bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Deep Learning Approach for Data Assimilation of Complex Hydrological Systems
Authors: Zhang Jiangjiang , Cao Chenglong , Nan Tongchao , Ju Lei , Zhou Hongxiang , Zeng Lingzao
Published: February 2024

In hydrological research, data assimilation (DA) is widely used to fuse the information contained in process‐based models and observational data to reduce simulation uncertainty. However, many popular DA methods are limited by low computational efficiency or their reliance on the Gaussian assumption. To address these limitations, we propose a novel DA method called DA(DL), which leverages the capabilities of DL to model non‐linear relationships and recognize complex patterns. DA(DL) first generates a large volume of training data from the prior ensemble, and then trains a DL model to update the system knowledge (e.g., model parameters in this study) from multiple predictors. For highly non‐linear models, an iterative form of DA(DL) can be implemented. Additionally, strategies of data augmentation and local updating are proposed to enhance DA(DL) for problems involving small ensemble size and the equifinality issue, respectively. In two hydrological DA cases involving Gaussian and non‐Gaussian distributions, DA(DL) shows promising performance compared to two ensemble smoother methods, that is, ES(K) and ES(DL), which respectively apply the Kalman‐ and DL‐based updates. Potential improvements to DA(DL) can be made by designing better DL model architectures, imposing physical constraints to the training of the DL model, and further updating other important variables like model states, forcings and error terms.
Safety, immunogenicity and protective effectiveness of heterologous boost with a recombinant COVID-19 vaccine (Sf9 cells) in adult recipients of inactivated vaccines
Authors: Luo Wenxin , Gan Jiadi , Luo Zhu , Li Shuangqing , Wang Zhoufeng , Wu Jiaxuan , Zhang Huohuo , Xian Jinghong , Cheng Ruixin , Tang Xiumei , Liu Yi , Yang Ling , Mou Qianqian , Zhang Xue , Chen Yi , Wang Weiwen , Wang Yantong , Bai Lin , Wei Xuan , Zhang Rui , Yang Lan , Chen Yaxin , Yang Li , Li Yalun , Liu Dan , Li Weimin , Chen Lei
Published: February 2024

Vaccines have proven effective in protecting populations against COVID-19, including the recombinant COVID-19 vaccine (Sf9 cells), the first approved recombinant protein vaccine in China. In this positive-controlled trial with 85 adult participants (Sf9 cells group: n = 44; CoronaVac group: n = 41), we evaluated the safety, immunogenicity, and protective effectiveness of a heterologous boost with the Sf9 cells vaccine in adults who had been vaccinated with the inactivated vaccine, and found a post-booster adverse events rate of 20.45% in the Sf9 cells group and 31.71% in the CoronaVac group (p = 0.279), within 28 days after booster injection. Neither group reported any severe adverse events. Following the Sf9 cells vaccine booster, the geometric mean titer (GMT) of binding antibodies to the receptor-binding domain of prototype SARS-CoV-2 on day 28 post-booster was significantly higher than that induced by the CoronaVac vaccine booster (100,683.37 vs. 9,451.69, p < 0.001). In the Sf9 cells group, GMTs of neutralizing antibodies against pseudo SARS-CoV-2 viruses (prototype and diverse variants of concern [VOCs]) increased by 22.23–75.93 folds from baseline to day 28 post-booster, while the CoronaVac group showed increases of only 3.29–10.70 folds. Similarly, neutralizing antibodies against live SARS-CoV-2 viruses (prototype and diverse VOCs) increased by 68.18–192.67 folds on day 14 post-booster compared with the baseline level, significantly greater than the CoronaVac group (19.67–37.67 folds). A more robust Th1 cellular response was observed with the Sf9 cells booster on day 14 post-booster (mean IFN-γ+ spot-forming cells per 2 × 105 peripheral blood mononuclear cells: 26.66 vs. 13.59). Protective effectiveness against symptomatic COVID-19 was approximately twice as high in the Sf9 cells group compared to the CoronaVac group (68.18% vs. 36.59%, p = 0.004). Our study findings support the high protective effectiveness of heterologous boosting with the recombinant COVID-19 vaccine (Sf9 cells) against symptomatic COVID-19 of diverse SARS-CoV-2 variants of concern, while causing no apparent safety concerns.
Cognitive and immunological effects of yoga compared to memory training in older women at risk for alzheimer’s disease
Authors: Grzenda Adrienne , Siddarth Prabha , Milillo Michaela M. , Aguilar-Faustino Yesenia , Khalsa Dharma S. , Lavretsky Helen
Published: February 2024

