bluuebunny/crossref_metadata_2025 huggingface dataset:
A pilot metabolomic study of drug interaction with the immune response to seasonal influenza vaccination
Authors: Siddiqa Amnah , Wang Yating , Thapa Maheshwor , Martin Dominique E. , Cadar Andreia N. , Bartley Jenna M. , Li Shuzhao
Published: June 2023

Many human diseases, including metabolic diseases, are intertwined with the immune system. The understanding of how the human immune system interacts with pharmaceutical drugs is still limited, and epidemiological studies only start to emerge. As the metabolomics technology matures, both drug metabolites and biological responses can be measured in the same global profiling data. Therefore, a new opportunity presents itself to study the interactions between pharmaceutical drugs and immune system in the high-resolution mass spectrometry data. We report here a double-blinded pilot study of seasonal influenza vaccination, where half of the participants received daily metformin administration. Global metabolomics was measured in the plasma samples at six timepoints. Metformin signatures were successfully identified in the metabolomics data. Statistically significant metabolite features were found both for the vaccination effect and for the drug-vaccine interactions. This study demonstrates the concept of using metabolomics to investigate drug interaction with the immune response in human samples directly at molecular levels.
Metal-dependent enzyme symmetry guides the biosynthetic flux of terpene precursors
Authors: Ecker Felix , Vattekkatte Abith , Boland Wilhelm , Groll Michael
Published: June 2023

Terpenoids account for more than 60% of all natural products, and their carbon skeletons originate from common isoprenoid units of different lengths such as geranyl pyrophosphate and farnesyl pyrophosphate. Here we characterize a metal-dependent, bifunctional isoprenyl diphosphate synthase from the leaf beetle Phaedon cochleariae by structural and functional analyses. Inter- and intramolecular cooperative effects in the homodimer strongly depend on the provided metal ions and regulate the biosynthetic flux of terpene precursors to either biological defence or physiological development. Strikingly, a unique chain length determination domain adapts to form geranyl or farnesyl pyrophosphate by altering enzyme symmetry and ligand affinity between both subunits. In addition, we identify an allosteric geranyl-pyrophosphate-specific binding site that shares similarity with end-product inhibition in human farnesyl pyrophosphate synthase. Our combined findings elucidate a deeply intertwined reaction mechanism in the P. cochleariae isoprenyl diphosphate synthase that integrates substrate, product and metal-ion concentrations to harness its dynamic potential.
Leveraging rail-based mobile energy storage to increase grid reliability in the face of climate uncertainty
Authors: Moraski Jill W. , Popovich Natalie D. , Phadke Amol A.
Published: June 2023

Maintaining reliability is increasingly challenging for electric grids as they endure more frequent extreme weather events and utilize more intermittent generation. Exploration of alternative reliability approaches is needed to effectively address these emerging issues. Here we examine the potential to use the US rail system as a nationwide backup transmission grid over which containerized batteries, or rail-based mobile energy storage (RMES), are shared among regions to meet demand peaks, relieve transmission congestion and increase resilience. We find that RMES is a feasible reliability solution for low-frequency, high-impact events and quantify its cost effectiveness relative to reliability-driven investments in transmission infrastructure and stationary capacity. Compared to new transmission lines and stationary battery capacity, deploying RMES for such events could save the power sector upwards of US$300 per kW-year and US$85 per kW-year, respectively. While no known technical barriers exclude RMES from grid participation, addressing interconnection challenges and revising regulatory frameworks is necessary for deployment at scale.
Mid-Proterozoic day length stalled by tidal resonance
Authors: Mitchell Ross N. , Kirscher Uwe
Published: June 2023

We present statistical analysis of a compilation of observational constraints on the Precambrian length of day and find that the day length stalled at about 19 h for about 1 billion years during the mid-Proterozoic. We suggest that the accelerative torque of atmospheric thermal tides from solar energy balanced the decelerative torque of lunar oceanic tides, temporarily stabilizing Earth’s rotation. This stalling coincides with a period of relatively limited biological evolution known as the boring billion.
Genome-wide association study of thoracic aortic aneurysm and dissection in the Million Veteran Program
Authors: Klarin Derek , Devineni Poornima , Sendamarai Anoop K. , Angueira Anthony R. , Graham Sarah E. , Shen Ying H. , Levin Michael G. , Pirruccello James P. , Surakka Ida , Karnam Purushotham R. , Roychowdhury Tanmoy , Li Yanming , Wang Minxian , Aragam Krishna G. , Paruchuri Kaavya , Zuber Verena , Shakt Gabrielle E. , Tsao Noah L. , Judy Renae L. , Vy Ha My T. , Verma Shefali S. , Rader Daniel J. , Do Ron , Bavaria Joseph E. , Nadkarni Girish N. , Ritchie Marylyn D. ,   VA Million Veteran Program, Burgess Stephen , Guo Dong-chuan , Ellinor Patrick T. , LeMaire Scott A. , Milewicz Dianna M. , Willer Cristen J. , Natarajan Pradeep , Tsao Philip S. , Pyarajan Saiju , Damrauer Scott M.
Published: June 2023

