bluuebunny/crossref_metadata_2025 huggingface dataset:
Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing
Authors: Reichart Nicholas J , Steiger Andrea K , Van Fossen Elise M , McClure Ryan , Overkleeft Herman S , Wright Aaron T
Published: September 2023

Multi-omic analyses can provide information on the potential for activity within a microbial community but often lack specificity to link functions to cell, primarily offer potential for function or rely on annotated databases. Functional assays are necessary for understanding in situ microbial activity to better describe and improve microbiome biology. Targeting enzyme activity through activity-based protein profiling enhances the accuracy of functional studies. Here, we introduce a pipeline of coupling activity-based probing with fluorescence-activated cell sorting, culturing, and downstream activity assays to isolate and examine viable populations of cells expressing a function of interest. We applied our approach to a soil microbiome using two activity-based probes to enrich for communities with elevated activity for lignocellulose-degradation phenotypes as determined by four fluorogenic kinetic assays. Our approach efficiently separated and identified microbial members with heightened activity for glycosyl hydrolases, and by expanding this workflow to various probes for other function, this process can be applied to unique phenotype targets of interest.
Combination Therapies Involving Photodynamic Therapy
Authors: Oluwafemi Oluwatobi , Songca Sandile Phinda
Published: September 2023

Photodynamic therapy (PDT) is increasingly used among health practitioners in combatting a variety of diseases, most notably various types of cancer, and is often utilised in combination with other therapeutic options to enhance efficacy or reduce adverse reactions. Combination Therapies Involving Photodynamic Therapy reviews the current state of development of PDT and presents the foreseeable advancements of combination approaches to therapeutic strategies.

This book represents a novel approach to the therapeutic applications of five different technologies including the combinations of photodynamic therapy, photothermal hyperthermia therapy, magnetic hyperthermia therapy, chemotherapy, and cold atmospheric pressure plasma therapy. An ideal companion for students, researchers and practitioners in biological sciences, biotechnology, and photobiological and photochemical sciences, as well as medicinal and pharmaceutical chemistry.
Engineered exosomes for tissue regeneration: from biouptake, functionalization and biosafety to applications
Authors: Zhang Mu , Wan Lei , Li Ruiqi , Li Xiaoling , Zhu Taifu , Lu Haibin
Published: September 2023

Exosomes are increasingly recognized as important effector molecules that regulate intercellular signaling pathways.
A ferrocene-modified stable metal–organic framework for efficient CO2 photoreduction reaction
Authors: Lai Gui-Qi , Li Ning , He Jun , Lan Ya-Qian
Published: September 2023

Ferrocene-grafted/loaded stable metal–organic frameworks (MOFs) as photocatalysts can improve the light absorption and photogenerated charge migration efficiently, and thus enhanced CO2-to-HCOOH photoreduction activity.
Copper-catalyzed nitration of electron-deficient BN-naphthalene
Authors: Fang Xiangdong
Published: September 2023

Under Cu-catalysis, a regioselective nitration of 1,8-dihalogenated BN-naphthalene (ABN) compounds (4a–4c) has been established with the use of tert-butyl nitrite as the nitrating reagent.
A trick of the tail: computing the entropic contribution to the energetics of quinone-protein unbindung
Authors: Haxhija Jetmir , Guischard Felix , Koslowski Thorsten
Published: September 2023

Quinones are vital redox carriers in cellular respiration. The conformational entropy of quinones confined to lipid bilayers can amount up to 12 kcal mol−1. We suggest an entropic zipper mechanism that triggers conformational changes in complex I.
Structural properties of Kudzu protein enzymatic hydrolysate and its repair effect on HepG2 cells damaged by H2O2 oxidation
Authors: Pang Huina , Yue Yihan , Dong Hongying , Jiang Ting , Zhang Hongyin , Zhao Yu , Cai Tiequan , Yan Mingming , Shao Shuai
Published: September 2023

We investigated the structural properties, foaming capacity and foaming stability, antioxidant activity, and amino acid composition of Kudzu protein (KP) and Kudzu protein hydrolysate (KPH).
C–F bond functionalizations via fluorinated carbenes
Authors: Li Yingmei , Luo Jiangbin , Jiang Yaojia
Published: September 2023

