bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid species identification of pathogenic bacteria from a minute quantity exploiting three-dimensional quantitative phase imaging and artificial neural network
Authors: Kim Geon , Ahn Daewoong , Kang Minhee , Park Jinho , Ryu DongHun , Jo YoungJu , Song Jinyeop , Ryu Jea Sung , Choi Gunho , Chung Hyun Jung , Kim Kyuseok , Chung Doo Ryeon , Yoo In Young , Huh Hee Jae , Min Hyun-seok , Lee Nam Yong , Park YongKeun 
Published: June 2022

AbstractThe healthcare industry is in dire need of rapid microbial identification techniques for treating microbial infections. Microbial infections are a major healthcare issue worldwide, as these widespread diseases often develop into deadly symptoms. While studies have shown that an early appropriate antibiotic treatment significantly reduces the mortality of an infection, this effective treatment is difficult to practice. The main obstacle to early appropriate antibiotic treatments is the long turnaround time of the routine microbial identification, which includes time-consuming sample growth. Here, we propose a microscopy-based framework that identifies the pathogen from single to few cells. Our framework obtains and exploits the morphology of the limited sample by incorporating three-dimensional quantitative phase imaging and an artificial neural network. We demonstrate the identification of 19 bacterial species that cause bloodstream infections, achieving an accuracy of 82.5% from an individual bacterial cell or cluster. This performance, comparable to that of the gold standard mass spectroscopy under a sufficient amount of sample, underpins the effectiveness of our framework in clinical applications. Furthermore, our accuracy increases with multiple measurements, reaching 99.9% with seven different measurements of cells or clusters. We believe that our framework can serve as a beneficial advisory tool for clinicians during the initial treatment of infections.
Surface plasmons interference nanogratings: wafer-scale laser direct structuring in seconds
Authors: Geng Jiao , Yan Wei , Shi Liping , Qiu Min 
Published: June 2022

AbstractIt is always a great challenge to bridge the nano- and macro-worlds in nanoscience, for instance, manufacturing uniform nanogratings on a whole wafer in seconds instead of hours even days. Here, we demonstrate a single-step while extremely high-throughput femtosecond laser scanning technique to obtain wafer-scale, highly regular nanogratings on semiconductor-on-metal thin films. Our technique takes advantage of long-range surface plasmons-laser interference, which is regulated by a self-initiated seed. By controlling the scanning speed, two types of nanogratings are readily manufactured, which are produced by either oxidation or ablation. We achieve a record manufacturing speed (>1 cm2 s−1), with tunable periodicity of Λ < 1 µm. The fractional variation of their periodicity is evaluated to be as low as ∆Λ/Λ ≈ 0.5%. Furthermore, by utilizing the semiconductor-on-metal film-endowed interference effects, an extremely high energy efficiency is achieved via suppressing light reflection during femtosecond laser nano-processing. As the fabricated nanogratings exhibit multi-functionality, we exemplify their practical applications in highly sensitive refractive index sensing, vivid structural colors, and durable superhydrophilicity.
HAO1-mediated oxalate metabolism promotes lung pre-metastatic niche formation by inducing neutrophil extracellular traps
Authors: Zeng Zhicheng , Xu Shaowan , Wang Feifei , Peng Xin , Zhang Wanning , Zhan Yizhi , Ding Yanqing , Liu Ziguang , Liang Li 
Published: June 2022

AbstractMetabolic reprogramming has been shown to be involved in cancer-induced pre-metastatic niche (PMN) formation, but the underlying mechanisms have been insufficiently explored. Here, we showed that hydroxyacid oxidase 1 (HAO1), a rate-limiting enzyme of oxalate synthesis, was upregulated in the alveolar epithelial cells of mice bearing metastatic breast cancer cells at the pre-metastatic stage, leading to oxalate accumulation in lung tissue. Lung oxalate accumulation induced neutrophil extracellular trap (NET) formation by activating NADPH oxidase, which facilitated the formation of pre-metastatic niche. In addition, lung oxalate accumulation promoted the proliferation of metastatic cancer cells by activating the MAPK signaling pathway. Pharmacologic inhibition of HAO1 could effectively suppress the lung oxalate accumulation induced by primary cancer, consequently dampening lung metastasis of breast cancer. Breast cancer cells induced HAO1 expression and oxalate accumulation in alveolar epithelial cells by activating TLR3-IRF3 signaling. Collectively, these findings underscore the role of HAO1-mediated oxalate metabolism in cancer-induced lung PMN formation and metastasis. HAO1 could be an appealing therapeutic target for preventing lung metastasis of cancer.
Structural insights into ligand recognition and selectivity of somatostatin receptors
Authors: Zhao Wenli , Han Shuo , Qiu Na , Feng Wenbo , Lu Mengjie , Zhang Wenru , Wang Mu , Zhou Qingtong , Chen Shutian , Xu Wei , Du Juan , Chu Xiaojing , Yi Cuiying , Dai Antao , Hu Liaoyuan , Shen Michelle Y. , Sun Yaping , Zhang Qing , Ma Yingli , Zhong Wenge , Yang Dehua , Wang Ming-Wei , Wu Beili , Zhao Qiang 
Published: June 2022

