bluuebunny/crossref_metadata_2025 huggingface dataset:
Tertiary structure and conformational dynamics of the anti-amyloidogenic chaperone DNAJB6b at atomistic resolution
Authors: Adupa Vasista , Ustyantseva Elizaveta , Kampinga Harm H. , Onck Patrick R.
Published: April 2024

DNAJB6b is a molecular chaperone of the heat shock protein network, shown to play a crucial role in preventing aggregation of several disease-related intrinsically disordered proteins. Using homology modeling and microsecond-long all-atom molecular dynamics (MD) simulations, we show that monomeric DNAJB6b is a transiently interconverting protein cycling between three states: a closed state, an open state (both abundant), and a less abundant extended state. Interestingly, the reported regulatory autoinhibitory anchor between helix V in the G/F1 region and helices II/III of the J-domain, which obstructs the access of Hsp70 to the J-domain remains present in all three states. This possibly suggests a mechanistically intriguing regulation in which DNAJB6b only becomes exposed when loaded with substrates that require Hsp70 processing. Our MD results of DNAJB6b carrying mutations in the G/F1 region that are linked to limb-girdle muscular dystrophy type D1 (LGMDD1) show that this G/F1 region becomes highly dynamic, pointing towards a spontaneous release of the autoinhibitory helix V from helices II/III. This would increase the probability of non-functional Hsp70 interactions to DNAJB6b without substrates. Our cellular data indeed confirm that non-substrate loaded LGMDD1 mutants have aberrant interactions with Hsp70.
Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality
Authors: Zheng Renyu , Zhao Mingfei , Du Jingshan S. , Sudarshan Tarunya Rao , Zhou Yicheng , Paravastu Anant K. , De Yoreo James J. , Ferguson Andrew L. , Chen Chun-Long
Published: April 2024

A long-standing challenge in bioinspired materials is to design and synthesize synthetic materials that mimic the sophisticated structures and functions of natural biomaterials, such as helical protein assemblies that are important in biological systems. Herein, we report the formation of a series of nanohelices from a type of well-developed protein-mimetics called peptoids. We demonstrate that nanohelix structures and supramolecular chirality can be well-controlled through the side-chain chemistry. Specifically, the ionic effects on peptoids from varying the polar side-chain groups result in the formation of either single helical fiber or hierarchically stacked helical bundles. We also demonstrate that the supramolecular chirality of assembled peptoid helices can be controlled by modifying assembling peptoids with a single chiral amino acid side chain. Computational simulations and theoretical modeling predict that minimizing exposure of hydrophobic domains within a twisted helical form presents the most thermodynamically favorable packing of these amphiphilic peptoids and suggests a key role for both polar and hydrophobic domains on nanohelix formation. Our findings establish a platform to design and synthesize chiral functional materials using sequence-defined synthetic polymers.
Host response during unresolved urinary tract infection alters female mammary tissue homeostasis through collagen deposition and TIMP1
Authors: Henry Samantha , Lewis Steven Macauley , Cyrill Samantha Leeanne , Callaway Mackenzie Kate , Chatterjee Deeptiman , Hanasoge Somasundara Amritha Varshini , Jones Gina , He Xue-Yan , Caligiuri Giuseppina , Ciccone Michael Francis , Diaz Isabella Andrea , Biswas Amelia Aumalika , Hernandez Evelyn , Ha Taehoon , Wilkinson John Erby , Egeblad Mikala , Tuveson David Arthur , dos Santos Camila Oresco
Published: April 2024

Exposure to pathogens throughout a lifetime influences immunity and organ function. Here, we explore how the systemic host-response to bacterial urinary tract infection (UTI) induces tissue-specific alterations to the mammary gland. Utilizing a combination of histological tissue analysis, single cell transcriptomics, and flow cytometry, we identify that mammary tissue from UTI-bearing mice displays collagen deposition, enlarged ductal structures, ductal hyperplasia with atypical epithelial transcriptomes and altered immune composition. Bacterial cells are absent in the mammary tissue and blood of UTI-bearing mice, therefore, alterations to the distal mammary tissue are mediated by the systemic host response to local infection. Furthermore, broad spectrum antibiotic treatment resolves the infection and restores mammary cellular and tissue homeostasis. Systemically, unresolved UTI correlates with increased plasma levels of the metalloproteinase inhibitor, TIMP1, which controls extracellular matrix remodeling and neutrophil function. Treatment of nulliparous and post-lactation UTI-bearing female mice with a TIMP1 neutralizing antibody, restores mammary tissue normal homeostasis, thus providing evidence for a link between the systemic host response during UTI and mammary gland alterations.
Bacterial peptidoglycan acts as a digestive signal mediating host adaptation to diverse food resources in C. elegans
Authors: Hao Fanrui , Liu Huimin , Qi Bin
Published: April 2024