The current understanding of the genetic determinants of thoracic aortic aneurysms and dissections (TAAD) has largely been informed through studies of rare, Mendelian forms of disease. Here, we conducted a genome-wide association study (GWAS) of TAAD, testing ~25 million DNA sequence variants in 8,626 participants with and 453,043 participants without TAAD in the Million Veteran Program, with replication in an independent sample of 4,459 individuals with and 512,463 without TAAD from six cohorts. We identified 21 TAAD risk loci, 17 of which have not been previously reported. We leverage multiple downstream analytic methods to identify causal TAAD risk genes and cell types and provide human genetic evidence that TAAD is a non-atherosclerotic aortic disorder distinct from other forms of vascular disease. Our results demonstrate that the genetic architecture of TAAD mirrors that of other complex traits and that it is not solely inherited through protein-altering variants of large effect size.
Direct stimulation of de novo nucleotide synthesis by O-GlcNAcylation
Authors: Chen Lulu , Zhou Qi , Zhang Pingfeng , Tan Wei , Li Yingge , Xu Ziwen , Ma Junfeng , Kupfer Gary M. , Pei Yanxin , Song Qibin , Pei Huadong
Published: June 2023

O-linked β-N-acetyl glucosamine (O-GlcNAc) is at the crossroads of cellular metabolism, including glucose and glutamine; its dysregulation leads to molecular and pathological alterations that cause diseases. Here we report thatO-GlcNAc directly regulates de novo nucleotide synthesis and nicotinamide adenine dinucleotide (NAD) production upon abnormal metabolic states. Phosphoribosyl pyrophosphate synthetase 1 (PRPS1), the key enzyme of the de novo nucleotide synthesis pathway, isO-GlcNAcylated byO-GlcNAc transferase (OGT), which triggers PRPS1 hexamer formation and relieves nucleotide product-mediated feedback inhibition, thereby boosting PRPS1 activity. PRPS1O-GlcNAcylation blocked AMPK binding and inhibited AMPK-mediated PRPS1 phosphorylation. OGT still regulates PRPS1 activity in AMPK-deficient cells. Elevated PRPS1O-GlcNAcylation promotes tumorigenesis and confers resistance to chemoradiotherapy in lung cancer. Furthermore, Arts-syndrome-associated PRPS1 R196W mutant exhibits decreased PRPS1O-GlcNAcylation and activity. Together, our findings establish a direct connection amongO-GlcNAc signals, de novo nucleotide synthesis and human diseases, including cancer and Arts syndrome.
H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
Authors: Pal Debosree , Patel Manthan , Boulet Fanny , Sundarraj Jayakumar , Grant Olivia A. , Branco Miguel R. , Basu Srinjan , Santos Silvia D. M. , Zabet Nicolae Radu , Scaffidi Paola , Pradeepa Madapura M.
Published: June 2023

Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here, we demonstrate that the male-specific lethal (MSL)-complex-mediated histone H4 acetylation at lysine 16 (H4K16ac) is enriched at TEs in human embryonic stem cells (hESCs) and cancer cells. This in turn activates transcription of subsets of full-length long interspersed nuclear elements (LINE1s, L1s) and endogenous retrovirus (ERV) long terminal repeats (LTRs). Furthermore, we show that the H4K16ac-marked L1 and LTR subfamilies display enhancer-like functions and are enriched in genomic locations with chromatin features associated with active enhancers. Importantly, such regions often reside at boundaries of topologically associated domains and loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac-marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape at specific genomic locations by maintaining an active chromatin landscape at TEs.
Hantzsch reaction using copper nitrate hydroxide-containing mesoporous silica nanoparticle with C3N4 framework as a novel powerful and reusable catalyst
Authors: Rahmati Ensiyeh , Rafiee Zahra
Published: June 2023

Copper nitrate hydroxide (CNH)-containing mesoporous silica nanoparticle (MSN) with g-C3N4 framework (MSN/C3N4/CNH) was fabricated via a four-step hydrothermal synthesis method. Functionalized MSN-based C3N4 was prepared, decorated with CNH, and identified by different physicochemical techniques such as FT-IR, XRD, SEM, EDX, and STA analyses. Then, MSN/C3N4/CNH composite was utilized as a robust catalyst for the fast fabrication of biologically active polyhydroquinoline derivatives with high yields between 88 and 97% via Hantzsch reaction under mild reaction conditions and short reaction time (within 15 min) owing to synergistic influence of Lewis acid and base sites. Moreover, MSN/C3N4/CNH can be straightforwardly recovered and used up to six reaction cycles without a conspicuous decrease in efficiency.
T cell repertoire breadth is associated with the number of acute respiratory infections in the LoewenKIDS birth cohort
Authors: Paschold Lisa , Gottschick Cornelia , Langer Susan , Klee Bianca , Diexer Sophie , Aksentijevich Ivona , Schultheiß Christoph , Purschke Oliver , Riese Peggy , Trittel Stephanie , Haase Roland , Dressler Frank , Eberl Wolfgang , Hübner Johannes , Strowig Till , Guzman Carlos A. , Mikolajczyk Rafael , Binder Mascha
Published: June 2023

