bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides
Authors: Sneideris Tomas , Erkamp Nadia A. , Ausserwöger Hannes , Saar Kadi L. , Welsh Timothy J. , Qian Daoyuan , Katsuya-Gaviria Kai , Johncock Margaret L. L. Y. , Krainer Georg , Borodavka Alexander , Knowles Tuomas P. J. 
Published: November 2023

AbstractAntimicrobial peptides (AMPs), which combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets, are naturally produced by a number of different organisms, and are increasingly also explored as therapeutics. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we identified a significant number of AMPs that have a strong tendency to form liquid-like condensates in the presence of nucleic acids through phase separation. We demonstrate that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. These results suggest that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. The development of antimicrobials that target nucleic acid phase transitions may become an attractive route to finding effective and long-lasting antibiotics.
Functional dissection of PRC1 subunits RYBP and YAF2 during neural differentiation of embryonic stem cells
Authors: Liu Yanjiang , Hu Gongcheng , Yang Shengxiong , Yao Mingze , Liu Zicong , Yan Chenghong , Wen Yulin , Ping Wangfang , Wang Juehan , Song Yawei , Dong Xiaotao , Pan Guangjin , Yao Hongjie 
Published: November 2023

AbstractPolycomb repressive complex 1 (PRC1) comprises two different complexes: CBX-containing canonical PRC1 (cPRC1) and RYBP/YAF2-containing variant PRC1 (vPRC1). RYBP-vPRC1 or YAF2-vPRC1 catalyzes H2AK119ub through a positive-feedback model; however, whether RYBP and YAF2 have different regulatory functions is still unclear. Here, we show that the expression of RYBP and YAF2 decreases and increases, respectively, during neural differentiation of embryonic stem cells (ESCs).Rybpknockout impairs neural differentiation by activating Wnt signaling and derepressing nonneuroectoderm-associated genes. However,Yaf2knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. Taken together, this study reveals that RYBP and YAF2 function differentially in regulating mESC neural differentiation.
Frequency stable and low phase noise THz synthesis for precision spectroscopy
Authors: Djevahirdjian Léo , Lechevallier Loïc , Martin-Drumel Marie-Aline , Pirali Olivier , Ducournau Guillaume , Kassi Rédha , Kassi Samir 
Published: November 2023

AbstractWe present a robust approach to generate a continuously tunable, low phase noise, Hz linewidth and mHz/s stability THz emission in the 0.1 THz to 1.4 THz range. This is achieved by photomixing two commercial telecom, distributed feedback lasers locked by optical-feedback onto a single highly stable V-shaped optical cavity. The phase noise is evaluated up to 1.2 THz, demonstrating Hz-level linewidth. To illustrate the spectral performances and agility of the source, low pressure absorption lines of methanol and water vapors have been recorded up to 1.4 THz. In addition, the hyperfine structure of a water line at 556.9 GHz, obtained by saturation spectroscopy, is also reported, resolving spectral features displaying a full-width at half-maximum of 10 kHz. The present results unambiguously establish the performances of this source for ultra-high resolution molecular physics.
Low-temperature hydroformylation of ethylene by phosphorous stabilized Rh sites in a one-pot synthesized Rh-(O)-P-MFI zeolite
Authors: Zhao Minjie , Li Chengeng , Gómez Daviel , Gonell Francisco , Diaconescu Vlad Martin , Simonelli Laura , Haro Miguel Lopez , Calvino Jose Juan , Meira Debora Motta , Concepción Patricia , Corma Avelino 
Published: November 2023

