bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increased hydraulic risk in assemblages of woody plant species predicts spatial patterns of drought-induced mortality
Authors: Sanchez-Martinez Pablo , Mencuccini Maurizio , García-Valdés Raúl , Hammond William M. , Serra-Diaz Josep M. , Guo Wen-Yong , Segovia Ricardo A. , Dexter Kyle G. , Svenning Jens-Christian , Allen Craig , Martínez-Vilalta Jordi 
Published: August 2023

AbstractPredicting drought-induced mortality (DIM) of woody plants remains a key research challenge under climate change. Here, we integrate information on the edaphoclimatic niches, phylogeny and hydraulic traits of species to model the hydraulic risk of woody plants globally. We combine these models with species distribution records to estimate the hydraulic risk faced by local woody plant species assemblages. Thus, we produce global maps of hydraulic risk and test for its relationship with observed DIM. Our results show that local assemblages modelled as having higher hydraulic risk present a higher probability of DIM. Metrics characterizing this hydraulic risk improve DIM predictions globally, relative to models accounting only for edaphoclimatic predictors or broad functional groupings. The methodology we present here allows mapping of functional trait distributions and elucidation of global macro-evolutionary and biogeographical patterns, improving our ability to predict potential global change impacts on vegetation.
Single-molecule mid-infrared spectroscopy and detection through vibrationally assisted luminescence
Authors: Chikkaraddy Rohit , Arul Rakesh , Jakob Lukas A. , Baumberg Jeremy J. 
Published: August 2023

AbstractRoom-temperature detection of molecular vibrations in the mid-infrared (MIR, λ = 3–30 µm) has numerous applications, including real-time gas sensing, medical imaging and quantum communication. However, existing technologies rely on cooled semiconductor detectors because of thermal noise limitations. One way to overcome this challenge is to upconvert the low-energy MIR photons into high-energy visible wavelengths (λ = 500–800 nm) where detection of single photons is easily achieved using silicon technologies. This process suffers from weak cross-sections and the MIR-to-visible wavelength mismatch, limiting its efficiency. Here we exploit molecular emitters possessing both MIR and visible transitions from molecular vibrations and electronic states, coupled through Franck–Condon factors. By assembling molecules into a plasmonic nanocavity resonant at both MIR and visible wavelengths, and optically pumping them below the electronic absorption band, we show transduction of MIR light. The upconverted signal is observed as enhanced visible luminescence. Combining Purcell-enhanced visible luminescence with enhanced rates of vibrational pumping gives transduction efficiencies of >10%. MIR frequency-dependent upconversion gives the vibrational signatures of molecules assembled in the nanocavity. Transient picocavity formation further confines MIR light down to the single-molecule level. This allows us to demonstrate single-molecule MIR detection and spectroscopy that is inaccessible to any previous detector.
Excited-state observation of active K-Ras reveals differential structural dynamics of wild-type versus oncogenic G12D and G12C mutants
Authors: Hansen Alexandar L. , Xiang Xinyao , Yuan Chunhua , Bruschweiler-Li Lei , Brüschweiler Rafael 
Published: August 2023

AbstractDespite the prominent role of the K-Ras protein in many different types of human cancer, major gaps in atomic-level information severely limit our understanding of its functions in health and disease. Here, we report the quantitative backbone structural dynamics of K-Ras by solution nuclear magnetic resonance spectroscopy of the active state of wild-type K-Ras bound to guanosine triphosphate (GTP) nucleotide and two of its oncogenic P-loop mutants, G12D and G12C, using a new nanoparticle-assisted spin relaxation method, relaxation dispersion and chemical exchange saturation transfer experiments covering the entire range of timescales from picoseconds to milliseconds. Our combined experiments allow detection and analysis of the functionally critical Switch I and Switch II regions, which have previously remained largely unobservable by X-ray crystallography and nuclear magnetic resonance spectroscopy. Our data reveal cooperative transitions of K-Ras·GTP to a highly dynamic excited state that closely resembles the partially disordered K-Ras·GDP state. These results advance our understanding of differential GTPase activities and signaling properties of the wild type versus mutants and may thus guide new strategies for the development of therapeutics.
Treatment of antibiotic-resistant bacteria colonizing diabetic foot ulcers by OLED induced antimicrobial photodynamic therapy
Authors: Piksa Marta , Fortuna Wojciech , Lian Cheng , Gacka Małgorzata , Samuel Ifor D. W. , Matczyszyn Katarzyna , Pawlik Krzysztof J. 
Published: August 2023

