or melting during measurement and some technical issues with optical techniques. When excluding SSA data for the surface layer, which metamorphosed remarkably during measurement, IceCube- and HISSGraS-derived SSAs correlated strongly with those obtained by gas adsorption and HISSGraS accuracy is 21–34%.
Exceptional thinning through the entire altitudinal range of Mont-Blanc glaciers during the 2021/22 mass balance year
Authors: Berthier Etienne , Vincent Christian , Six Delphine
Published: November 2023

Widespread glacier losses have been observed in most glaciated regions on Earth during recent decades, with a typical pattern of strong thinning in their lower reaches and limited elevation changes in their accumulation areas. Here, we use Pléiades satellite stereo-images of the Mont-Blanc massif (Alps) to reveal that thinning took place through the entire elevation range during the exceptional 2021/22 mass-balance year. Above 3000 m a.s.l. on Argentière glacier and Mer de Glace, thinning rates exceeded 3.5 m a−1 while almost no change occurred during the previous 9 years. Below 3000 m a.s.l., these anomalous thinning rates are essentially explained by changes in surface mass balance. At higher altitudes, other processes such as firn densification may play a role. Our analysis shows that high altitude glaciers, mostly stable during the last 100 years, are now responding to the impact of climate change.
THE UNCANNY AFTERLIVES OF AUGUSTUS: READING ACROSS SUETONIUS’LIVES OF THE CAESARS
Authors: Koltermann Jannis F.
Published: November 2023

This article examines the appearances of Augustus in Suetonius’Lives of the Caesarsoutside Augustus' ownLife. It shows how Suetonius contrasts the positive image of Augustus drawn in theLife of Augustuswith the distortion of this image by Augustus’ successors, depicted in the laterLives. In their reception, he is still presented as an ideal to follow, yet as a role model for cruelty (Tiberius), adultery and military failure (Caligula), or lyre-playing (Nero)—roles which Suetonius’ real Augustus never or only marginally assumed. Thus in a series of close and intratextual readings, this article invites a more general reassessment of Suetonius’ work: it suggests that theLives of the Caesarsdraw a more critical image of the Principate than has often been said, that they are more consciously part of an image-making process and, above all, that they should more commonly be understood as one whole work, rather than read individually and in isolation.
Governing Through Gridlock: Bill Composition under Divided Government
Authors: Craig Alison W.
Published: November 2023

What is the effect of divided government on issue attention in state legislatures? Much of the research on divided government examines how it affects the enactment of significant legislation but does not consider other effects on legislative behavior. In this article, I propose a new theory of the relationship between divided government and legislative activity. Regardless of partisan control, reelection-minded legislators face pressure to deliver benefits to voters, yet divided government can make substantive policy change difficult. As a result of these competing pressures, under divided government legislators increasingly turn their focus to bills that benefit their local constituents, which are seen as easier to enact and allow them to engage in advertising, credit claiming, and position taking. Consistent with this theory, I find that under divided government, legislators introduce bills at the same rate, but the type of legislation introduced shifts away from statewide policy changes and towards district-specific legislation.
Observation of Non‐Resonance Interactions Between Cold Protons and EMIC Waves of Different Polarizations in the Inner Magnetosphere
Authors: Li Xinmin , Wang Rongsheng , Gao Xinliang , Lu Quanming , Chen Huayue , Ma Jiuqi
Published: November 2023

Using the high‐quality measurements of plasma by the Magnetospheric Multiscale (MMS) spacecraft, we investigate the wave‐particle interaction between cold protons and Electromagnetic ion cyclotron (EMIC) waves of different polarizations in the inner magnetosphere. Both the left‐hand and right‐hand polarized EMIC waves can interact with cold protons via non‐resonance interaction, and energize the cold protons (∼eV) up to suprathermal energies (∼tens of eV), resulting in a series of bridge‐like arcs in the ion energy spectrogram. Cold protons experience different types of phase bunching in left‐hand and right‐hand polarized EMIC waves. However, the relative angles between the velocities of bunched protons and wave magnetic or electric fields are independent of the polarizations of EMIC waves. Thus, the energy transfer process is not affected by the polarization of EMIC waves. The observations indicate that EMIC waves can affect the magnetospheric particle dynamics by energizing the cold protons.
On the Creation, Depletion, and End of Life of Polar Cap Patches
Authors: Eriksen Nina Kristine , Lorentzen Dag A. , Oksavik Kjellmar , Baddeley Lisa , Hosokawa Keisuke , Shiokawa Kazuo , Bland Emma , Paxton Larry , Zhang Yongliang , McWilliams Kathryn , Yeoman Tim , Themens David R.
Published: November 2023