We set out to gain insight into peripheral blood B and T cell repertoires from 120 infants of the LoewenKIDS birth cohort to investigate potential determinants of early life respiratory infections. Low antigen-dependent somatic hypermutation of B cell repertoires, as well as low T and B cell repertoire clonality, high diversity, and high richness especially in public T cell clonotypes reflected the immunological naivety at 12 months of age when high thymic and bone marrow output are associated with relatively few prior antigen encounters. Infants with inadequately low T cell repertoire diversity or high clonality showed higher numbers of acute respiratory infections over the first 4 years of life. No correlation of T or B cell repertoire metrics with other parameters such as sex, birth mode, older siblings, pets, the onset of daycare, or duration of breast feeding was noted. Together, this study supports that—regardless of T cell functionality—the breadth of the T cell repertoire is associated with the number of acute respiratory infections in the first 4 years of life. Moreover, this study provides a valuable resource of millions of T and B cell receptor sequences from infants with available metadata for researchers in the field.
Prognostic value of central blood pressure on the outcomes of embolic stroke of undetermined source
Authors: Han Minho , Heo JoonNyung , Lee Il Hyung , Kim Joon Ho , Lee Hyungwoo , Jung Jae Wook , Lim In Hwan , Hong Soon-Ho , Kim Young Dae , Nam Hyo Suk
Published: June 2023

We investigated the prognostic impact of central blood pressure (BP) on outcomes in patients with embolic stroke of undetermined source (ESUS). The prognostic value of central BP according to ESUS subtype was also evaluated. We recruited patients with ESUS and data on their central BP parameters (central systolic BP [SBP], central diastolic BP [DBP], central pulse pressure [PP], augmentation pressure [AP], and augmentation index [AIx]) during admission. ESUS subtype classification was arteriogenic embolism, minor cardioembolism, two or more causes, and no cause. Major adverse cardiovascular event (MACE) was defined as recurrent stroke, acute coronary syndrome, hospitalization for heart failure, or death. Over a median of 45.8 months, 746 patients with ESUS were enrolled and followed up. Patients had a mean age of 62.8 years, and 62.2% were male. Multivariable Cox regression analysis showed that central SBP and PP were associated with MACE. All-cause mortality was independently associated with AIx. In patients with no cause ESUS, central SBP and PP, AP, and AIx were independently associated with MACE. AP and AIx were independently associated with all-cause mortality (all p < 0.05). We demonstrated that central BP can predict poor long-term prognosis in patients with ESUS, especially those with the no cause ESUS subtype.
NISNet3D: three-dimensional nuclear synthesis and instance segmentation for fluorescence microscopy images
Authors: Wu Liming , Chen Alain , Salama Paul , Winfree Seth , Dunn Kenneth W. , Delp Edward J.
Published: June 2023

The primary step in tissue cytometry is the automated distinction of individual cells (segmentation). Since cell borders are seldom labeled, cells are generally segmented by their nuclei. While tools have been developed for segmenting nuclei in two dimensions, segmentation of nuclei in three-dimensional volumes remains a challenging task. The lack of effective methods for three-dimensional segmentation represents a bottleneck in the realization of the potential of tissue cytometry, particularly as methods of tissue clearing present the opportunity to characterize entire organs. Methods based on deep learning have shown enormous promise, but their implementation is hampered by the need for large amounts of manually annotated training data. In this paper, we describe 3D Nuclei Instance Segmentation Network (NISNet3D) that directly segments 3D volumes through the use of a modified 3D U-Net, 3D marker-controlled watershed transform, and a nuclei instance segmentation system for separating touching nuclei. NISNet3D is unique in that it provides accurate segmentation of even challenging image volumes using a network trained on large amounts of synthetic nuclei derived from relatively few annotated volumes, or on synthetic data obtained without annotated volumes. We present a quantitative comparison of results obtained from NISNet3D with results obtained from a variety of existing nuclei segmentation techniques. We also examine the performance of the methods when no ground truth is available and only synthetic volumes were used for training.
Improving efficiency of semitransparent organic solar cells by constructing semitransparent microcavity
Authors: Annabi Milani Elmira , Piralaee Mina , Asgari Asghar
Published: June 2023

Semitransparent organic solar cells have become attractive recently because of their photon harvesting in the near-infrared and ultraviolet range and passing in the visible light region. Semitransparent organic solar cells with Glass/MoO3/Ag/MoO3/PBDB-T:ITIC/TiO2/Ag/PML/1DPCs structure have been studied in this work and the effects microcavity with 1-dimensional photonic crystals (1DPCs) on the solar cell performance such as the power conversion efficiency, the average visible transmittance, Light utilization efficiency (LUE), the color coordinates in the CIE color space, and CIE LAB are investigated. The analytical calculation including the density of exactions and their displacement is used to model the devices. The model shows that the presence of microcavity can improve the power conversion efficiency by about %17 in comparison with the absence of microcavity. Although the transmission is decreasing slightly, microcavity does not change the color coordinates much. The device can transmit high-quality light with a near-white sensation to the human eye.
Designing Ising machines with higher order spin interactions and their application in solving combinatorial optimization
Authors: Bashar Mohammad Khairul , Shukla Nikhil
Published: June 2023