Subjective cognitive decline (SCD) and mild cognitive impairment (MCI) accompanied by cerebrovascular risk factors (CVRFs) are known to increase the risk of developing dementia. Mind-body practices such as yoga and meditation, have been recognized as safe techniques with beneficial effects on cognitive functions in older adults at risk for cognitive decline. We conducted a randomized, controlled trial to assess the efficacy of Kundalini yoga training (KY) compared to memory enhancement training (MET) on mood and cognitive functioning in a group of older women with CVRFs and SCD (clinicaltrials.gov = NCT03503669). The KY intervention consisted of weekly, 60-min in-person classes with a certified instructor for 12 weeks, with a 12-min guided recording for daily homework practice at home. MET involved 12 weekly in-person group classes with 12-min daily homework exercises. Objective and subjective memory performance were the primary outcomes. Peripheral whole blood samples were collected at baseline, 12-weeks, and 24-weeks follow-up for RNA sequencing and cytokine/chemokine assays. A total of 79 patients (KY = 40; MET = 39) were randomized, and 63 completed the 24-week follow-up (KY = 65% completion rate; MET = 95%; χ2(1) = 10.9, p < 0.001). At 24-weeks follow-up, KY yielded a significant, large effect size improvement in subjective cognitive impairment measures compared to MET. KYOn a transcriptional level, at 12- and 24-week follow-up, KY uniquely altered aging-associated signatures, including interferon gamma and other psycho-neuro-immune pathways. Levels of chemokine eotaxin-1, an aging marker, increased over time in MET but not KY participants. These results suggest clinical and biological benefits to KY for SCD, linking changes in cognition to the anti-inflammatory effects of yoga.
SALL4 promotes cancer stem-like cell phenotype and radioresistance in oral squamous cell carcinomas via methyltransferase-like 3-mediated m6A modification
Authors: Huang Junhong , Li Huan , Yang Zihui , Liu Rong , Li Yahui , Hu Yating , Zhao Shengnan , Gao Xiang , Yang Xinjie , Wei Jianhua
Published: February 2024

Radioresistance imposes a great challenge in reducing tumor recurrence and improving the clinical prognosis of individuals having oral squamous cell carcinoma (OSCC). OSCC harbors a subpopulation of CD44(+) cells that exhibit cancer stem-like cell (CSC) characteristics are involved in malignant tumor phenotype and radioresistance. Nevertheless, the underlying molecular mechanisms in CD44( + )-OSCC remain unclear. The current investigation demonstrated that methyltransferase-like 3 (METTL3) is highly expressed in CD44(+) cells and promotes CSCs phenotype. Using RNA-sequencing analysis, we further showed that Spalt-like transcription factor 4 (SALL4) is involved in the maintenance of CSCs properties. Furthermore, the overexpression of SALL4 in CD44( + )-OSCC cells caused radioresistance in vitro and in vivo. In contrast, silencing SALL4 sensitized OSCC cells to radiation therapy (RT). Mechanistically, we illustrated that SALL4 is a direct downstream transcriptional regulation target of METTL3, the transcription activation of SALL4 promotes the nuclear transport of β-catenin and the expression of downstream target genes after radiation therapy, there by activates the Wnt/β-catenin pathway, effectively enhancing the CSCs phenotype and causing radioresistance. Herein, this study indicates that the METTL3/SALL4 axis promotes the CSCs phenotype and resistance to radiation in OSCC via the Wnt/β-catenin signaling pathway, and provides a potential therapeutic target to eliminate radioresistant OSCC.
Long noncoding RNA H19: functions and mechanisms in regulating programmed cell death in cancer
Authors: Xia Yuyang , Pei Tianjiao , Zhao Junjie , Wang Zilin , Shen Yu , Yang Yang , Liang Jiayu
Published: February 2024

Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs with transcript lengths of >200 nucleotides. Mounting evidence suggests that lncRNAs are closely associated with tumorigenesis. LncRNA H19 (H19) was the first lncRNA to function as an oncogene in many malignant tumors. Apart from the established role of H19 in promoting cell growth, proliferation, invasion, migration, epithelial-mesenchymal transition (EMT), and metastasis, it has been recently discovered that H19 also inhibits programmed cell death (PCD) of cancer cells. In this review, we summarize the mechanisms by which H19 regulates PCD in cancer cells through various signaling pathways, molecular mechanisms, and epigenetic modifications. H19 regulates PCD through the Wnt/β-catenin pathway and the PI3K–Akt–mTOR pathway. It also acts as a competitive endogenous RNA (ceRNA) in PCD regulation. The interaction between H19 and RNA-binding proteins (RBP) regulates apoptosis in cancer. Moreover, epigenetic modifications, including DNA and RNA methylation and histone modifications, are also involved in H19-associated PCD regulation. In conclusion, we summarize the role of H19 signaling via PCD in cancer chemoresistance, highlighting the promising research significance of H19 as a therapeutic target. We hope that our study will contribute to a broader understanding of H19 in cancer development and treatment.
Heavy fermions vs doped Mott physics in heterogeneous Ta-dichalcogenide bilayers
Authors: Crippa Lorenzo , Bae Hyeonhu , Wunderlich Paul , Mazin Igor I. , Yan Binghai , Sangiovanni Giorgio , Wehling Tim , Valentí Roser
Published: February 2024

Controlling and understanding electron correlations in quantum matter is one of the most challenging tasks in materials engineering. In the past years a plethora of new puzzling correlated states have been found by carefully stacking and twisting two-dimensional van der Waals materials of different kind. Unique to these stacked structures is the emergence of correlated phases not foreseeable from the single layers alone. In Ta-dichalcogenide heterostructures made of a good metallic “1H”- and a Mott insulating “1T”-layer, recent reports have evidenced a cross-breed itinerant and localized nature of the electronic excitations, similar to what is typically found in heavy fermion systems. Here, we put forward a new interpretation based on first-principles calculations which indicates a sizeable charge transfer of electrons (0.4-0.6 e) from 1T to 1H layers at an elevated interlayer distance. We accurately quantify the strength of the interlayer hybridization which allows us to unambiguously determine that the system is much closer to a doped Mott insulator than to a heavy fermion scenario. Ta-based heterolayers provide therefore a new ground for quantum-materials engineering in the regime of heavily doped Mott insulators hybridized with metallic states at a van der Waals distance.
TGF-β blockade drives a transitional effector phenotype in T cells reversing SIV latency and decreasing SIV reservoirs in vivo
Authors: Kim Jinhee , Bose Deepanwita , Araínga Mariluz , Haque Muhammad R. , Fennessey Christine M. , Caddell Rachel A. , Thomas Yanique , Ferrell Douglas E. , Ali Syed , Grody Emanuelle , Goyal Yogesh , Cicala Claudia , Arthos James , Keele Brandon F. , Vaccari Monica , Lorenzo-Redondo Ramon , Hope Thomas J. , Villinger Francois , Martinelli Elena
Published: February 2024