This feature article summarizes the developments in fluorinated carbene transformations, and their consequent C–F functionalization in a cascade platform.
Building fast and selective Zn ion channels for highly stable quasi-solid-state Zn-ion batteries
Authors: Kao Chun-Chuan , Liu Jiahao , Ye Chao , Zhang Shao-Jian , Hao Junnan , Qiao Shi-Zhang
Published: September 2023

Ordered ion channels constructed by confining a gel electrolyte in intercalated halloysite nanotubes exhibit fast and selective Zn ion transportation and therefore enhance the cycling stability of the quasi-solid-state Zn-ion batteries.
A modulized lane‐follower for driverless vehicles using multi‐frame
Authors: Luan Honggang , Gao Yang , Wang Zhenxu , Liu Jinyuan , Wang Shuqi , Zhao Yihui , Wang Junchao
Published: September 2023

As a fundamental function, lane following plays an important role for driverless vehicles. Unfortunately, lane followers generally confront great difficulty in lane line missed situations caused by vague line, shadows etc. However, for most lane line missed situation, clues of the line may be hidden in prior view of it. Consequently, a lane follower called UNL Lane Follower, which contains two deep learning network modules is proposed. The first module is a lane line detection model called UNET_CLB. Here, the sequence of image frames is utilised rather than only the current frame to deal with the missing lane lines. The second module is a lane‐following model called LSTM_DTS, which combines a deep learning attention mechanism (temporal attention network and spatial attention network) with a recurrent neural network. As a result, the proposed UNL Lane Follower produces smoother driving behaviour, especially when a lane line is temporally missed. For better explain ability, the role of each part of the network structure is analysed and explained intuitively. As a modularised network, the UNET_CLB is firstly trained and tested on the TuSimple dataset and CULane dataset. The LSTM_DTS lane follow is then trained and tested on our actual lane following dataset. Finally, the UNL Lane Follower is trained and tested as a whole in a simulation running on Webots, after importing the weight of the two modules trained separately. All testing results showed that the UNL Lane Follower can provide better robustness and accuracy for lane line following mission in the line missed situations.
Null‐space beamforming strategy for secrecy rate balancing of two‐way MIMO relay networks
Authors: Fazeli Samad , Akhlaghi Soroush
Published: September 2023

Here, the issue of physical layer security in a two‐way multi‐antenna relay network) is studied. In such a network, two multi‐antenna transceivers attempt to exchange their secret messages via a multi‐antenna relay node in the presence of an eavesdropper. Throughout the first hop, two sources send their messages to the relay node, while an eavesdropper tries to overhear these messages. Then, in the second hop, the relay attempts to send its signal in the null‐space direction of relay‐to‐eavesdropper channel to prevent eavesdropping. The main goal is to obtain effective receive and transmit beamforming vectors at transceivers as well as the beamforming matrix at the relay node to address the secrecy rate balancing problem. The underlying problem is not convex in general. To overcome this issue, the original problem is divided into three subproblems. In the first subproblem the beamforming design at the relay is optimized while in the second subproblem the receive beamforming in a closed form solution is obtained. Finally, in the last subproblem the transmit beamforming is solved using the semi‐definite relaxation and Taylor series expansion. Numerical results represent the effectiveness of the proposed method compared to the previous works in the literature.
Using EtherCAT technology to launch online automated guided vehicle manipulation with unity‐based platform for smart warehouse management
Authors: Nguyen Hung , Nguyen Thanh Phuong , Ngo Ha Quang Thinh
Published: September 2023

