bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell, whole-embryo phenotyping of mammalian developmental disorders
Authors: Huang Xingfan , Henck Jana , Qiu Chengxiang , Sreenivasan Varun K. A. , Balachandran Saranya , Amarie Oana V. , Hrabě de Angelis Martin , Behncke Rose Yinghan , Chan Wing-Lee , Despang Alexandra , Dickel Diane E. , Duran Madeleine , Feuchtinger Annette , Fuchs Helmut , Gailus-Durner Valerie , Haag Natja , Hägerling Rene , Hansmeier Nils , Hennig Friederike , Marshall Cooper , Rajderkar Sudha , Ringel Alessa , Robson Michael , Saunders Lauren M. , da Silva-Buttkus Patricia , Spielmann Nadine , Srivatsan Sanjay R. , Ulferts Sascha , Wittler Lars , Zhu Yiwen , Kalscheuer Vera M. , Ibrahim Daniel M. , Kurth Ingo , Kornak Uwe , Visel Axel , Pennacchio Len A. , Beier David R. , Trapnell Cole , Cao Junyue , Shendure Jay , Spielmann Malte
Published: November 2023

Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be ‘decomposable’ through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.
The social and structural architecture of the yeast protein interactome
Authors: Michaelis André C. , Brunner Andreas-David , Zwiebel Maximilian , Meier Florian , Strauss Maximilian T. , Bludau Isabell , Mann Matthias
Published: November 2023

Cellular functions are mediated by protein–protein interactions, and mapping the interactome provides fundamental insights into biological systems. Affinity purification coupled to mass spectrometry is an ideal tool for such mapping, but it has been difficult to identify low copy number complexes, membrane complexes and complexes that are disrupted by protein tagging. As a result, our current knowledge of the interactome is far from complete, and assessing the reliability of reported interactions is challenging. Here we develop a sensitive high-throughput method using highly reproducible affinity enrichment coupled to mass spectrometry combined with a quantitative two-dimensional analysis strategy to comprehensively map the interactome of Saccharomyces cerevisiae. Thousand-fold reduced volumes in 96-well format enabled replicate analysis of the endogenous GFP-tagged library covering the entire expressed yeast proteome1. The 4,159 pull-downs generated a highly structured network of 3,927 proteins connected by 31,004 interactions, doubling the number of proteins and tripling the number of reliable interactions compared with existing interactome maps2. This includes very-low-abundance epigenetic complexes, organellar membrane complexes and non-taggable complexes inferred by abundance correlation. This nearly saturated interactome reveals that the vast majority of yeast proteins are highly connected, with an average of 16 interactors. Similar to social networks between humans, the average shortest distance between proteins is 4.2 interactions. AlphaFold-Multimer provided novel insights into the functional roles of previously uncharacterized proteins in complexes. Our web portal (www.yeast-interactome.org) enables extensive exploration of the interactome dataset.
A chromosome-level genome assembly of the Knoxia roxburghii (Rubiaceae)
Authors: Zhang Yingmin , Zhang Fan , Jin Ling , Zhang Ticao , Pu Xinying , Qiu Bin , Li Guodong
Published: November 2023

Knoxia roxburghii is a well-known medicinal plant that is widely distributed in southern China and Southeast Asia. Its dried roots, known as hongdaji in traditional Chinese medicine, are used to treat a range of diseases, including cancers, carbuncles, and ascites. In this study, we report a de novo chromosome-level genome sequence for this diploid plant, which has a length of approximately 446.30 Mb with a contig N50 size of 42.26 Mb and scaffold N50 size of 44.38 Mb. Approximately 99.78% of the assembled sequences were anchored to 10 pseudochromosomes and 3 gapless assembled chromosomes were included in this assembly. A total of 24,507 genes were annotated, along with 68.92% of repetitive elements. Overall, our results will facilitate further active component biosynthesis for K. roxburghii and provide insights for future functional genomic studies and DNA-informed breeding.
Physiological response and drought resistance evaluation of Gleditsia sinensis seedlings under drought-rehydration state
Authors: Liu Fuhua , Zhao Yang , Wang Xiurong , Wang Biao , Xiao Feng , He Kequan
Published: November 2023