HIV-1 persistence during ART is due to the establishment of long-lived viral reservoirs in resting immune cells. Using an NHP model of barcoded SIVmac239 intravenous infection and therapeutic dosing of anti-TGFBR1 inhibitor galunisertib (LY2157299), we confirm the latency reversal properties of in vivo TGF-β blockade, decrease viral reservoirs and stimulate immune responses. Treatment of eight female, SIV-infected macaques on ART with four 2-weeks cycles of galunisertib leads to viral reactivation as indicated by plasma viral load and immunoPET/CT with a 64Cu-DOTA-F(ab’)2-p7D3-probe. Post-galunisertib, lymph nodes, gut and PBMC exhibit lower cell-associated (CA-)SIV DNA and lower intact pro-virus (PBMC). Galunisertib does not lead to systemic increase in inflammatory cytokines. High-dimensional cytometry, bulk, and single-cell (sc)RNAseq reveal a galunisertib-driven shift toward an effector phenotype in T and NK cells characterized by a progressive downregulation in TCF1. In summary, we demonstrate that galunisertib, a clinical stage TGF-β inhibitor, reverses SIV latency and decreases SIV reservoirs by driving T cells toward an effector phenotype, enhancing immune responses in vivo in absence of toxicity.
Epigenetic regulation of CD38/CD48 by KDM6A mediates NK cell response in multiple myeloma
Authors: Liu Jiye , Xing Lijie , Li Jiang , Wen Kenneth , Liu Ning , Liu Yuntong , Wu Gongwei , Wang Su , Ogiya Daisuke , Song Tian-Yu , Kurata Keiji , Penailillo Johany , Morelli Eugenio , Wang Tingjian , Hong Xiaoning , Gulla Annamaria , Tai Yu-Tzu , Munshi Nikhil , Richardson Paul , Carrasco Ruben , Hideshima Teru , Anderson Kenneth C.
Published: February 2024

Anti-CD38 monoclonal antibodies like Daratumumab (Dara) are effective in multiple myeloma (MM); however, drug resistance ultimately occurs and the mechanisms behind this are poorly understood. Here, we identify, via two in vitro genome-wide CRISPR screens probing Daratumumab resistance, KDM6A as an important regulator of sensitivity to Daratumumab-mediated antibody-dependent cellular cytotoxicity (ADCC). Loss of KDM6A leads to increased levels of H3K27me3 on the promoter of CD38, resulting in a marked downregulation in CD38 expression, which may cause resistance to Daratumumab-mediated ADCC. Re-introducing CD38 does not reverse Daratumumab-mediated ADCC fully, which suggests that additional KDM6A targets, including CD48 which is also downregulated upon KDM6A loss, contribute to Daratumumab-mediated ADCC. Inhibition of H3K27me3 with an EZH2 inhibitor resulted in CD38 and CD48 upregulation and restored sensitivity to Daratumumab. These findings suggest KDM6A loss as a mechanism of Daratumumab resistance and lay down the proof of principle for the therapeutic application of EZH2 inhibitors, one of which is already FDA-approved, in improving MM responsiveness to Daratumumab.
Oncoprotein SET-associated transcription factor ZBTB11 triggers lung cancer metastasis
Authors: Xu Wenbin , Yao Han , Wu Zhen , Yan Xiaojun , Jiao Zishan , Liu Yajing , Zhang Meng , Wang Donglai
Published: February 2024

Metastasis is the major cause of lung cancer-related death, but the mechanisms governing lung tumor metastasis remain incompletely elucidated. SE translocation (SET) is overexpressed in lung tumors and correlates with unfavorable prognosis. Here we uncover SET-associated transcription factor, zinc finger and BTB domain-containing protein 11 (ZBTB11), as a prometastatic regulator in lung tumors. SET interacts and collaborates with ZBTB11 to promote lung cancer cell migration and invasion, primarily through SET-ZBTB11 complex-mediated transcriptional activation of matrix metalloproteinase-9 (MMP9). Additionally, by transcriptional repression of proline-rich Gla protein 2 (PRRG2), ZBTB11 links Yes-associated protein 1 (YAP1) activation to drive lung tumor metastasis independently of SET-ZBTB11 complex. Loss of ZBTB11 suppresses distal metastasis in a lung tumor mouse model. Overexpression of ZBTB11 is recapitulated in human metastatic lung tumors and correlates with diminished survival. Our study demonstrates ZBTB11 as a key metastatic regulator and reveals diverse mechanisms by which ZBTB11 modulates lung tumor metastasis.
Sequential stacking link prediction algorithms for temporal networks
Authors: He Xie , Ghasemian Amir , Lee Eun , Clauset Aaron , Mucha Peter J.
Published: February 2024