AbstractSomatostatin receptors (SSTRs) play versatile roles in inhibiting the secretion of multiple hormones such as growth hormone and thyroid-stimulating hormone, and thus are considered as targets for treating multiple tumors. Despite great progress made in therapeutic development against this diverse receptor family, drugs that target SSTRs still show limited efficacy with preferential binding affinity and conspicuous side-effects. Here, we report five structures of SSTR2 and SSTR4 in different states, including two crystal structures of SSTR2 in complex with a selective peptide antagonist and a non-peptide agonist, respectively, a cryo-electron microscopy (cryo-EM) structure of Gi1-bound SSTR2 in the presence of the endogenous ligand SST-14, as well as two cryo-EM structures of Gi1-bound SSTR4 in complex with SST-14 and a small-molecule agonist J-2156, respectively. By comparison of the SSTR structures in different states, molecular mechanisms of agonism and antagonism were illustrated. Together with computational and functional analyses, the key determinants responsible for ligand recognition and selectivity of different SSTR subtypes and multiform binding modes of peptide and non-peptide ligands were identified. Insights gained in this study will help uncover ligand selectivity of various SSTRs and accelerate the development of new molecules with better efficacy by targeting SSTRs.
Evolution of determinant factors of maximal sprinting and repeated sprint ability in women soccer players
Authors: González-Fernández Francisco Tomás , García-Taibo Olalla , Vila Moisés , Nobari Hadi , Clemente Filipe Manuel 
Published: June 2022

AbstractThe present study aimed to determine the influence of force–power–velocity, vertical and horizontal jumps, and repeated sprint ability on the sprinting performance of adult women soccer players. Eighteen women soccer players from one team participating in the first female national Spanish soccer league were analyzed. Fitness assessments were performed twice in a period of three months. The following assessments were made to reach the aim of the study: (1) anthropometric measures, (2) CMJ (0%, 20% and 40%), (3) hop test (dominant and nondominant leg), (4) linear sprinting at 30 m and (5) RSA test. The main evidence of this study revealed the meaningful contribution of lower-limb power (vertical and horizontal jump), maximal sprint and peak power on sprinting time performance, while stride frequency was meaningfully explained by vertical jump and maximal sprinting. In fact, positive moderate and large correlations were found between Time and CMJ, CMJ 20%, CMJ 40%, Hop Test Dominant and Non-dominant, and Pmaxand MS of Force–Power–Velocity (r = − 0.73,p = 0.001; r = − 0.68,p = 0.002; r = − 0.51,p = 0.03; r = − 0.64,p = 0.004; r = − 0.57,p = 0.013; r = − 0.78,p = 0.001, and r = − 0.83,p = 0.001, respectively). In sum, peak power, maximal speed, and lower-limb power (in vertical and horizontal jumps) were significant determinants of sprinting performance (time), while vertical jump was the determinant of stride frequency. In addition, our findings suggest that potentiation and explosive vertical power could be the emphasis for sustaining the stride frequency of women soccer players, while sprinting performance should be supported by strong acceleration and maximal velocity sustained by both vertical and horizontal force and concentric and eccentric strength and power.
Elucidating macular structure–function correlations in glaucoma
Authors: Giammaria Sara , Sharpe Glen P. , Dyachok Oksana , Rafuse Paul E. , Shuba Lesya M. , Nicolela Marcelo T. , Vianna Jayme R. , Chauhan Balwantray C. 
Published: June 2022