The Ising model provides a natural mapping for many computationally hard combinatorial optimization problems (COPs). Consequently, dynamical system-inspired computing models and hardware platforms that minimize the Ising Hamiltonian, have recently been proposed as a potential candidate for solving COPs, with the promise of significant performance benefit. However, prior work on designing dynamical systems as Ising machines has primarily considered quadratic interactions among the nodes. Dynamical systems and models considering higher order interactions among the Ising spins remain largely unexplored, particularly for applications in computing. Therefore, in this work, we propose Ising spin-based dynamical systems that consider higher order (> 2) interactions among the Ising spins, which subsequently, enables us to develop computational models to directly solve many COPs that entail such higher order interactions (i.e., COPs on hypergraphs). Specifically, we demonstrate our approach by developing dynamical systems to compute the solution for the Boolean NAE-K-SAT (K ≥ 4) problem as well as solve the Max-K-Cut of a hypergraph. Our work advances the potential of the physics-inspired ‘toolbox’ for solving COPs.
Effect of contact number among graphene nanosheets on the conductivities of tunnels and polymer composites
Authors: Zare Yasser , Kim Tae-Hoon , Gharib Nima , Chang Young-Wook
Published: June 2023

Simple equations are expressed for tunnel conductivity, tunnel resistance and conductivity of a graphene-filled composite by the number of contacts and interphase part. More specially, the active filler amount is suggested by interphase depth, which changes the contact number. The conductivity of nanocomposite is presented by filler content, filler dimensions, tunneling length and interphase depth. The innovative model is surveyed by the experimented conductivity of real examples. Too, the impacts of numerous issues on the tunnel resistance, tunnel conductivity and conductivity of nanocomposite are discussed to validate the novel equations. The estimates agree with the experimented data and the impacts of several terms on the tunnel resistance, tunnel conductivity and conductivity of system are sensible. Thin and big nanosheets positively affect the nanocomposite’s conductivity, but thick nanosheets improve the tunnel conductivity. High conductivity is found at short tunnels, while the nanocomposite’s conductivity directly depends on the tunneling length. The dissimilar effects of these features on the tunneling properties and conductivity are described.
LKC-Net: large kernel convolution object detection network
Authors: Wang Weina , Li Shuangyong , Shao Jiapeng , Jumahong Huxidan
Published: June 2023

Deep learning-based object detection methods have achieved great performance improvement. However, since small kernel convolution has been widely used, the semantic feature is difficult to obtain due to the small receptive fields, and the key information cannot be highlighted, resulting in a series of problems such as wrong detection, missing detection, and repeated detection. To overcome these problems, we propose a large kernel convolution object detection network based on feature capture enhancement and vast receptive field attention, called LKC-Net. Firstly, a feature capture enhancement block based on large kernel convolution is proposed to improve the semantic feature capturing ability, and depth convolution is used to reduce the number of parameters. Then, the vast receptive filed attention mechanism is constructed to enhance channel direction information extraction ability, and it is more compatible with the proposed backbone than other existing attention mechanisms. Finally, the loss function is improved by introducing the SIoU, which can overcome the angle mismatch problem between the ground truth and prediction box. Experiments are conducted on Pascal VOC and MS COCO datasets for demonstrating the performance of LKC-Net.
Host defense peptides combined with MTA extract increase the repair in dental pulp cells: in vitro and ex vivo study
Authors: Silva Poliana Amanda Oliveira , Martins Danilo César Mota , de Castro Cantuária Ana Paula , de Andrade Rosangela V. , Lacorte Cristiano , de Almeida Jeeser Alves , Aguiar Lana Ribeiro , Corrêa José Raimundo , da Silva Ingrid Gracielle Martins , Franco Octávio Luiz , Rezende Taia Maria Berto
Published: June 2023

Host Defense Peptides (HDPs) have, in previous studies, been demonstrating antimicrobial, anti-inflammatory, and immunomodulatory capacity, important factors in the repair process. Knowing these characteristics, this article aims to evaluate the potential of HDPs IDR1018 and DJK-6 associated with MTA extract in the repair process of human pulp cells. Antibacterial activity of HDPs, MTA and HDPs combined with MTA in Streptococcus mutans planktonic bacteria and antibiofilm activity was evaluated. Cell toxicity was assayed with MTT and cell morphology was observed by scanning electron microscopy (SEM). Proliferation and migration of pulp cells were evaluated by trypan blue and wound healing assay. Inflammatory and mineralization related genes were evaluated by qPCR (IL-6, TNFRSF, DSPP, TGF-β). Alkaline phosphatase, phosphate quantification and alizarin red staining were also verified. The assays were performed in technical and biological triplicate (n = 9). Results were submitted for the calculation of the mean and standard deviation. Then, normality verification by Kolmogorov Smirnov test, analyzing one-way ANOVA. Analyses were considered at a 95% significance level, with a p-value < 0.05. Our study demonstrated that HDPs combined with MTA were able to reduce biofilms performed in 24 h and biofilm performed over 7 days S. mutans biofilm (p < 0.05). IDR1018 and MTA, as well as their combination, down-regulated IL-6 expression (p < 0.05). Tested materials were not cytotoxic to pulp cells. IDR1018 induced high cell proliferation and combined with MTA induced high cellular migration rates in 48 h (p < 0.05). Furthermore, the combination of IDR1018 and MTA also induced high expression levels of DSPP, ALP activity, and the production of calcification nodules. So, IDR-1018 and its combination with MTA could assist in pulp-dentine complex repair process in vitro.
Momentum-resolved spin-conserving two-triplon bound state and continuum in a cuprate ladder
Authors: Tseng Yi , Paris Eugenio , Schmidt Kai P. , Zhang Wenliang , Asmara Teguh Citra , Bag Rabindranath , Strocov Vladimir N. , Singh Surjeet , Schlappa Justine , Rønnow Henrik M. , Schmitt Thorsten
Published: June 2023