Link prediction algorithms are indispensable tools in many scientific applications by speeding up network data collection and imputing missing connections. However, in many systems, links change over time and it remains unclear how to optimally exploit such temporal information for link predictions in such networks. Here, we show that many temporal topological features, in addition to having high computational cost, are less accurate in temporal link prediction than sequentially stacked static network features. This sequential stacking link prediction method uses 41 static network features that avoid detailed feature engineering choices and is capable of learning a highly accurate predictive distribution of future connections from historical data. We demonstrate that this algorithm works well for both partially observed and completely unobserved target layers, and on two temporal stochastic block models achieves near-oracle-level performance when combined with other single predictor methods as an ensemble learning method. Finally, we empirically illustrate that stacking multiple predictive methods together further improves performance on 19 real-world temporal networks from different domains.
Hierarchical Li electrochemistry using alloy-type anode for high-energy-density Li metal batteries
Authors: Cao Jiaqi , Shi Yuansheng , Gao Aosong , Du Guangyuan , Dilxat Muhtar , Zhang Yongfei , Cai Mohang , Qian Guoyu , Lu Xueyi , Xie Fangyan , Sun Yang , Lu Xia
Published: February 2024

Exploiting thin Li metal anode is essential for high-energy-density battery, but is severely plagued by the poor processability of Li, as well as the uncontrollable Li plating/stripping behaviors and Li/electrolyte interface. Herein, a thickness/capacity-adjustable thin alloy-type Li/LiZn@Cu anode is fabricated for high-energy-density Li metal batteries. The as-formed lithophilic LiZn alloy in Li/LiZn@Cu anode can effectively regulate Li plating/stripping and stabilize the Li/electrolyte interface to deliver the hierarchical Li electrochemistry. Upon charging, the Li/LiZn@Cu anode firstly acts as Li source for homogeneous Li extraction. At the end of charging, the de-alloy of LiZn nanostructures further supplements the Li extraction, actually playing the Li compensation role in battery cycling. While upon discharging, the LiZn alloy forms just at the beginning, thereby regulating the following Li homogeneous deposition. The reversibility of such an interesting process is undoubtedly verified from the electrochemistry and in-situ XRD characterization. This work sheds light on the facile fabrication of practical Li metal anodes and useful Li compensation materials for high-energy-density Li metal batteries.
Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application
Authors: Li Bingyan , Duan Yuange , Du Zhenyong , Wang Xuan , Liu Shanlin , Feng Zengbei , Tian Li , Song Fan , Yang Hailin , Cai Wanzhi , Lin Zhonglong , Li Hu
Published: February 2024

Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.
Ripples in the bottom of the potential energy landscape of metallic glass
Authors: Zella Leo , Moon Jaeyun , Egami Takeshi
Published: February 2024

In the absence of periodicity, the structure of glass is ill-defined, and a large number of structural states are found at similar energy levels. However, little is known about how these states are connected to each other in the potential energy landscape. We simulate mechanical relaxation by molecular dynamics for a prototypical $${{{\rm{C}}}}{{{{\rm{u}}}}}_{64.5}{{{\rm{Z}}}}{{{{\rm{r}}}}}_{35.5}$$
C

u

64.5

Z

r

35.5

metallic glass and follow the mechanical energy loss of each atom to track the change in the state. We find that the energy barriers separating these states are remarkably low, only of the order of 1 meV, implying that even quantum fluctuations can overcome these potential energy barriers. Our observation of numerous small ripples in the bottom of the potential energy landscape puts many assumptions regarding the thermodynamic states of metallic glasses into question and suggests that metallic glasses are not totally frozen at the local atomic level.
Three dimensional classification of dislocations from single projections
Authors: Niermann Tore , Niermann Laura , Lehmann Michael
Published: February 2024

Many material properties are governed by dislocations and their interactions. The reconstruction of the three-dimensional structure of a dislocation network so far is mainly achieved by tomographic tilt series with high angular ranges, which is experimentally challenging and additionally puts constraints on possible specimen geometries. Here, we show a way to reveal the three dimensional location of dislocations and simultaneously classify their type from single 4D scanning transmission electron microscopy measurements. The dislocation’s strain field causes inter-band scattering between the electron’s Bloch waves within the crystal. This scattering in turn results in characteristic interference patterns with sufficient information to identify the dislocations type and depth in beam direction by comparison with multi-beam calculations. We expect the presented measurement principle will lead to fully automated methods for reconstruction of the three dimensional strain fields from such measurements with a wide range of applications in material and physical sciences and engineering.
Iodide manipulation using zinc additives for efficient perovskite solar minimodules
Authors: Uddin Md Aslam , Rana Prem Jyoti Singh , Ni Zhenyi , Yang Guang , Li Mingze , Wang Mengru , Gu Hangyu , Zhang Hengkai , Dou Benjia Dak , Huang Jinsong
Published: February 2024