AbstractCorrelation between structural data from optical coherence tomography and functional data from the visual field may be suboptimal because of poor mapping of OCT measurement locations to VF stimuli. We tested the hypothesis that stronger structure–function correlations in the macula can be achieved with fundus-tracking perimetery, by precisely mapping OCT measurements to VF sensitivity at the same location. The conventional 64 superpixel (3° × 3°) OCT grid was mapped to VF sensitivities averaged in 40 corresponding VF units with standard automated perimetry (conventional mapped approach, CMA) in 38 glaucoma patients and 10 healthy subjects. Similarly, a 144 superpixel (2° × 2°) OCT grid was mapped to each of the 68 locations with fundus-tracking perimetry (localized mapped approach, LMA). For each approach, the correlation between sensitivity at each VF unit and OCT superpixel was computed. Vector maps showing the maximum correlation between each VF unit and OCT pixel was generated. CMA yielded significantly higher structure–function correlations compared to LMA. Only 20% of the vectors with CMA and < 5% with LMA were within corresponding mapped OCT superpixels, while most were directed towards loci with structural damage. Measurement variability and patterns of structural damage more likely impact correlations compared to precise mapping of VF stimuli.
Functional regulations between genetic alteration-driven genes and drug target genes acting as prognostic biomarkers in breast cancer
Authors: Wang Li , Yu Lei , Shi Jian , Li Feng , Zhang Caiyu , Xu Haotian , Yin Xiangzhe , Wang Lixia , Lin Shihua , Litvinova Anastasiia , Ping Yanyan , Ning Shangwei , Zhao Hongying 
Published: June 2022

AbstractDifferences in genetic molecular features including mutation, copy number alterations and DNA methylation, can explain interindividual variability in response to anti-cancer drugs in cancer patients. However, identifying genetic alteration-driven genes and characterizing their functional mechanisms in different cancer types are still major challenges for cancer studies. Here, we systematically identified functional regulations between genetic alteration-driven genes and drug target genes and their potential prognostic roles in breast cancer. We identified two mutation and copy number-driven gene pairs (PARP1-ACSL1 and PARP1-SRD5A3), three DNA methylation-driven gene pairs (PRLR-CDKN1C, PRLR-PODXL2 and PRLR-SRD5A3), six gene pairs between mutation-driven genes and drug target genes (SLC19A1-SLC47A2, SLC19A1-SRD5A3, AKR1C3-SLC19A1, ABCB1-SRD5A3, NR3C2-SRD5A3 and AKR1C3-SRD5A3), and four copy number-driven gene pairs (ADIPOR2-SRD5A3, CASP12-SRD5A3, SLC39A11-SRD5A3 and GALNT2-SRD5A3) that all served as prognostic biomarkers of breast cancer. In particular, RARP1 was found to be upregulated by simultaneous copy number amplification and gene mutation. Copy number deletion and downregulated expression of ACSL1 and upregulation of SRD5A3 both were observed in breast cancers. Moreover, copy number deletion of ACSL1 was associated with increased resistance to PARP inhibitors. PARP1-ACSL1 pair significantly correlated with poor overall survival in breast cancer owing to the suppression of the MAPK, mTOR and NF-kB signaling pathways, which induces apoptosis, autophagy and prevents inflammatory processes. Loss of SRD5A3 expression was also associated with increased sensitivity to PARP inhibitors. The PARP1-SRD5A3 pair significantly correlated with poor overall survival in breast cancer through regulating androgen receptors to induce cell proliferation. These results demonstrate that genetic alteration-driven gene pairs might serve as potential biomarkers for the prognosis of breast cancer and facilitate the identification of combination therapeutic targets for breast cancers.
Fibrillin-1 mutant mouse captures defining features of human primary open glaucoma including anomalous aqueous humor TGF beta-2
Authors: Ko MinHee K. , Woo Jeong-Im , Gonzalez Jose M. , Kim Gayeoun , Sakai Lynn , Peti-Peterdi Janos , Kelber Jonathan A. , Hong Young-Kwon , Tan James C. 
Published: June 2022