AbstractWe evaluate the efficacy of antimicrobial Photodynamic Therapy (APDT) for inactivating a variety of antibiotic-resistant clinical strains from diabetic foot ulcers. Here we are focused on APDT based on organic light-emitting diodes (OLED). The wound swabs from ten patients diagnosed with diabetic foot ulcers were collected and 32 clinical strains comprising 22 bacterial species were obtained. The isolated strains were identified with the use of mass spectrometry coupled with a protein profile database and tested for antibiotic susceptibility. 74% of isolated bacterial strains exhibited adaptive antibiotic resistance to at least one antibiotic. All strains were subjected to the APDT procedure using an OLED as a light source and 16 µM methylene blue as a photosensitizer. APDT using the OLED led to a large reduction in all cases. For pathogenic bacteria, the reduction ranged from 1.1-log to > 8 log (Klebsiella aerogenes, Enterobacter cloaca, Staphylococcus hominis) even for high antibiotic resistance (MRSA 5-log reduction). Opportunistic bacteria showed a range from 0.4-log reduction for Citrobacter koseri to > 8 log reduction for Kocuria rhizophila. These results show that OLED-driven APDT is effective against pathogens and opportunistic bacteria regardless of drug resistance.
Comparative performances of machine learning algorithms in radiomics and impacting factors
Authors: Decoux Antoine , Duron Loic , Habert Paul , Roblot Victoire , Arsovic Emina , Chassagnon Guillaume , Arnoux Armelle , Fournier Laure 
Published: August 2023

AbstractThere are no current recommendations on which machine learning (ML) algorithms should be used in radiomics. The objective was to compare performances of ML algorithms in radiomics when applied to different clinical questions to determine whether some strategies could give the best and most stable performances regardless of datasets. This study compares the performances of nine feature selection algorithms combined with fourteen binary classification algorithms on ten datasets. These datasets included radiomics features and clinical diagnosis for binary clinical classifications including COVID-19 pneumonia or sarcopenia on CT, head and neck, orbital or uterine lesions on MRI. For each dataset, a train-test split was created. Each of the 126 (9 × 14) combinations of feature selection algorithms and classification algorithms was trained and tuned using a ten-fold cross validation, then AUC was computed. This procedure was repeated three times per dataset. Best overall performances were obtained with JMI and JMIM as feature selection algorithms and random forest and linear regression models as classification algorithms. The choice of the classification algorithm was the factor explaining most of the performance variation (10% of total variance). The choice of the feature selection algorithm explained only 2% of variation, while the train-test split explained 9%.
Nature-inspired spider web shaped UHF RFID reader antenna for IoT and healthcare applications
Authors: Sharif Abubakar , kumar Rajesh , Arshad Kamran , Assaleh Khaled , Chattha Hassan Tariq , Imran Muhammad Ali , Abbasi Qammer Hussain 
Published: August 2023

AbstractThis paper proposes a nature-inspired spider web-shaped ultra-high frequency (UHF) radio frequency identification (RFID) reader antenna and battery-free sensor-based system for healthcare applications. This antenna design consists of eight concentric decagons of various sizes and five straight microstrip lines.These lines are connected to the ground using 50$$\Omega $$Ωresistors from both ends, except for one microstrip line that is reserved for connecting a feeding port. The reader antenna design features fairly strong and uniform electric and magnetic field characteristics. It also exhibits wideband characteristics, covering whole UHF RFID band (860–960 MHz) and providing a tag reading volume of 200$$\times $$×200$$\times $$×20 mm$${^3}$$3. Additionally, it has low gain characteristics, which are necessary for the majority of nearfield applications to prevent the misreading of other tags. Moreover, the current distribution in this design is symmetric throughout the structure, effectively resolving orientation sensitivity issues commonly encountered in low-cost linearly polarized tag antennas. The measurement results show that the reader antenna can read medicine pills tagged using low-cost passive/battery-free RFID tags, tagged expensive jewelry, intervenes solution, and blood bags positioned in various orientations. As a result, the proposed reader antenna-based system is a strong contender for near-field RFID, healthcare, and IoT applications.
Developmental genetic underpinnings of a symbiosis-associated organ in the fungus-farming ambrosia beetle Euwallacea validus
Authors: Spahr Ellie J. , Wasef Fady , Kasson Matt T. , Kijimoto Teiya 
Published: August 2023

