bluuebunny/crossref_metadata_2025 huggingface dataset:
Geometrically modulated contact forces enable hula hoop levitation
Authors: Zhu Xintong , Pomerenk Olivia , Ristroph Leif
Published: December 2024

Mechanical systems with moving points of contact—including rolling, sliding, and impacts—are common in engineering applications and everyday experiences. The challenges in analyzing such systems are compounded when an object dynamically explores the complex surface shape of a moving structure, as arises in familiar but poorly understood contexts such as hula hooping. We study this activity as a unique form of mechanical levitation against gravity and identify the conditions required for the stable suspension of an object rolling around a gyrating body. We combine robotic experiments involving hoops twirling on surfaces of various geometries and a model that links the motions and shape to the contact forces generated. The in-plane motions of the hoop involve synchronization to the body gyration that is shown to require damping and sufficiently high launching speed. Further, vertical equilibrium is achieved only for bodies with “hips” or a critical slope of the surface, while stability requires an hourglass shape with a “waist” and whose curvature exceeds a critical value. Analysis of the model reveals dimensionless factors that successfully organize and unify observations across a wide range of geometries and kinematics. By revealing and explaining the mechanics of hula hoop levitation, these results motivate strategies for motion control via geometry-dependent contact forces and for accurately predicting the resulting equilibria and their stability.
Comparing integrative ventilatory and renal acid–base acclimatization in lowlanders and Tibetan highlanders during ascent to 4,300 m
Authors: Johnson Nicole A. , Dickenson Jessica A. , MacKenzie Benjamin W.L. , Isakovich Rodion , Kalker Anne , Bouten Janne , Strzalkowski Nicholas D.J. , Harman Taylor S. , Holmström Pontus , Kunwar Ajaya J. , Thakur Nilam , Dhungel Sunil , Sherpa Nima , Bigham Abigail W. , Brutsaert Tom D. , Day Trevor A.
Published: December 2024

With over 14 million people living above 3,500 m, the study of acclimatization and adaptation to high altitude in human populations is of increasing importance, where exposure to high altitude (HA) imposes a blood oxygenation and acid–base challenge. A sustained and augmented hypoxic ventilatory response protects oxygenation through ventilatory acclimatization, but elicits hypocapnia and respiratory alkalosis. A subsequent renally mediated compensatory metabolic acidosis corrects pH toward baseline values, with a high degree of interindividual variability. Differential renal compensation between acclimatizing lowlanders (LL) and Tibetan highlanders (TH; Sherpa) with ascent was previously unknown. We assessed ventilatory and renal acclimatization between unacclimatized LL and TH during incremental ascent from 1,400 m to 4,300 m in age- and sex-matched groups of 15-LL (8F) and 14-TH (7F) of confirmed Tibetan ancestry. We compared respiratory and renally mediated blood acid–base acclimatization (PCO
2
, [HCO
3
−
], pH) in both groups before (1,400 m) and following day 8 to 9 of incremental ascent to 4,300 m. We found that following ascent to 4,300 m, LL had significantly lower PCO
2
(
P
<0.0001) and [HCO
3
−
] (
P
<0.0001), and higher pH (
P
= 0.0037) than 1,400 m, suggesting respiratory alkalosis and only partial renal compensation. Conversely, TH had significantly lower PCO
2
(
P
< 0.0001) and [HCO
3
−
] (
P
< 0.0001), but unchanged pH (
P
= 0.1), suggesting full renal compensation, with significantly lower PCO
2
(
P
= 0.01), [HCO
3
−
] (
P
< 0.0001) and pH (
P
= 0.005) than LL at 4,300 m. This demonstration of differential integrative respiratory–renal responses between acclimatizing LL and TH may indicate selective pressure on TH, and highlights the important role of the kidneys in acclimatization.
Computational-aided rational mutation design of pertuzumab to overcome active HER2 mutation S310F through antibody–drug conjugates
Authors: Bai Xuefei , Xu Lingyi , Wang Zhe , Zhuang Xinlei , Ning Jiangtao , Sun Yanping , Wang Haibin , Guo Yugang , Xu Yingchun , Guo Jiangtao , Chen Shuqing , Pan Liqiang
Published: December 2024

Recurrent missense mutations in the human epidermal growth factor receptor 2 (HER2) have been identified across various human cancers. Among these mutations, the active S310F mutation in the HER2 extracellular domain stands out as not only oncogenic but also confers resistance to pertuzumab, an antibody drug widely used in clinical cancer therapy, by impeding its binding. In this study, we have successfully employed computational-aided rational design to undertake directed evolution of pertuzumab, resulting in the creation of an evolved pertuzumab variant named Ptz-SA. This variant, with only two mutations (T30S/D31A) located on its heavy chain, effectively reinstates binding to the mutated antigen, at the expense of a 35-fold reduction in binding affinity to HER2 (S310F) compared to the wild-type pair. Subsequently, Ptz-SA demonstrates potent killing capacity through antigen-dependent cytotoxicity. Moreover, upon engineering Ptz-SA into antibody–drug conjugates, such as Ptz-SA-MMAE, it manifests notable in vitro and in vivo antitumor efficacy by efficiently delivering cytotoxic payload into tumor cells expressing HER2 (S310F). Cryoelectron microscopy studies elucidate the molecular mechanism underlying the restored binding ability of Ptz-SA toward the S310F mutation. The steric hindrance induced by the S310F mutation is efficiently circumvented by the T30S and D31A mutations, which provides adequate space to accommodate the larger phenylalanine. Additionally, Ptz-SA also exhibits binding capacity to HER2 (S310Y), another mutation occurring at the S310 site of HER2 with high frequency. The computational-aided evolution of pertuzumab provides an alternative strategy for overcoming point mutation-mediated resistance to therapeutic antibodies.
Confined cell migration along extracellular matrix space in vivo
Authors: Chepizhko Oleksandr , Armengol-Collado Josep-Maria , Alexander Stephanie , Wagena Esther , Weigelin Bettina , Giomi Luca , Friedl Peter , Zapperi Stefano , La Porta Caterina A. M.
Published: December 2024