Interstitial iodides are the most critical type of defects in perovskite solar cells that limits efficiency and stability. They can be generated during solution, film, and device processing, further accelerating degradation. Herein, we find that introducing a small amount of a zinc salt- zinc trifluoromethane sulfonate (Zn(OOSCF3)2) in the perovskite solution can control the iodide defects in resultant perovskites ink and films. CF3SOO̶ vigorously suppresses molecular iodine formation in the perovskites by reducing it to iodide. At the same time, zinc cations can precipitate excess iodide by forming a Zn-Amine complex so that the iodide interstitials in the resultant perovskite films can be suppressed. The perovskite films using these additives show improved photoluminescence quantum efficiency and reduce deep trap density, despite zinc cations reducing the perovskite grain size and iodide interstitials. The zinc additives facilitate the formation of more uniform perovskite films on large-area substrates (78-108 cm2) in the blade-coating process. Fabricated minimodules show power conversion efficiencies of 19.60% and 19.21% with aperture areas of 84 and 108 cm2, respectively, as certified by National Renewable Energy Laboratory (NREL), the highest efficiency certified for minimodules of these sizes.
Multigenerational paternal obesity enhances the susceptibility to male subfertility in offspring via Wt1 N6-methyladenosine modification
Authors: Xiong Yong-Wei , Zhu Hua-Long , Zhang Jin , Geng Hao , Tan Lu-Lu , Zheng Xin-Mei , Li Hao , Fan Long-Long , Wang Xin-Run , Zhang Xu-Dong , Wang Kai-Wen , Chang Wei , Zhang Yu-Feng , Yuan Zhi , Duan Zong-Liu , Cao Yun-Xia , He Xiao-Jin , Xu De-Xiang , Wang Hua
Published: February 2024

There is strong evidence that obesity is a risk factor for poor semen quality. However, the effects of multigenerational paternal obesity on the susceptibility to cadmium (a reproductive toxicant)-induced spermatogenesis disorders in offspring remain unknown. Here, we show that, in mice, spermatogenesis and retinoic acid levels become progressively lower as the number of generations exposed to a high-fat diet increase. Furthermore, exposing several generations of mice to a high fat diet results in a decrease in the expression of Wt1, a transcription factor upstream of the enzymes that synthesize retinoic acid. These effects can be rescued by injecting adeno-associated virus 9-Wt1 into the mouse testes of the offspring. Additionally, multigenerational paternal high-fat diet progressively increases METTL3 and Wt1 N6-methyladenosine levels in the testes of offspring mice. Mechanistically, treating the fathers with STM2457, a METTL3 inhibitor, restores obesity-reduced sperm count, and decreases Wt1 N6-methyladenosine level in the mouse testes of the offspring. A case-controlled study shows that human donors who are overweight or obese exhibit elevated N6-methyladenosine levels in sperm and decreased sperm concentration. Collectively, these results indicate that multigenerational paternal obesity enhances the susceptibility of the offspring to spermatogenesis disorders by increasing METTL3-mediated Wt1 N6-methyladenosine modification.
Cross-catenation between position-isomeric metallacages
Authors: Wang Yiliang , Liu Taotao , Zhang Yang-Yang , Li Bin , Tan Liting , Li Chunju , Shen Xing-Can , Li Jun
Published: February 2024

The study of cross-catenated metallacages, which are complex self-assembly systems arising from multiple supramolecular interactions and hierarchical assembly processes, is currently lacking but could provide facile insights into achieving more precise control over low-symmetry/high-complexity hierarchical assembly systems. Here, we report a cross-catenane formed between two position-isomeric Pt(II) metallacages in the solid state. These two metallacages formed [2]catenanes in solution, whereas a 1:1 mixture selectively formed a cross-catenane in crystals. Varied temperature nuclear magnetic resonance experiments and time-of-flight mass spectra are employed to characterize the cross-catenation in solutions, and the dynamic library of [2]catenanes are shown. Additionally, we searched for the global-minimum structures of three [2]catenanes and re-optimized the low-lying structures using density functional theory calculations. Our results suggest that the binding energy of cross-catenanes is significantly larger than that of self-catenanes within the dynamic library, and the selectivity in crystallization of cross-catenanes is thermodynamic. This study presents a cross-catenated assembly from different metallacages, which may provide a facile insight for the development of low-symmetry/high-complexity self-assemble systems.
PySAGES: flexible, advanced sampling methods accelerated with GPUs
Authors: Zubieta Rico Pablo F. , Schneider Ludwig , Pérez-Lemus Gustavo R. , Alessandri Riccardo , Dasetty Siva , Nguyen Trung D. , Menéndez Cintia A. , Wu Yiheng , Jin Yezhi , Xu Yinan , Varner Samuel , Parker John A. , Ferguson Andrew L. , Whitmer Jonathan K. , de Pablo Juan J.
Published: February 2024

Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of the relevant underlying free energy landscapes. In this sense, software that can be seamlessly adapted to a broad range of complex systems is essential. Building on past efforts to provide open-source community-supported software for advanced sampling, we introduce PySAGES, a Python implementation of the Software Suite for Advanced General Ensemble Simulations (SSAGES) that provides full GPU support for massively parallel applications of enhanced sampling methods such as adaptive biasing forces, harmonic bias, or forward flux sampling in the context of molecular dynamics simulations. By providing an intuitive interface that facilitates the management of a system’s configuration, the inclusion of new collective variables, and the implementation of sophisticated free energy-based sampling methods, the PySAGES library serves as a general platform for the development and implementation of emerging simulation techniques. The capabilities, core features, and computational performance of this tool are demonstrated with clear and concise examples pertaining to different classes of molecular systems. We anticipate that PySAGES will provide the scientific community with a robust and easily accessible platform to accelerate simulations, improve sampling, and enable facile estimation of free energies for a wide range of materials and processes.
Germline mutations of 4567 patients with hereditary breast-ovarian cancer spectrum in Thailand
Authors: Kansuttiviwat Chalermkiat , Lertwilaiwittaya Pongtawat , Roothumnong Ekkapong , Nakthong Panee , Dungort Peerawat , Meesamarnpong Chutima , Tansa-Nga Warisara , Pongsuktavorn Khontawan , Wiboonthanasarn Supakit , Tititumjariya Warunya , Phuphuripan Nannipa , Lertbussarakam Chittapat , Wattanarangsan Jantanee , Sritun Jiraporn , Punuch Kittiporn , Kammarabutr Jirayu , Mutirangura Pornthira , Thongnoppakhun Wanna , Limwongse Chanin , Pithukpakorn Manop
Published: February 2024