AbstractZeolites containing Rh single sites stabilized by phosphorous were prepared through a one-pot synthesis method and are shown to have superior activity and selectivity for ethylene hydroformylation at low temperature (50 °C). Catalytic activity is ascribed to confined Rh2O3clusters in the zeolite which evolve under reaction conditions into single Rh3+sites. These Rh3+sites are effectively stabilized in a Rh-(O)-P structure by using tetraethylphosphonium hydroxide as a template, which generates in situ phosphate species after H2activation. In contrast to Rh2O3, confined Rh0clusters appear less active in propanal production and ultimately transform into Rh(I)(CO)2under similar reaction conditions. As a result, we show that it is possible to reduce the temperature of ethylene hydroformylation with a solid catalyst down to 50 °C, with good activity and high selectivity, by controlling the electronic and morphological properties of Rh species and the reaction conditions.
Interface-type tunable oxygen ion dynamics for physical reservoir computing
Authors: Liu Zhuohui , Zhang Qinghua , Xie Donggang , Zhang Mingzhen , Li Xinyan , Zhong Hai , Li Ge , He Meng , Shang Dashan , Wang Can , Gu Lin , Yang Guozhen , Jin Kuijuan , Ge Chen 
Published: November 2023

AbstractReservoir computing can more efficiently be used to solve time-dependent tasks than conventional feedforward network owing to various advantages, such as easy training and low hardware overhead. Physical reservoirs that contain intrinsic nonlinear dynamic processes could serve as next-generation dynamic computing systems. High-efficiency reservoir systems require nonlinear and dynamic responses to distinguish time-series input data. Herein, an interface-type dynamic transistor gated by an Hf0.5Zr0.5O2 (HZO) film was introduced to perform reservoir computing. The channel conductance of Mott material La0.67Sr0.33MnO3 (LSMO) can effectively be modulated by taking advantage of the unique coupled property of the polarization process and oxygen migration in hafnium-based ferroelectrics. The large positive value of the oxygen vacancy formation energy and negative value of the oxygen affinity energy resulted in the spontaneous migration of accumulated oxygen ions in the HZO films to the channel, leading to the dynamic relaxation process. The modulation of the channel conductance was found to be closely related to the current state, identified as the origin of the nonlinear response. In the time series recognition and prediction tasks, the proposed reservoir system showed an extremely low decision-making error. This work provides a promising pathway for exploiting dynamic ion systems for high-performance neural network devices.
Multi-state quantum simulations via model-space quantum imaginary time evolution
Authors: Tsuchimochi Takashi , Ryo Yoohee , Tsang Siu Chung , Ten-no Seiichiro L. 
Published: November 2023

AbstractWe introduce the framework of model space into quantum imaginary time evolution (QITE) to enable stable estimation of ground and excited states using a quantum computer. Model-space QITE (MSQITE) propagates a model space to the exact one by retaining its orthogonality, and hence is able to describe multiple states simultaneously. The quantum Lanczos (QLanczos) algorithm is extended to MSQITE to accelerate the convergence. The present scheme is found to outperform both the standard QLanczos and the recently proposed folded-spectrum QITE in simulating excited states. Moreover, we demonstrate that spin contamination can be effectively removed by shifting the imaginary time propagator, and thus excited states with a particular spin quantum number are efficiently captured without falling into the different spin states that have lower energies. We also investigate how different levels of the unitary approximation employed in MSQITE can affect the results. The effectiveness of the algorithm over QITE is demonstrated by noise simulations for the H4model system.
DeepPatent2: A Large-Scale Benchmarking Corpus for Technical Drawing Understanding
Authors: Ajayi Kehinde , Wei Xin , Gryder Martin , Shields Winston , Wu Jian , Jones Shawn M. , Kucer Michal , Oyen Diane 
Published: November 2023