Collective migration of cancer cells is often interpreted using concepts derived from the physics of active matter, but the experimental evidence is mostly restricted to observations made in vitro. Here, we study collective invasion of metastatic cancer cells injected into the mouse deep dermis using intravital multiphoton microscopy combined with a skin window technique and three-dimensional quantitative image analysis. We observe a multicellular but low-cohesive migration mode characterized by rotational patterns which self-organize into antiparallel persistent tracks with orientational nematic order. We analyze the deformations induced by the cells in the extracellular matrix and find broadly distributed strain bands with a prevalence of compression. A model of active nematic hydrodynamics is able to describe several statistical features of the experimentally observed flow, suggesting that collective cancer cell invasion can be interpreted as a nematic active fluid in the turbulent regime. Our results help elucidate the migration patterns of cancer cells in vivo and provide quantitative guidance for the development of realistic in vitro and in silico models for collective cell migration.
VCP controls KCC2 degradation through FAF1 recruitment and accelerates emergence from anesthesia
Authors: Chen Peng , Hu Jiang-Jian , Liu Yuexin , Cao Boxu , Song Xue-Jun
Published: December 2024

Ubiquitin-proteasomal degradation of K
+
/Cl
−
cotransporter 2 (KCC2) in the ventral posteromedial nucleus (VPM) has been demonstrated to serve as a common mechanism by which the brain emerges from anesthesia and regains consciousness. Ubiquitin-proteasomal degradation of KCC2 during anesthesia is driven by E3 ligase Fbxl4. However, the mechanism by which ubiquitinated KCC2 is targeted to the proteasome has not been elucidated. We report in cultured neuro-2a cells that the valosin-containing protein (VCP) transported ubiquitinated KCC2 to the proteasome and in mice in vivo experiments that inhibition of VCP restored KCC2 expression in the VPM and enhanced the effects of anesthesia. In cultured neuro-2a cells, propofol-induced degradation of KCC2 was inhibited by VCP inhibitor DBeQ and VCP knockout plasmid sgRNA(VCP). Propofol-induced enhanced interaction between VCP and KCC2 was inhibited by knockout of Fbxl4 or Fas-associated factor 1 (FAF1). In in vivo studies, pharmacological or genetic inhibition of VCP in the VPM significantly prevented KCC2 degradation and enhanced propofol anesthesia; these effects were abrogated by a KCC2 antagonist VU0463271. These results demonstrate that the VCP controls ubiquitin-proteasomal degradation of KCC2 dependent on FAF1 recruitment and serves as a mechanism for the ubiquitin-proteasomal degradation of KCC2, which is responsible for the subsequent emergence from anesthesia.
The unequal adoption of ChatGPT exacerbates existing inequalities among workers
Authors: Humlum Anders , Vestergaard Emilie
Published: December 2024

We study the adoption of ChatGPT, the icon of Generative AI, using a large-scale survey linked to comprehensive register data in Denmark. Surveying 18,000 workers from 11 exposed occupations, we document that ChatGPT is widespread, especially among younger and less-experienced workers. However, substantial inequalities have emerged. Women are 16 percentage points less likely to have used the tool for work. Furthermore, despite its potential to lift workers with less expertise, users of ChatGPT earned slightly more already before its arrival, even given their lower tenure. Workers see a substantial productivity potential in ChatGPT but are often hindered by employer restrictions and a perceived need for training.
Genesis and regulation of C-terminal cyclic imides from protein damage
Authors: Xu Wenqing , Zhao Zhenguang , Su Matthew , Jain Atul D. , Lloyd Hannah C. , Feng Ethan Yang , Cox Nick , Woo Christina M.
Published: December 2024

C-Terminal cyclic imides are posttranslational modifications that can arise from spontaneous intramolecular cleavage of asparagine or glutamine residues resulting in a form of irreversible protein damage. These protein damage events are recognized and removed by the E3 ligase substrate adapter cereblon (CRBN), indicating that these aging-related modifications may require cellular quality control mechanisms to prevent deleterious effects. However, the factors that determine protein or peptide susceptibility to C-terminal cyclic imide formation or their effect on protein stability have not been explored in detail. Here, we characterize the primary and secondary structures of peptides and proteins that promote intrinsic formation of C-terminal cyclic imides in comparison to deamidation, a related form of protein damage. Extrinsic effects from solution properties and stressors on the cellular proteome additionally promote C-terminal cyclic imide formation on proteins like glutathione synthetase that are susceptible to aggregation if the protein damage products are not removed by CRBN. This systematic investigation provides insight into the regions of the proteome that are prone to these unexpectedly frequent modifications, the effects of this form of protein damage on protein stability, and the biological role of CRBN.
The 1831 CE mystery eruption identified as Zavaritskii caldera, Simushir Island (Kurils)
Authors: Hutchison William , Sugden Patrick , Burke Andrea , Abbott Peter , Ponomareva Vera V. , Dirksen Oleg , Portnyagin Maxim V. , MacInnes Breanyn , Bourgeois Joanne , Fitzhugh Ben , Verkerk Magali , Aubry Thomas J. , Engwell Samantha L. , Svensson Anders , Chellman Nathan J. , McConnell Joseph R. , Davies Siwan , Sigl Michael , Plunkett Gill
Published: December 2024