Food availability and usage is a major adaptive force for the successful survival of animals in nature, yet little is known about the specific signals that activate the host digestive system to allow for the consumption of varied foods. Here, by using a food digestion system inC. elegans, we discover that bacterial peptidoglycan (PGN) is a unique food signal that activates animals to digest inedible food. We identified that a glycosylated protein, Bacterial Colonization Factor-1 (BCF-1), in the gut interacts with bacterial PGN, leading to the inhibition of the mitochondrial unfolded protein response (UPRmt) by regulating the release of Neuropeptide-Like Protein (NLP-3). Interestingly, activating UPRmtwas found to hinder food digestion, which depends on the innate immune p38 MAPK/PMK-1 pathway. Conversely, inhibiting PMK-1 was able to alleviate digestion defects inbcf-1mutants. Furthermore, we demonstrate that animals with digestion defects experience reduced natural adaptation capabilities. This study reveals that PGN-BCF-1 interaction acts as “good-food signal” to promote food digestion and animal growth, which facilitates adaptation of the host animals by increasing ability to consume a wide range of foods in their natural environment.
Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells
Authors: Kubo Naoki , Uehara Ryuji , Uemura Shuhei , Ohishi Hiroaki , Shirane Kenjiro , Sasaki Hiroyuki
Published: April 2024

DNA methyltransferase 3A (DNMT3A) and its catalytically inactive cofactor DNA methyltransferase 3-Like (DNMT3L) proteins form functional heterotetramers to deposit DNA methylation in mammalian germ cells. While both proteins have an ATRX-DNMT3-DNMT3L (ADD) domain that recognizes histone H3 tail unmethylated at lysine-4 (H3K4me0), the combined and differential roles of the domains in the two proteins have not been fully defined in vivo. Here we investigate DNA methylation landscapes in female and male germ cells derived from mice with loss-of-function amino acid substitutions in the ADD domains of DNMT3A and/or DNMT3L. Mutations in either the DNMT3A-ADD or the DNMT3L-ADD domain moderately decrease global CG methylation levels, but to different degrees, in both germ cells. Furthermore, when the ADD domains of both DNMT3A and DNMT3L lose their functions, the CG methylation levels are much more reduced, especially in oocytes, comparable to the impact of the Dnmt3a/3L knockout. In contrast, aberrant accumulation of non-CG methylation occurs at thousands of genomic regions in the double mutant oocytes and spermatozoa. These results highlight the critical role of the ADD-H3K4me0 binding in proper CG and non-CG methylation in germ cells and the various impacts of the ADD domains of the two proteins.
Revisiting Copenhagen climate mitigation targets
Authors: Li Shuping , Meng Jing , Hubacek Klaus , Eskander Shaikh M. S. U. , Li Yuan , Chen Peipei , Guan Dabo
Published: April 2024

Many economies set climate mitigation targets for 2020 at the 2009 15th Conference of the Parties conference of the United Nations Framework Convention on Climate Change in Copenhagen. Yet no retrospective review of the implementation and actual mitigation associated with these targets has materialized. Here we track the national CO2 emissions from both territory and consumption (trade adjusted) perspectives to assess socioeconomic factors affecting changes in emissions. Among the 34 countries analysed, 12 failed to meet their targets (among them Portugal, Spain and Japan) and 7 achieved the target for territorial emissions, albeit with carbon leakage through international trade to meet domestic demand while increasing emissions in other countries. Key factors in meeting targets were intensity reduction of energy and the improvement of the energy mix. However, many countries efforts fell short of their latest nationally determined contributions. Timely tracking and review of mitigation efforts are critical for meeting the Paris Agreement targets.
Smartphone-based ecological momentary assessment reveals an incremental association between natural diversity and mental wellbeing
Authors: Hammoud Ryan , Tognin Stefania , Smythe Michael , Gibbons Johanna , Davidson Neil , Bakolis Ioannis , Mechelli Andrea
Published: April 2024

Using smartphone-based ecological momentary assessment, this study investigated an association between natural diversity on mental wellbeing. A sample of 1,998 participants completed 41,448 assessments between April 2018 and September 2023. Environments which included a larger range of natural features, such as trees, plants and birdlife (high natural diversity) were associated with greater mental wellbeing than environments including a smaller range of natural features (low natural diversity). There was evidence of a mediating effect of natural diversity on the association between natural environments and mental wellbeing. These results highlight the importance of policies and practices that support richness of biodiversity for public mental health.
ECG signal quality in intermittent long-term dry electrode recordings with controlled motion artifacts
Authors: Joutsen Atte , Cömert Alper , Kaappa Emma , Vanhatalo Kirsi , Riistama Jarno , Vehkaoja Antti , Eskola Hannu
Published: April 2024

Wearable long-term monitoring applications are becoming more and more popular in both the consumer and the medical market. In wearable ECG monitoring, the data quality depends on the properties of the electrodes and on how they interface with the skin. Dry electrodes do not require any action from the user. They usually do not irritate the skin, and they provide sufficiently high-quality data for ECG monitoring purposes during low-intensity user activity. We investigated prospective motion artifact–resistant dry electrode materials for wearable ECG monitoring. The tested materials were (1) porous: conductive polymer, conductive silver fabric; and (2) solid: stainless steel, silver, and platinum. ECG was acquired from test subjects in a 10-min continuous settling test and in a 48-h intermittent long-term test. In the settling test, the electrodes were stationary, whereas both stationary and controlled motion artifact tests were included in the long-term test. The signal-to-noise ratio (SNR) was used as the figure of merit to quantify the results. Skin–electrode interface impedance was measured to quantify its effect on the ECG, as well as to leverage the dry electrode ECG amplifier design. The SNR of all electrode types increased during the settling test. In the long-term test, the SNR was generally elevated further. The introduction of electrode movement reduced the SNR markedly. Solid electrodes had a higher SNR and lower skin–electrode impedance than porous electrodes. In the stationary testing, stainless steel showed the highest SNR, followed by platinum, silver, conductive polymer, and conductive fabric. In the movement testing, the order was platinum, stainless steel, silver, conductive polymer, and conductive fabric.
Enhancement of acousto-optic interaction using a phoxonic cavity with structural hierarchy
Authors: An Junyong , Park Seongmin , Jeon Wonju
Published: April 2024