G. sinensis is a crucial tree species in China, possessing important economic and ecological value, and having a wide geographical distribution. G. sinensis seedlings is highly vulnerable to the drought-rehydration-drought cycle during their growth, and there is a lack of quantitative and systematic research on the physiological mechanisms of drought resistance and rehydration in G. sinensis. There is also a lack of good drought-resistant families and reliable methods for evaluating drought resistance, which severely hinders the selection and promotion of drought-resistant G. sinensis families and the industry's development. Therefore, this study selection 58 families seedlings of G. sinensis to drought stress and rehydration using an artificial simulated water control method in potted seedlings. The aim was to compare the effects of different levels of drought and rehydration on the growth and physiological indices of seedlings from different families. Identification of drought-resistant families and dependable drought related indices and techniques, the explanation of divergence in drought stress effects on various drought-resistant seedlings and the mechanisms underpinning growth and physiological responses, and the provision of theoretical reference for G. sinensis drought-resistant variety selection and cultivation. The Drought Resistance Index (DRI) served as the primary indicator, supplemented by growth, leaf morphology, and photosynthetic physiological indicators, to thoroughly assess and identify five distinct drought tolerant taxa while also selecting five representative families. Soluble protein (SP), proline (Pro), and malondialdehyde (MDA) contents, as well as the activities of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) in seedlings from the five families, increased as the degree of drought intensified. The highest values were appeared during periods of severe drought, and gradually decreased after subsequent rehydration. Principal component analysis (PCA) revealed MDA and soluble sugars (SS) as the primary predictors of drought and rehydration response in G. sinensis seedlings respectively. Changes in osmoregulatory substance content and increased antioxidant enzyme activity may be crucial for responding to drought tolerance mechanisms. Leaf morphological indicators, seedling height, soil plant analysis development (SPAD) value, photosynthetic indicators, and MDA are dependable parameters for assessing the drought tolerance of G. sinensis seedlings. When assessing the drought-resistance of seedlings using physiological indicators such as photosynthesis, a comprehensive analysis should incorporate multiple indicators and methods. This evaluation approach could serve as a reference for screening exceptional drought-resistant families of G. sinensis.
Innovative spectrofluorometric method for determination of harmaline and harmine in different matrices
Authors: Abdelazim Ahmed H. , Algarni Majed A. , Almalki Atiah H.
Published: November 2023

Harmaline and harmine are naturally occurring closely related β-carboline alkaloids found in Peganum and Banisteriopsis plants. They have historical significance in traditional practices due to their potential psychoactive and therapeutic properties. Herein, a highly sensitive spectrofluorometric method was developed for the quantifying of harmaline and harmine in diverse matrices, including pure forms, seed samples, and spiked plasma. The procedures lie in addressing the challenge of overlapping fluorescence spectra exhibited by harmaline and harmine through the incorporation of hydroxypropyl-β-cyclodextrin, altering their chemical properties and fluorescence characteristics. Synchronous fluorescence measurements coupled with first derivative mathematical technique make it possible to distinguish between the harmaline and harmine at 419 and 456 nm, respectively. The method effectiveness is demonstrated through spectral analysis, optimization of the measurement conditions, adopting validation parameters and application to the pure form, seed samples and spiked human plasma. This methodology facilitates accurate determination of these alkaloids over the concentration range of 10─200 ng/mL. Thus, the developed approach provides a robust mean for the precise determination of harmaline and harmine, contributing to analytical chemistry's ongoing efforts to address complex challenges in quantification across diverse matrices.
Nesfatin-1 protects the reproductive health of male Sprague Dawley rats exposed to blue and white LED lights
Authors: Chekani Azar Saeid , Sabuncuoğlu Çoban Nilüfer
Published: November 2023

There is little information on the effects of exposure to light emitting diode (LED) illumination on the welfare of laboratory animals. Nesfatin-1, a satiety-regulation peptide present in various tissues, is found in the central nervous system and participates in the stress response. The present study investigated whether exposure to blue and white LED lights for 14 weeks affected growth and reproductive, biochemical and histopathological parameters in male Sprague Dawley (SD) rats as well as whether subcutaneous (SC) injection of nesfatin-1 (0.5 mg/kg bodyweight) in the last two weeks of the experimental period alleviated these effects. Forty male SD rats (21 days of age) were randomly allotted to 6 groups. The animals were exposed to routine fluorescent light (the control [C] and control + sesame oil [CS] groups) or blue/white LEDs (the blue-LED and white-LED groups), accompanied by nesfatin-1 administration (the blue-LED-N1 and white-LED-N1 groups). White-LED rats had significantly higher testis weights (p < 0.05) than control and blue-LED rats. Serum melatonin levels were significantly lower in blue-LED rats, but nesfatin-1 injection rescued melatonin levels in blue-LED-N1 rats (p < 0.05). Blue-LED rats showed the highest serum nesfatin-1 levels, but nesfatin-1 injection decreased nesfatin-1 levels in blue-LED-N1 rats (p < 0.0001). Blue-LED rats showed a significant reduction in sperm motility compared to the other groups (p < 0.0001). White and blue LED exposure caused significant negative histopathological changes in the testes, but nesfatin-1 administration reduced edema in the intertubular spaces, hyperemia in the interstitial cells, degeneration of spermatocytes and thinning of the tubular wall in the testicular tissues; these restorative effects were larger in blue-LED-N1 rats than white-LED-N1 rats. Blue and white LED exposures had negative effects on melatonin levels, testis weights and tissue health. Nesfatin-1 alleviated some of the negative effects of LED lighting.
Green and sustainable synthesis of CaO nanoparticles: Its solicitation as a sensor material and electrochemical detection of urea
Authors: Naik T. S. Sunil Kumar , Singh Simranjeet , Narasimhappa Pavithra , Varshney Radhika , Singh Joginder , Khan Nadeem A , Zahmatkesh Sasan , Ramamurthy Praveen C. , Shehata Nabila , Kiran G. N. , Sunil K.
Published: November 2023