AbstractMutualistic interactions between organisms often mediate the innovation of traits essential to maintain the relationship. Yet our understanding of these interactions has been stymied due to various hurdles in studying the genetics of non-model animals. To understand the genetic mechanisms by which such traits develop, we examined the function of genes breathless (btl), trachealess (trh), and doublesex in the development of a novel fungus-carrying organ (mycangium) that facilitates an obligate relationship between fungus-farming ambrosia beetles and specific fungal partners. Gene knockdown by RNA interference and subsequent micro-computed tomography visualization suggest btl and trh are required for initiation of mycangia and that tubulogenesis may have been co-opted for early mycangial development.
Lymphocyte detection for cancer analysis using a novel fusion block based channel boosted CNN
Authors: Rauf Zunaira , Khan Abdul Rehman , Sohail Anabia , Alquhayz Hani , Gwak Jeonghwan , Khan Asifullah 
Published: August 2023

AbstractTumor-infiltrating lymphocytes, specialized immune cells, are considered an important biomarker in cancer analysis. Automated lymphocyte detection is challenging due to its heterogeneous morphology, variable distribution, and presence of artifacts. In this work, we propose a novel Boosted Channels Fusion-based CNN “BCF-Lym-Detector” for lymphocyte detection in multiple cancer histology images. The proposed network initially selects candidate lymphocytic regions at the tissue level and then detects lymphocytes at the cellular level. The proposed “BCF-Lym-Detector” generates diverse boosted channels by utilizing the feature learning capability of different CNN architectures. In this connection, a new adaptive fusion block is developed to combine and select the most relevant lymphocyte-specific features from the generated enriched feature space. Multi-level feature learning is used to retain lymphocytic spatial information and detect lymphocytes with variable appearances. The assessment of the proposed “BCF-Lym-Detector” show substantial improvement in terms of F-score (0.93 and 0.84 on LYSTO and NuClick, respectively), which suggests that the diverse feature extraction and dynamic feature selection enhanced the feature learning capacity of the proposed network. Moreover, the proposed technique’s generalization on unseen test sets with a good recall (0.75) and F-score (0.73) shows its potential use for pathologists’ assistance.
LAMP1 as a novel molecular biomarker to predict the prognosis of the children with autism spectrum disorder using bioinformatics approaches
Authors: Deng Sisi , Feng Xiang , Yang Miao , Yu Wenjing , Wu Zixuan , Zhu Xu , Song Zhenyan , Cheng Shaowu 
Published: August 2023

AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder that usually manifests in childhood and is thought to be caused by a complex interaction of genetic, environmental, and immune factors. The majority of current ASD diagnostic methods rely on subjective behavioral observation and scale assessment, making early detection difficult. In this study, we confirmed that lysosomal-associated membrane protein 1 (LAMP1), a functional marker of immune cell activation and cytotoxic degranulation, was upregulated in ASD blood, brain cortex, and various genetic animal models or cells using bioinformatics approaches. The prognostic value of LAMP1 was investigated by correlating its expression with clinical ASD rating scales, and the receiver operating characteristic (ROC) curve analysis in ASD also revealed that it has a favorable diagnostic ability in distinguishing ASD from control cohort. According to gene set enrichment analysis (GSEA) results, LAMP1 correlated with genes that were enriched in natural kill and T cell immune function. Taking all of the evidence into account, we discovered that abnormal elevations of LAMP1 mRNA and protein in the blood of ASD children, may influence the development of ASD through its involvement in immune cell activity regulation. This report highlights a novel marker for ASD early detection as well as potential therapeutic targets.
Using domain adaptation for classification of healthy and disease conditions from mobile-captured images of standard 12-lead electrocardiograms
Authors: Gliner Vadim , Makarov Vladimir , Avetisyan Arutyun I. , Schuster Assaf , Yaniv Yael 
Published: August 2023