Polar ice cores and historical records evidence a large-magnitude volcanic eruption in 1831 CE. This event was estimated to have injected ~13 Tg of sulfur (S) into the stratosphere which produced various atmospheric optical phenomena and led to Northern Hemisphere climate cooling of ~1 °C. The source of this volcanic event remains enigmatic, though one hypothesis has linked it to a modest phreatomagmatic eruption of Ferdinandea in the Strait of Sicily, which may have emitted additional S through magma–crust interactions with evaporite rocks. Here, we undertake a high-resolution multiproxy geochemical analysis of ice-core archives spanning the 1831 CE volcanic event. S isotopes confirm a major Northern Hemisphere stratospheric eruption but, importantly, rule out significant contributions from external evaporite S. In multiple ice cores, we identify cryptotephra layers of low K andesite-dacite glass shards occurring in summer 1831 CE and immediately prior to the stratospheric S fallout. This tephra matches the chemistry of the youngest Plinian eruption of Zavaritskii, a remote nested caldera on Simushir Island (Kurils). Radiocarbon ages confirm a recent (<300 y) eruption of Zavaritskii, and erupted volume estimates are consistent with a magnitude 5 to 6 event. The reconstructed radiative forcing of Zavaritskii (−2 ± 1 W m
−2
) is comparable to the 1991 CE Pinatubo eruption and can readily account for the climate cooling in 1831–1833 CE. These data provide compelling evidence that Zavaritskii was the source of the 1831 CE mystery eruption and solve a confounding case of multiple closely spaced observed and unobserved volcanic eruptions.
Liquid-nano-liquid interface–oriented anisotropic encapsulation
Authors: Zhan Yating , Huang Xirui , Liu Minchao , Lin Runfeng , Yu Hongyue , Kou Yufang , Xing Enyun , Elzatahry Ahmed A. , Mady Mohamed F. , Zhao Dongyuan , Zhao Tiancong , Li Xiaomin
Published: December 2024

Emulsion interface engineering has been widely employed for the synthesis of nanomaterials with various morphologies. However, the instability of the liquid–liquid interface and uncertain interfacial interactions impose significant limitations on controllable fabrications. Here, we developed a liquid-nano-liquid interface–oriented anisotropic encapsulation strategy for fabricating asymmetric nanohybrids. Specifically, functional nanoparticles such as magnetic nanoparticles, lanthanide fluorescent nanoparticles, and Au nanorods were anisotropically encapsulated by mesoporous polydopamine (mPDA). In this emulsion system, the wetting behavior of functional nanoparticles at the water/oil interface could be manipulated by the stabilizer of the emulsion (surfactant), leading to the anisotropic assembly of mPDA shell and resulting in various nanostructures, including core–shell, yolk–shell with small opening, ball-in-bowl, and multipetal structures. Due to their structural asymmetry, inherent magnetic properties, and photothermal properties, the ball-in-bowl structured Fe
3
O
4
@SiO
2
&mPDA nanohybrids, serving as proof of concept for nanomotors, demonstrated effective penetration of bacterial biofilm and promotion of infected wound healing. Overall, our approach offers a different perspective for designing morphologically controllable asymmetric structures based on liquid-nano-liquid interface in microemulsion systems that hold great potential for establishing innovative functional nanomaterials.
The interaction of
Serratia
bacteria and harmonine in harlequin ladybird confers an interspecies competitive edge
Authors: Zhang Chaowei , Zhou Hang , He Kang , Xiao Yiqi , Chen Mengyao , Zuo Zhangqi , Shu Runguo , Geng Yuhang , Jin Shuo , Mei Yang , He Bingbing , Li Fei
Published: December 2024

The harlequin ladybird,
Harmonia axyridis
, is a predatory beetle used globally to control pests such as aphids and scale insects. Originating from East Asia, this species has become highly invasive since its introduction in the late 19th century to Europe and North America, posing a threat to local biodiversity. Intraguild predation is hypothesized to drive the success of this invasive species, but the underlying mechanisms remain unknown. In this study, a feeding assay revealed that while harlequin ladybirds survive feeding on seven-spotted ladybird eggs, the reverse is not true. However, seven-spotted ladybirds that had fed on harlequin ladybird eggs were able to survive the feeding assay when treated with penicillin. Microbiome sequencing and whole genome analysis of harlequin ladybird eggs revealed a newly discovered pathogenic bacterium strain named
Serratia harmoniae.
The median lethal concentration (LC50) of
S. harmoniae
was found to be 2.1 × 10
5
times higher in the harlequin ladybird compared to the seven-spotted ladybird. The high tolerance observed in harlequin ladybirds was attributed to harmonine, specifically produced in the fat body of this species. Silencing three key genes in the harmonine biosynthesis pathway—
Spidey
,
Sca2
, and
Desat—
reduced the production of the compound, leading to increased
S. harmoniae
levels and higher mortality. Treating RNAi-altered individuals with penicillin reversed this effect, successfully reducing
S. harmoniae
presence and increasing insect survival. Taken together, these findings demonstrate that
S. harmoniae
, a newly identified pathogenic bacterium carried by harlequin ladybirds, interacts with harmonine to confer an interspecies competitive advantage over native ladybird species in nonnative regions.
Palmitoylation-dependent association with Annexin II directs hepatitis E virus ORF3 sorting into vesicles and quasi-enveloped virions
Authors: Liu Xing , Liu Tianxu , Shao Zhen , Xiong Xiaoyan , Qi Shuhui , Guan Junyong , Wang Menghang , Tang Yan-Dong , Feng Zongdi , Wang Lin , Yin Xin
Published: December 2024