Urea is recognized as one of the most frequently used adulterants in milk to enhance artificial protein content, and whiteness. Drinking milk having high urea concentrations which causes innumerable health disputes like ulcers, indigestion, and kidney-related problems. Therefore, herein, a simple and rapid electroanalytical platform was developed to detect the presence of urea in milk using a modified electrode sensor. Calcium oxide nanoparticles (CaO NPs) were green synthesized and used as a catalyst material for developing the sensor. Synthesized materials formation was confirmed by different techniques like FTIR, UV–visible, XRD, SEM–EDX, and Raman spectroscopy. The carbon paste electrode (CPE) was modified using the CaO NPs and used as a working electrode during the analysis followed by cyclic voltammetry and differential pulse voltammetry (DPV) techniques. The fabricated calcium oxide modified carbon paste electrode (CaO/CPE) successfully detected the presence of urea in the lower concentration range (lower limit of detection (LLOD) = 0.032 µM) having a wide linear detection range of 10–150 µM. Adsorption-controlled electrode process was achieved at the scan rate variation parameter. The leading parameters like the selectivity, repeatability, and stability of the CaO/CPE were investigated. The relative standard deviation of sensor was ± 3.8% during the interference and stability study.
Causal influence of muscle weakness on cardiometabolic diseases and osteoporosis
Authors: Mou Xiaoqing , He Bin , Zhang Muzi , Zhu Yong , Ou Yunsheng , Chen Xiaojun
Published: November 2023

The causal roles of muscle weakness in cardiometabolic diseases and osteoporosis remain elusive. This two-sample Mendelian randomization (MR) study aims to explore the causal roles of muscle weakness in the risk of cardiometabolic diseases and osteoporosis. 15 single nucleotide polymorphisms (SNPs, P < 5 × 10−8) associated with muscle weakness were used as instrumental variables. Genetic predisposition to muscle weakness led to increased risk of coronary artery disease (inverse variance weighted [IVW] analysis, beta-estimate: 0.095, 95% confidence interval [CI]: 0.023 to 0.166, standard error [SE]:0.036, P-value = 0.009) and reduced risk of heart failure (weight median analysis, beta-estimate: − 0.137, 95% CI − 0.264 to − 0.009, SE:0.065, P-value = 0.036). In addition, muscle weakness may reduce the estimated bone mineral density (eBMD, weight median analysis, beta-estimate: − 0.059, 95% CI − 0.110 to − 0.008, SE:0.026, P-value = 0.023). We found no MR associations between muscle weakness and atrial fibrillation, type 2 diabetes or fracture. This study provides robust evidence that muscle weakness is causally associated with the incidence of coronary artery disease and heart failure, which may provide new insight to prevent and treat these two cardiometabolic diseases.
Exploratory graph analysis on the Connor–Davidson Resilience Scale (CD-RISC) among older adults in China
Authors: Wang Yujie , Xu Jixiang , Yang Shitong , Jiang Junjia , Gao Junling
Published: November 2023

It is important for healthy aging to understand resilience in depth. This study aims to examine the dimensional structure underlying the Connor–Davidson Resilience Scale (CD-RISC) among Chinese older adults. Exploratory Graph Analysis (EGA) was used to evaluate the dimensional structure of CD-RISC in two large samples: training sample (n = 11,493) and cross-validation sample (n = 7662). Then, Confirmatory Factor Analysis (CFA) was used to compare the fit of the theoretical dimensions with the EGA dimensions. Finially, Generalized Linear Model was used to examine the association between resilience scores and self-rated health (SRH) after controlling other covariates in order to evaluate the predictive value of the EGA dimensions. The EGA indicated two demensions(named foresight and self-adjustment) of the 25-item CD-RISC. The CFA comparison found that the two-demension structure of CD-RISC fit significantly better than the theoretical three-demension structure. After controlling for sociodemographic characteristics, generalized linear model showed that the EGA dimensions has better protective value with SRH. Compared with older adults with lowest quartile of foresight, those with second (odds ratio, OR = 0.68, 95% CI = 0.62 ~ 0.75), third (OR = 0.50, 95% CI = 0.45 ~ 0.56) and fourth quartile (OR = 0.42, 95% CI  =  0.37 ~ 0.48) of foresight had lower odds ratio of poor SRH. Similarly, older adults with the second (OR = 1.11, 95% CI = 1.01 ~ 1.23) and fourth (OR = 0.79, 95% CI = 0.69 ~ 0.90) quartile of self-adjustment also had lower OR of poor SRH than those with lowest quartile of self-adjustment. These findings show that EGA outperforms the traditional methods, which may be helpful to understand resilience deeply. CD-RISC should be interpreted into two aspects among community-dwelling older adults in China, highlighting the significance of the practical value and cultural context of resilience.
Algorithmic assessment of shoulder function using smartphone video capture and machine learning
Authors: Darevsky David M. , Hu Daniel A. , Gomez Francisco A. , Davies Michael R. , Liu Xuhui , Feeley Brian T.
Published: November 2023