Abstract12-lead electrocardiogram (ECG) recordings can be collected in any clinic and the interpretation is performed by a clinician. Modern machine learning tools may make them automatable. However, a large fraction of 12-lead ECG data is still available in printed paper or image only and comes in various formats. To digitize the data, smartphone cameras can be used. Nevertheless, this approach may introduce various artifacts and occlusions into the obtained images. Here we overcome the challenges of automating 12-lead ECG analysis using mobile-captured images and a deep neural network that is trained using a domain adversarial approach. The net achieved an average 0.91 receiver operating characteristic curve on tested images captured by a mobile device. Assessment on image from unseen 12-lead ECG formats that the network was not trained on achieved high accuracy. We further show that the network accuracy can be improved by including a small number of unlabeled samples from unknown formats in the training data. Finally, our models also achieve high accuracy using signals as input rather than images. Using a domain adaptation approach, we successfully classified cardiac conditions on images acquired by a mobile device and showed the generalizability of the classification using various unseen image formats.
Pollution of the Niger Delta with total petroleum hydrocarbons, heavy metals and nutrients in relation to seasonal dynamics
Authors: Anyanwu Ihuoma N. , Beggel Sebastian , Sikoki Francis D. , Okuku Eric O. , Unyimadu John-Paul , Geist Juergen 
Published: August 2023

AbstractThe African Niger Delta is among the world’s most important wetlands in which the ecological effects of intensive oil exploitation and global change are not well documented. We characterized the seasonal dynamics and pollution with total-petroleum-hydrocarbons (TPHs), heavy-metals (HMs) and nutrient-loads in relation to climate-driven variables. High TPH concentrations up to 889 mg/L and HMs up to 13.119 mg/L were found in water samples, with pronounced spatio-temporal variation throughout the year. HM pollution index and contamination factor indicate serious ecological and human health hazards, especially for Cd, Cu, Hg, and Ni. Significant differences in TPHs/HMs were observed between sites and seasons, with correlations between TPHs-HMs, and climate-variables and TPHs-HMs. Nutrient levels, turbidity, salinity, temperature, and SO42- were high and interlinked with the variability of TPHs/HMs being greatest during wet season. These findings suggest an urgent need for improved pollution control in the Niger Delta taking into account the observed spatio-temporal variation and the exacerbation of effects in light of climate change. Given the high levels of contamination, further assessments of exposure effects and bioaccumulation in biota should include future climate change scenarios and effects on humans who intensively depend on the system for drinking water, food supply and livelihood.
RNA-Seq reveals ACTH-induced steroid hormone pathway participating in goat adrenal gland response to castration
Authors: Jing Haijing , Ding Yi , Jiang Xunping , Liu Guiqiong , Sha Yiyu 
Published: August 2023

AbstractThe content of androgen from adrenal is elevated under castration, and the mechanisms of compensatory secretion of adrenal androgen remain unknown. This study was designed to compare the transcript profiles between adrenals from noncastrated, orchiectomized and immunocastrated Yiling goats. Fifteen goats were randomly divided into three groups: pVAX-asd injection (control) group, pVAX-B2L-(G4S)3-kisspeptin-54-asd immunization (PBK-asd) group, and surgical castration (SC) group. Subsequently, serum was collected every two weeks after the initial immunization for hormone assays. At week 14 after immunization, adrenal glands were collected for transcriptome sequencing and qPCR. Serum testosterone concentration was significantly reduced in PBK-asd and SC group, demonstrating the effectiveness of castration. Both surgical and immunized castration resulted in adrenal hyperplasia, and thickness of adrenal cortex elevated. The specific genes involving castration were enriched in many pathways, including Steroid hormone biosynthesis pathway. The adrenocorticotropic hormone (ACTH), which promotes the production of adrenal steroids, and dehydroepiandrosterone (DHEA), a steroid hormone secreted by adrenal glands, both increased after castration. Further construction of co-expression network for transcription genes and traits (including adrenal weight and cortex thickness, ACTH and DHEA concentration) showed that the trait-related genes were enriched in multiple steroid-related pathways. These results showed that adrenal compensatory hyperplasia and androgen secretion caused by castration may involve in ACTH-induced steroid hormone synthesis.
Modern PID/FOPID controllers for frequency regulation of interconnected power system by considering different cost functions
Authors: Mohamed Mohamed Ahmed Ebrahim , Jagatheesan K. , Anand B. 
Published: August 2023