Historically considered to be nonenveloped, hepatitis E virus (HEV), an important zoonotic pathogen, has recently been discovered to egress from infected cells as quasi-enveloped virions. These quasi-enveloped virions circulating in the blood are resistant to neutralizing antibodies, thereby facilitating the stealthy spread of infection. Despite abundant evidence of the essential role of the HEV-encoded ORF3 protein in quasi-enveloped virus formation, the underlying mechanism remains unclear. Here, we demonstrate that the HEV ORF3 protein possesses an inherent capacity for self-secretion and that palmitoylation at two cysteine residues within the ORF3 N-terminal region is essential for its secretion and quasi-enveloped virus formation. We further found that only palmitoylated ORF3 proteins hijacked Annexin II for transport to the cytoskeleton and are then directed into multivesicular bodies through the nSMase-endosomal sorting complexes required for transport-III pathway for secretion. Finally, we show that infection of gerbils with HEV mutants harboring mutations at palmitoylation sites within ORF3 showed no fecal viral shedding but competent replication in the liver. Our study fills a gap in the understanding of the assembly and release of quasi-enveloped virions mediated by ORF3 and offers the potential for designing therapeutic strategies to control HEV infection.
Learning the language of antibody hypervariability
Authors: Singh Rohit , Im Chiho , Qiu Yu , Mackness Brian , Gupta Abhinav , Joren Taylor , Sledzieski Samuel , Erlach Lena , Wendt Maria , Fomekong Nanfack Yves , Bryson Bryan , Berger Bonnie
Published: December 2024

Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose “foundational” PLMs have limited performance in modeling antibodies due to the latter’s hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples. Our learned feature representations accurately predict mutational effects on antigen binding, paratope identification, and other key antibody properties. We experimentally validate AbMAP for antibody optimization by applying it to refine a set of antibodies that bind to a SARS-CoV-2 peptide, and obtain an 82% hit-rate and up to 22-fold increase in binding affinity. AbMAP also unlocks large-scale analyses of immune repertoires, revealing that B-cell receptor repertoires of individuals, while remarkably different in sequence, converge toward similar structural and functional coverage. Importantly, AbMAP’s transfer learning approach can be readily adapted to advances in foundational PLMs. We anticipate AbMAP will accelerate the efficient design and modeling of antibodies, expedite the discovery of antibody-based therapeutics, and deepen our understanding of humoral immunity.
A hybrid meta on-top functional for multiconfiguration pair-density functional theory
Authors: Bao Jie J. , Zhang Dayou , Zhang Shaoting , Gagliardi Laura , Truhlar Donald G.
Published: December 2024

Multiconfiguration pair-density functional theory (MC-PDFT) was proposed a decade ago, but it is still in the early stage of density functional development. MC-PDFT uses functionals that are called on-top functionals; they depend on the density and the on-top pair density. Most MC-PDFT calculations to date have been unoptimized translations of generalized gradient approximations (GGAs) of Kohn–Sham density functional theory (KS-DFT). A hybrid MC-PDFT has also been developed, in which one includes a fraction of the complete active space self-consistent-field wave function energy in the total energy. Meta-GGA functionals, which use kinetic-energy densities in addition to GGA ingredients, have shown higher accuracy than GGAs in KS-DFT, yet the translation of meta-GGAs has not been previously proposed for MC-PDFT. In this paper, we propose a way to include kinetic energy density in a hybrid on-top functional for MC-PDFT, and we optimize the parameters of the resulting functional by training with a database developed as part of the present work that contains a wide variety of systems with diverse characters. The resulting hybrid meta functional is called the MC23 functional. We find that MC23 has improved performance as compared to KS-DFT functionals for both strongly and weakly correlated systems. We recommend MC23 for future MC-PDFT calculations.
Across the firewall: Foreign media’s role in shaping Chinese social media narratives on the Russo-Ukrainian War
Authors: Hanley Hans W. A. , Lu Yingdan , Pan Jennifer
Published: December 2024

There is a widespread perception that China’s digital censorship distances its people from the global internet, and the Chinese Communist Party, through state-controlled media, is the main gatekeeper of information about foreign affairs. Our analysis of narratives about the Russo-Ukrainian War circulating on the Chinese social media platform Weibo challenges this view. Comparing narratives on Weibo with 8.26 million unique news articles from 2,500 of some of the most trafficked websites in China, Russia, Ukraine, and the United States (totaling 10,000 sites), we find that Russian news websites published more articles matching narratives found on Weibo than news websites from China, Ukraine, or the United States. Similarly, a plurality of Weibo narratives were most associated with narratives found on Russian news websites while less than ten percent were most associated with narratives from Chinese news sites. Narratives later appearing on Weibo were more likely to first appear on Russian rather than Chinese, Ukrainian, or US news websites, and Russian websites were highly influential for narratives appearing on Weibo. Altogether, these results show that Chinese state media was not the main gatekeeper of information about Russia’s invasion of Ukraine for Weibo users.
Complex tissue regeneration in
Lophuromys
reveals a phylogenetic signal for enhanced regenerative ability in deomyine rodents
Authors: Riddell Brennan , McDonough Molly , Ferguson Adam , Kimani John M. , Gawriluk Thomas R. , Peng Chi , Kiama Stephen G. , Ezenwa Vanessa O. , Seifert Ashley W.
Published: December 2024