AbstractPrimary open angle glaucoma (POAG) features an optic neuropathy, elevated aqueous humor (AH) TGFβ2, and major risk factors of central corneal thickness (CCT), increasing age and intraocular pressure (IOP). We examined Tight skin (Tsk) mice to see if mutation of fibrillin-1, a repository for latent TGFβ, is associated with characteristics of human POAG. We measured: CCT by ocular coherence tomography (OCT); IOP; retinal ganglion cell (RGC) and optic nerve axon counts by microscopic techniques; visual electrophysiologic scotopic threshold responses (STR) and pattern electroretinogram (PERG); and AH TGFβ2 levels and activity by ELISA and MINK epithelial cell-based assays respectively. Tsk mice had open anterior chamber angles and compared with age-matched wild type (WT) mice: 23% thinner CCT (p < 0.003); IOP that was higher (p < 0.0001), more asymmetric (p = 0.047), rose with age (p = 0.04) and had a POAG-like frequency distribution. Tsk mice also had RGCs that were fewer (p < 0.04), declined with age (p = 0.0003) and showed increased apoptosis and glial activity; fewer optic nerve axons (p = 0.02); abnormal axons and glia; reduced STR (p < 0.002) and PERG (p < 0.007) visual responses; and higher AH TGFβ2 levels (p = 0.0002) and activity (p = 1E−11) especially with age. Tsk mice showed defining features of POAG, implicating aberrant fibrillin-1 homeostasis as a pathogenic contributor to emergence of a POAG phenotype.
Physiological and transcriptome analyses reveal the response of Ammopiptanthus mongolicus to extreme seasonal temperatures in a cold plateau desert ecosystem
Authors: Yang Zimeng , Liu Yiying , Han Hang , Zhao Xinyu , Chen Siyu , Li Guofang , Shi Sha , Feng Jinchao 
Published: June 2022

AbstractAmmopiptanthus mongolicus is the only evergreen broad-leaved shrub present in arid areas of Northwest China and plays an important role in maintaining the stability of the local desert ecosystem. It can survive under extreme temperatures (e.g., extreme low temperature: − 24.8 °C and extreme high temperature: 37.7 °C). To understand the gene expression-physiological regulation network of A. mongolicus in extreme temperature environments, we monitored the changes in gene expression and photosynthetic traits of the leaves. The results showed that at low temperatures, the net photosynthetic rates (A), Fv'/Fm' and electron transport rate (ETR) decreased, the Fv/Fm ratio was only 0.32, and the proportion of nonregulatory heat dissipation Y(NO) increased. Based on a KEGG analysis of the differentially expressed genes, 15 significantly enriched KEGG pathways were identified, which were mainly related to circadian rhythm, photosynthesis, lipid metabolism, carbohydrate metabolism, plant hormones and other life activities. At high temperatures, the A value increased, and the proportion of regulatory energy dissipation Y(NPQ) increased. The KEGG analysis identified 24 significantly enriched KEGG pathways, which are mainly related to circadian rhythm, carbon sequestration of photosynthesis, carotenoid biosynthesis, secondary metabolites, cofactors and vitamin metabolism. In general, at the expense of photosynthesis, A. mongolicus can ensure the survival of leaves by increasing Y(NO) levels, regulating the circadian rhythm, increasing the synthesis of unsaturated fatty acids and changing the role of plant hormones. Under high-temperature stress, a high photosynthetic capacity was maintained by adjusting the stomatal conductance (gsw), increasing Y(NPQ), consuming excess light energy, continuously assembling and maintaining PSII, and changing the production of antioxidants.
Randomized clinical trial comparing intravitreal aflibercept combined with subthreshold laser to intravitreal aflibercept monotherapy for diabetic macular edema
Authors: Tatsumi Tomoaki , Takatsuna Yoko , Oshitari Toshiyuki , Kaiho Tomomi , Kawasaki Yohei , Shiko Yuki , Sugawara Takeshi , Baba Takayuki , Yamamoto Shuichi 
Published: June 2022

AbstractTo compare the efficacy and safety of intravitreal aflibercept with three loading doses + pro re nata regimen combined with subthreshold laser application to that of IVA monotherapy on eyes with diabetic macular edema. This was a phase 4 clinical trial with a prospective, randomized, and parallel investigator-driven protocol. Patients with DME were randomly assigned to the IVA monotherapy group (n = 25) or the IVA + SL combination therapy group (n = 26). The main outcome measures were the number of IVA injections and the changes in the best-corrected visual acuity (BCVA) and the central retinal thickness (CRT) at the final evaluation at 96 weeks. The mean number of IVA injections in the monotherapy group was 5.86 ± 2.43 and it was 6.05 ± 2.73 in the IVA + SL group at 96 weeks, and this difference was not significant (P = 0.83). The differences in the mean changes of the CRT (P = 0.17) and the BCVA (P = 0.31) were also not significant between the two groups throughout the follow-up period. We conclude that adjunct of SL to anti-VEGF therapy does not reduce the number of necessary intravitreal injections.
Abundance and distribution patterns of cetaceans and their overlap with vessel traffic in the Humboldt Current Ecosystem, Chile
Authors: Bedriñana-Romano Luis , Zarate Patricia M. , Hucke-Gaete Rodrigo , Viddi Francisco A. , Buchan Susannah J. , Cari Ilia , Clavijo Ljubitza , Bello Robert , Zerbini Alexandre N. 
Published: June 2022