Multi-gene panel testing has led to the detection of pathogenic/likely pathogenic (P/LP) variants in many cancer susceptibility genes in patients with breast-ovarian cancer spectrum. However, the clinical and genomic data of Asian populations, including Thai cancer patients, was underrepresented, and the clinical significance of multi-gene panel testing in Thailand remains undetermined. In this study, we collected the clinical and genetic data from 4567 Thai patients with cancer in the hereditary breast-ovarian cancer (HBOC) spectrum who underwent multi-gene panel testing. Six hundred and ten individuals (13.4%) had germline P/LP variants. Detection rates of germline P/LP variants in breast, ovarian, pancreatic, and prostate cancer were 11.8%, 19.8%, 14.0%, and 7.1%, respectively. Non-BRCA gene mutations accounted for 35% of patients with germline P/LP variants. ATM was the most common non-BRCA gene mutation. Four hundred and thirty-two breast cancer patients with germline P/LP variants (80.4%) met the current NCCN genetic testing criteria. The most common indication was early-onset breast cancer. Ten patients harbored double pathogenic variants in this cohort. Our result showed that a significant proportion of non-BRCA P/LP variants were identified in patients with HBOC-related cancers. These findings support the benefit of multi-gene panel testing for inherited cancer susceptibility among Thai HBOC patients. Some modifications of the testing policy may be appropriate for implementation in diverse populations.
Differences in brain aging between sexes in Parkinson’s disease
Authors: Beheshti Iman , Booth Samuel , Ko Ji Hyun
Published: February 2024

Parkinson’s disease (PD) is linked to faster brain aging. Male sex is associated with higher prevalence, severe symptoms, and a faster progression rate in PD. There remains a significant gap in understanding the function of sex in the process of brain aging in PD. The structural T1-weighted MRI-driven brain-predicted age difference (i.e., Brain-PAD: the actual age subtracted from the brain-predicted age) was computed in a group of 373 people with PD (mean age ± SD: 61.37 ± 9.81, age range: 33–85, 34% female) from the Parkinson’s Progression Marker Initiative database using a robust brain-age estimation framework that was trained on 949 healthy subjects. Linear regression models were used to investigate the association between Brain-PAD and clinical variables in PD, stratified by sex. Males with Parkinson’s disease (PD-M) exhibited a significantly higher mean Brain-PAD than their female counterparts (PD-F) (t(256) = 2.50, p = 0.012). In the propensity score-matched PD-M group (PD-M*), Brain-PAD was found to be associated with a decline in general cognition, a worse degree of sleep behavior disorder, reduced visuospatial acuity, and caudate atrophy. Conversely, no significant links were observed between these factors and Brain-PAD in the PD-F group. Having ‘older’ looking brains in PD-M than PD-F supports the idea that sex plays a vital function in PD, such that the PD mechanism may be different in males and females. This study has the potential to broaden our understanding of dissimilarities in brain aging between sexes in the context of PD.
Air-gap-assisted solvothermal process to synthesize unprecedented graphene-like two-dimensional TiO2 nanosheets for Na+ electrosorption/desalination
Authors: Salhi Billel , Baig Nadeem , Abdulazeez Ismail
Published: February 2024

Designing a high-performance capacitive deionization setup is limited due to the slow salt removal and charge storage capacities. Efforts are being made to replace traditional electrodes with advanced 2D materials. We introduce a simple method for synthesizing two-dimensional titanium dioxide graphene-like nanosheets via a unique air-gap-assisted solvothermal method. Crystalline 2D graphene-like anatase-TiO2 sheets of unprecedented quality were obtained by tuning the air gap in the solvothermal reactor. The 2D TiO2 synthesized by air-gap-assisted solvothermal process has shown an exceptionally high surface area of 934.5 m2/g compared to the pristine TiO2 (249.5 m2/g). The sheets were used as Faradaic electrodes in ion-electrosorption and their capacitive deionization capabilities were evaluated. The electrochemical conductivity was examined via an in situ investigation of Na+-ion migration and storage. The adsorption capacity of 2D TiO2 sheets increased with higher applied potential while keeping the adsorption time constant at 15 min. At adsorption potentials of –0.8 V, –1.0 V, and –1.2 V, desalting rates of 2.09, 2.18, and 2.20 mg g−1 min−1 resulted in adsorption capacities of 31.33, 32.73, and 33.023 mg g–1, respectively. The 2D TiO2 electrode demonstrated high electron-transfer rates, a large desalination capacity, and a rapid average desalting rate. The specific capacity of the 2D-layered TiO2 electrode was found to be about 45.68 F g−1. These results can be attributed to the large specific surface area, short ionic diffusion paths, numerous active adsorption sites, surface defects, and pseudocapacitance. This air-gap-assisted solvothermal method is expected to open new avenues for the synthesis of high-quality 2D materials.
A Clinical Breathomics Dataset
Authors: Kuo Ping-Hung , Jhong Yue-Chen , Kuo Tien-Chueh , Hsu Yu-Ting , Kuo Ching-Hua , Tseng Yufeng Jane
Published: February 2024