AbstractRecent advances in computer vision (CV) and natural language processing have been driven by exploiting big data on practical applications. However, these research fields are still limited by the sheer volume, versatility, and diversity of the available datasets. CV tasks, such as image captioning, which has primarily been carried out on natural images, still struggle to produce accurate and meaningful captions on sketched images often included in scientific and technical documents. The advancement of other tasks such as 3D reconstruction from 2D images requires larger datasets with multiple viewpoints. We introduce DeepPatent2, a large-scale dataset, providing more than 2.7 million technical drawings with 132,890 object names and 22,394 viewpoints extracted from 14 years of US design patent documents. We demonstrate the usefulness of DeepPatent2 with conceptual captioning. We further provide the potential usefulness of our dataset to facilitate other research areas such as 3D image reconstruction and image retrieval.
A novel model for predicting the prognosis of postoperative intrahepatic cholangiocarcinoma patients
Authors: Lv Yinghao , Liu Hu , He Penghui , Xie Sinan , Yin Xiuchun , Cai Yunshi , Wu Hong 
Published: November 2023

AbstractIntrahepatic cholangiocarcinoma (ICC) accounts for 20% of liver malignancies with a 5-year survival rate of 35% at best with limited prognostic predictors. Lung Immune Prognostic Index (LIPI) is a novel prognostic factor in pulmonary cancers. In this study, we developed a modified prognostic model from LIPI called intrahepatic immune prognostic index (IIPI) for ICC. A retrospectively study was conducted at Liver Transplant Center of West China Hospital between January 2015 and January 2023. Hematological factors and clinical features of ICC patients were collected and analyzed. The area under curve (AUC) and optimal cuff-off of each single hematological factor was calculated. In this study, derived neurtrophil to lymphocyte ratio (dNLR), arbohydrate antigen199 (CA199) and carcinoembryonic antigen (CEA) have higher AUC values. LIPI was composed of dNLR and was further modified by combing CA199 and CEA, forming the IIPI. The IIPI consists of four grades which are None, Light, Moderate and Severe. Compared to other prognostic factors, IIPI exhibited better ability to predict overall survival. The multivariate analysis indicated that cirrhosis, differentiation, hilar invasion and IIPI were independent prognostic factors for ICC patients. An IIPI-based nomogram was also established and could predict the overall survival. In addition, the subgroup analyses based on clinical prognostic factors showed that the IIPI exhibited excellent prognostic influence. IIPI model is suitable for predicting the prognosis of postoperative ICC patients. Further research is needed to explore the relationship between postoperative recurrence and metastasis of ICC patients and IIPI.
Ni/Mn metal–organic framework decorated bacterial cellulose (Ni/Mn-MOF@BC) and nickel foam (Ni/Mn-MOF@NF) as a visible-light photocatalyst and supercapacitive electrode
Authors: Ebrahimi-Koodehi Soheila , Ghodsi Farhad Esmaeili , Mazloom Jamal 
Published: November 2023

AbstractRecently, metal–organic frameworks (MOFs) and hybrids with biomaterial are broadly investigated for a variety of applications. In this work, a novel dual-phase MOF has been grown on bacterial cellulose (BC) as a biopolymer nano-fibrous film (Ni/Mn-MOF@BC), and nickel foam (Ni/Mn-MOF@NF) using a simple reflux method to explore their potential for photocatalyst and energy storage applications. The studies showed that the prepared Mn and Ni/Mn-MOFs display different structures. Besides, the growth of MOFs on BC substantially changed the morphology of the samples by reducing their micro sized scales to nanoparticles. The nanosized MOF particles grown on BC served as a visible-light photocatalytic material. Regarding the high surface area of BC and the synergistic effect of two metal ions, Ni/Mn-MOF@BC with a lower band gap demonstrates remarkable photocatalytic degradation efficiency (ca. 84% within 3 h) against methylene blue (MB) dye under visible light, and the catalyst retained 65% of its initial pollutant removal properties after four cycles of irradiation. Besides, MOF powders deposited on nickel foam have been utilized as highly capacitive electrochemical electrodes. There, Ni/Mn-MOF@NF electrode also possesses outstanding electrochemical properties, showing a specific capacitance of 2769 Fg−1 at 0.5 Ag−1, and capacity retention of 94% after 1000 cycles at 10 Ag−1.
Development and validation of a prognostic model of survival for classic heatstroke patients: a multicenter study
Authors: Wang Yu , Li Donglin , Wu Zongqian , Zhong Chuan , Tang Shengjie , Hu Haiyang , Lin Pei , Yang Xianqing , Liu Jiangming , He Xinyi , Zhou Haining , Liu Fake 
Published: November 2023