We propose a phoxonic cavity with structural hierarchy to enhance acousto-optic interaction in acoustically dissipative media. In a conventional phoxonic cavity, interaction between infrared light and hypersound with the same wavelength scale became weak due to large acoustic attenuation whose coefficient is proportional to the square of the frequency. To alleviate the acoustic attenuation, it is necessary to use low-frequency sound with much longer wavelength than the infrared light, but the conventional phoxonic cavity is not suitable for confining such hypersound and infrared light simultaneously. In this study, we employ the concept of structural hierarchy into the phoxonic cavity to control infrared light and hypersound with different wavelength scales. A phoxonic cavity with two different scales achieves the acousto-optic interaction approximately 1.6 times that in the conventional one. To further enhance the interaction, we adjust geometrical constitution and material properties of the two-scale phoxonic cavity using quasi-static homogenization theory, leading to the interaction about 2.1 times that in the conventional cavity.
Revealing the global emission gaps for fully fluorinated greenhouse gases
Authors: Guo Liya , Fang Xuekun
Published: April 2024

In response to the global trend of climate change, it is important to accurately quantify emissions of fully fluorinated greenhouse gases (FFGHGs, referring to SF6/NF3/CF4/C2F6/C3F8/c-C4F8 here). Atmospheric observation-based top-down methods and activity-based bottom-up methods are usually used together to estimate FFGHG emissions at the global and regional levels. In this work, emission gaps at global and regional levels are discussed among top-down studies, between the top-down and bottom-up FFGHG emissions, and among bottom-up emissions. Generally, trends and magnitudes of individual FFGHG emissions among top-down estimates are close to each other within the uncertainties. However, global bottom-up inventories show discrepancies in FFGHG emissions among each other in trends and magnitudes. The differences in emission magnitudes are up to 93%, 90%, 88%, 83%, 87%, and 85% for SF6, NF3, CF4, C2F6, C3F8, and c-C4F8, respectively. Besides, we reveal the insufficient regional TD studies and the lack of atmospheric observation data/stations especially in areas with potential FFGHG emissions. We make recommendations regarding the best practices for improving our understanding of these emissions, including both top-down and bottom-up methods.
A machine-learning algorithm using claims data to identify patients with homozygous familial hypercholesterolemia
Authors: Gu Jing , Epland Matthew , Ma Xinshuo , Park Jina , Sanchez Robert J. , Li Ying
Published: April 2024

Homozygous familial hypercholesterolemia (HoFH) is an underdiagnosed and undertreated ultra-rare disease. We utilized claims data from the Komodo Healthcare Map database to develop a machine-learning model to identify potential HoFH patients. We tokenized patients enrolled in MyRARE (patient support program for those prescribed evinacumab-dgnb in the United States) and linked them with their Komodo claims. A true positive HoFH cohort (n = 331) was formed by including patients from MyRARE and patients with prescriptions for evinacumab-dgnb or lomitapide. The negative cohort (n = 1423) comprised patients with or at risk for cardiovascular disease. We divided the cohort into an 80% training and 20% testing set. Overall, 10,616 candidate features were investigated; 87 were selected due to clinical relevance and importance on prediction performance. Different machine-learning algorithms were explored, with fast interpretable greedy-tree sums selected as the final machine-learning tool. This selection was based on its satisfactory performance and its easily interpretable nature. The model identified four useful features and yielded precision (positive predicted value) of 0.98, recall (sensitivity) of 0.88, area under the receiver operating characteristic curve of 0.98, and accuracy of 0.97. The model performed well in identifying HoFH patients in the testing set, providing a useful tool to facilitate HoFH screening and diagnosis via healthcare claims data.
Sirolimus-coated Eustachian tube balloon dilatation for treating Eustachian tube dysfunction in a rat model
Authors: Kang Jeon Min , Kim Song Hee , Ryu Dae Sung , Park Yubeen , Won Dong-Sung , Kim Ji Won , Park Jun-Kyu , Park Hong Ju , Park Jung-Hoon
Published: April 2024