Ionospheric convection patterns from the Super Dual Auroral Radar Network are used to determine the trajectories, transit times, and decay rates of three polar cap patches from their creation in the dayside polar cap ionosphere to their end of life on the nightside. The first two polar cap patches were created within 12 min of each other and traveled through the dayside convection throat, before entering the nightside auroral oval after 104 and 92 min, respectively. When the patches approached the nightside auroral oval, an intensification in the poleward auroral boundary occurred close to their exit point, followed by a decrease in the transit velocity. The last patch (patch 3) decayed completely within the polar cap and had a lifetime of only 78 min. After a change in drift direction, patch 3 had a radar backscatter power half‐life of 4.23 min, which reduced to 1.80 min after a stagnation, indicating a variable decay rate. 28 minutes after the change in direction, and 16 min after coming to a halt within the Clyde River radar field‐of‐view, patch 3 appeared to reach its end of life. We relate this rapid decay to increased frictional heating, which speeds up the recombination rate. Therefore, we suggest that the slowed patch motion within the polar cap convection pattern is a major factor in determining whether the patch survives as a recognizable density enhancement by the time the flux tubes comprising the initial patch cross into the nightside auroral oval.
Phosphorylation of USP27X by GSK3β maintains the stability and oncogenic functions of CBX2
Authors: Xing Yushu , Ba-tu Jirimu , Dong Chongyang , Cao Xiaodong , Li Bing , Jia Xin , Juan Yu , Lv Xiaojie , Zhang Huiwen , Qin Na , Han Wuri , Wang Dongfeng , Qi Xiao , Wang Yutong , Hao Xulu , Zhang Shuang , Du Xiaoli , Wang Huanyun , Wang Minjie
Published: November 2023

Chromobox protein homolog 2 (CBX2) exerts a multifaceted impact on the progression of aggressive cancers. The proteasome-dependent pathway is crucial for modulating CBX2 regulation, while the specific regulatory roles and mechanisms of deubiquitinating enzymes targeting CBX2 remain poorly understood. Mass spectrometry analysis identified ubiquitin-specific peptidase 27X (USP27X) as a deubiquitinating enzyme that targets CBX2. Overexpression of USP27X significantly enhances CBX2 levels by promoting deubiquitination, while deficiency of USP27X leads to CBX2 degradation, thereby inhibiting tumorigenesis. Furthermore, it has been revealed that glycogen synthase kinase 3 beta (GSK3β) can directly bind to and phosphorylate USP27X, thereby enhancing the interaction between USP27X and CBX2 and leading to further stabilization of the CBX2 protein. Clinically, the co-expression of high levels of USP27X and CBX2 in breast cancer tissues is indicative of a poor prognosis for patients with this disease. These findings collectively underscore the critical regulatory role played by USP27X in modulating CBX2, thereby establishing the GSK3β-USP27X-CBX2 axis as a pivotal driver of malignant progression in breast cancer.
CerS6-dependent ceramide synthesis in hypothalamic neurons promotes ER/mitochondrial stress and impairs glucose homeostasis in obese mice
Authors: Hammerschmidt Philipp , Steculorum Sophie M. , Bandet Cécile L. , Del Río-Martín Almudena , Steuernagel Lukas , Kohlhaas Vivien , Feldmann Marvin , Varela Luis , Majcher Adam , Quatorze Correia Marta , Klar Rhena F. U. , Bauder Corinna A. , Kaya Ecem , Porniece Marta , Biglari Nasim , Sieben Anna , Horvath Tamas L. , Hornemann Thorsten , Brodesser Susanne , Brüning Jens C.
Published: November 2023

Dysregulation of hypothalamic ceramides has been associated with disrupted neuronal pathways in control of energy and glucose homeostasis. However, the specific ceramide species promoting neuronal lipotoxicity in obesity have remained obscure. Here, we find increased expression of the C16:0 ceramide-producing ceramide synthase (CerS)6 in cultured hypothalamic neurons exposed to palmitate in vitro and in the hypothalamus of obese mice. Conditional deletion of CerS6 in hypothalamic neurons attenuates high-fat diet (HFD)-dependent weight gain and improves glucose metabolism. Specifically, CerS6 deficiency in neurons expressing pro-opiomelanocortin (POMC) or steroidogenic factor 1 (SF-1) alters feeding behavior and alleviates the adverse metabolic effects of HFD feeding on insulin sensitivity and glucose tolerance. POMC-expressing cell-selective deletion of CerS6 prevents the diet-induced alterations of mitochondrial morphology and improves cellular leptin sensitivity. Our experiments reveal functions of CerS6-derived ceramides in hypothalamic lipotoxicity, altered mitochondrial dynamics, and ER/mitochondrial stress in the deregulation of food intake and glucose metabolism in obesity.
A physiological approach for assessing human survivability and liveability to heat in a changing climate
Authors: Vanos Jennifer , Guzman-Echavarria Gisel , Baldwin Jane W. , Bongers Coen , Ebi Kristie L. , Jay Ollie
Published: November 2023