Tears within the stabilizing muscles of the shoulder, known as the rotator cuff (RC), are the most common cause of shoulder pain—often presenting in older patients and requiring expensive advanced imaging for diagnosis. Despite the high prevalence of RC tears within the elderly population, there is no previously published work examining shoulder kinematics using markerless motion capture in the context of shoulder injury. Here we show that a simple string pulling behavior task, where subjects pull a string using hand-over-hand motions, provides a reliable readout of shoulder mobility across animals and humans. We find that both mice and humans with RC tears exhibit decreased movement amplitude, prolonged movement time, and quantitative changes in waveform shape during string pulling task performance. In rodents, we further note the degradation of low dimensional, temporally coordinated movements after injury. Furthermore, a logistic regression model built on our biomarker ensemble succeeds in classifying human patients as having a RC tear with > 90% accuracy. Our results demonstrate how a combined framework bridging animal models, motion capture, convolutional neural networks, and algorithmic assessment of movement quality enables future research into the development of smartphone-based, at-home diagnostic tests for shoulder injury.
Variable sensitivity multimaterial robotic e-skin combining electronic and ionic conductivity using electrical impedance tomography
Authors: Costa Cornellà Aleix , Hardman David , Costi Leone , Brancart Joost , Van Assche Guy , Iida Fumiya
Published: November 2023

Electronic skins (e-skins) aim to replicate the capabilities of human skin by integrating electronic components and advanced materials into a flexible, thin, and stretchable substrate. Electrical impedance tomography (EIT) has recently been adopted in the area of e-skin thanks to its robustness and simplicity of fabrication compared to previous methods. However, the most common EIT configurations have limitations in terms of low sensitivities in areas far from the electrodes. Here we combine two piezoresistive materials with different conductivities and charge carriers, creating anisotropy in the sensitive part of the e-skin. The bottom layer consists of an ionically conducting hydrogel, while the top layer is a self-healing composite that conducts electrons through a percolating carbon black network. By changing the pattern of the top layer, the resulting distribution of currents in the e-skin can be tuned to locally adapt the sensitivity. This approach can be used to biomimetically adjust the sensitivities of different regions of the skin. It was demonstrated how the sensitivity increased by 500% and the localization error reduced by 40% compared to the homogeneous case, eliminating the lower sensitivity regions. This principle enables integrating the various sensing capabilities of our skins into complex 3D geometries. In addition, both layers of the developed e-skin have self-healing capabilities, showing no statistically significant difference in localization performance before the damage and after healing. The self-healing bilayer e-skin could recover full sensing capabilities after healing of severe damage.
Optimized design of permanent magnet for disk permanent magnet governor
Authors: Xu Manman , Fu Yili , Shao Long , Wang Xiangdong , Lu Yimin , Cao Chuqing
Published: November 2023

To research the magnetic field and mechanical characteristics of the permanent magnet governor, the static magnetic field of the sector permanent magnet is analyzed by the molecular current method in the permanent magnet governor. The magnetic flux distribution is acquired at any spatial position. Comparing the analytical value with the simulation value, the results show that they are basically consistent. Based on the analytical formula, the influence of the radial position, radial length, thickness, and pole number on the magnetic induction intensity of the permanent magnet governor is studied. Thus, it provides the theoretical reference for the structural optimized design. At the same time, a test bench was set up to measure the magnetic induction intensity. The calculation and experimental results show that the magnetic induction strength of the permanent magnet is increased by 27.5%, the axial component of the air gap flux density is increased by 14.3%, and the permanent magnet material is reduced by 7.84%.
A blocking ELISA based on virus-like nanoparticles chimerized with an antigenic epitope of ASFV P54 for detecting ASFV antibodies
Authors: Huang Chaohua , Cao Chenfu , Xu Zhichao , Lin Yanxing , Wu Jiang , Weng Qiaoyu , Liu Zheng , Jin Ye , Chen Peng , Hua Qunyi
Published: November 2023

African swine fever virus (ASFV) is a highly lethal pathogen of domestic and wild pigs. Due to no vaccines or drugs available, early accurate diagnosis and eradication of infected animals are the most important measures for ASFV prevention and control. Bluetongue virus (BTV) core-like particles (CLPs) are non-infectious hollow nanoparticles assembled from the BTV VP3 and VP7 proteins, which could be used as a platform for presenting foreign epitopes. In this study, the secondary structure of BTV VP7 protein was analyzed and predicted using the IEDB Analysis resource. Based on the prediction results of the VP7 protein, the chimeric CLPs with an ASFV P54 epitope were successfully prepared through the BAC-to-BAC baculovirus expression system and sucrose gradient centrifugation. Based on the chimeric CLPs and mAb 2E4 against AFSV P54 epitope, a blocking ELISA for detecting AFSV antibodies was established, and its reaction conditions were optimized. Through comprehensive evaluation of the method, the results showed the chimeric CLPs-based blocking ELISA displayed the best detection performance, with an AUC of 0.9961, a sensitivity of 97.65%, and a specificity of 95.24% in ROC analysis. Compared with western blot and a commercial c-ELISA for detecting anti-ASFV antibodies, this method had an excellent agreement of 96.35% (kappa value = 0.911) and 97.76% (kappa value = 0.946) with the other tests, respectively. This ELISA also had high repeatability, with CV < 10%, and no cross-reaction with the serum antibodies against other swine viruses or Orbivirus. In brief, this was the first report on developing a blocking ELISA based on virus-like nanoparticles chimerized with an antigenic epitope of ASFV P54 for serological diagnosis of ASFV.
Microbial associates of an endemic Mediterranean seagrass enhance the access of the host and the surrounding seawater to inorganic nitrogen under ocean acidification
Authors: Pfister Catherine A. , Cardini Ulisse , Mirasole Alice , Montilla Luis M. , Veseli Iva , Gattuso Jean-Pierre , Teixido Nuria
Published: November 2023