Eustachian tube balloon dilatation (ETBD) has shown promising results in the treatment of ET dysfunction (ETD); however, recurrent symptoms after ETBD frequently occur in patients with refractory ETD. The excessive pressure of balloon catheter during ETBD may induce the tissue hyperplasia and fibrotic changes around the injured mucosa. Sirolimus (SRL), an antiproliferative agent, inhibits tissue proliferation. An SRL-coated balloon catheter was fabricated using an ultrasonic spray coating technique with a coating solution composed of SRL, purified shellac, and vitamin E. This study aimed to investigate effectiveness of ETBD with a SRL-coated balloon catheter to prevent tissue proliferation in the rat ET after ETBD. In 21 Sprague–Dawley rats, the left ET was randomly divided into the control (drug-free ETBD; n = 9) and the SRL (n = 9) groups. All rats were sacrificed for histological examination immediately after and at 1 and 4 weeks after ETBD. Three rats were used to represent the normal ET. The SRL-coated ETBD significantly suppressed tissue proliferation caused by mechanical injuries compared with the control group. ETBD with SRL-coated balloon catheter was effective and safe to maintain ET luminal patency without tissue proliferation at the site of mechanical injuries for 4 weeks in a rat ET model.
A two-phase spatiotemporal chaos-based protocol for data integrity in IoT
Authors: Alkhonaini Mimouna Abdullah , Alenizi Farhan A. , Jazyah Yahia Hasan , Lee Sangkeum
Published: April 2024

One of the biggest problems with Internet of Things (IoT) applications in the real world is ensuring data integrity. This problem becomes increasingly significant as IoT expands quickly across a variety of industries. This study presents a brand-new data integrity methodology for Internet of Things applications. The “sequence sharing” and “data exchange” stages of the suggested protocol are divided into two parts. During the first phase, each pair of nodes uses a new chaotic model for securely exchanging their identity information to generate a common sequence. This phase’s objectives include user authentication and timing calculations for the second phase of the recommended method’s packet validation phase. The recommended approach was tested in numerous settings, and various analyses were taken into account to guarantee its effectiveness. Also, the results were compared with the conventional data integrity control protocol of IoT. According to the results, the proposed method is an efficient and cost-effective integrity-ensuring mechanism with eliminates the need for third-party auditors and leads to reducing energy consumption and packet overhead. The results also show that the suggested approach is safe against a variety of threats and may be used as a successful integrity control mechanism in practical applications.
Impact of time-history terms on reservoir dynamics and prediction accuracy in echo state networks
Authors: Ebato Yudai , Nobukawa Sou , Sakemi Yusuke , Nishimura Haruhiko , Kanamaru Takashi , Sviridova Nina , Aihara Kazuyuki
Published: April 2024

The echo state network (ESN) is an excellent machine learning model for processing time-series data. This model, utilising the response of a recurrent neural network, called a reservoir, to input signals, achieves high training efficiency. Introducing time-history terms into the neuron model of the reservoir is known to improve the time-series prediction performance of ESN, yet the reasons for this improvement have not been quantitatively explained in terms of reservoir dynamics characteristics. Therefore, we hypothesised that the performance enhancement brought about by time-history terms could be explained by delay capacity, a recently proposed metric for assessing the memory performance of reservoirs. To test this hypothesis, we conducted comparative experiments using ESN models with time-history terms, namely leaky integrator ESNs (LI-ESN) and chaotic echo state networks (ChESN). The results suggest that compared with ESNs without time-history terms, the reservoir dynamics of LI-ESN and ChESN can maintain diversity and stability while possessing higher delay capacity, leading to their superior performance. Explaining ESN performance through dynamical metrics are crucial for evaluating the numerous ESN architectures recently proposed from a general perspective and for the development of more sophisticated architectures, and this study contributes to such efforts.
Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes
Authors: Ridley Rodney S. , Conrad Roth E. , Lindner Blake G. , Woo Seongwook , Konstantinidis Konstantinos T.
Published: April 2024

Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes—these may be useful for deeper investigation of nature’s ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)—accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.
Empagliflozin in children with glycogen storage disease-associated inflammatory bowel disease: a prospective, single-arm, open-label clinical trial
Authors: Li Zhiling , Zhang Xiaoyan , Chen Huan , Zeng Hanshi , Wu Jiaxing , Wang Ying , Ma Ni , Lan Jiaoli , Zhang Yuxin , Niu Huilin , Shang Lei , Jiang Xun , Yang Min
Published: April 2024

Glycogen storage disease type Ib (GSD-Ib) is a rare inborn error of glycogen metabolism caused by mutations in SLC37A4. Patients with GSD-Ib are at high risk of developing inflammatory bowel disease (IBD). We evaluated the efficacy of empagliflozin, a renal sodium‒glucose cotransporter protein 2 (SGLT2) inhibitor, on colonic mucosal healing in patients with GSD-associated IBD. A prospective, single-arm, open-label clinical trial enrolled eight patients with GSD-associated IBD from Guangdong Provincial People's Hospital in China from July 1, 2022 through December 31, 2023. Eight patients were enrolled with a mean age of 10.34 ± 2.61 years. Four male and four female. The endoscopic features included deep and large circular ulcers, inflammatory hyperplasia, obstruction and stenosis. The SES-CD score significantly decreased at week 48 compared with before empagliflozin. Six patients completed 48 weeks of empagliflozin therapy and endoscopy showed significant improvement or healing of mucosal ulcers, inflammatory hyperplasia, stenosis, and obstruction. One patient had severe sweating that required rehydration and developed a urinary tract infection. No serious or life-threatening adverse events. This study suggested that empagliflozin may promote colonic mucosal healing and reduce hyperplasia, stenosis, and obstruction in children with GSD-associated IBD.
Refraction and topographic risk factors for early myopic regression after small-incision lenticule extraction surgery
Authors: Lee Chia-Yi , Jeng Yu-Ting , Chao Chen-Cheng , Lian Ie-Bin , Huang Jing-Yang , Yang Shun-Fa , Chang Chao-Kai
Published: April 2024