Studying multi-particle elementary excitations has provided unique access to understand collective many-body phenomena in correlated electronic materials, paving the way towards constructing microscopic models. In this work, we perform O K-edge resonant inelastic X-ray scattering (RIXS) on the quasi-one-dimensional cuprate $${{{{{{\rm{Sr}}}}}}}_{14}{{{{{{\rm{Cu}}}}}}}_{24}{{{{{{\rm{O}}}}}}}_{41}$$

Sr

14

Cu

24

O

41

with weakly-doped spin ladders. The RIXS signal is dominated by a dispersing sharp mode ~ 270 meV on top of a damped incoherent component ~ 400-500 meV. Comparing with model calculations using the perturbative continuous unitary transformations method, the two components resemble the spin-conserving ΔS = 0 two-triplon bound state and continuum excitations in the spin ladders. Such multi-spin response with long-lived ΔS = 0 excitons is central to several exotic magnetic properties featuring Majorana fermions, yet remains unexplored given the generally weak cross-section with other experimental techniques. By investigating a simple spin-ladder model system, our study provides valuable insight into low-dimensional quantum magnetism.
A neural machine code and programming framework for the reservoir computer
Authors: Kim Jason Z. , Bassett Dani S.
Published: June 2023

From logical reasoning to mental simulation, biological and artificial neural systems possess an incredible capacity for computation. Such neural computers offer a fundamentally novel computing paradigm by representing data continuously and processing information in a natively parallel and distributed manner. To harness this computation, prior work has developed extensive training techniques to understand existing neural networks. However, the lack of a concrete and low-level machine code for neural networks precludes us from taking full advantage of a neural computing framework. Here we provide such a machine code along with a programming framework by using a recurrent neural network—a reservoir computer—to decompile, code and compile analogue computations. By decompiling the reservoir’s internal representation and dynamics into an analytic basis of its inputs, we define a low-level neural machine code that we use to program the reservoir to solve complex equations and store chaotic dynamical systems as random-access memory. We further provide a fully distributed neural implementation of software virtualization and logical circuits, and even program a playable game of pong inside of a reservoir computer. Importantly, all of these functions are programmed without requiring any example data or sampling of state space. Finally, we demonstrate that we can accurately decompile the analytic, internal representations of a full-rank reservoir computer that has been conventionally trained using data. Taken together, we define an implementation of neural computation that can both decompile computations from existing neural connectivity and compile distributed programs as new connections.
Proteomic characterization of acute kidney injury in patients hospitalized with SARS-CoV2 infection
Authors: Paranjpe Ishan , Jayaraman Pushkala , Su Chen-Yang , Zhou Sirui , Chen Steven , Thompson Ryan , Del Valle Diane Marie , Kenigsberg Ephraim , Zhao Shan , Jaladanki Suraj , Chaudhary Kumardeep , Ascolillo Steven , Vaid Akhil , Gonzalez-Kozlova Edgar , Kauffman Justin , Kumar Arvind , Paranjpe Manish , Hagan Ross O. , Kamat Samir , Gulamali Faris F. , Xie Hui , Harris Joceyln , Patel Manishkumar , Argueta Kimberly , Batchelor Craig , Nie Kai , Dellepiane Sergio , Scott Leisha , Levin Matthew A. , He John Cijiang , Suarez-Farinas Mayte , Coca Steven G. , Chan Lili , Azeloglu Evren U. , Schadt Eric , Beckmann Noam , Gnjatic Sacha , Merad Miram , Kim-Schulze Seunghee , Richards Brent , Glicksberg Benjamin S. , Charney Alexander W. , Nadkarni Girish N.
Published: June 2023

Background

Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms.

Methods

Using measurements of ~4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N = 437), we identified 413 higher plasma abundances of protein targets and 30 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p < 0.05). Of these, 62 proteins were validated in an external cohort (p < 0.05, N = 261).

Results

We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p < 0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury.

Conclusions

Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.
Sum frequency generation spectroscopy of fluorinated organic material-based interfaces: a tutorial review
Authors: Sakunkaewkasem Siwakorn , Deleon Daniela , Choi Yunsoo , Tran Hung-Vu , Marquez Maria D. , Baldelli Steven , Lee T. Randall
Published: June 2023

Molecular interactions at interfaces have a significant effect on the wetting properties of surfaces on a macroscale.
Steady-state monitoring of oxygen in a high-throughput organ-on-chip platform enables rapid and non-invasive assessment of drug-induced nephrotoxicity
Authors: Kann Samuel H. , Shaughnessey Erin M. , Zhang Xin , Charest Joseph L. , Vedula Else M.
Published: June 2023

Measurement of steady-state oxygen levels in a high-throughput organ-on-chip platform enabled rapid and non-invasive monitoring of dose and time-dependent injury responses of human kidney cells to cisplatin, a drug with toxic effects in the kidney.
Enhanced mechanical strength of a highly de-lithiated single-crystal Ni-rich cathode to suppress irreversible planar gliding
Authors: Yang Jiachao , Xu Shenyang , Yu Jian , Li Yunjiao , He Zhenjiang , Wu Feixiang , Zhang Tao , Hao Shuaipeng , Jiang Shijie , Pan Jiawei , Xi Xiaoming , Liu Shuaiwei
Published: June 2023