In Industry 4.0, the innovative concept of a smart warehouse is defined as a progressive development in logistics and operations management. Numerous advanced techniques are recommended for integration, including wearable devices, communication, loading/unloading, optimization, robotics, and automated transportation, among others. Currently, the growing demand for swift cargo distribution, cost‐effective labour utilization, and enhanced productivity stands as an urgent topic for both enterprises and scholars. This paper presents an EtherCAT‐based model of automated guided vehicle (AGV)‐manipulation introduced within the Unity platform for smart warehouse management. The working environment selected for this model is a cross‐docking warehouse with a chessboard layout. Initially, theoretical computations pertaining to mechanical design are established to provide accurate parameters. Subsequently, the structure of the TwinCAT Human–Machine Interface Server and the configuration within the Unity environment are outlined. Following that, the software architecture, encompassing data exchange and a set of motion commands, is meticulously explained. To validate the proposed approach, several laboratory tests are conducted under identical conditions. This research offers several contributions: firstly, it introduces the innovative use of real‐time technology to represent AGV systems; secondly, it elucidates the potential connection between virtual reality and the physical model; and thirdly, it employs fluid motion techniques to illustrate and visualize driving performance. These findings hold significant promise not only for the advancement of smart warehouse management but also for the broader landscape of digital trade.
Computationally efficient angle estimation of bistatic MIMO radar based on multimodal optimization
Authors: Du Yanan , Gao Hongyuan , Liu Yapeng , Sun Rongchen
Published: September 2023

In this letter, a computationally efficient multiple signal classification (MUSIC)‐based evolutionary algorithm for angle estimation of bistatic multiple‐input multiple‐output (MIMO) radar is proposed. The existing MUSIC algorithms require a computationally cumbersome two‐dimensional (2D) peak searching and the performance is highly related to the grid that set, which leads to a conflict between the computational efficiency and estimation performance. To address this difficulty, a multimodal quantum‐inspired salp swarm algorithm, integrating kmeans clustering technique, is proposed to substitute the 2D peak searching to obtain multiple maxima of the MUSIC algorithm. The resulting computationally efficient algorithm obviously reduces the computational complexity of the MUSIC algorithm, avoids grid errors, and further exploits the potential of the MUSIC algorithm. Numerical simulations in various scenarios are carried out to verify the superiority of the method.
Research on prediction method of expressway section traffic flow considering anomaly detection probability
Authors: Wang Zhiyu , Li Linheng , Qu Xu , Mao Peipei , Ran Bin
Published: September 2023

Real‐time and accurate short‐term traffic flow prediction can provide a scientific basis for decision making by travellers and traffic management, and alleviate traffic congestion to a certain extent. The existing traffic flow prediction methods often encounter limitations in real‐time performance and accuracy due to the post‐processing required to rectify anomaly detection results during data pre‐processing. This paper presents a novel traffic flow prediction model, termed the With‐Anomaly Detection Probability (ADP) Attention‐Bidirectional Long‐Short Term Memory (BiLSTM) model. This model takes the probability of anomaly detection into consideration, integrating the anomaly detection outcomes as an inherent parameter into the traffic flow prediction framework. Additionally, the model incorporates an attention mechanism within the long‐short term memory network. Through a comprehensive simulation study utilizing actual measured traffic flow data from the Shanghai‐Chongqing Expressway, the effectiveness of the proposed model is rigorously evaluated. The prediction results show that the model proposed in this paper is a real‐time and accurate short‐time traffic flow prediction model compared with the basic models.
Refined convolution‐based measures for real‐time harmonic distortions estimation in power system dominated by inverter‐based resources
Authors: Kandezy Reza Saeed , Safarishaal Masoud , Hemmati Rasul , Jiang John Ning
Published: September 2023

Real‐time estimating harmonic distortion levels near the Point of Interconnections of grid‐connected inverter‐based resources (IBRs) is critical for maintaining the operational reliability and security of the power grid, particularly during transients when IBRs generate excessive harmonics. Traditional methods like Total Harmonic Distortion (THD) are unsuitable for time‐varying waveforms as they suffer from aliasing, spectral leakage, and picket‐fence effects. This paper proposes a novel approach that utilizes convolution‐based measures for estimating harmonic distortion, which offers a more suitable way for ongoing real‐time applications. The first measure uses a 60 Hz sinusoidal function as the convolution kernel, while an enhanced measure employs the Gaussian function as the kernel. Two convolution‐based measures are proposed and compared with THD. The comparison criteria are based on the two significant features describing the variation of harmonics: min/max values and variation curvature of harmonics showing the accurate performance of proposed measures. Moreover, short‐term estimations of harmonic distortion are used to validate the effectiveness of the proposed measures, while long‐term estimations are used to determine the ability of the proposed measures to determine harmonic distortion contributions among power network components. The proposed technique's intrinsic characteristics provide a sampling window with low sensitivity to deviations in the fundamental frequency and signal's stationary condition to prevent aliasing and spectral leakage and rule out the impact of the picket‐fence effect on the harmonic distortion level estimation.
Higher accuracy detection strategy for electroluminescent defects in photovoltaic modules based on improved Yolov5
Authors: Ding Sheng , Chen Tiansheng , Chen Hao , Chen Congyan
Published: September 2023