We sought to evaluate the topographic risk factors for early myopic regression after small-incision lenticule extraction (SMILE). A retrospective case‒control study was conducted, and individuals who underwent SMILE surgery were enrolled. Among them, 406 and 14 eyes were categorized into the nonregression and regression groups, respectively. The preoperative and postoperative parameters in the two groups were collected, including spherical refraction (SE), axial length (AXL) and topographic data. A generalized linear model was adopted to analyze the difference in each parameter between the two groups. After 6 months, UCVA decreased in the regression group, and SE increased in the regression group (both P < 0.05). The increase in the CCT at the thinnest point (P = 0.044), flat corneal curvature (P = 0.012) and TCRP (P = 0.001) were significantly greater in the regression group. Regarding the risk factors for myopic regression, preoperative SE, preoperative sphere power, preoperative AXL, preoperative flat corneal curvature, preoperative SA, early postoperative SE, early postoperative sphere power, early postoperative AXL and early postoperative CCT difference were significantly greater in the regression group (all P < 0.05). The SE, sphere power, AXL, preoperative flat corneal curvature, preoperative SA, and postoperative CCT difference correlate with early myopic regression after SMILE.
A six degrees-of-freedom cable-driven robotic platform for head–neck movement
Authors: Bales Ian , Zhang Haohan
Published: April 2024

This paper introduces a novel cable-driven robotic platform that enables six degrees-of-freedom (DoF) natural head–neck movements. Poor postural control of the head–neck can be a debilitating symptom of neurological disorders such as amyotrophic lateral sclerosis and cerebral palsy. Current treatments using static neck collars are inadequate, and there is a need to develop new devices to empower movements and facilitate physical rehabilitation of the head–neck. State-of-the-art neck exoskeletons using lower DoF mechanisms with rigid linkages are limited by their hard motion constraints imposed on head–neck movements. By contrast, the cable-driven robot presented in this paper does not constrain motion and enables wide-range, 6-DoF control of the head–neck. We present the mechatronic design, validation, and control implementations of this robot, as well as a human experiment to demonstrate a potential use case of this versatile robot for rehabilitation. Participants were engaged in a target reaching task while the robot applied both assistive and resistive moments on the head during the task. Our results show that neck muscle activation increased by 19% when moving the head against resistance and decreased by 28–43% when assisted by the robot. Overall, these results provide a scientific justification for further research in enabling movement and identifying personalized rehabilitation for motor training. Beyond rehabilitation, other applications such as applying force perturbations on the head to study sensory integration and applying traction to achieve pain relief may benefit from the innovation of this robotic platform which is capable of applying controlled 6-DoF forces/moments on the head.
Impacts of spatio-temporal change of landscape patterns on habitat quality across Zayanderud Dam watershed in central Iran
Authors: Abolmaali Seyed Mohammad-reza , Tarkesh Mostafa , Mousavi Seyed Alireza , Karimzadeh Hamidreza , Pourmanafi Saeid , Fakheran Sima
Published: April 2024

The biodiversity of an ecosystem is greatly influenced by the spatio-temporal pattern of the landscape. Understanding how landscape type affects habitat quality (HQ) is important for maintaining environmental and ecological sustainability, preserving biodiversity, and guaranteeing ecological health. This research examined the relationship between the HQ and landscape pattern. The study presented an interpretation of the biodiversity variation associated with the landscape pattern in the Zayanderud Dam watershed area by integrating the Land Change Modeler and the InVEST model. Landsat images and maximum likelihood classification were used to analyze the spatio-temporal characteristics of the landscape pattern in 1991 and 2021. The future landscape pattern in 2051 was simulated using a Land Change Modeler. Subsequently, the InVEST model and the landscape maps were used to identify the spatial distribution of HQ and its changes over three periods. The mean values of the HQ in the study area were 0.601, 0.489, and 0.391, respectively, demonstrating a decreasing trend. The effect of landscape pattern change on HQ was also assessed based on landscape metrics, including PD, NP, SHDI, and CONTAG. HQ had a significant positive correlation with the CONTAG parameter (R = 0.78). Additionally, it had a significant inverse correlation with NP (R = − 0.83), PD (R = − 0.61), and SHDI (R = − 0.42). The results showed that the habitats in the northern region had lower quality compared to those in the southern parts of the Zayanderud Dam watershed. The density, diversity, and connectivity of landscape patches significantly influence the HQ in the study area. This research has the potential to enhance understanding of the impacts of land change patterns on biodiversity and establish a scientific basis for the conservation of natural habitats. Additionally, it can facilitate efficient decision-making and planning related to biodiversity conservation and landscape management.
A unified SVPWM fault tolerant control algorithm for single leg fault reconstruction topology of two-level inverter
Authors: Zhiduan Cai , Lihao Xu
Published: April 2024