Seagrasses are important primary producers in oceans worldwide. They live in shallow coastal waters that are experiencing carbon dioxide enrichment and ocean acidification. Posidonia oceanica, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we tested whether microbial metabolisms associated with P. oceanica and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we showed that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that the presence of P. oceanica enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6–17.4 with the greatest effect at CO2 vent sites. However, microbial ammonification was reduced at lower pH, suggesting that future ocean climate change will compromise this microbial process. Thus, the seagrass holobiont enhances water column productivity, even in the context of ocean acidification.
A simulation study to investigate an extension to the point cluster technique
Authors: Karmarkar Vivek , Vitali Rachel V.
Published: November 2023

Joint kinematics are an important and widely utilized metric in quantitative human movement analysis. Typically, trajectory data for skin-mounted markers are collected using stereophotogrammetry, sometimes referred to as optical motion capture, and processed using various mathematical models to estimate joint kinematics (e.g., angles). Among the various sources of noise in optical motion capture data, soft tissue artifacts (STAs) remain a critical source of error. This study investigates the performance of the point cluster technique (PCT), an extension of the PCT using perturbation theory (PCT-PT), and singular value decomposition least squares (SVD-LS) method (as a reference) for 100 different marker configurations on the thigh and shank during treadmill walking. This study provides additional evidence that the PCT method is significantly limited by the underlying mathematical constraints governing its optimization process. Furthermore, the results suggest the PCT-PT method outperforms the PCT method across all performance metrics for both body segments during the entire gait cycle. For position-based metrics, the PCT-PT method provides better estimates than the SVD-LS method for the thigh during majority of the stance phase and provides comparable estimates for the shank during the entire gait cycle. For knee angle estimates, the PCT-PT method provides equivalent results as the SVD-LS method.
Evaluation of retinal vascularization in retinopathy of prematurity regressed after intravitreal ranibizumab monotherapy or without treatment based on fluorescein angiography
Authors: Wu Lei , Li Manhong , Wang Liang , Yan Hongxiang , Zhou Ziyi , Fan Jing , Zhou Yi , Gou Kaili , Guo Changmei , Wang Yusheng , Zhang Zifeng
Published: November 2023

To investigate the fluorescein angiography (FA) findings and compare the extent of retinal vascularization in retinopathy of prematurity (ROP), recovered after intravitreal ranibizumab (IVR) monotherapy and those regressed spontaneously. Infants with a history of ROP who underwent FA between April 2018 and November 2021 were retrospectively included. The patients were divided into two groups based on whether they had received IVR (IVR group) or had ROP that regressed spontaneously without treatment (untreated group). The differences between the two groups in zone II ROP were also compared, to equalize the subgroups as much as possible in terms of disease severity. FA findings were recorded. The extent of vascularization was measured by the ratio of the distance from the center of the disk to the border of the vascularized zone (DB) and the distance from the center of the disk to the center of the fovea (DF). The width of the persistent avascular retina (PAR) was counted by disc diameters (DD). One hundred and ten eyes of 55 infants were included in the IVR group and 76 eyes of 38 babies in the untreated group. The ratio of abnormal shape of vessels was significantly higher in the IVR group than in the untreated group (50.9% vs. 35.5%; P = 0.038), while the linear choroidal filling pattern, tortuosity of vessels over the posterior pole, dye leakage, anomalous branching of vessels, circumferential vessels, arteriovenous shunt, abnormal capillary bed, and macular abnormalities were similarly. There was a smaller temporal DB/DF ratio (4.48 vs. 4.63; P = 0.003) and greater PAR (2.63 vs. 1.76; P < 0.001) in the IVR group compared to the untreated group. In zone II ROP, the progression of retinal vascularization was significantly larger in the IVR group than that in the untreated group (P = 0.003), while no statistical differences were observed in FA features, the DB/DF ratio, and PAR between the two subgroups. The residual vascular abnormalities and PAR may be common results of ROP regression. The DB/DF ratio of 4.0 temporally and 3.3 nasally could be used as the preliminary indicators for safe retinal vascularization in the completion of ROP regression.
Tailoring the dispersion characteristics in planar arrays of discrete and coalesced split ring resonators
Authors: Spanos Ioannis , Stevens Christopher John , Solymar Laszlo , Shamonina Ekaterina
Published: November 2023

In this report, the coupling and dispersion characteristics of discrete and coalesced square resonators was investigated in the MHz regime. Resonators with one and three gaps were considered. When the resonators are not in direct contact, the number of gaps has little effect upon the total coupling, which is negative. When the resonators are connected so that they share one side, the coupling can change drastically depending on the number of gaps. In particular, when the shared side has a gap, the total coupling coefficient switches to positive values, making it possible for forward travelling waves to propagate on arrays. Experimental, numerical and analytical data verify this behaviour.
Prediction of ovulation: new insight into an old challenge
Authors: Maman Ettie , Adashi Eli Y. , Baum Micha , Hourvitz Ariel
Published: November 2023