At present, the domestic photovoltaic (PV) industry is developing rapidly. In order to improve the production efficiency of PV cells, a fast and accurate automatic detection model of PV modules’ defects that can be applied in the production line is essential. In this paper, based on the characteristics of significant differences in PV module defect size and a large number of fine defects, an improved defect detection algorithm based on Yolov5 is proposed. Thirteen mainstream defects are divided into two categories according to size, and a series‐connected detection network is constructed for a two‐stage detection. In order to better detect fine defects, this paper proposes the TR‐ResNet module, a residual module composed of the self‐attention, based on the self‐attention mechanism, to replace some fully convolutional residual modules (CNN‐ResNet module) in the Yolov5 backbone network. After testing, the Precision, Recall and mAP of the model are greatly improved and gained 0.904, 0.845, and 0.840. Moreover, the model performs well in stability detection, which can adapt to different production environments and quality requirements. The present study may make the detection work more efficient and improve productivity.
Decision‐dependent distributionally robust integrated generation, transmission, and storage expansion planning: An enhanced Benders decomposition approach
Authors: Qiu Lu , Dan Yangqing , Li Xukun , Cao Ye
Published: September 2023

Integrated generation, transmission, and storage expansion planning (IGT&SP) is the cornerstone to realize low‐carbon transition considering security constraints in the long run. A novel IGT&SP planning scheme is proposed to balance the planning cost, i.e. renewable energy sources (RESs) and energy storage systems, based on the distributionally ambiguity sets. A novel decision‐dependent ambiguity set is proposed to capture the relation between the uncertainties of RES output and long‐term planning. A two‐stage risk‐averse distributionally robust optimization is formulated, where the RESs, energy storage systems, and transmission line expansion are optimized in the first stage and a unit commitment problem is proposed in the second‐stage optimization to assess the performance of the expanded system. This problem is reformulated into a two‐stage optimization problem with complete mixed‐integer recourse, where the state variable is binary. A novel enhanced Benders decomposition algorithm is proposed to solve the IGT&SEP efficiently, where the cutting planes are generated by a primal‐dual relaxation of the recourse problem. Simulations are conducted on the modified IEEE‐30 test system and modified IEEE‐118 test system. Compared with adjustable robust optimization and L1‐norm Wasserstein distance‐based distributionally robust optimization, numerical results verify the effectiveness of the proposed IGT&SP, together with the solution algorithm.
Heuristic algorithm for univariate stratification problem
Authors: Brito José André , Semaan Gustavo , de Lima Leonardo , Fadel Augusto
Published: September 2023

In sampling theory, stratification corresponds to a technique used in surveys, which allows segmenting a population into homogeneous subpopulations (strata) to produce statistics with a higher level of precision. In particular, this article proposes a heuristic to solve the univariate stratification problem – widely studied in the literature. One of its versions sets the number of strata and the precision level and seeks to determine the limits that define such strata to minimize the sample size allocated to the strata. A heuristic-based on a stochastic optimization method and an exact optimization method was developed to achieve this goal. The performance of this heuristic was evaluated through computational experiments, considering its application in various populations used in other works in the literature, based on 20 scenarios that combine different numbers of strata and levels of precision. From the analysis of the obtained results, it is possible to verify that the heuristic had a performance superior to four algorithms in the literature in more than 94% of the cases, particularly concerning the known algorithm of Lavallée–Hidiroglou.
Complete Hydatidiform Mole with a Coexisting Viable Male Fetus Detected by Cell-Free DNA
Authors: Lemieux Mackenzie , Kus Lauren , Stewart Kali , He Mai , Rowe Jackson , Brady Matthew , Bligard Katherine , Lawlor Megan , Kelly Jeannie
Published: September 2023