To improve the reliability of Two-level three phase voltage source inverters, a uniform fault tolerant strategy based on space vector pulse width modulation is proposed for different leg faults. The reconstructed topologies of inverters with different bridge arm faults are different, which makes the basic voltage vector phase of each reconstructed topology inconsistent, resulting in different calculations. Therefore, the coordinate transformation is applied to place the basic voltage vectors of each reconstructed topology on the synchronous stationary αβ coordinate system so that the calculations of the reconstructed topology under different bridge arm faults are unified, thus reducing the complexity of fault-tolerant control. Aiming at the three-phase current asymmetry caused by the neutral point voltage oscillation in inverter topology reconstruction, a transient compensation method of neutral point voltage offset for the α-axis component of the reference voltage vector is introduced to suppress the adverse effects. The compensation method directly offers a neutral point voltage offset value after Clarke transformation and corrects the α-axis component of the reference voltage vector, avoiding the integral calculation in the conventional voltage compensation algorithm. The correctness and effectiveness of the proposed fault-tolerant control strategy are verified experimentally.
Circular ZDHHC11 supports Burkitt lymphoma growth independent of its miR-150 binding capacity
Authors: Liu Yichen , Zhao Xing , Seitz Annika , Hooijsma Annie A. , Ravanbakhsh Reyhaneh , Sheveleva Sofia , de Jong Debora , Koerts Jasper , Dzikiewicz-Krawczyk Agnieszka , van den Berg Anke , Ziel-Swier Lotteke J. Y. M. , Kluiver Joost
Published: April 2024

We previously showed that MYC promoted Burkitt lymphoma (BL) growth by inhibiting the tumor suppressor miR-150, resulting in release of miR-150 targets MYB and ZDHHC11. The ZDHHC11 gene encodes three different transcripts including a mRNA (pcZDHHC11), a linear long non-coding RNA (lncZDHHC11) and a circular RNA (circZDHHC11). All transcripts contain the same region with 18 miR-150 binding sites. Here we studied the relevance of circZDHHC11, including this miR-150 binding site region, for growth of BL cells. CircZDHHC11 was mainly present in the cytoplasmic fraction in BL cells and its localization was not altered upon miR-150 overexpression. Knockdown of circZDHHC11 caused a strong inhibition of BL growth without affecting the expression levels of MYC, MYB, miR-150 and other genes. Overexpression of circZDHHC11 neither affected cell growth, nor rescued the phenotype induced by miR-150 overexpression. Genomic deletion of the miR-150 binding site region did not affect growth, nor did it change the effect of circZDHHC11 knockdown. This indicated that the miR-150 binding site region is dispensable for the growth promoting role of circZDHHC11. To conclude, our results show that circZDHHC11 is a crucial factor supporting BL cell growth independent of its ability to sponge miR-150.
Effect of thermal treatment on microcracking characteristics of granite under tensile condition based on bonded-particle model and moment tensor
Authors: Zhao Jinsheng , Sun Wei , Luo Hao , Wu Shunchuan , Hou Zhiqiang
Published: April 2024

It is known that the heterogeneity caused by thermally induced micro-cracks and thermal stress can affect the mechanical behavior of granite. The laboratory-scale tests have the intrinsic limitation of non-repeatability and lack of effective methods to characterize the interaction effect between thermal micro-cracks and thermal stresses. In this study, we demonstrate how advancements in particle bonded model and moment tensor can help better understand the roles of high temperature in weakening granite and thermally induced cracking process in Brazilian test. Our results show that the types of micro-cracks (intergranular, intragranular, and transcrystalline ones) are related to their thermal expansion coefficients of mineralogical compositions. The intergranular tensile micro-cracks are predominant during the heating and heating–cooling processes. An obvious weakening of granite and non-central initiation is associated with the heterogeneity caused by the thermal damage and thermal stress. We also quantitatively evaluate the thermal damage based on orientation distribution, b-value, and nature of the sources, which gives a new microcracking perspective on tensile characteristics subjected to high temperature.
Comparison and evaluation of overcoring and hydraulic fracturing stress measurements
Authors: Li Peng , Cai Meifeng , Miao Shengjun , Li Yuan , Sun Liang , Wang Jiangtao , Gorjian Mostafa
Published: April 2024

The stress measurements determined by both the overcoring (OC) and hydraulic fracturing (HF) methods in the Shuichang iron mine and Sanshandao gold mine were compared and evaluated, respectively. The results indicate that the independent OC and HF data in the two mines reveal the same dominant faulting stress regime. The σH orientations derived from the OC and HF methods in the Shuichang iron mine are dominantly oriented in the N81.1°W–N89.4°W and N77.0°E–N88.0°E, respectively, and the σH orientations yielded from the OC and HF techniques in the Sanshandao gold mine are predominantly in the N30°W–N90°W and N55.5°W–N60.4°W, respectively; hence, the σH orientations obtained by the two different methods in the two mines are comparatively similar. In addition, the shapes of the probability density diagrams using an improved Bayesian regression approach of the three principal stresses measured by the OC and HF methods in the same mine are quite similar, and all the obtained Kolmogorov–Smirnov test p-values are larger than the selected significance level of 0.01, indicating that the stress data interpreted by the two methods approximately follow the same distribution law. Thus, the performance of the two techniques and the reliability of the measured data are satisfactory.
Simulation of a randomly percolated CNT network for an improved analog physical unclonable function
Authors: Yang Hyo-In , Lee Hanbin , Ko Jeonghee , An Yulim , Min Gyeongsu , Kim Dong Myong , Kim Dae Hwan , Bae Jong-Ho , Lim Meehyun , Choi Sung-Jin
Published: April 2024