AbstractClassic heatstroke (CHS) is a life-threatening illness characterized by extreme hyperthermia, dysfunction of the central nervous system and multiorgan failure. Accurate predictive models are useful in the treatment decision-making process and risk stratification. This study was to develop and externally validate a prediction model of survival for hospitalized patients with CHS. In this retrospective study, we enrolled patients with CHS who were hospitalized from June 2022 to September 2022 at 3 hospitals in Southwest Sichuan (training cohort) and 1 hospital in Central Sichuan (external validation cohort). Prognostic factors were identified utilizing least absolute shrinkage and selection operator (LASSO) regression analysis and multivariate Cox regression analysis in the training cohort. A predictive model was developed based on identified prognostic factors, and a nomogram was built for visualization. The areas under the receiver operator characteristic (ROC) curves (AUCs) and the calibration curve were utilized to assess the prognostic performance of the model in both the training and external validation cohorts. The Kaplan‒Meier method was used to calculate survival rates. A total of 225 patients (median age, 74 [68–80] years) were included. Social isolation, self-care ability, comorbidities, body temperature, heart rate, Glasgow Coma Scale (GCS), procalcitonin (PCT), aspartate aminotransferase (AST) and diarrhea were found to have a significant or near-significant association with worse prognosis among hospitalized CHS patients. The AUCs of the model in the training and validation cohorts were 0.994 (95% [CI], 0.975–0.999) and 0.901 (95% [CI], 0.769–0.968), respectively. The model's prediction and actual observation demonstrated strong concordance on the calibration curve regarding 7-day survival probability. According to K‒M survival plots, there were significant differences in survival between the low-risk and high-risk groups in the training and external validation cohorts. We designed and externally validated a prognostic prediction model for CHS. This model has promising predictive performance and could be applied in clinical practice for managing patients with CHS.
Investigation of N-polar InGaN growth on misoriented ScAlMgO4 substrates
Authors: Najmi Mohammed A. , Kirilenko Pavel , Iida Daisuke , Ohkawa Kazuhiro 
Published: November 2023

AbstractWe report the growth of N-polar InGaN layers on misoriented ScAlMgO4 (SAM) substrates with offset of 0.3 to 5.8° toward the m-plane. The surface of N-polar InGaN with small-offset substrates exhibited hexagonal hillocks similar to those commonly observed in N-polar GaN layers. Larger misorientation angles resulted in smoother surfaces of the InGaN layers. In contrast, the crystalline quality of InGaN indicated an opposite trend with significantly improved quality observed at smaller misorientation angles. We obtained an unprecedented crystalline quality of N-polar InGaN using SAM substrates with a 0.5° offset, which exhibited a $${000}\overline{2}$$

000

2
¯

X-ray rocking curve full width at half maximum value of 223 arcsec. The crystalline quality and surface morphology of InGaN were significantly influenced by the step surface of substrates according to atomic force microscopy observations.
Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA
Authors: Jena N. R. , Shukla P. K. 
Published: November 2023

AbstractA triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about − 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about − 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12–14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16–21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.
A Drosophila model relevant to chemotherapy-related cognitive impairment
Authors: Torre Matthew , Bukhari Hassan , Nithianandam Vanitha , Zanella Camila A. , Mata Douglas A. , Feany Mel B. 
Published: November 2023