Most studies projecting human survivability limits to extreme heat with climate change use a 35 °C wet-bulb temperature (Tw) threshold without integrating variations in human physiology. This study applies physiological and biophysical principles for young and older adults, in sun or shade, to improve current estimates of survivability and introduce liveability (maximum safe, sustained activity) under current and future climates. Our physiology-based survival limits show a vast underestimation of risks by the 35 °C Tw model in hot-dry conditions. Updated survivability limits correspond to Tw~25.8–34.1 °C (young) and ~21.9–33.7 °C (old)—0.9–13.1 °C lower than Tw = 35 °C. For older female adults, estimates are ~7.2–13.1 °C lower than 35 °C in dry conditions. Liveability declines with sun exposure and humidity, yet most dramatically with age (2.5–3.0 METs lower for older adults). Reductions in safe activity for younger and older adults between the present and future indicate a stronger impact from aging than warming.
Internal states as a source of subject-dependent movement variability are represented by large-scale brain networks
Authors: Breault Macauley Smith , Sacré Pierre , Fitzgerald Zachary B. , Gale John T. , Cullen Kathleen E. , González-Martínez Jorge A. , Sarma Sridevi V.
Published: November 2023

Humans’ ability to adapt and learn relies on reflecting on past performance. These experiences form latent representations called internal states that induce movement variability that improves how we interact with our environment. Our study uncovered temporal dynamics and neural substrates of two states from ten subjects implanted with intracranial depth electrodes while they performed a goal-directed motor task with physical perturbations. We identified two internal states using state-space models: one tracking past errors and the other past perturbations. These states influenced reaction times and speed errors, revealing how subjects strategize from trial history. Using local field potentials from over 100 brain regions, we found large-scale brain networks such as the dorsal attention and default mode network modulate visuospatial attention based on recent performance and environmental feedback. Notably, these networks were more prominent in higher-performing subjects, emphasizing their role in improving motor performance by regulating movement variability through internal states.
Dominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility
Authors: Yew Chow-Lih , Tsuchimatsu Takashi , Shimizu-Inatsugi Rie , Yasuda Shinsuke , Hatakeyama Masaomi , Kakui Hiroyuki , Ohta Takuma , Suwabe Keita , Watanabe Masao , Takayama Seiji , Shimizu Kentaro K.
Published: November 2023

The evolutionary transition to self-compatibility facilitates polyploid speciation. In Arabidopsis relatives, the self-incompatibility system is characterized by epigenetic dominance modifiers, among which small RNAs suppress the expression of a recessive SCR/SP11 haplogroup. Although the contribution of dominance to polyploid self-compatibility is speculated, little functional evidence has been reported. Here we employ transgenic techniques to the allotetraploid plant A. kamchatica. We find that when the dominant SCR-B is repaired by removing a transposable element insertion, self-incompatibility is restored. This suggests that SCR was responsible for the evolution of self-compatibility. By contrast, the reconstruction of recessive SCR-D cannot restore self-incompatibility. These data indicate that the insertion in SCR-B conferred dominant self-compatibility to A. kamchatica. Dominant self-compatibility supports the prediction that dominant mutations increasing selfing rate can pass through Haldane’s sieve against recessive mutations. The dominance regulation between subgenomes inherited from progenitors contrasts with previous studies on novel epigenetic mutations at polyploidization termed genome shock.
A click chemistry-mediated all-peptide cell printing hydrogel platform for diabetic wound healing
Authors: Huang Jinjian , Yang Rong , Jiao Jiao , Li Ze , Wang Penghui , Liu Ye , Li Sicheng , Chen Canwen , Li Zongan , Qu Guiwen , Chen Kang , Wu Xiuwen , Chi Bo , Ren Jianan
Published: November 2023

High glucose-induced vascular endothelial injury is a major pathological factor involved in non-healing diabetic wounds. To interrupt this pathological process, we design an all-peptide printable hydrogel platform based on highly efficient and precise one-step click chemistry of thiolated γ-polyglutamic acid, glycidyl methacrylate-conjugated γ-polyglutamic acid, and thiolated arginine-glycine-aspartate sequences. Vascular endothelial growth factor 165-overexpressed human umbilical vein endothelial cells are printed using this platform, hence fabricating a living material with high cell viability and precise cell spatial distribution control. This cell-laden hydrogel platform accelerates the diabetic wound healing of rats based on the unabated vascular endothelial growth factor 165 release, which promotes angiogenesis and alleviates damages on vascular endothelial mitochondria, thereby reducing tissue hypoxia, downregulating inflammation, and facilitating extracellular matrix remodeling. Together, this study offers a promising strategy for fabricating tissue-friendly, high-efficient, and accurate 3D printed all-peptide hydrogel platform for cell delivery and self-renewable growth factor therapy.
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase
Authors: Nemergut Michal , Pluskal Daniel , Horackova Jana , Sustrova Tereza , Tulis Jan , Barta Tomas , Baatallah Racha , Gagnot Glwadys , Novakova Veronika , Majerova Marika , Sedlackova Karolina , Marques Sérgio M. , Toul Martin , Damborsky Jiri , Prokop Zbynek , Bednar David , Janin Yves L. , Marek Martin
Published: November 2023