Identifying why complex tissue regeneration is present or absent in specific vertebrate lineages has remained elusive. One also wonders whether the isolated examples where regeneration is observed represent cases of convergent evolution or are instead the product of phylogenetic inertia from a common ancestral program. Testing alternative hypotheses to identify genetic regulation, cell states, and tissue physiology that explain how regenerative healing emerges in some species requires sampling multiple species among which there is variation in regenerative ability across a phylogenetic framework. Here, we interrogate tissue healing across eleven rodents and show that brush-furred mice (
Lophuromys zena
) are capable of musculoskeletal regeneration where new tissue faithfully maintains axial polarity and tissue identity as previously observed in spiny mice (
Acomys spp.
). In contrast, we find that all nondeomyine rodents heal identical ear pinna injuries via fibrotic repair with scar tissue. Together, these data reveal a phylogenetic signal for enhanced regenerative ability in Deomyinae which is key to testing evolutionary hypotheses about the emergence of regenerative ability in mammals.
Evidence for a metal–bosonic insulator–superconductor transition in compressed sulfur
Authors: Wang Kui , Zhao Hongjian , Liu Guangtao , Zhou Mi , Chen Yinqi , Li Qiushi , Ma Guangchen , Wang Hongbo , Hemley Russell J. , Ma Yanming
Published: December 2024

The abrupt drop of resistance to zero at a critical temperature is a key signature of the current paradigm of the metal–superconductor transition. However, the emergence of an intermediate bosonic insulating state characterized by a resistance peak preceding the onset of the superconducting transition has challenged this traditional understanding. Notably, this phenomenon has been predominantly observed in disordered or chemically doped low-dimensional systems, raising intriguing questions about the generality of the effect and its underlying fundamental physics. Here, we present a systematic experimental study of compressed elemental sulfur, an undoped three-dimensional (3D) high-pressure superconductor, with detailed measurements of electrical resistance as a function of temperature, magnetic field, and current. The anomalous resistance peak observed in this 3D system is interpreted based on an empirical model of a metal–bosonic insulator–superconductor transition, potentially driven by vortex dynamics under magnetic field and energy dissipation processes. These findings offer a fresh platform for theoretical analysis of the decades-long enigmatic of the underlying mechanism of this phenomenon.
Deletion of metal transporter Zip14 reduces major histocompatibility complex II expression in murine small intestinal epithelial cells
Authors: Jimenez-Rondan Felix R. , Ruggiero Courtney H. , Riva Alberto , Yu Fahong , Stafford Lauren S. , Cross Tyler R. , Larkin Joseph , Cousins Robert J.
Published: December 2024

Documented worldwide, impaired immunity is a cardinal signature resulting from loss of dietary zinc, an essential micronutrient. A steady supply of zinc to meet cellular requirements is regulated by an array of zinc transporters. Deletion of the transporter Zip14 (Slc39a14) in mice produced intestinal inflammation. Elevated fecal lipocalin-2, calprotectin, IgG levels, and dysbiosis support the inflammatory phenotype. Here, we show through RNA-sequencing, using purified intestinal epithelial cells (IECs), that
Zip14
deletion produces markedly reduced expression of major histocompatibility complex class II (MHCII) molecules and the master MHCII transactivator (
Ciita
). qPCR, western analysis, and immunohistochemistry confirmed loss of MHCII. Spectrofluorimetry with zinc probe FluoZin-3 showed reduced labile zinc in IECs from knockout mice. Chromatin immunoprecipitation assays, using Ciita antibody and IEC chromatin, suggest decreased transcription accounts for depressed expression of specific MHCII genes. Assay for Transposase-Accessible Chromatin (ATAC) sequencing (ATAC-seq) demonstrated that
H2-Aa
,
H2-Ab1
and other MHCII genes result from chromatin remodeling yielding closed chromatin at regulatory regions of these genes. In agreement, ATAC-seq showed peak density of the chromosomal regulatory region of Ciita is consistent with down regulation of specific MHCII genes in IECs with
Zip14
loss. Finally, dietary zinc supplementation of knockout mice and zinc supplementation of intestinal organoids with
Zip14
deletion restored transcript levels. Taken together, our data suggest that cellular zinc delivery, via Zip14, is necessary for proper chromatin occupancy, required for normal MHCII expression and effective immune functions, and to preclude inflammatory disorders of the small intestine.
Income inequality and the erosion of democracy in the twenty-first century
Authors: Rau Eli G. , Stokes Susan
Published: December 2024

Among the most pressing problems societies face today are economic inequality and the erosion of democratic norms and institutions. In fact the two problems—inequality and democratic erosion—are linked. In a large cross-national statistical study of risk factors for democratic erosion, we establish that economic inequality is one of the strongest predictors of where and when democracy erodes. Even wealthy and longstanding democracies are vulnerable if they are highly unequal (though national wealth might provide some resiliency). The association between inequality and risk of democratic backsliding is robust, and holds under different measures and structures of both income inequality and wealth inequality. The association is unlikely to be a case of reverse causation. For concerned citizens seeking to understand why so many democracies are eroding and how to stop this process, our study indicates that policies for ameliorating inequality are a promising path forward.
A novel circular two-party semiquantum private comparison of size relationship based on d-level single-particle state without any preshared key
Authors: Shi Yan-Hua
Published: December 2024