Carbon nanotube networks (CNTs)-based devices are well suited for the physically unclonable function (PUF) due to the inherent randomness of the CNT network, but CNT networks can vary significantly during manufacturing due to various controllable process conditions, which have a significant impact on PUF performance. Therefore, optimization of process conditions is essential to have a PUF with excellent performance. However, because it is time-consuming and costly to fabricate directly under various conditions, we implement randomly formed CNT network using simulation and confirm the variable correlation of the CNT network optimized for PUF performance. At the same time, by implementing an analog PUF through simulation, we present a 2D patterned PUF that has excellent security and can compensate for error occurrence problems. To evaluate the performance of analog PUF, a new evaluation method different from the existing digital PUF is proposed, and the PUF performance is compared according to two process variables, CNT density and metallic CNT ratio, and the correlation with PUF performance is confirmed. This study can serve as a basis for research to produce optimized CNT PUF by applying simulation according to the needs of the process of forming a CNT network.
Performance and robustness of small molecule retention time prediction with molecular graph neural networks in industrial drug discovery campaigns
Authors: Vik Daniel , Pii David , Mudaliar Chirag , Nørregaard-Madsen Mads , Kontijevskis Aleksejs
Published: April 2024

This study explores how machine-learning can be used to predict chromatographic retention times (RT) for the analysis of small molecules, with the objective of identifying a machine-learning framework with the robustness required to support a chemical synthesis production platform. We used internally generated data from high-throughput parallel synthesis in context of pharmaceutical drug discovery projects. We tested machine-learning models from the following frameworks: XGBoost, ChemProp, and DeepChem, using a dataset of 7552 small molecules. Our findings show that two specific models, AttentiveFP and ChemProp, performed better than XGBoost and a regular neural network in predicting RT accurately. We also assessed how well these models performed over time and found that molecular graph neural networks consistently gave accurate predictions for new chemical series. In addition, when we applied ChemProp on the publicly available METLIN SMRT dataset, it performed impressively with an average error of 38.70 s. These results highlight the efficacy of molecular graph neural networks, especially ChemProp, in diverse RT prediction scenarios, thereby enhancing the efficiency of chromatographic analysis.
Serum autotaxin is a prognostic indicator of liver-related events in patients with non-alcoholic fatty liver disease
Authors: Iwadare Takanobu , Kimura Takefumi , Okumura Taiki , Wakabayashi Shun-ichi , Nakajima Taro , Kondo Shohei , Kobayashi Hiroyuki , Yamashita Yuki , Sugiura Ayumi , Fujimori Naoyuki , Yamazaki Tomoo , Kunimoto Hideo , Shimamoto Satoshi , Igarashi Koji , Joshita Satoru , Tanaka Naoki , Umemura Takeji
Published: April 2024

Background

Circulating autotaxin (ATX) levels have been reported to correlate with liver inflammation activity and liver fibrosis severity in patients with non-alcoholic fatty liver disease (NAFLD). The objective of this study is to investigate whether serum ATX could predict liver-related events (LRE) in NAFLD patients.

Methods

This retrospective investigation includes 309 biopsy-proven NAFLD patients registered at Shinshu University Hospital. All patients are followed for at least 1 year, during which time the prevalence of LRE, including newly developing hepatocellular carcinoma, hepatic encephalopathy, ascites, and esophagogastric varices, is investigated in relation to ATX levels at the time of liver biopsy.

Results

During the median follow-up period of 7.0 years, LRE are observed in 20 patients (6.5%). The area under the receiver operating characteristic curve and cut-off value of serum ATX for predicting LRE are 0.81 and 1.227 mg/l, respectively. Multivariate Cox proportional hazards models for LRE determine ATX and advanced fibrosis as independently associated factors. Furthermore, in a competing risk analysis that considered non-liver-related death as a competing event, ATX (HR 2.29, 95% CI 1.22–4.30, p = 0.010) is identified as an independent factor associated with LRE, along with advanced fibrosis (HR 8.01, 95% CI 2.10–30.60, p = 0.002). The predictive utility of ATX for LRE is validated in an independent cohort.