NanoLuc, a superior β-barrel fold luciferase, was engineered 10 years ago but the nature of its catalysis remains puzzling. Here experimental and computational techniques are combined, revealing that imidazopyrazinone luciferins bind to an intra-barrel catalytic site but also to an allosteric site shaped on the enzyme surface. Structurally, binding to the allosteric site prevents simultaneous binding to the catalytic site, and vice versa, through concerted conformational changes. We demonstrate that restructuration of the allosteric site can boost the luminescent reaction in the remote active site. Mechanistically, an intra-barrel arginine coordinates the imidazopyrazinone component of luciferin, which reacts with O2 via a radical charge-transfer mechanism, and then it also protonates the resulting excited amide product to form a light-emitting neutral species. Concomitantly, an aspartate, supported by two tyrosines, fine-tunes the blue color emitter to secure a high emission intensity. This information is critical to engineering the next-generation of ultrasensitive bioluminescent reporters.
HDAC8-mediated inhibition of EP300 drives a transcriptional state that increases melanoma brain metastasis
Authors: Emmons Michael F. , Bennett Richard L. , Riva Alberto , Gupta Kanchan , Carvalho Larissa Anastasio Da Costa , Zhang Chao , Macaulay Robert , Dupéré-Richér Daphne , Fang Bin , Seto Edward , Koomen John M. , Li Jiannong , Chen Y. Ann , Forsyth Peter A. , Licht Jonathan D. , Smalley Keiran S. M.
Published: November 2023

Melanomas can adopt multiple transcriptional states. Little is known about the epigenetic drivers of these cell states, limiting our ability to regulate melanoma heterogeneity. Here, we identify stress-induced HDAC8 activity as driving melanoma brain metastasis development. Exposure of melanocytes and melanoma cells to multiple stresses increases HDAC8 activation leading to a neural crest-stem cell transcriptional state and an amoeboid, invasive phenotype that increases seeding to the brain. Using ATAC-Seq and ChIP-Seq we show that increased HDAC8 activity alters chromatin structure by increasing H3K27ac and enhancing accessibility at c-Jun binding sites. Functionally, HDAC8 deacetylates the histone acetyltransferase EP300, causing its enzymatic inactivation. This, in turn, increases binding of EP300 to Jun-transcriptional sites and decreases binding to MITF-transcriptional sites. Inhibition of EP300 increases melanoma cell invasion, resistance to stress and increases melanoma brain metastasis development. HDAC8 is identified as a mediator of transcriptional co-factor inactivation and chromatin accessibility that drives brain metastasis.
TRS: a method for determining transcript termini from RNAtag-seq sequencing data
Authors: Bar Amir , Argaman Liron , Eldar Michal , Margalit Hanah
Published: November 2023

In bacteria, determination of the 3’ termini of transcripts plays an essential role in regulation of gene expression, affecting the functionality and stability of the transcript. Several experimental approaches were developed to identify the 3’ termini of transcripts, however, these were applied only to a limited number of bacteria and growth conditions. Here we present a straightforward approach to identify 3’ termini from widely available RNA-seq data without the need for additional experiments. Our approach relies on the observation that the RNAtag-seq sequencing protocol results in overabundance of reads mapped to transcript 3’ termini. We present TRS (Termini by Read Starts), a computational pipeline exploiting this property to identify 3’ termini in RNAtag-seq data, and show that the identified 3’ termini are highly reliable. Since RNAtag-seq data are widely available for many bacteria and growth conditions, our approach paves the way for studying bacterial transcription termination in an unprecedented scope.
Dermis resident macrophages orchestrate localized ILC2 eosinophil circuitries to promote non-healing cutaneous leishmaniasis
Authors: Lee Sang Hun , Kang Byunghyun , Kamenyeva Olena , Ferreira Tiago Rodrigues , Cho Kyoungin , Khillan Jaspal S. , Kabat Juraj , Kelsall Brian L. , Sacks David L.
Published: November 2023

Tissue-resident macrophages are critical for tissue homeostasis and repair. We previously showed that dermis-resident macrophages produce CCL24 which mediates their interaction with IL-4+ eosinophils, required to maintain their M2-like properties in the TH1 environment of the Leishmania major infected skin. Here, we show that thymic stromal lymphopoietin (TSLP) and IL-5+ type 2 innate lymphoid cells are also required to maintain dermis-resident macrophages and promote infection. Single cell RNA sequencing reveals the dermis-resident macrophages as the sole source of TSLP and CCL24. Generation of Ccl24-cre mice permits specific labeling of dermis-resident macrophages and interstitial macrophages from other organs. Selective ablation of TSLP in dermis-resident macrophages reduces the numbers of IL-5+ type 2 innate lymphoid cells, eosinophils and dermis-resident macrophages, and ameliorates infection. Our findings demonstrate that dermis-resident macrophages are self-maintained as a replicative niche for L. major by orchestrating localized type 2 circuitries with type 2 innate lymphoid cells and eosinophils.
Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting
Authors: Ronson George E. , Starowicz Katarzyna , Anthony Elizabeth J. , Piberger Ann Liza , Clarke Lucy C. , Garvin Alexander J. , Beggs Andrew D. , Whalley Celina M. , Edmonds Matthew J. , Beesley James F. J. , Morris Joanna R.
Published: November 2023

A synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.
DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms
Authors: Carrión Ornella , Li Chun-Yang , Peng Ming , Wang Jinyan , Pohnert Georg , Azizah Muhaiminatul , Zhu Xiao-Yu , Curson Andrew R. J. , Wang Qing , Walsham Keanu S. , Zhang Xiao-Hua , Monaco Serena , Harvey James M. , Chen Xiu-Lan , Gao Chao , Wang Ning , Wang Xiu-Juan , Wang Peng , Giovanonni Stephen J. , Lee Chih-Ping , Suffridge Christopher P. , Zhang Yu , Luo Ziqi , Wang Dazhi , Todd Jonathan D. , Zhang Yu-Zhong
Published: November 2023

Dimethylsulfoxonium propionate (DMSOP) is a recently identified and abundant marine organosulfur compound with roles in oxidative stress protection, global carbon and sulfur cycling and, as shown here, potentially in osmotolerance. Microbial DMSOP cleavage yields dimethyl sulfoxide, a ubiquitous marine metabolite, and acrylate, but the enzymes responsible, and their environmental importance, were unknown. Here we report DMSOP cleavage mechanisms in diverse heterotrophic bacteria, fungi and phototrophic algae not previously known to have this activity, and highlight the unappreciated importance of this process in marine sediment environments. These diverse organisms, including Roseobacter, SAR11 bacteria and Emiliania huxleyi, utilized their dimethylsulfoniopropionate lyase ‘Ddd’ or ‘Alma’ enzymes to cleave DMSOP via similar catalytic mechanisms to those for dimethylsulfoniopropionate. Given the annual teragram predictions for DMSOP production and its prevalence in marine sediments, our results highlight that DMSOP cleavage is likely a globally significant process influencing carbon and sulfur fluxes and ecological interactions.
Customisable IT tool for on-field assessments to support disaster management
Authors: Grimaz Stefano , Malisan Petra , Zorzini Fabio , Grimaz Loris , Bettuzzi Mauro
Published: November 2023

Information and technology (IT) based tools are widely used in all phases of the disaster management cycle (DMC), improving the effectiveness of the prevision-prevention, preparedness, response, and recovery phases. The availability of on-field collected data provides an answer to the need to represent the scenario in which decision-makers will intervene. In this context, disaster management experience has shown that in many cases the users of on-field assessment outcomes (i.e., decision-makers) need: a data collection tool quickly and simply adaptable to better respond to specific and conditional needs; the automated elaboration of situation results; and the ability to exchange the information between the different phases of the DMC. This paper illustrates the IT tool, called "SPRINT-Engine", which was developed to meet these requirements. The SPRINT-Engine has been specifically developed and improved to permit easy and rapid customizability, even in near real-time. The paper presents some applications in real cases of on-field assessment managed by SPRINT-Lab researchers in support of institutions in various activities and projects at different scales and in different phases of the DMC.
Cellular dynamics as a marker of normal-to-cancer transition in human cells
Authors: Marques M. P. M. , de Carvalho A. L. M. Batista , Martins C. B. , Silva J. D. , Sarter M. , García Sakai V. , Stewart J. R. , de Carvalho L. A. E. Batista
Published: November 2023

Normal-to-cancer (NTC) transition is known to be closely associated to cell´s biomechanical properties which are dependent on the dynamics of the intracellular medium. This study probes different human cancer cells (breast, prostate and lung), concomitantly to their healthy counterparts, aiming at characterising the dynamical profile of water in distinct cellular locations, for each type of cell, and how it changes between normal and cancer states. An increased plasticity of the cytomatrix is observed upon normal-to-malignant transformation, the lung carcinoma cells displaying the highest flexibility followed by prostate and breast cancers. Also, lung cells show a distinct behaviour relative to breast and prostate, with a higher influence from hydration water motions and localised fast rotations upon NTC transformation. Quasielastic neutron scattering techniques allowed to accurately distinguish the different dynamical processes taking place within these highly heterogeneous cellular systems. The results thus obtained suggest that intracellular water dynamics may be regarded as a specific reporter of the cellular conditions—either healthy or malignant.
Association between serum vitamin D levels and lipid profiles: a cross-sectional analysis
Authors: Gholamzad Amir , Khakpour Niloofar , Kabipour Tina , Gholamzad Mehrdad
Published: November 2023