In order to cut down the resource expended by the preshared key, this paper uses

d

-level single-particle states to design a novel circular two-party semiquantum private comparison scheme with a quantum semi-honest third party who does not need any preshared key. This scheme is capable of determining the size relationship of two integer sequences from two semiquantum communicants. The traveling particles are transmitted in a circular way. This protocol does not use quantum entangled states, quantum entanglement swapping, unitary operations or delay lines. This protocol does not require the semiquantum communicants to use any quantum memory either. Its security toward external attacks and internal attacks is fairly good.
Light Pollution Monitoring Through Zenithal Sky Brightness at Selected Malaysian Observatories
Authors: Bely Ahmad Hariz , Umar Roslan , Sabri Nor Hazmin , Abidin Zamri Zainal , Nasir Ahmad Lutfi Afifi Mohamad , Ismail Ihsanuddin , Hussaini Razalie , Zulkifli Emma Zulaiha , Rakhmadi Arwin Juli
Published: December 2024

Sky brightness magnitude is crucial for optical astronomical observations that require the dark skies area. This study focuses on the effect of artificial light pollution on astronomical observations by measuring the zenithal brightness at some selected observatories in Malaysia. Data were collected from eight observatories representing both pristine and rural areas using the Sky Quality Meter (SQM). The results show huge differences in sky brightness levels like pristine areas such as Balai Cerap KUSZA, Terengganu and the suggestion site Pusat Astronomi Borneo, Sarawak have less light pollution, making them ideal for astronomical observatory. On the other hand, due to surrounding urban growth and artificial light, rural observatories such as Stesen Hilal Permandangan Indah in Langkawi and Tapak Cerapan Bukit Geliga, Terengganu have low sky brightness. The study shows how urbanization has a significant impact and how artificial light pollution control are needed to maintain the quality of astronomical observations in Malaysia.
Astrophysical study of dust collision using molecular dynamics method: an overview
Authors: Rosandi Yudi , Urbassek Herbert M. , Nietiadi Maureen L. , Alfaridzi Raihan
Published: December 2024

Understanding dust collisions in astrophysical environments is essential for comprehending the formation and evolution of cosmic structures, such as planetary rings and interstellar clouds. This article reviews briefly studies on dust collision dynamics using the molecular dynamics (MD) method during the early stages of protoplanet formation. By simulating interactions at the atomic and molecular levels, researchers have actively explored the fundamental processes governing dust aggregation and fragmentation. This method incorporates essential aspects such as surface energy and viscoelastic behavior through interaction potentials between atomic particles. MD simulations cover a wide range of physical conditions, including varying impact velocities, particle sizes, and material compositions, to provide a thorough understanding of collision outcomes. The results identify critical thresholds for sticking, bouncing, and fragmentation, enhancing broader astrophysical models of dust evolution. This work underscores the significance of cohesive forces and material properties in determining collision behavior. The presented model involves the collision of two dust aggregates, each consisting of a few million atomic particles, at impact velocities around the threshold value, known as the bouncing velocity (Vb
), evaluated using the macroscopic Johnson-Kendall-Roberts (JKR) model. The model material mainly consists of silica, as the main material of rocky planets and water, which is widely distributed across the solar system. The findings demonstrate the range of validity of the JKR theory at the atomic scale, influenced by the complexity of the internal structure of the colliding agents. These insights contribute to our understanding of dust growth mechanisms in protoplanetary disks, advancing knowledge of cosmic dust dynamics and its implications for planet formation and the interstellar medium. The simulation data can also refine larger-scale modeling methods, such as granular mechanics.
Exploring solar flares and solar radio bursts associated with β-γ-δ active regions during the ascending phase of the solar cycle 25
Authors: Afandi Nur Zulaikha Mohd , Umar Roslan , Zafar Sharifah Nurul Aisyah Syed , Sabri Nor Hazmin , Monstein Christian
Published: December 2024

This paper presents an exploration of solar flares and solar radio bursts(SRBs) associated with β-γ-δ class active regions (ARs) during the ascending phase of solar cycle 25th, spanning from January 2022 to May 2024. The β-γ-δ ARs have complex magnetic fields with bipolar configurations, which are conducive to the production of intense solar flares. During solar flares, powerful electromagnetic (EM) radiation including solar radio bursts (SRBs) penetrates the outside of the Sun. The investigation was started by collecting the number of β-γ-δ, solar flares and SRBs for statistical evaluation. The details of AR such as the date and number of the active region of β-γ-δ were obtained from the Space Weather Live website. Then, the associated number of solar flares in all classes (Class-B, Class-C, Class-M and Class-X) from SWPC, NOAA and SRBs of Type II, Type III and Type IV from the CALLISTO spectrometer were calculated and recorded. In order to observe changes over the years, the data for solar flares and SRBs were analyzed separately for 2022, 2023, and 2024 and plotted in histograms. The results show that the average occurrence of β-γ-δ ARs in 2024 was 6 days and it was higher than compared to in 2023 and 2022 which had averages of 2 and 3 days, respectively. The production of Class-C, Class-M, and Class-X flares demonstrated significant trends with the ascending phase of the solar cycle. The highest number of Class-X flares occurred in AR 13664, with 10 flares recorded over 9 days. Moreover, the number of SRBs included 12 Type II bursts and 6 Type IV bursts, with the majority of days having both types of bursts. Additional factors contributing to the production number of solar flares and SRBs from β-γ-δ ARs have been studied and discussed in this paper.
Danau Rayo from the geoscience perspective: Is it a product of a meteor crater?
Authors: Sari Marlinda , Setiawan Budhi , Idarwati
Published: December 2024