The mechanical strength of de-lithiated state particles decreases significantly, which is caused by planar gliding. In-modification improves the compression hardness of Ni-rich single crystalline particles, even at a voltage of 4.3 V.
Efficient inverted CsPbI3inorganic perovskite solar cells achieved by facile surface treatment with ethanolamine
Authors: Liu Ning , Xu Zuxiong , Pan Yi , Wang Jianwei , Liu Zhongyu , Zhang Jing , Huang Like , Hu Ziyang , Zhu Yuejin , Liu Xiaohui
Published: June 2023

A facile and effective surface treatment strategy is proposed to modify the CsPbI3surface with ethanolamine. Thus, a champion power conversion efficiency of 18.41% with improved stability is achieved for the inverted CsPbI3solar cells.
Recent advances in enhancing stereocomplexation between poly(lactide) enantiomeric chains
Authors: Guo Mingwei , Wu Weixin , Wu Wenjing , Wang Ruizhe , Huang Liming , Gao Qinwei
Published: June 2023

Over the past three decades, its excellent biodegradability and biocompatibility have enabled poly(lactide) (PLA) to be extensively explored as a replacement for oil-based thermoplastics in biomedical and industrial applications.
Electrochemical assessment of a tripodal thiourea-based anion receptor at the liquid|liquid interface
Authors: Al Nasser Hussain A. , Martinez-Crespo Luis , Webb Simon J. , Dryfe Robert A. W.
Published: June 2023

Thiourea-based receptors for anions have been widely studied due to their ability to transport anions across phospholipid bilayers.
Colossal room-temperature electrocaloric strength aided by hydrostatic pressure in lead-free multiferroic solid solutions
Authors: Menéndez César , Rurali Riccardo , Cazorla Claudio
Published: June 2023

We propose an innovative approach for the enhancement of electrocaloric effects that consists of the application of multiple external fields on lead-free multiferroic materials able to undergo sharp first-order phase transitions.
State of the art and prospectives of heterogeneous photocatalysts based on metal–organic frameworks (MOFs): design, modification strategies, and their applications and mechanisms in photodegradation, water splitting, and CO2reduction
Authors: Ma Zeren , Guan Bin , Guo Jiangfeng , Wu Xingze , Chen Yujun , Zhang Jinhe , Jiang Xing , Bao Shibo , Chen Lei , Shu Kaiyou , Dang Hongtao , Guo Zelong , Li Zekai , Yao Shunyu , Huang Zhen
Published: June 2023

We review the design of MOFs as heterogeneous photocatalysts, analysing research on their use in water pollutant degradation, water splitting and CO2reduction. Advantages and disadvantages of MOFs-based photocatalysts, catalytic mechanisms and future research are evaluated.
Organometallic Ir(iii) complexes: post-synthetic modification, photophysical properties and binuclear complex construction
Authors: Gitlina Anastasia Yu. , Khistiaeva Viktoria , Melnikov Alexey , Ivonina Mariia , Sizov Vladimir , Spiridonova Dar'ya , Makarova Anna , Vyalikh Denis , Grachova Elena
Published: June 2023

The post-synthetic modification of Ir(iii) complexes [Ir(C^N)2N^N]+ allows to control construction of d–d and d–f binuclear dyads.
Structural verification and new reactivity for Stang's reagent, [PhI(CN)][OTf]
Authors: Bennetts Jason D. , Barwise Lachlan , Sharp-Bucknall Lachlan , White Keith F. , Hogan Conor F. , Dutton Jason L.
Published: June 2023

The solid-state structure of Stang's reagent is revealed, with confirmation of its existence as an ion-pair with triflate in solution. Further reactivity successfully delivers CN to pyridyl ligands.
Direct frequency comb spectroscopy of HCN to evaluate line lists
Authors: Bailey D. Michelle , Crump Eric M. , Hodges Joseph T. , Fleisher Adam J.
Published: June 2023

Direct frequency comb spectroscopy of HCN is performed using a high resolution, cross-dispersed spectrometer. Short-wave and mid-wave infrared instrumentation for precision molecular spectroscopy to test line lists is discussed.
A vascularized crypt-patterned colon model for high-throughput drug screening and disease modelling
Authors: Sotra Alexander , Jozani Kimia Asadi , Zhang Boyang
Published: June 2023

Stepwise development of a vascularized crypt-patterned colon monolayer in a high-throughput microfluidic platform (IFlowPlate384). The platform can be applied to preclinical drug screens and in vitro disease modelling.
Synthesis and rheological investigations of gum-ghatti-cl-poly(NIPA-co-AA)-graphene oxide based hydrogels
Authors: Dave Pragnesh N. , Macwan Pradip M. , Kamaliya Bhagvan
Published: June 2023

The purpose of the present work is to study the rheological properties of gum ghatti-cl-poly(NIPA-co-AA)/GO (GNAGO) hydrogels reinforced with graphene oxide (GO) to modify their mechanical and thermal properties.
Theoretical design of molecularly imprinted polypyrrole biosensor for the detection of renal failure biomarkers
Authors: Rajaee Elham , Izadyar Mohammad , Housaindokht Mohammad Reza
Published: June 2023