AbstractThe Humboldt Current Ecosystem (HCE) is one of the most productive marine ecosystems, sustaining one of the largest fishing industries in the world. Although several species of cetaceans are known to inhabit these productive waters, quantitative assessments of their abundance and distribution patterns are scarce and patchy. Here, we present the first abundance and distribution estimates for fin whale (Balaenoptera physalus), southeast Pacific blue whales (Balaenoptera musculus), sperm whale (Physeter macrocephalus), dusky dolphin (Lagenorhynchus obscurus), and common dolphin (Delphinusspp.) in the entire Chilean portion of the HCE. Line transect surveys were conducted during 2016–2021 between 18° S and 41° S and up to ~ 200 km offshore, and data were analyzed using distance sampling methods. Group counts were modelled as a function of environmental variables using single step Bayesian Binomial N-mixture model (BNMM), which allows full uncertainty propagation between model components. By using spatially explicit predictions of cetacean densities and observed vessel densities in the HCE, we provide quantitative assessments on the relative probability of cetaceans encountering vessels (RPCEV). Dusky dolphin and fin whale showed the largest distribution overlap with industrial and artisanal fishery fleets. Our results highlight areas where effort should be prioritized to address the extant but unquantified negative interactions between vessels and cetaceans in Chilean HCE.
Nonlinear control of switchable wavelength-selective absorption in a one-dimensional photonic crystal including ultrathin phase transition material-vanadium dioxide
Authors: Saleki Ziba 
Published: June 2022

AbstractBased on the transfer matrix theory, I realize a nearly perfect wavelength-selective absorption of near-IR waves in a one-dimensional defective photonic crystal, $$(AB)^ND(BA)^M$$

(
A
B
)

N

D

(
B
A
)

M

, containing a vanadium dioxide (VO$$_2$$

2

) phase transition layer as a defect. Firstly, the effect of the period numbers, N and M, on the absorption spectrum is studied to achieve a perfect absorption peak. It is shown that optimal period numbers of the structure to maximize the absorption peak are N = 7 and M = 16. Our results also indicate that a narrow-band, almost perfect absorption is achieved due to the symmetry of the structure with respect to VO$$_2$$

2

. Also, the absorption amount of the considered structure is about 50 times larger than that of a free-standing VO$$_2$$

2

. Furthermore, the absorption peak value and resonant wavelength can be continuously tuned while VO$$_2$$

2

transits from semiconductor to metal phase at 340 K temperature. In addition, how different parameters such as the polarization and incident angle affect the absorption spectra is discussed. Finally, the nonlinear absorption spectra of the structure are graphically demonstrated beside the linear case. The current system can be applied in designing practical tunable optical devices such as IR sensors, limiters, and switches.
Physical activity, screen time and the incidence of neck and shoulder pain in school-aged children
Authors: Pirnes Katariina Pauliina , Kallio Jouni , Hakonen Harto , Hautala Arto , Häkkinen Arja Helena , Tammelin Tuija 
Published: June 2022

AbstractThis study investigated the associations of accelerometer-measured physical activity, sedentary time and screen time with the incidence of neck and shoulder pain in school-aged children over a two-year follow-up. Children (aged 10–15) were measured at baseline 2013 (T0) (n = 970) and at follow-ups 2014 (T1) and 2015 (T2). Neck and shoulder pain frequency and screen time were determined with a web-based questionnaire. Daytime moderate to vigorous physical activity and sedentary time were measured with an accelerometer. Logistic regression was applied, and the results were adjusted for age, gender, body mass index and bedtime. Accelerometer-measured physical activity or sedentary time at baseline were not associated with the incidence of neck and shoulder pain at the two-year follow-up. Associations of neck and shoulder pain incidence with overall screen time (p = 0.020), and especially with passive gaming time (p = 0.036) and social media time (p = 0.023) were found at the first but not the second follow-up. The neck and shoulder pain incidence associated with overall screen time, passive gaming time and social media time at the first follow-up. The importance of limiting screen time, should be explored in order to find new approaches in preventing neck and shoulder pain in school-aged children.