Complete hydatidiform mole with coexisting fetus (CHMCF) is rare, and diagnosis is challenging due to limited data. Here, we present the case of a patient with noninvasive prenatal test (NIPT) resulting in “likely molar pregnancy” in the second trimester. Subsequent ultrasound confirmed a cystic appearing portion of the placenta. At 22 weeks, the patient delivered a demised fetus and two placentas. Pathology was consistent with CHMCF. This case is the first to show primary detection of a CHMCF with single-nucleotide polymorphism (SNP)-based NIPT prior to ultrasound identification. Our case suggests the use of SNP-based NIPT as an alternative noninvasive method to guide shared decision-making and clinical management for patients with this diagnosis.
Nourishing social solidarity in exchanging gifts: a study on social exchange in Shanghai communities during COVID-19 lockdown
Authors: Zhou Youjia , Dong Chen
Published: September 2023

During the COVID-19 lockdown in Shanghai, we found many social exchanges within communities. In this study, we focus on exploring the driving forces behind social exchanges and their impacts on the social solidarity of local communities. Twenty-eight residents of separate communities are interviewed, and grounded theory is applied to have the motivation for social exchanges coded and analyzed. We find that reciprocal and generalized exchanges, rather than negotiated exchanges, occur in most communities. Among these exchanges, the willingness to share is stimulated by the traditional cultural norms taking place in online social groups. Residents will be propelled to carry on exchanges through sentiments cultivated within and to develop the micro social order through interactions in the media space. Social exchanges bring social solidarity to communities and develop it into a noticeable form consisting of functional, emotional, and communal aspects.
Isolated Nocturnal Hypertension in People Living With Human Immunodeficiency Virus: A Cross-Sectional Study
Authors: Zanuzzi Matias G , López Silvina M , Cattaneo Máximo J , Pérez-Maure María A , Lahiri Cecile D , Romero Cesar A
Published: September 2023

BACKGROUND

Nocturnal hypertension (NH) is a potent cardiovascular risk factor described frequently in people with HIV (PWH). Isolated NH (INH) is less well reported in PWH because of the need for ambulatory blood pressure monitoring (ABPM) in office normotensive patients. We aim to document the prevalence of NH and INH and the clinical factors associated with these phenotypes.

METHODS

Cross-sectional study from an HIV program in Argentina. Office and ABPM measurements, as well as clinical and laboratory exploration, were performed. We defined INH as NH with daytime normotension in patients with office normotension.

RESULTS

We obtained ABPM in 66 PWH, 60% male, aged 44.7 (IQR 27–69) years; 87% receiving antiretroviral therapy, and 86.2% virologically suppressed. ABPM-based hypertension prevalence was 54.7% (95% CI: 42.5–66.3). The prevalence of NH was 48.5% (32/66), while the INH prevalence was 19.7% (95% CI: 11.7–30.9). No differences were found regarding sex, HIV viral load, CD4+ T lymphocytes count, or years of infection between normotensive and INH patients. Multiple linear regression model adjusted for sex and age determined that body mass index (β = 0.93, P < 0.01), plasma uric acid (β = 0.25, P = 0.04), plasma potassium (β = −10.1, P = 0.01), and high-sensitivity C-reactive protein (hs-CRP) (β = 0.78, P = 0.02) independently predicted nocturnal systolic blood pressure (BP) in PWH. In a multiple logistic regression model adjusted for age and sex, the presence of sedentariness, plasma potassium <4 mEq/L, BMI, and hs-CRP levels were predictors of INH.