This study aimed to perform a rational design for molecularly imprinted polymer (MIP) preparation by using pyrrole as the functional monomer for the detection of renal failure biomarkers.
Highly selective reduction of CO2 to HCOOH by a ZnO/SnO2 electrocatalyst with heterogeneous interfaces
Authors: He Jing-Nan , Ding Xin , Liu Qi , Gao Yan
Published: June 2023

ZnO/SnO2 was designed and prepared for highly selective CO2 reduction for HCOOH. A faraday efficiency (FE) of 93.8% and a yield of 0.16 mmol h−1 cm−2 were obtained at the potential of −1.05 V.
Highly stereoselective synthesis of trans-alkenes via electrochemical Ni-catalyzed hydroarylation of alkynes with aryl iodides
Authors: Zhang Haoxiang , Guo Lin , Yang Chao , Xia Wujiong
Published: June 2023

An electrochemical nickel catalyzed hydroarylation reaction of alkynes with aryl iodides is herein described.
Dicarbofunctionalization of unactivated alkenes via organo-photoredox catalysis in water: access to cyanoalkylated fused quinazolinones
Authors: Ghouse Abuthayir Mohamathu , Akondi Srirama Murthy
Published: June 2023

An organophotocatalyzed synthesis of polycyclic quinazolinones with a distal nitrile group is reported in the aqueous medium.
Expanded triazolophanes: a topological analysis of vesicular assembly
Authors: Sapala Appa Rao , Maurya Govind P. , Singh Hanuman , Mehta Neha , Karmakar Tarak , Haridas V.
Published: June 2023

We describe a unique topology-based approach for fabrication of vesicles. Studies on various designer cyclic and acyclic systems revealed that adequate curvature is essential for vesicle formation.
Stochastic platform based on calix[6]arene and TiO2-modified reduced graphene oxide electrode for on-site determination of nonivamide in pharmaceutical and water samples
Authors: Tuchiu Bianca-Maria , Stefan-van Staden Raluca-Ioana , van Staden Jacobus (Koos) Frederick
Published: June 2023

Calix[6]arene recognised nonivamide in topical ointments and in water samples.
Physico-chemical and tribological properties of commercial oil – bio-lubricant mixtures dispersed with graphene nanoplatelets
Authors: Banavathu Koteswara Rao , Chebattina Kodanda Rama Rao , Srinivas V. , Moorthy Ch V. K. N. S. N. , Pullagura Gandhi
Published: June 2023

This study focuses on the physicochemical and tribological properties of bio-lubricants and commercial lubricant blends dispersed with graphene nanoplatelets.
Effects of piston shapes and swirl ratios on combustion and emissions of a micro diesel pilot-ignition natural gas engine
Authors: Fu Jianqin , Li Chao , Zhou Feng , Shu Jun , Liu Jingping
Published: June 2023

To improve the performance of a micro diesel pilot-ignition (DPI) natural gas (NG) engine, four groups of pistons were designed and the effects of piston shapes and swirl ratios were discussed based on computational fluid dynamics (CFD) simulation.
Insights and guidelines to interpret forces and deformations at the nanoscale by using a tapping mode AFM simulator: dForce 2.0
Authors: Gisbert Victor G. , Garcia Ricardo
Published: June 2023

dForce 2.0 simulates tapping and bimodal AFM observables and properties. The code incorporates 26 interaction force models. It might be freely downloaded from the article. It might be run from a personal computer.
Self-templated synthesis of novel and robust honeycomb-like N-doped highly graphitized carbon from low-temperature carbonization
Authors: Lee Ha-Young , Gyan-Barimah Caleb , Shin Cheol-Hwan , Yu Jong-Sung
Published: June 2023

Honeycomb-like N-doped highly graphitized carbon is prepared by self-templated magnesiothermic reduction. Porosity and graphiticity of the prepared carbon support greatly improve the catalytic performance and durability of PtCo alloy in PEMFCs.
Machine learning-assisted screening of effective passivation materials for P–I–N type perovskite solar cells
Authors: Huang Di , Guo Chaorong , Li Zhennan , Zhou Haixin , Zhao Xiaojie , Feng Zhimin , Zhang Rui , Liu Menglong , Liang Jiaojiao , Zhao Ling , Meng Juan
Published: June 2023

The effective passivation material (ITIC) for P–I–N type perovskite solar cells is selected by machine learning. In the verification experiment, the defect density of the perovskite layer is significantly decreased after treatment with ITIC.
Position of gold dictates the photophysical and photocatalytic properties of Cu2O in Cu2O/Au multicomponent nanoparticles
Authors: Kovács Dávid , Deák András , Radnóczi György Z. , Horváth Zsolt E. , Sulyok Attila , Schiller Róbert , Czömpöly Ottó , Zámbó Dániel
Published: June 2023

Decorating Cu2O nanooctahedra with small Au nanograins is a superior strategy to utilize photogenerated charge carriers without generating hot electrons. Photocatalytic activity in these heteronanoparticles is improved even upon low-power excitation.
Compressing fully connected layers of deep neural networks using permuted features
Authors: Nagaraju Dara , Chandrachoodan Nitin
Published: June 2023