This study entailed a comprehensive GC‒MS analysis conducted on 121 patient samples to generate a clinical breathomics dataset. Breath molecules, indicative of diverse conditions such as psychological and pathological states and the microbiome, were of particular interest due to their non-invasive nature. The highlighted noninvasive approach for detecting these breath molecules significantly enhances diagnostic and monitoring capacities. This dataset cataloged volatile organic compounds (VOCs) from the breath of individuals with asthma, bronchiectasis, and chronic obstructive pulmonary disease. Uniform and consistent sample collection protocols were strictly adhered to during the accumulation of this extensive dataset, ensuring its reliability. It encapsulates extensive human clinical breath molecule data pertinent to three specific diseases. This consequential clinical breathomics dataset is a crucial resource for researchers and clinicians in identifying and exploring important compounds within the patient’s breath, thereby augmenting future diagnostic and therapeutic initiatives.
An implicit measure of growth mindset uniquely predicts post-failure learning behavior
Authors: Sik Kata , Cummins Jamie , Job Veronika
Published: February 2024

Research on implicit theories of intelligence (a.k.a. intelligence mindset) has shown that endorsing a stronger growth mindset (the belief that intelligence can be improved) is adaptive in the face of difficulties. Although the theory presumes implicit processes (i.e., unaware beliefs, guiding behaviors and actions automatically), the concept is typically assessed with self-reports. In this project we brought together research on intelligence mindset with research on implicit social cognition. Harnessing recent innovations from research on implicit measures, we assessed intelligence mindsets on an implicit level with a mousetracking Propositional Evaluation Paradigm. This measure captures the spontaneous truth evaluation of growth- and fixed-mindset statements to tap into implicit beliefs. In two preregistered laboratory studies (N = 184; N = 193), we found that implicitly measured growth mindsets predicted learning engagement after an experience of failure above and beyond the explicitly measured growth mindset. Our results suggest that implicit and explicit aspects of intelligence mindsets must be differentiated. People might be in a different mindset when making learning-related decisions under optimal conditions (i.e., with ample time and capacity) or under suboptimal conditions (i.e., when time pressure is high). This advancement in the understanding of implicit theories of intelligence is accompanied with substantial implications for theory and practice.
Analysis of solitary wave solutions in the fractional-order Kundu–Eckhaus system
Authors: Alshammari Saleh , Moaddy Khaled , Shah Rasool , Alshammari Mohammad , Alsheekhhussain Zainab , Al-sawalha M. Mossa , Yar Mohammad
Published: February 2024

The area of fractional partial differential equations has recently become prominent for its ability to accurately simulate complex physical events. The search for traveling wave solutions for fractional partial differential equations is a difficult task, which has led to the creation of numerous mathematical approaches to tackle this problem. The primary objective of this research work is to provide optical soliton solutions for the Frictional Kundu–Eckhaus equation (FKEe) by utilizing generalized coefficients. This strategy utilizes the Riccati–Bernoulli sub-ODE technique to effectively discover the most favorable traveling wave solutions for fractional partial differential equations. As a result, it facilitates the extraction of optical solitons and intricate wave solutions. The Backlund transformation is used to methodically construct a sequence of solutions for the specified equations. The study additionally showcases 3D and Density graphics that visually depict chosen solutions for certain parameter selections, hence improving the understanding of the outcomes.
Development of an ostrich-derived single-chain variable fragment (scFv) against PTPRN extracellular domain
Authors: Dabiri Hamed , Sadeghizadeh Majid , Ziaei Vahab , Moghadasi Zahra , Maham Ali , Hajizadeh-Saffar Ensiyeh , Habibi-Anbouhi Mahdi
Published: February 2024

In type 1 diabetes, the immune system destroys pancreatic beta cells in an autoimmune condition. To overcome this disease, a specific monoclonal antibody that binds to pancreatic beta cells could be used for targeted immunotherapy. Protein tyrosine phosphatase receptor N (PTPRN) is one of the important surface antigen candidates. Due to its high sequence homology among mammals, so far, no single-chain monoclonal antibody has been produced against this receptor. In this study, we developed a novel single-chain variable fragment (scFv) against the PTPRN extracellular domain. To this aim, ostrich species was used as a host is far phylogenetically birds from mammals to construct a phage display library for the first time. An ostrich-derived scfv phage display library was prepared and biopanning steps were done to enrich and screen for isolating the best anti-PTPRN binders. An scFv with appropriate affinity and specificity to the PTPRN extracellular domain was selected and characterized by ELISA, western blotting, and flow cytometry. The anti-PTPRN scFv developed in this study could be introduced as an effective tool that can pave the way for the creation of antibody-based targeting systems in cooperation with the detection and therapy of type I diabetes.
Mathematical modelling of a single tethered aerostat using longitudinal stability derivatives
Authors: Sasidharan Anoop , Velamati Ratna Kishore , Mohammad Akram , Benaissa Sabrina
Published: February 2024