Ultrasound monitoring and hormonal blood testing are considered by many as an accurate method to predict ovulation time. However, uniform and validated algorithms for predicting ovulation have yet to be defined. Daily hormonal tests and transvaginal ultrasounds were recorded to develop an algorithm for ovulation prediction. The rupture of the leading ovarian follicle was a marker for ovulation day. The model was validated retrospectively on natural cycles frozen embryo transfer cycles with documented ovulation. Circulating levels of LH or its relative variation failed, by themselves, to reliably predict ovulation. Any decrease in estrogen was 100% associated with ovulation emergence the same day or the next day. Progesterone levels > 2 nmol/L had low specificity to predict ovulation the next day (62.7%), yet its sensitivity was high (91.5%). A model for ovulation prediction, combining the three hormone levels and ultrasound was created with an accuracy of 95% to 100% depending on the combination of the hormone levels. Model validation showed correct ovulation prediction in 97% of these cycles. We present an accurate ovulation prediction algorithm. The algorithm is simple and user-friendly so both reproductive endocrinologists and general practitioners can use it to benefit their patients.
Quantum-anomalous-Hall current patterns and interference in thin slabs of chiral topological superconductors
Authors: Di Miceli Daniele , Serra Llorenç
Published: November 2023

The chiral topological superconductor, which supports propagating nontrivial edge modes while maintaining a gapped bulk, can be realized hybridizing a quantum-anomalous-Hall thin slab with an ordinary s-wave superconductor. We show that by sweeping the voltage bias in a normal-hybrid-normal double junction, the pattern of electric currents in the normal leads spans three main regimes. From single-mode edge-current quantization at low bias, to double-mode edge-current oscillations at intermediate voltages and up to diffusive bulk currents at larger voltages. Observing such patterns by resolving the spatial distribution of the local current in the thin slab could provide additional evidence, besides the global conductance, on the physics of chiral topological superconductors.
High-sensitivity deuterium metabolic MRI differentiates acute pancreatitis from pancreatic cancers in murine models
Authors: Montrazi Elton T. , Sasson Keren , Agemy Lilach , Peters Dana C. , Brenner Ori , Scherz Avigdor , Frydman Lucio
Published: November 2023

Deuterium metabolic imaging (DMI) is a promising tool for investigating a tumor’s biology, and eventually contribute in cancer diagnosis and prognosis. In DMI, [6,6′-2H2]-glucose is taken up and metabolized by different tissues, resulting in the formation of HDO but also in an enhanced formation of [3,3′-2H2]-lactate at the tumor site as a result of the Warburg effect. Recent studies have shown DMI’s suitability to highlight pancreatic cancer in murine models by [3,3′-2H2]-lactate formation; an important question is whether DMI can also differentiate between these tumors and pancreatitis. This differentiation is critical, as these two diseases are hard to distinguish today radiologically, but have very different prognoses requiring distinctive treatments. Recent studies have shown the limitations that hyperpolarized MRI faces when trying to distinguish these pancreatic diseases by monitoring the [1-13C1]-pyruvate→[1-13C1]-lactate conversion. In this work, we explore DMI’s capability to achieve such differentiation. Initial tests used a multi-echo (ME) SSFP sequence, to identify any metabolic differences between tumor and acute pancreatitis models that had been previously elicited very similar [1-13C1]-pyruvate→[1-13C1]-lactate conversion rates. Although ME-SSFP provides approximately 5 times greater signal-to-noise ratio (SNR) than the standard chemical shift imaging (CSI) experiment used in DMI, no lactate signal was observed in the pancreatitis model. To enhance lactate sensitivity further, we developed a new, weighted-average, CSI-SSFP approach for DMI. Weighted-average CSI-SSFP improved DMI’s SNR by another factor of 4 over ME-SSFP—a sensitivity enhancement that sufficed to evidence natural abundance 2H fat in abdominal images, something that had escaped the previous approaches even at ultrahigh (15.2 T) MRI fields. Despite these efforts to enhance DMI’s sensitivity, no lactate signal could be detected in acute pancreatitis models (n = 10; [3,3′-2H2]-lactate limit of detection < 100 µM; 15.2 T). This leads to the conclusion that pancreatic tumors and acute pancreatitis may be clearly distinguished by DMI, based on their different abilities to generate deuterated lactate.
Prediction of alternative pre-mRNA splicing outcomes
Authors: Najjar Rayan , Mustelin Tomas
Published: November 2023

To understand the biological impact of alternative pre-mRNA splicing, it is vital to know which exons are involved, what protein domains they encode, and how the translated isoforms differ. Therefore, we developed a computational pipeline (RiboSplitter) focused on functional effect prediction. It builds on event-based alternative splicing detection with additional filtering steps leading to more efficient statistical testing, and with detection of isoform-specific protein changes. A key methodological advance is reading frame prediction by translating exonic DNA in all possible frames, then finding a single open reading frame, or a single frame with matches to known proteins of the gene. This allowed unambiguous translation in 93.9% of alternative splicing events when tested on RNA-sequencing data of B cells from Sjögren’s syndrome patients. RiboSplitter does not depend on reference annotations and translates events even when one or both isoform(s) are novel (unannotated). RiboSplitter’s visualizations illustrate each event with translation outcomes, show event location within the gene, and align exons to protein domains.
Modeling personalized heart rate response to exercise and environmental factors with wearables data
Authors: Nazaret Achille , Tonekaboni Sana , Darnell Gregory , Ren Shirley You , Sapiro Guillermo , Miller Andrew C.
Published: November 2023