Vitamin D is an essential nutrient that plays a crucial role in calcium homeostasis and bone health. Recent research suggests that vitamin D may also have an impact on lipid metabolism, specifically the level of circulating lipids in the blood. We aim to investigate it role among healthy participate. We conducted a cross-sectional study of 15,600 patients who were referred to the laboratories of university hospitals. We measured the serum levels of Vitamin D as well as triglycerides, total cholesterol, LDL, and HDL using ELISA. We found that the mean serum level of Vitamin D was 40.31 ± 20.79 ng/mL. Of the participants, 16.7% had a serum level of Vitamin D less than 20 ng/mL, 57.7% had a level between 21 and 40 ng/mL, and 13.5% had a level between 41 and 60 ng/mL. Additionally, 12.2% had a level greater than 60 ng/mL. We performed a one-way analysis of variance and found that as the serum level of Vitamin D increased, the mean LDL level decreased significantly. Our study provides evidence of a significant relationship between serum levels of Vitamin D and LDL levels in patients. The findings suggest that vitamin D status may play a role in regulating lipid metabolism and may have implications for the prevention and treatment of cardiovascular disease. Further research is needed to elucidate the underlying mechanisms of this relationship and to determine optimal levels of vitamin D intake for maintaining lipid profiles.
Opportunistic assessment of ischemic heart disease risk using abdominopelvic computed tomography and medical record data: a multimodal explainable artificial intelligence approach
Authors: Zambrano Chaves Juan M. , Wentland Andrew L. , Desai Arjun D. , Banerjee Imon , Kaur Gurkiran , Correa Ramon , Boutin Robert D. , Maron David J. , Rodriguez Fatima , Sandhu Alexander T. , Rubin Daniel , Chaudhari Akshay S. , Patel Bhavik N.
Published: November 2023

Current risk scores using clinical risk factors for predicting ischemic heart disease (IHD) events—the leading cause of global mortality—have known limitations and may be improved by imaging biomarkers. While body composition (BC) imaging biomarkers derived from abdominopelvic computed tomography (CT) correlate with IHD risk, they are impractical to measure manually. Here, in a retrospective cohort of 8139 contrast-enhanced abdominopelvic CT examinations undergoing up to 5 years of follow-up, we developed multimodal opportunistic risk assessment models for IHD by automatically extracting BC features from abdominal CT images and integrating these with features from each patient’s electronic medical record (EMR). Our predictive methods match and, in some cases, outperform clinical risk scores currently used in IHD risk assessment. We provide clinical interpretability of our model using a new method of determining tissue-level contributions from CT along with weightings of EMR features contributing to IHD risk. We conclude that such a multimodal approach, which automatically integrates BC biomarkers and EMR data, can enhance IHD risk assessment and aid primary prevention efforts for IHD. To further promote research, we release the Opportunistic L3 Ischemic heart disease (OL3I) dataset, the first public multimodal dataset for opportunistic CT prediction of IHD.
Breathing sounds analysis system for early detection of airway problems in patients with a tracheostomy tube
Authors: Kim Hyunbum , Koh Daeyeon , Jung Yohan , Han Hyunjun , Kim Jongbaeg , Joo Younghoon
Published: November 2023

To prevent immediate mortality in patients with a tracheostomy tube, it is essential to ensure timely suctioning or replacement of the tube. Breathing sounds at the entrance of tracheostomy tubes were recorded with a microphone and analyzed using a spectrogram to detect airway problems. The sounds were classified into three categories based on the waveform of the spectrogram according to the obstacle status: normal breathing sounds (NS), vibrant breathing sounds (VS) caused by movable obstacles, and sharp breathing sounds (SS) caused by fixed obstacles. A total of 3950 breathing sounds from 23 patients were analyzed. Despite neither the patients nor the medical staff recognizing any airway problems, the number and percentage of NS, VS, and SS were 1449 (36.7%), 1313 (33.2%), and 1188 (30.1%), respectively. Artificial intelligence (AI) was utilized to automatically classify breathing sounds. MobileNet and Inception_v3 exhibited the highest sensitivity and specificity scores of 0.9441 and 0.9414, respectively. When classifying into three categories, ResNet_50 showed the highest accuracy of 0.9027, and AlexNet showed the highest accuracy of 0.9660 in abnormal sounds. Classifying breathing sounds into three categories is very useful in deciding whether to suction or change the tracheostomy tubes, and AI can accomplish this with high accuracy.
1,3-Diphenylureido hydroxamate as a promising scaffold for generation of potent antimalarial histone deacetylase inhibitors
Authors: Tavares Maurício T. , Krüger Arne , Yan Sun L. Rei , Waitman Karoline B. , Gomes Vinícius M. , de Oliveira Daffiny Sumam , Paz Franciarli , Hilscher Sebastian , Schutkowski Mike , Sippl Wolfgang , Ruiz Claudia , Toledo Mônica F. Z. J. , Hassimotto Neuza M. A. , Machado-Neto João A. , Poso Antti , Cameron Michael D. , Bannister Thomas D. , Palmisano Giuseppe , Wrenger Carsten , Kronenberger Thales , Parise-Filho Roberto
Published: November 2023