Lighter-than-air (LTA) aerial vehicles such as airships and aerostats can be found in various strategic and commercial applications, primarily due to their capability to hover and stealth. The mathematical model of these vehicles helps in understanding their complex dynamics and designing and developing proper stabilisation systems for them. Stability derivatives have been used for developing mathematical models for heavier-than-air aerial vehicles since their introduction. This paper presents a methodology to develop a mathematical model of an aerostat based on stability derivatives. One of the major contributions of this study is the estimation of aerostat’s added mass terms expressed as longitudinal stability derivatives due to acceleration of the longitudinal motion variables. A longitudinally decoupled linear mathematical model of a single-tethered aerostat using stability derivatives is investigated in this study. A computational fluid dynamics (CFD)-based analysis of the 3D model of the vehicle is used to obtain the stability derivatives. The methodology presented considers the aerostat and tether models separately before coupling them to create the full model. The stability derivative analysis is carried out using ANSYS Fluent, and the coupled tethered aerostat model is investigated using MATLAB 2020. The negative pitch angle of the aerostat is caused by the selection of the pitching centre as the aerostat centre of volume instead of the tether confluence point. The tension force on the tether, which is proportional to the wind velocity, and aerostat velocity components are found to be stabilised within 200–400 s.
The effects of eccentric training on hamstring flexibility and strength in young dance students
Authors: Liang Feng , Hongfeng Huo , Ying Zhu
Published: February 2024

The objective of this research is to examine the impact of eccentric training on hamstring flexibility and strength in young dancers during the concluding stages of their foundational dance training program. A total of 24 female, second-year dance students from Hebei Normal University were selected as participants. They were divided into three distinct groups: Nordic hamstring exercise and single-leg deadlift group (NHE&SLD), forward bending exercises and standing leg lift group (FBE&SLL), and a control group (CG). The study was designed around a 6-week training regimen. An isokinetic dynamometer was used to measure seated knee flexor–extensor strength, while electronic goniometry was employed to measure hamstring flexibility in the supine position. Paired sample t-tests were conducted within each group, and one-way analysis of covariance (ANCOVA) was utilized for comparisons between groups. In the NHE&SLD group, significant disparities were observed in both concentric (T = − 5.687, P = 0.001) and eccentric (T = − 3.626, P = 0.008) hamstring strength pre and post-intervention. The pre-intervention dominant leg concentric strength test values significantly influenced the post-intervention outcomes (F = 5.313, P = 0.001, η2 = 0.840). Similarly, the pre-intervention dominant leg eccentric strength test values impacted the post-intervention results (F = 4.689, P = 0.043, η2 = 0.190). Following the intervention, the NHE&SLD group displayed marked changes in the active straight leg raising angle on both left (T = − 4.171, P = 0.004) and right (T = − 6.328, P = 0.001) sides. The FBE&SLL group also revealed significant changes in the active straight leg raising angle on both left (T = − 4.506, P = 0.003) and right (T = − 4.633, P = 0.002) sides following the intervention. The pre-intervention left leg concentric strength test value significantly influenced the post-intervention outcomes (F = 25.067, P = 0.001, η2 = 0.556). Likewise, the pre-intervention right leg eccentric strength test value significantly influenced the post-intervention results (F = 85.338, P = 0.01, η2 = 0.810). Eccentric training can better enhance the flexibility and strength of hamstring muscles in dance students. Traditional stretching training significantly improves the flexibility of the hamstring muscles. Eccentric training has more training benefits than traditional stretching training. It is recommended for dance students to use eccentric training when increasing hamstring flexibility and strength.
The enhancement effect of mungbean on the physical, functional, and sensory characteristics of soy yoghurt
Authors: An Gyeongseon , Park Sunghoon , Ha Jungmin
Published: February 2024

Vegetable drinks offer a convenient way to increase the daily intake of vegetables containing vitamins, antioxidants, and fiber. In this study, we discovered that mungbean milk serves as a carbohydrate source during fermentation using lactic acid bacteria (LAB) and enhances the nutritional value of vegetable yoghurt. Mungbean milk reduces pH while titratable acidity increases faster than soybean milk during fermentation. M0S, Soybean milk 100% with added sucrose exhibited the highest titratable acidity after 16 h of fermentation. The acetic acid content of all samples did not show significant changes during fermentation, but the lactic acid content increased. Proximate analysis showed no significant change during fermentation, regardless of the fermentation time and mixing ratio of mungbean to soybean milk. The sucrose content of samples except M0S decreased after 16 h of fermentation. Mungbean milk exhibited high antioxidant activity both before and after fermentation, while M0S showed the lowest antioxidant activity. The results of this study demonstrated the potential application of mungbean milk to improve fermented vegetable drinks using LAB functionally. Fermented mungbean milk yoghurt can be a valuable addition to a healthy and balanced diet for those who consume plant-based diets.
Life on Earth can grow on extraterrestrial organic carbon
Authors: Waajen Annemiek C. , Lima Cassio , Goodacre Royston , Cockell Charles S.
Published: February 2024

The universe is a vast store of organic abiotic carbon that could potentially drive heterotrophy on habitable planets. Meteorites are one of the transporters of this carbon to planetary surfaces. Meteoritic material was accumulating on early Earth when life emerged and proliferated. Yet it is not known if this organic carbon from space was accessible to life. In this research, an anaerobic microbial community was grown with the CM2 carbonaceous chondrite Aguas Zarcas as the sole carbon, energy and nutrient source. Using a reversed 13C-stable isotope labelling experiment in combination with optical photothermal infrared (O-PTIR) spectroscopy of single cells, this paper demonstrates the direct transfer of carbon from meteorite into microbial biomass. This implies that meteoritic organics could have been used as a carbon source on early Earth and other habitable planets, and supports the potential for a heterotrophic metabolism in early living systems.