CONCLUSION

INH is highly prevalent in PWH. Metabolic and inflammatory markers predict nocturnal SBP in PWH.
Sex biases and the scarcity of sex metadata in global herpetology collections
Authors: Wainwright Tara , Trevena Morwenna , Alewijnse Sarah R , Campbell Patrick D , Jones Marc E H , Streicher Jeffrey W , Cooper Natalie
Published: September 2023

Natural history specimens are a widely used and valuable resource for conservation, ecology, and evolutionary biology. One might assume that these collections are representative of natural populations, but recent work has suggested that many collections have disproportionately more male than female specimens. Here, we investigate sex ratios in > 5 000 000 amphibian and reptile specimen records from global natural history collections. We found a slight bias towards males in amphibians (39% females) and reptiles (47% females), but this varied among orders and families. Body size, sexual size dimorphism, and year of collection had little effect. Strikingly however, > 95% of herpetology specimen records had no sex data associated with them at all, even from recent collections. This lack of sex data substantially limits the utility of herpetological museum collections in many ways. We propose that enhanced efforts to train taxonomic specialists and support their careers would unlock the potential of sex-based research using museum collections and their associated public databases.
BCEDB: a linear B-cell epitopes database for SARS-CoV-2
Authors: Tai Chengzheng , Li Hongjun , Zhang Jing
Published: September 2023

The 2019 Novel Coronavirus (SARS-CoV-2) has infected millions of people worldwide and caused millions of deaths. The virus has gone numerous mutations to replicate faster, which can overwhelm the immune system of the host. Linear B-cell epitopes are becoming promising in prevention of various deadly infectious diseases, breaking the general idea of their low immunogenicity and partial protection. However, there is still no public repository to host the linear B-cell epitopes for facilitating the development vaccines against SARS-CoV-2. Therefore, we developed BCEDB, a linear B-cell epitopes database specifically designed for hosting, exploring and visualizing linear B-cell epitopes and their features. The database provides a comprehensive repository of computationally predicted linear B-cell epitopes from Spike protein; a systematic annotation of epitopes including sequence, antigenicity score, genomic locations of epitopes, mutations in different virus lineages, mutation sites on the 3D structure of Spike protein and a genome browser to visualize them in an interactive manner. It represents a valuable resource for peptide-based vaccine development.

Database URL: http://www.oncoimmunobank.cn/bcedbindex
Submucosal Injection of the RNA Oligonucleotide GUT-1 in Active Ulcerative Colitis Patients: A Randomized, Double-Blind, Placebo-Controlled Phase 2a Induction Trial
Authors: Atreya Raja , Kühbacher Tanja , Waldner Maximilian J , Hirschmann Simon , Drvarov Oliver , Abu Hashem Raed , Maaser Christian , Kucharzik Torsten , Dinter Johanna , Mertens Jessica , Schramm Christoph , Holler Babett , Mössner Joachim , Suzuki Kenji , Yokoyama Junji , Terai Shuji , Uter Wolfgang , Yoneyama Hiroyuki , Asakura Hitoshi , Hibi Toshifumi , Neurath Markus F
Published: September 2023

Background and Aims

Carbohydrate sulfotransferase 15 [CHST15] biosynthesizes sulphated matrix glycosaminoglycans and is implicated in intestinal inflammation and fibrosis. Here, we evaluate the efficacy and safety of the double-stranded RNA oligonucleotide GUT-1, a specific blocker of CHST15, as induction therapy in patients with ulcerative colitis [UC].

Methods

In this randomized, double-blind, placebo-controlled, phase 2a study, we enrolled endoscopically active UC patients, refractory to conventional therapy, in five hospital centres across Germany. Patients were randomized 1:1:1 using a block randomized technique to receive a single dosing of 25 nM GUT-1, 250 nM GUT-1, or placebo by endoscopic submucosal injections. The primary outcome measure was improvement of endoscopic lesions at weeks 2 or 4. The secondary outcome measures included clinical and histological responses. Safety was assessed in all patients who received treatment.

Results

Twenty-eight patients were screened, 24 were randomized, and 21 were evaluated. Endoscopic improvement at weeks 2 or 4 was achieved by 71.4% in the GUT-1 250 nM, 0% in the GUT-1 25 nM, and 28.6% in the placebo group. Clinical remission was shown by 57.1% in the GUT-1 250 nM, 0% in the GUT-1 25 nM, and 14.3% in the placebo groups. Histological improvement was shown by 42.9% in the GUT-1 250 nM, 0% in the GUT-1 25 nM, and 0% in the placebo groups. GUT-1 250 nM reduced CHST15 expression significantly and suppressed mucosal inflammation and fibrosis. GUT-1 application was well tolerated.