Conclusions

Serum ATX may serve as a predictive marker for LRE in patients with NAFLD.
The case for longtermism: concern for the far future as a catalyst for pro-climate action
Authors: Syropoulos Stylianos , Law Kyle Fiore , Young Liane
Published: April 2024

Amid escalating climate challenges, we examine relationships between longtermism beliefs with policy-level and grassroots climate-protective attitudes and actions. Across four primary pre-registered studies (N = 4451) and two supplementary pilots (N = 1858), we find that a significant portion, approximately 25% of our participants, who endorse the longtermism ethical philosophy, report heightened climate change concerns. Furthermore, longtermists show stronger support for pro-climate policies, advocate for initiatives in line with climate justice for future generations and present-day minoritized groups and make proactive contributions to environmental causes and initiatives. Moreover, we find that responsibility to distant future generations drives these associations. Through a targeted intervention, we boosted intergenerational responsibility and increased donations to an environmental charity. These findings highlight how longtermism beliefs shape pro-environmental attitudes and actions, offering valuable insights for climate advocacy strategies and cultivating more widespread support for comprehensive environmental policies.
Brain mechanisms underlying the emotion processing bias in treatment-resistant depression
Authors: Fan Xiaoxu , Mocchi Madaline , Pascuzzi Bailey , Xiao Jiayang , Metzger Brian A. , Mathura Raissa K. , Hacker Carl , Adkinson Joshua A. , Bartoli Eleonora , Elhassa Salma , Watrous Andrew J. , Zhang Yue , Allawala Anusha , Pirtle Victoria , Mathew Sanjay J. , Goodman Wayne , Pouratian Nader , Bijanki Kelly R.
Published: April 2024

Depression is associated with a cognitive bias towards negative information and away from positive information. This biased emotion processing may underlie core depression symptoms, including persistent feelings of sadness and a reduced capacity to experience pleasure. The neural mechanisms responsible for this biased emotion processing remain unknown. Here we had a unique opportunity to record stereotactic electroencephalography signals in the amygdala and prefrontal cortex (PFC) from 5 patients with treatment-resistant depression (TRD) and 12 patients with epilepsy (as control) while they participated in an affective bias task in which happy and sad faces were evaluated. First, compared with the control group, patients with TRD showed increased amygdala responses to sad faces in the early stage (around 300 ms) and decreased amygdala responses to happy faces in the late stage (around 600 ms) following the onset of faces. Furthermore, during the late stage of happy-face processing, alpha-band activity in the PFC as well as alpha-phase locking between the amygdala and the PFC were significantly greater in patients with TRD compared with the control group. The increased amygdala activation during the early stage of sad-face processing suggests an overactive bottom-up processing system in TRD. Meanwhile, the reduced amygdala response during the late stage of happy-face processing could be attributed to increased top-down inhibition by the PFC through alpha-band oscillation, which may be relieved following deep brain stimulation in the subcallosal cingulate and the ventral capsule/ventral striatum.
The impact of solvation on the structure and electric field strength in Li+GlyGly complexes
Authors: Meyer Katharina A. E. , Garand Etienne
Published: April 2024

To scrutinise the impact of electric fields on the structure and vibrations of biomolecules in the presence of water, we study the sequential solvation of lithium diglycine up to three water molecules with cryogenic infrared action spectroscopy.
Automated odor-blending with one-pot Bayesian optimization
Authors: Fukui Yota , Minami Kosuke , Shiba Kota , Yoshikawa Genki , Tsuda Koji , Tamura Ryo
Published: April 2024

To enable robots to perform the creation of new odors by blending existing ones automatically, we developed an automated odor-blending system using membrane-type surface stress sensors and machine learning.
Data-driven representative models to accelerate scaled-up atomistic simulations of bitumen and biobased complex fluids
Authors: York Daniel , Vidal-Daza Isaac , Segura Cristina , Norambuena-Contreras Jose , Martin-Martinez Francisco J.
Published: April 2024

Automated generation of data driven representative models of bitumen-like materials for large scale atomistic simulations.
Extrusion and chlorogenic acid treatment increase the ordered structure and resistant starch levels in rice starch with amelioration of gut lipid metabolism in obese rats
Authors: Zeng Xixi , Chen Ling , Zheng Bo
Published: April 2024

This work proves the dietary intervention effect of chlorogenic acid coupled with extruded rice starch (CGA-ES) in rats with lipid metabolism disorders, which is associated with the improvement of intestinal microecology.
The study of the synergistic effect of the oxysilane and phosphite-based flame retardant additive and its application in lithium-ion batteries
Authors: Chen YuChao , Liang Jin , Cao Jiang
Published: April 2024

Lithium-ion batteries are widely used in electronic devices due to their high energy density and long cycle life.
Synthesis of different types of nano-hydroxyapatites for efficient photocatalytic degradation of textile dye (Congo red): a crystallographic characterization
Authors: Kawsar Md. , Sahadat Hossain Md. , Tabassum Sumaya , Bahadur Newaz Mohammed , Ahmed Samina
Published: April 2024

Exploration of the crystallographic parameters of various nano-hydroxyapatites for enhanced photocatalytic degradation of Congo red dye.
Lock-key microfluidics: simulating nematic colloid advection along wavy-walled channels
Authors: Wamsler Karolina , Head Louise C. , Shendruk Tyler N.
Published: April 2024

Liquid crystalline media mediate interactions between suspended particles and confining geometries, which not only has potential to guide patterning and bottom-up colloidal assembly, but can also control colloidal migration in microfluidic devices.
C–H arylation of thiopyran derivatives with aryl halides
Authors: Su Yangzhe , Wang Min , Xu Jianping , Chen Weinan , Zhou Gang
Published: April 2024

A C–H arylation of thiopyran derivatives with aryl halides, including aryl chlorides, has been successfully developed.