We report a series of 1,3-diphenylureido hydroxamate HDAC inhibitors evaluated against sensitive and drug-resistant P. falciparum strains. Compounds 8a–d show potent antiplasmodial activity, indicating that a phenyl spacer allows improved potency relative to cinnamyl and di-hydrocinnamyl linkers. In vitro, mechanistic studies demonstrated target activity for PfHDAC1 on a recombinant level, which agreed with cell quantification of the acetylated histone levels. Compounds 6c, 7c, and 8c, identified as the most active in phenotypic assays and PfHDAC1 enzymatic inhibition. Compound 8c stands out as a remarkable inhibitor, displaying an impressive 85% inhibition of PfHDAC1, with an IC50 value of 0.74 µM in the phenotypic screening on Pf3D7 and 0.8 µM against multidrug-resistant PfDd2 parasites. Despite its potent inhibition of PfHDAC1, 8c remains the least active on human HDAC1, displaying remarkable selectivity. In silico studies suggest that the phenyl linker has an ideal length in the series for permitting effective interactions of the hydroxamate with PfHDAC1 and that this compound series could bind as well as in HsHDAC1. Taken together, these results highlight the potential of diphenylurea hydroxamates as a privileged scaffold for the generation of potent antimalarial HDAC inhibitors with improved selectivity over human HDACs.
Investigation on the organic–inorganic hybrid crystal [NH2(CH3)2]2CuBr4: structure, phase transition, thermal property, structural geometry, and dynamics
Authors: Na Changyub , Lim Ae Ran
Published: November 2023

Understanding the physical properties of the organic–inorganic hybrid [NH2(CH3)2]2CuBr4 is essential to expand its applications. The single [NH2(CH3)2]2CuBr4 crystals were grown and their comprehensive properties were investigated. The crystals had a monoclinic structure with the space group P21/n and lattice constants of a = 8.8651 (5) Å, b = 11.9938 (6) Å, c = 13.3559 (7) Å, and β = 91.322°. The transition temperature from phase I to phase II was determined to be 388 K. Variations in the 1H nuclear magnetic resonance chemical shifts of NH2 and 14N NMR chemical shifts according to the temperature changes in the cation were attributed to vibrations of NH2 groups at their localization sites. The 1H and 13C spin–lattice relaxation times (T1ρ) in phase II changed significantly with temperature, indicating that these values are governed by molecular motion. The T1ρ values were much longer in phase I than in phase II, which means energy transfer was difficult. Finally, the activation energies for phases I and II were considered. According to the basic mechanism of [NH2(CH3)2]2CuBr4 crystals, organic–inorganic materials may have potential applications in various fields.
A multimodal screening system for elderly neurological diseases based on deep learning
Authors: Park Sangyoung , No Changho , Kim Sora , Han Kyoungmin , Jung Jin-Man , Kwon Kyum-Yil , Lee Minsik
Published: November 2023

In this paper, we propose a deep-learning-based algorithm for screening neurological diseases. We proposed various examination protocols for screening neurological diseases and collected data by video-recording persons performing these protocols. We converted video data into human landmarks that capture action information with a much smaller data dimension. We also used voice data which are also effective indicators of neurological disorders. We designed a subnetwork for each protocol to extract features from landmarks or voice and a feature aggregator that combines all the information extracted from the protocols to make a final decision. Multitask learning was applied to screen two neurological diseases. To capture meaningful information about these human landmarks and voices, we applied various pre-trained models to extract preliminary features. The spatiotemporal characteristics of landmarks are extracted using a pre-trained graph neural network, and voice features are extracted using a pre-trained time-delay neural network. These extracted high-level features are then passed onto the subnetworks and an additional feature aggregator that are simultaneously trained. We also used various data augmentation techniques to overcome the shortage of data. Using a frame-length staticizer that considers the characteristics of the data, we can capture momentary tremors without wasting information. Finally, we examine the effectiveness of different protocols and different modalities (different body parts and voice) through extensive experiments. The proposed method achieves AUC scores of 0.802 for stroke and 0.780 for Parkinson’s disease, which is effective for a screening system.
Patterns of host-parasite associations between marine meiofaunal flatworms (Platyhelminthes) and rhytidocystids (Apicomplexa)
Authors: Van Steenkiste Niels W. L. , Wakeman Kevin C. , Söderström Bill , Leander Brian S.
Published: November 2023