Conclusion

Single dosing by submucosal injection of GUT-1 repressed CHST15 mucosal expression and may represent a novel induction therapy by modulating tissue remodelling in UC.
Crimes without a body: reflections on a case series of online crimes
Authors: Barbieri Cristiano , Grattagliano Ignazio , Catanesi Roberto
Published: September 2023

There is a large volume of online crimes. The aim of this work is to reflect on virtual crimes that are apparently different but actually have commonalities. In these cases, the corporeal sphere that mediates interpersonal relationships is absent, and perceptions of the real world and emotional regulation may be altered, which poses the risk of destructive behaviours. From this standpoint, self/hetero-directed aggression is the result of a certain type of transition from the real to the virtual world, where the body either is not involved at all or is experienced in an aberrant manner. In this study, we present three cases that clearly illustrate this concept.
Dynamic Evolution of Bacterial Ligand Recognition by Formyl Peptide Receptors
Authors: Paterson Nicole M , Al-Zubieri Hussein , Ragona Joseph , Kohler Kristin M , Tirado Juan , Geisbrecht Brian V , Barber Matthew F
Published: September 2023

The detection of invasive pathogens is critical for host immune defense. Cell surface receptors play a key role in the recognition of diverse microbe-associated molecules, triggering leukocyte recruitment, phagocytosis, release of antimicrobial compounds, and cytokine production. The intense evolutionary forces acting on innate immune receptor genes have contributed to their rapid diversification across plants and animals. However, the functional consequences of immune receptor divergence are often unclear. Formyl peptide receptors (FPRs) comprise a family of animal G protein–coupled receptors which are activated in response to a variety of ligands including formylated bacterial peptides, pathogen virulence factors, and host-derived antimicrobial peptides. FPR activation in turn promotes inflammatory signaling and leukocyte migration to sites of infection. Here we investigate patterns of gene loss, diversification, and ligand recognition among FPRs in primates and carnivores. We find that FPR1, which plays a critical role in innate immune defense in humans, has been lost in New World primates. Amino acid variation in FPR1 and FPR2 among primates and carnivores is consistent with a history of repeated positive selection acting on extracellular domains involved in ligand recognition. To assess the consequences of FPR divergence on bacterial ligand interactions, we measured binding between primate FPRs and the FPR agonist Staphylococcus aureus enterotoxin B, as well as S. aureus FLIPr-like, an FPR inhibitor. We found that few rapidly evolving sites in primate FPRs are sufficient to modulate recognition of bacterial proteins, demonstrating how natural selection may serve to tune FPR activation in response to diverse microbial ligands.
Identification of Dementia in Medicare Claims Compared to Rigorous Clinical Assessments in African Americans
Authors: Grodstein Francine , James Bryan D , Chen Yi , Capuano Ana W , Power Melinda C , Bennett David A , Bynum Julie P W , Barnes Lisa L
Published: September 2023

Background

Evidence indicates the health care system disproportionately misses dementia in African American compared to White individuals. In preliminary data, we examined factors related to dementia identification by the health care system among African Americans.

Methods

We leveraged linked Medicare fee-for-service claims and detailed annual cohort evaluations in African Americans from 4 cohorts at Rush Alzheimer’s Disease Center.

Results

Among 88 African Americans with cognitive impairment (mean = 10 years follow-up), Medicare claims identified dementia <2 years from cohort diagnosis in 55%; 27% were identified 2–9.9 years after cohort diagnosis, and in 18% there was either no claims diagnosis during the study period, or claims identified dementia 10+ years after cohort diagnosis. Claims identification of dementia was related to older age at cohort diagnosis (eg, <2 years between cohort and claims: mean = 82 years; 10+ years/no diagnosis: mean = 77 years, p = .04), lower Mini-Mental State Examination (MMSE) score (<2 years: mean = 24; 10+ years/no diagnosis: mean = 26, p = .04), more depressive symptoms (<2 years: mean = 2.1 symptoms; 10+ years/no diagnosis: mean = 1.2, p = .04), and more comorbidity (<2 years: mean = 5.6 comorbidities; 10+ years/no diagnosis, mean = 3.0, p = .02).