Heart rate (HR) response to workout intensity reflects fitness and cardiorespiratory health. Physiological models have been developed to describe such heart rate dynamics and characterize cardiorespiratory fitness. However, these models have been limited to small studies in controlled lab environments and are challenging to apply to noisy—but ubiquitous—data from wearables. We propose a hybrid approach that combines a physiological model with flexible neural network components to learn a personalized, multidimensional representation of fitness. The physiological model describes the evolution of heart rate during exercise using ordinary differential equations (ODEs). ODE parameters are dynamically derived via a neural network connecting personalized representations to external environmental factors, from area topography to weather and instantaneous workout intensity. Our approach efficiently fits the hybrid model to a large set of 270,707 workouts collected from wearables of 7465 users from the Apple Heart and Movement Study. The resulting model produces fitness representations that accurately predict full HR response to exercise intensity in future workouts, with a per-workout median error of 6.1 BPM [4.4–8.8 IQR]. We further demonstrate that the learned representations correlate with traditional metrics of cardiorespiratory fitness, such as VO2 max (explained variance 0.81 ± 0.003). Lastly, we illustrate how our model is naturally interpretable and explicitly describes the effects of environmental factors such as temperature and humidity on heart rate, e.g., high temperatures can increase heart rate by 10%. Combining physiological ODEs with flexible neural networks can yield interpretable, robust, and expressive models for health applications.
Population mobility data provides meaningful indicators of fast food intake and diet-related diseases in diverse populations
Authors: Horn Abigail L. , Bell Brooke M. , Bulle Bueno Bernardo García , Bahrami Mohsen , Bozkaya Burçin , Cui Yan , Wilson John P. , Pentland Alex , Moro Esteban , de la Haye Kayla
Published: November 2023

The characteristics of food environments people are exposed to, such as the density of fast food (FF) outlets, can impact their diet and risk for diet-related chronic disease. Previous studies examining the relationship between food environments and nutritional health have produced mixed findings, potentially due to the predominant focus on static food environments around people’s homes. As smartphone ownership increases, large-scale data on human mobility (i.e., smartphone geolocations) represents a promising resource for studying dynamic food environments that people have access to and visit as they move throughout their day. This study investigates whether mobility data provides meaningful indicators of diet, measured as FF intake, and diet-related disease, evaluating its usefulness for food environment research. Using a mobility dataset consisting of 14.5 million visits to geolocated food outlets in Los Angeles County (LAC) across a representative sample of 243,644 anonymous and opted-in adult smartphone users in LAC, we construct measures of visits to FF outlets aggregated over users living in neighborhood. We find that the aggregated measures strongly and significantly correspond to self-reported FF intake, obesity, and diabetes in a diverse, representative sample of 8,036 LAC adults included in a population health survey carried out by the LAC Department of Public Health. Visits to FF outlets were a better predictor of individuals’ obesity and diabetes than their self-reported FF intake, controlling for other known risks. These findings suggest mobility data represents a valid tool to study people’s use of dynamic food environments and links to diet and health.
Mixed quantum-classical dynamics for near term quantum computers
Authors: Bultrini Daniel , Vendrell Oriol
Published: November 2023

Mixed quantum-classical dynamics is a set of methods often used to understand systems too complex to treat fully quantum mechanically. Many techniques exist for full quantum mechanical evolution on quantum computers, but mixed quantum-classical dynamics are less explored. We present a modular algorithm for general mixed quantum-classical dynamics where the quantum subsystem is coupled with the classical subsystem. We test it on a modified Shin-Metiu model in the first quantization through Ehrenfest propagation. We find that the Time-Dependent Variational Time Propagation algorithm performs well for short-time evolutions and retains qualitative results for longer-time evolutions.
Exciton formation dynamics at the SiO2/Si interface
Authors: Revuelta Sergio , Cánovas Enrique
Published: November 2023

Excitons can operate as carriers for energy transduction in optoelectronics, and engineering their dynamics is of great interest. Here, we employ time-resolved terahertz spectroscopy to analyze exciton formation dynamics as a function of temperature for a (100) N-type silicon substrate passivated by native SiO2. By analyzing the frequency-resolved complex conductivity as a function of temperature we resolve the photophysics for the formation of free carriers into excitons. Notably, we observe a relatively long-lived ~300 ps transient population of free carriers at temperatures well below the Mott transition (4 K). We rationalize this by transient photophysics at the SiO2/N-type-Si surface, where holes localize and release under high injection conditions due to a transient surface photovoltage effect. We believe our results have implications for the design of excitonic-based electronic applications operating at cryogenic temperatures and accessed optically.
NaYF4:Yb/Ho upconversion nanoprobe incorporated gold nanoparticle (AuNP) based FRET immunosensor for the “turn-on” detection of cardiac troponin I
Authors: Abraham Merin K. , Madanan Anju S. , Varghese Susan , Shkhair Ali Ibrahim , Indongo Geneva , Rajeevan Greeshma , Vijila N. S. , George Sony
Published: November 2023