AbstractChemotherapy-related cognitive impairment (CRCI) is a common adverse effect of treatment and is characterized by deficits involving multiple cognitive domains including memory. Despite the significant morbidity of CRCI and the expected increase in cancer survivors over the coming decades, the pathophysiology of CRCI remains incompletely understood, highlighting the need for new model systems to study CRCI. Given the powerful array of genetic approaches and facile high throughput screening ability inDrosophila, our goal was to validate aDrosophilamodel relevant to CRCI. We administered the chemotherapeutic agents cisplatin, cyclophosphamide, and doxorubicin to adultDrosophila. Neurologic deficits were observed with all tested chemotherapies, with doxorubicin and in particular cisplatin also resulting in memory deficits. We then performed histologic and immunohistochemical analysis of cisplatin-treatedDrosophilatissue, demonstrating neuropathologic evidence of increased neurodegeneration, DNA damage, and oxidative stress. Thus, ourDrosophilamodel relevant to CRCI recapitulates clinical, radiologic, and histologic alterations reported in chemotherapy patients. Our newDrosophilamodel can be used for mechanistic dissection of pathways contributing to CRCI (and chemotherapy-induced neurotoxicity more generally) and pharmacologic screens to identify disease-modifying therapies.
Efficacy and safety of platelet-rich plasma and autologous-serum eye drops for dry eye in primary Sjögren’s syndrome: a randomized trial
Authors: Kang Min-Ji , Lee Jee Hye , Hwang Jehyung , Chung So-Hyang 
Published: November 2023

AbstractWe compared the efficacy and safety of autologous-serum (AS) and platelet-rich plasma (PRP) eye drops for dry eye (DE) treatment in primary Sjögren’s syndrome (SS). This prospective, randomized, double-blinded clinical study included patients diagnosed with primary SS DE. Thirty-eight participants were randomly assigned to the AS or PRP groups. Corneal and conjunctival staining scores, Schirmer I test, tear film break-up time (TBUT), and ocular surface disease index (OSDI) scores were evaluated at 4 and 12 weeks. Conjunctival impression cytology (CIC) metaplasia grade and goblet cell density grade at 12 weeks were compared with those at baseline. Corneal and conjunctival staining scores and TBUT significantly improved at 4 and 12 weeks in both groups (all p < 0.005). No significant difference between the AS and PRP groups was observed at 4 and 12 weeks. The Schirmer I values, OSDI scores, CIC metaplasia grade, and goblet cell density grade did not significantly change at 4 and 12 weeks in either group. Both AS and PRP eye drops are effective for primary SS DE without a significant difference. Considering that the preparation time of PRP is shorter than that of AS, PRP can be a good alternative treatment for primary SS DE.
A comprehensive analysis of multi-circulatory disorders in early pressure injury and their diagnostic significance in rat models
Authors: Chen Lu , Takashi En , Kamijo Akio , Miura Daiji , Lu Jian , Zhang Lan , Ten Hirotomo , Fan Jianglin 
Published: November 2023

AbstractEarly pressure injury (PI) progression is associated with multi-circulatory disorders and they interplay with each other, resulting in a lack of a satisfactory diagnostic method. We generated early PI and blanchable erythema hairless rat models. Transparent disc method and capillary refilling time test (CRTT) results were recorded with ultraviolet camera to capture the dynamics changes, and the blanching index and refilling index were set for comprehensive analysis. The deteriorated areas of early PI showed non-blanchable erythema (NBE) and an increase in erythema at 0.5 and 6 h with the transparent disc method. CRTT showed a marked refilling delay at 12 h. The comprehensive analysis of blanching index and refilling index showed a significant change in erythema from NBE at 0.5 h and ischemia progressing to hemorrhage at 18 h. There was also a marked difference in the deteriorating and improving areas within the same erythema. Pathological analysis showed inflammatory cell infiltration, with marked edema accompanied by increased hemorrhage and tissue necrosis. Furthermore, small arteries and veins with thrombosis and microthrombi were observed. Consistent ischemia after decompression and subsequent hemorrhage are important indicators, and comprehensive analysis can help increase the positive diagnosis rate over that for other circulatory disorders alone.