AbstractThis article presents frequency regulation of an interconnected three-area power system (Thermal + Wind + Hydro). Fractional Order PID (FOPID) and Proportional-Integral-Derivative (PID) controllers are applied as subsidiary regulators to control the electrical power interconnected system at the time of sudden load variation. To accomplish this study, Genetic Algorithm (GA), Grey Wolf Optimizer (GWO), Sine Cosine Inspired Algorithm (SCIA) and Atom Search Inspired Algorithm (ASIA) are implemented to optimize the secondary regulators' gains (PID and FOPID) by considering various cost functions such as Integral Absolute Error (IAE), Integral Time Absolute Error (ITAE), Integral Square Error (ISE), and Integral Time Square Error (ITSE). Performance analysis in this work is conducted using various cost functions based on GA, GWO, SCIA and ASIA. The comparative analysis of the attained results reveals that GWO-PID and ASIA–PID settle at (83.83 s) and (30.31 s), respectively and ASIA-FOPID at (25.12 s). The controllers based on ITSE as a cost function outperform the comptrollers with other cost functions (ISE, IAE and ITAE). In addition, the ISE-based GA–PID and SCIA–PID settle at (113.92 s) and (35.1 s), respectively and SCIA-FOPID at (24.78 s). The ISE-based regulators yield improved response equated to other cost functions (ITSE, IAE and ITAE) optimized controllers. The robustness test also is carried out to validate the effectiveness of the proposed optimization techniques by changing the system parameters within ± 25% and ± 50% from their nominal values as well as changing the load pattern.
The kisspeptin-1 receptor antagonist peptide-234 aggravates uremic cardiomyopathy in a rat model
Authors: Dinh Hoa , Kovács Zsuzsanna Z. A. , Márványkövi Fanni , Kis Merse , Kupecz Klaudia , Szűcs Gergő , Freiwan Marah , Lauber Gülsüm Yilmaz , Acar Eylem , Siska Andrea , Ibos Katalin Eszter , Bodnár Éva , Kriston András , Kovács Ferenc , Horváth Péter , Földesi Imre , Cserni Gábor , Podesser Bruno K. , Pokreisz Peter , Kiss Attila , Dux László , Csabafi Krisztina , Sárközy Márta 
Published: August 2023

AbstractUremic cardiomyopathy is characterized by diastolic dysfunction, left ventricular hypertrophy (LVH), and fibrosis. Dysregulation of the kisspeptin receptor (KISS1R)-mediated pathways are associated with the development of fibrosis in cancerous diseases. Here, we investigated the effects of the KISS1R antagonist peptide-234 (P234) on the development of uremic cardiomyopathy. Male Wistar rats (300–350 g) were randomized into four groups: (i) Sham, (ii) chronic kidney disease (CKD) induced by 5/6 nephrectomy, (iii) CKD treated with a lower dose of P234 (ip. 13 µg/day), (iv) CKD treated with a higher dose of P234 (ip. 26 µg/day). Treatments were administered daily from week 3 for 10 days. At week 13, the P234 administration did not influence the creatinine clearance and urinary protein excretion. However, the higher dose of P234 led to reduced anterior and posterior wall thicknesses, more severe interstitial fibrosis, and overexpression of genes associated with left ventricular remodeling (Ctgf, Tgfb, Col3a1, Mmp9), stretch (Nppa), and apoptosis (Bax, Bcl2, Casp7) compared to the CKD group. In contrast, no significant differences were found in the expressions of apoptosis-associated proteins between the groups. Our results suggest that the higher dose of P234 hastens the development and pathophysiology of uremic cardiomyopathy by activating the fibrotic TGF-β-mediated pathways.