A “turn-on” NaYF4:Yb/Ho upconversion nanoprobe for the detection of cTnI is developed, in which AuNP is incorporated facilitating FRET mechanism. The probe exhibits appreciable sensitivity towards cTnI sensing in human serum.
Ultrasensitive electrochemical detection and inhibition evaluation of DNA methyltransferase based on cascade strand displacement amplification
Authors: Liu Ruizhi , Wang Yuge , Chai Hua , Miao Peng
Published: November 2023

An electrochemical sensing approach for ultrasensitive MTase activity assay is proposed based on cascade strand displacement polymerization after specific cleavage reaction in the methylated state.
Application of boehmite as a fiber coating for headspace solid-phase microextraction of chlorophenols from aqueous samples
Authors: Saraji Mohammad , Fouladi Monir , Mohammadnezhad Gholamhossein , Mehrafza Narges
Published: November 2023

The boehmite molecular structure was used as SPME fibers for the extraction of chlorophenols from water samples followed by GC-ECD.
Aptamer-based kinetically controlled DNA reactions coupled with metal–organic framework nanoprobes for sensitive detection of SARS-CoV-2 spike protein
Authors: Liu Yan , Zhou Yuanlin , Xu Wanting , Li Jiarong , Wang Shuning , Shen Xiaojia , Wen Xiaobin , Liu Li
Published: November 2023

A new aptamer-based fluorescence method is developed for SARS-CoV-2 spike protein detection based on using kinetically controlled DNA reactions.
Advances in colorimetric aptasensors for heavy metal ion detection utilizing nanomaterials: a comprehensive review
Authors: Zhu Jiangxiong , Wang Danfeng , Yu Hong , Yin Hao , Wang Lumei , Shen Guoqing , Geng Xueqing , Yang Linnan , Fei Yongcheng , Deng Yun
Published: November 2023

Heavy metal ion contamination poses significant environmental and health risks, necessitating rapid and efficient detection methods.
Genetically engineered probiotics for an optical imaging-guided tumor photothermal therapy/immunotherapy
Authors: Chen Xue , Li Puze , Xie Shiqiang , Yang Xiangliang , Luo Ban , Hu Jun
Published: November 2023

It is important to visualize the precise localization and real-time distribution of bacteria in vivo to guide bacteria-based cancer therapy.
The pitfalls of using JHF spin–spin coupling constants to infer hydrogen bond formation in organofluorine compounds
Authors: Cariello Guilherme , Zeoly Lucas A. , Piscelli Bruno A. , Lectka Thomas , Cormanich Rodrigo A.
Published: November 2023

Shedding light on 'through space' spin–spin coupling constants (SSCCs), this study challenges hydrogen bonding's dominance in JFH SSCC transmission on organofluorine compounds. Steric, substituent and solvent effects considerably alter SSCC pathways.
Trapping and thermal migration of the first- and second-row atoms in Ar, Kr and Xe crystals
Authors: Leibin Iosif V. , Bezrukov Dmitry S. , Buchachenko Alexei A.
Published: November 2023

Trapping and temperature-induced migration of atoms from H to Ne in the face-centered cubic Ar, Kr and Xe crystals are investigated within the classical crystal model parameterized by the empirically-modified pairwise potentials.
The network structure in transient telechelic polymer networks: extension of the Miller–Macosko model
Authors: Ahmadi Mostafa , Yazdanimoghaddam Rosha , Sharif Farhad
Published: November 2023

A mean-field theory is developed for forecasting the network connectivity of transient telechelic polymer networks made with various polymer functionalities and transient connectivities represented by metal–ligand complexes.
The NO reduction by CO over NiOx/CeO2 catalysts with a fixed Ni surface density: pretreatment effects on the catalyst structure and catalytic activity
Authors: Lee Kyung-Min , Kim Byeongseok , Lee Juwon , Kwon Gihan , Yoon Kwangsuk , Song Hocheol , Min Kyung Hoon , Shim Sang Eun , Hwang Sungwon , Kim Taejin
Published: November 2023

NiOx/CeO2 catalysts were synthesized under various pretreatment conditions. Different pretreatment conditions significantly influenced the activity of the NO reduction by CO reaction.
Preparation of CuNi/NH2-MIL-125(Ti) for the photocatalytic synthesis of 1,4-dihydropyridines and β-acetamido ketones
Authors: Movahedi Shayan , Jafarzadeh Mohammad
Published: November 2023

Bimetallic CuNi nanoparticles were successfully grown on the surface of a Ti-based metal–organic framework, NH2-MIL-125, via impregnation and chemical reduction processes.
Mechanistic insights into methanol carbonylation to methyl acetate over an efficient organic template-free Cu-exchanged mordenite
Authors: Luque-Álvarez L. A. , González-Arias J. , Romero-Sarria F. , Reina T. R. , Bobadilla L. F. , Odriozola J. A.
Published: November 2023

A new approach for determining the mechanism of methanol carbonylation to methyl acetate over a green template-free Cu-MOR solid catalyst.