Danau Rayo, one of the candidate’s geosites, is located in Kecamatan Rupit, Musi Rawa Utara Regency, and consists of the Kasai Formation as the Quaternary volcanic product. This study intends to Aind Danau Rayo’s uniqueness from the geoscience perspective, especially a morphological approach. The shape of the lake, which looks like a perfect circle with a diameter of about 645 meters in the middle of a plain that is not connected to a river, shows its geological uniqueness. The results of 3-dimensional modeling show that there are elevations on several sides, especially the southeast side, allowing the hypothesis that the lake is a meteor fall that formed a crater. The intensive weathering and erosion processes cause the features of the crater rim—characterized by rounded lithology, excellent sorting, open packing, high porosity, and good permeability— to convert into a slip plane when a meteor impacts the northwest lake rim, leaving no trace behind. The unique geological feature of this geosite may add its geological value for geotourism development in this area.
Potential for Geotourism Development in the Wewengkon Adat Kasepuhan Citorek, Bayah Dome Geopark Area, Lebak Regency, Banten Province
Authors: Daru Prabowo Yogan
Published: December 2024

Lebak Regency as one of the regions in Indonesia, has been known to the world for its unique geology through the process of forming the Bayah Dome. Evidence of the process millions of years ago also presents a high-value earth heritage that is quite widely spread in the Wewengkon Adat Kasepuhan Citorek, but this potential has not been packaged and utilized properly. The purpose of this study is to identify the potential for geotourism development based on geological heritage, biodiversity, and cultural diversity in the Wewengkon Adat Kasepuhan Citorek through the Geopark concept. The research method used is a qualitative descriptive analysis technique. The results of the study show that the Wewengkon Adat Kasepuhan Citorek has the potential for geological heritage, biodiversity, and cultural diversity that are related to each other. In order to integrate all existing potentials, it is necessary to develop geotourism in the Wewengkon Adat Kasepuhan Citorek with a potential visiting time of 3 days 2 nights. The key to the success of the realization of this geotourism activity requires the active involvement of the local community in one management management through BUMDes Bersama with the hope of improving the community’s economy and forming a tourism-aware society.
Unlocking Geotourism Potential: An Assessment of Sangiang Island’s Geological Heritage
Authors: Sabillana Rabbanni Naufal , Fatimah Rosana Mega , Ramadian Aldrin , Sena Ajie Nugraha Katon
Published: December 2024

Sangiang Island, nestled in the Sunda Strait of Indonesia, is a hidden gem renowned for its unique geological and ecological features. The island is characterized by its volcanic origins, with dramatic coastal cliffs and rugged landscapes shaped by ancient volcanic activity, offering valuable insights into the Earth’s past volcanic processes. A systematic investigation has been conducted in several selected sites on Sangiang Island, including inventory, characterization, classification, assessment, and evaluation. This study aims to assess the potential of Sangiang Island as a geoheritage and geotourism destination. The sites examined include Sangiang Harbour, Begal Hill, Harapan Summit, Panjang Beach, and Bat Cave. Both qualitative and quantitative assessments were conducted, focusing on geoheritage values like Intrinsic and Scientific Value, Educational Value, Economic Value, Conservation Value, and Added Value. The analysis reveals that Sangiang Island’s geodiversity holds promising potential as geoheritage, with final scores ranging from 56.94% to 69.44%. Despite its uniqueness, Sangiang Island remains slightly renowned due to lack of maintenance and promotion. Geoconservation efforts are necessary at all these sites to support research, education, and geotourism.
Geological Disaster Mitigation In Air Batu Village, Merangin Jambi Geopark UGGP Area
Authors: Anggi Deliana S , Novia Ramadani Dinda , Angkat Suriadi , Misnawati  , Magdalena Ritonga D. M. , Agus
Published: December 2024

Merangin Geopark is a very valuable natural resource, namely the discovery of several potential geological diversity along the Merangin River and Mengkarang River. These potentials include Jambi flora and fauna fossils around 250-290 million years old (Late Perem Period), and plant fossils in the form of giant terracotta logs dated to the late Tertiary-early Quaternary. The natural scenery of the tourist route and the geosite location of the research area itself is in the hills and rivers such as tributaries and the Main River. Each geosite has a hilly area and right below it is the main river, namely the Batang Merangin river, which at any time can cause landslides or floods or overflow. Landslides are a natural phenomenon that occur in mountainous, hilly areas, and the rainy season greatly influences the occurrence of landslides. Therefore, this research was carried out to carry out disaster mitigation at geosites, especially at the Tantan Granitoid Geosite, Jeram Ladeh Geosite, Teluk Gedang Geosite, and Muara Karing Geosite to minimize and provide good information to the public, pupils or students who come to the geosite.. as well as visitors from within or outside the country.
Analysis of Rice Plant Age Based on NDVI Value Using MODIS Imagery (Case Study of Koto Tangah District, Padang City)
Authors: Safitri Imelda , Yanti Delvi , Irsyad Fadli
Published: December 2024