Microturbellarians are abundant and ubiquitous members of marine meiofaunal communities around the world. Because of their small body size, these microscopic animals are rarely considered as hosts for parasitic organisms. Indeed, many protists, both free-living and parasitic ones, equal or surpass meiofaunal animals in size. Despite several anecdotal records of “gregarines”, “sporozoans”, and “apicomplexans” parasitizing microturbellarians in the literature—some of them dating back to the nineteenth century—these single-celled parasites have never been identified and characterized. More recently, the sequencing of eukaryotic microbiomes in microscopic invertebrates have revealed a hidden diversity of protist parasites infecting microturbellarians and other meiofaunal animals. Here we show that apicomplexans isolated from twelve taxonomically diverse rhabdocoel taxa and one species of proseriate collected in four geographically distinct areas around the Pacific Ocean (Okinawa, Hokkaido, and British Columbia) and the Caribbean Sea (Curaçao) all belong to the apicomplexan genus Rhytidocystis. Based on comprehensive molecular phylogenies of Rhabdocoela and Proseriata inferred from both 18S and 28S rDNA sequences, as well as a molecular phylogeny of Marosporida inferred from 18S rDNA sequences, we determine the phylogenetic positions of the microturbellarian hosts and their parasites. Multiple lines of evidence, including morphological and molecular data, show that at least nine new species of Rhytidocystis infect the microturbellarian hosts collected in this study, more than doubling the number of previously recognized species of Rhytidocystis, all of which infect polychaete hosts. A cophylogenetic analysis examining patterns of phylosymbiosis between hosts and parasites suggests a complex picture of overall incongruence between host and parasite phylogenies, and varying degrees of geographic signals and taxon specificity.
Warming affects routine swimming activity and novel odour response in larval zebrafish
Authors: Sourisse Jade M. , Bonzi Lucrezia C. , Semmelhack Julie , Schunter Celia
Published: November 2023

Temperature is a primary factor affecting the physiology of ectothermic animals and global warming of water bodies may therefore impact aquatic life. Understanding the effects of near-future predicted temperature changes on the behaviour and underlying molecular mechanisms of aquatic animals is of particular importance, since behaviour mediates survival. In this study, we investigate the effects of developmental temperature on locomotory behaviour and olfactory learning in the zebrafish,Danio rerio. We exposed zebrafish from embryonic stage to either control (28 °C) or elevated temperature (30 °C) for seven days. Overall, warming reduced routine swimming activity and caused upregulation of metabolism and neuron development genes. When exposed to olfactory cues, namely catfish cue, a non-alarming but novel odour, and conspecifics alarming cue, warming differently affected the larvae response to the two cues. An increase in locomotory activity and a large transcriptional reprogramming was observed at elevated temperature in response to novel odour, with upregulation of cell signalling, neuron development and neuron functioning genes. As this response was coupled with the downregulation of genes involved in protein translation and ATP metabolism, novel odour recognition in future-predicted thermal conditions would require energetic trade-offs between expensive baseline processes and responsive functions. To evaluate their learning abilities at both temperatures, larvae were conditioned with a mixture of conspecifics alarm cue and catfish cue. Regardless of temperature, no behavioural nor gene expression changes were detected, reinforcing our findings that warming mainly affects zebrafish molecular response to novel odours. Overall, our results show that future thermal conditions will likely impact developing stages, causing trade-offs following novel olfactory detection in the environment.
Factors promoting hunting groups’ sustainable harvest of moose in a co-management system
Authors: Tuominen Laura S. , Wikström Mikael , Helanterä Heikki , Karell Patrik , Pusenius Jyrki , Rapeli Lauri , Ruha Leena , Vuorisalo Timo , Brommer Jon E.
Published: November 2023

Collaboration between and within management levels and involvement of local communities (co-management) increases sustainable management of natural resources. In Finland, moose (Alces alces) are harvested by hunting groups within a co-management system, providing meat and social benefits. We computed the 14-year change in moose harvest (2007–2020) for 4320 hunting groups. Moose harvest declined on average 1.1% per year, but with substantial variation in moose harvest changes between the hunting groups. We extracted information describing the collaboration between the hunting groups, their democratic status as well as leader dynamics, and the year of establishment. A hunting group’s moose harvest was more stable (i.e. declined less) when the hunting group was (1) established a longer time ago; (2), had more changes in leadership over time, but did not depend on collaboration with other local hunting groups (in terms of jointly holding moose hunting licenses), whether the hunting group was a registered society (presumed to be more democratic than a non-registered one) or had consecutive leaders that shared a surname (presumed to be related). We conclude that encouraging resource users’ early establishment in groups and groups’ long-term persistence and promoting democratic leadership roles improves stable benefits from a natural resource in a co-management system.
Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction
Authors: Chiou Chien-Shun , Chen Bo-Han , Wang You-Wun , Kuo Nang-Ting , Chang Chih-Hsiang , Huang Yao-Ting
Published: November 2023

The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modification types untrained in the basecalling models can seriously reduce the quality. Here we reports a set of ONT-sequenced genomes with unexpected low quality due to novel modification types. Demodification by whole-genome amplification significantly improved the quality but lost the epigenome. We also developed a reference-based method, Modpolish, for correcting modification-mediated errors while retaining the epigenome when a sufficient number of closely-related genomes is publicly available (default: top 20 genomes with at least 95% identity). Modpolish not only significantly improved the quality of in-house sequenced genomes but also public datasets sequenced by R9.4 and R10.4 (simplex). Our results suggested that novel modifications are prone to ONT systematic errors. Nevertheless, these errors are correctable by nucleotide demodification or Modpolish without prior knowledge of modifications.