Modern deep neural networks typically have some fully connected layers at the final classification stages. These stages have large memory requirements that can be expensive on resource‐constrained embedded devices and also consume significant energy just to read the parameters from external memory into the processing chip. The authors show that the weights in such layers can be modelled as permutations of a common sequence with minimal impact on recognition accuracy. This allows the storage requirements of FC layer(s) to be significantly reduced, which reflects in the reduction of total network parameters from 1.3× to 36× with a median of 4.45× on several benchmark networks. The authors compare the results with existing pruning, bitwidth reduction, and deep compression techniques and show the superior compression that can be achieved with this method. The authors also showed 7× reduction of parameters on VGG16 architecture with ImageNet dataset. The authors also showed that the proposed method can be used in the classification stage of the transfer learning networks.
Recurrent mini-outbursts and a magnetic white dwarf in the symbiotic system FN Sgr
Authors: Magdolen J. , Dobrotka A. , Orio M. , Mikołajewska J. , Vanderburg A. , Monard B. , Aloisi R. , Bezák P.
Published: June 2023

Aims. We investigated the optical variability of the symbiotic binary FN Sgr with photometric monitoring over a period of ≃55 years and with a high-cadence Kepler light curve lasting 81 days.

Methods. The data obtained in the V and I bands were reduced with standard photometric methods. The Kepler data were divided into subsamples and were analysed with the Lomb-Scargle algorithm.

Results. The V and I band light curves show a phenomenon never before observed with such recurrence in any symbiotic system, namely short outbursts starting between orbital phases 0.3 and 0.5 and lasting about 1 month, with a fast rise, a slower decline, and amplitudes of 0.5–1 mag. In the Kepler light curve, we discovered three frequencies with sidebands. We attribute a stable frequency of 127.5 d−1 (corresponding to a period of 11.3 min) to the white dwarf rotation. We suggest that this detection probably implies that the white dwarf accretes through a magnetic stream, as in intermediate polars. The small outbursts may be ascribed to the stream–disc interaction. Another possibility is that they are due to localised thermonuclear burning, perhaps confined by the magnetic field, such as those recently inferred in intermediate polars, albeit on different timescales. We also measured a second frequency around 116.9 d−1 (corresponding to about 137 min), which is much less stable and has a drift. This latter may be due to rocky detritus around the white dwarf, but is more likely caused by an inhomogeneity in the accretion disc. Finally, there is a third frequency close to the first one that appears to correspond to the beating between the rotation and the second frequency.
High-contrast detection of exoplanets with a kernel-nuller at the VLTI
Authors: Chingaipe Peter Marley , Martinache Frantz , Cvetojevic Nick , Ligi Roxanne , Mary David , N’Diaye Mamadou , Defrère Denis , Ireland Michael J.
Published: June 2023

Context. The conventional approach to direct imaging is to use a single aperture coronagraph with wavefront correction via extreme adaptive optics (AO). Such systems are limited to observing beyond an inner working angle (IWA) of a few λ/D. Nulling interferometry with two or more apertures will enable detections of companions at separations at and beyond the formal diffraction limit.

Aims. In this paper, we evaluate the astrophysical potential of a kernel-nuller as the prime high-contrast imaging mode of the Very Large Telescope Interferometer (VLTI).

Methods. By taking into account baseline projection effects induced by Earth rotation, we introduce some diversity in the response of the nuller as a function of time. This response is depicted by transmission maps. We also determine whether we can extract the astrometric parameters of a companion from the kernel outputs, which are the primary intended observable quantities of the kernel-nuller. This then leads us to comment on the characteristics of a possible observing program for the discovery of exoplanets.

Results. We present transmission maps for both the raw nuller outputs and their subsequent kernel outputs. To further examine the properties of the kernel-nuller, we introduce maps of the absolute value of the kernel output. We also identify 38 targets for the direct detection of exoplanets with a kernel-nuller at the focus of the VLTI.

Conclusions. With continued upgrades of the VLTI infrastructure, which will reduce fringe tracking residuals, a kernel-nuller would enable the detection of young giant exoplanets at separations <10 AU, where radial velocity and transit methods are more sensitive.
iNNterpol: High-precision interpolation of stellar atmospheres with a deep neural network using a 1D convolutional auto encoder for feature extraction
Authors: Westendorp Plaza C. , Asensio Ramos A. , Allende Prieto C.
Published: June 2023

Context. Given the widespread availability of grids of models for stellar atmospheres, it is necessary to recover intermediate atmospheric models by means of accurate techniques that go beyond simple linear interpolation and capture the intricacies of the data.

Aims. Our goal is to establish a reliable, precise, lightweight, and fast method for recovering stellar model atmospheres, that is to say the stratification of mass column, temperature, gas pressure, and electronic density with optical depth given any combination of the defining atmospheric specific parameters: metallicity, effective temperature, and surface gravity, as well as the abundances of other key chemical elements.

Methods. We employed a fully connected deep neural network which in turn uses a 1D convolutional auto-encoder to extract the nonlinearities of a grid using the ATLAS9 and MARCS model atmospheres.

Results. This new method we call iNNterpol effectively takes into account the nonlinearities in the relationships of the data as opposed to traditional machine-learning methods, such as the light gradient boosting method (LightGBM), that are repeatedly used for their speed in well-known competitions with reduced datasets. We show a higher precision with a convolutional auto-encoder than using principal component analysis as a feature extractor. We believe it constitutes a useful tool for generating fast and precise stellar model atmospheres, mitigating convergence issues, as well as a framework for future developments. The code and data for both training and direct interpolation are available online for full reproducibility and to serve as a practical starting point for other continuous 1D data in the field and elsewhere.