Determining the growth phase of rice is an estimation technique that has been carried out universally using satellite images. However, an estimation model cannot applied in other areas due to different regional characteristics. Lowland areas have different environmental factors than highland areas. Padang City with the characteristics of a coastal area dan including the capital of West Sumatra Province has productive rice fields as one of the rice supplies in Padang City. This study aims to determine a model for estimating the growth phase of rice plants in Padang City using MODIS Imagery. The data used were MODIS image recordings from January 2021 to July 2024 with 60 image output data. Observation locations with grids or image pixels with rice field areas ≥ 50%. Based on the results of image analysis, a model was obtained for estimating the age of rice plants in Padang City, namely y = −0.000095x2+ 0.013743x + 0.310743 with y being the NDVI value and x is the age of the rice plant with a coefficient of determination (R2) value of 0.9554 in the forceful category and an RMSE value of 0.0383. The range of NDVI values for each phase of rice growth in Koto Tangah District, Padang City, is water phase < 0.5063; vegetative phase (1) 0.5063-0.7515; vegetative phase (2) 0.7515-0.8022; generative phase (1) 0.8022-0.7546; generative phase (2) 0.7546-0.5134 and fallow phase 0.5134-0.3198.
Evaluation of internal quality and shelf life of chicken eggs coated with shellac nanoemulsion
Authors: Harimurti Niken , Permana Asep W , Agustinisari Iceu , Yuliani Sri , Wiguna Bangkit , Khulafaur Rosyidin Ahmad , Winarti Christina
Published: December 2024

It was investigated whether shellac nanoemulsion coating might preserve the internal quality of chicken eggs and increase their shelf life. Using a high energy approach with an ultraturrax set at 16,000 rpm, shellac, purified water, tween 80, and biosilica were emulsified. A total of 120 chicken eggs were divided into 4 groups: 1) uncoated (control), 2) coated with 0.5% w/w of biosilica, 3) coated with 1.0 % w/w of biosilica, 4) coated with 1.5% w/w of biosilica in shellac nanoemulsion. The eggs were stored at room temperature for 6 weeks and their quality parameters were observed weekly. The results showed that coating eggs with shellac nanoemulsion and biosilica at concentrations of 0-1.5% w/w significantly affected their internal quality (p<0.05) compared to uncoated eggs. The shellac nanoemulsion formulation with 1% w/w of biosilica concentration showed the best internal quality parameter values up to week 6 of storage as follows: yolk index 0.18; egg white index 0.03; pH 9.10; HU value 42; weight loss 2.89%. The addition of biosilica to a shellac-based nanoemulsion shows promise as an eco-friendly coating material that can prolong the shelf life and maintain the internal quality of chicken eggs.
Application of aloe vera gel edible coating modified by VCO to maintain post-harvest guava quality
Authors: Gustira D , Yefrida Y , Hanifa D , Refilda R
Published: December 2024

Guava (Psidium guajava L.) is a very popular tropical fruit that is rich in nutrients, but its shelf life is short due to its climacteric nature. In this study, the effect of coating with aloe vera gel (AVG) modified by virgin coconut oil (VCO) to preserve post-harvest guava fruit was investigated. The coating formula was prepared by mixing 75% AVG with variations of VCO (0.0%, 1.0%, 2.0%, 3.0%, and 4.0%), along with other additives such as Tween 80 (0.6%), CMC (1.5%), glycerol (1%), and distilled water. The physicochemical properties of the guava were measured over a storage period of 0, 3, 6, 9, 12, and 15 days. The optimal coating, which can extend the shelf life to 15 days compared to 3 days for the uncoated fruit, was found with the addition of 2.0% VCO, resulting in a weight loss of 28.25%, a decay incidence of 10.00%, texture of 4.37N, total soluble solids of 10.67 °BRIX, water content of 78.28%, total titratable acidity of 0.66%, total phenolics of 774.69 mg GAE/gFW and total antioxidants of 679.64 mg AAE/gFW. In conclusion, the addition of VCO to aloe vera gel-based edible coatings effectively preserves the post-harvest quality of guava fruit.
GOS dual-metal split-gate step channel dielectrically modulated DG-TFET biosensor: A label-free non-ideal case study and analysis
Authors: Shaw Namrata , Mukhopadhyay Bratati
Published: December 2024

This article performs an extensive analysis of the ideal and non-ideal case of hybridization of biomolecules in the nano-gap cavity present in a biosensor device. A gate-on-source (GOS) dual metal, split-gate, step channel dielectrically modulated (DM) double gate TFET-based label-free biosensor is proposed in this paper. The commercial TCAD simulation software (Silvaco TCAD) is used to simulate the proposed device. The paper focusses on both the performance improvement of the TFET device used to implement the biosensor and the sensitivity of the biosensor device. This proposed label-free bio-sensing device exhibits a high drain current sensitivity ∼ 108 (for dielectric constant k in the range of 15) irrespective of the presence/absence of charge on the biomolecules. A high ION/IOFF ratio of the range ∼ 108 is obtained for the proposed device. A low sub-threshold swing (less than 60 mV dec−1) is seen to be given by the proposed device. There are several non-ideal cases investigated in this work to allow the comprehension of the viability of this biosensor in practical applications. The non-ideal cases with fill factors ranging from 30% to 80% are analysed alongwith steric hindrance effects n the device sensitivity. The integration of electrical FET device with the biological sensing module to develop a biosensor is successfully achieved in this work to allow the attainment of a feasible solution for everyday needs.