Conclusions

Among African Americans, preliminary data indicate the health care system most rapidly identifies dementia in older individuals, with worse cognitive and physical health. The health care system may miss opportunities for early support of African Americans with dementia, and caregivers.
Confound-leakage: confound removal in machine learning leads to leakage
Authors: Hamdan Sami , Love Bradley C , von Polier Georg G , Weis Susanne , Schwender Holger , Eickhoff Simon B , Patil Kaustubh R
Published: September 2023

Background

Machine learning (ML) approaches are a crucial component of modern data analysis in many fields, including epidemiology and medicine. Nonlinear ML methods often achieve accurate predictions, for instance, in personalized medicine, as they are capable of modeling complex relationships between features and the target. Problematically, ML models and their predictions can be biased by confounding information present in the features. To remove this spurious signal, researchers often employ featurewise linear confound regression (CR). While this is considered a standard approach for dealing with confounding, possible pitfalls of using CR in ML pipelines are not fully understood.

Results

We provide new evidence that, contrary to general expectations, linear confound regression can increase the risk of confounding when combined with nonlinear ML approaches. Using a simple framework that uses the target as a confound, we show that information leaked via CR can increase null or moderate effects to near-perfect prediction. By shuffling the features, we provide evidence that this increase is indeed due to confound-leakage and not due to revealing of information. We then demonstrate the danger of confound-leakage in a real-world clinical application where the accuracy of predicting attention-deficit/hyperactivity disorder is overestimated using speech-derived features when using depression as a confound.

Conclusions

Mishandling or even amplifying confounding effects when building ML models due to confound-leakage, as shown, can lead to untrustworthy, biased, and unfair predictions. Our expose of the confound-leakage pitfall and provided guidelines for dealing with it can help create more robust and trustworthy ML models.
Radial shear in the flow at the Earth’s core surface
Authors: Firsov I , Jault D , Gillet N , Aubert J , Mandea M
Published: September 2023

The Earth’s magnetic field at the core–mantle boundary is the gradient of a harmonic potential function if the mantle is electrically insulating, and the horizontal components of the field can be derived from its radial component in the mantle. Therefore, these components give no further observational information on the core dynamics. However, it can still be envisioned that the horizontal components of the induction equation at Earth’s core surface yield further knowledge on the fluid motions at the top of the core independently of the observations. Here, we show that they provide a linear relationship between the surface velocity and the surface shear (strain shear) that depends on the mantle electrical conductivity. This offers a protocol to calculate the surface shear that we validate with synthetics obtained from dynamo simulations in the limit of a weak mantle conductance. First, using numerical simulations with stress-free boundary condition at the core surface, we retrieve the expected relationship between the horizontal flow uΣ and the shear, ${\bf u}_\Sigma =r\partial _r {\bf u}_{\Sigma }$. Next, we investigate simulations with no-slip boundary condition and insulating mantle, and we obtain the same relationship, even though the shear is not imposed as a boundary condition. Finally, we calculate the flow shear at the top of the core from a magnetic field model based on satellite measurements. The application to geophysical data indicates larger values of the surface flow shear than in the synthetic case, suggesting a possible role of the mantle electrical conductivity. The surface flow shear, in the simulations, much differs from the radial shear in the flow, deeper in the core, which is influenced by the mostly quasi-geostrophic geometry. This implies that we cannot rely on the relationship between the flow and the radial shear for quasi-geostrophic motions to exploit the horizontal components of the induction equation and gain further information on the flow at the Earth’s core surface.
Whole-genome and genome-wide association studies improve key agricultural traits of safflower for industrial and medicinal use
Authors: Chen Jiang , Guo Shuai , Hu Xueli , Wang Rui , Jia Donghai , Li Qiang , Yin Xianmei , Liao Xuejiao , Hu Zunhong , Wang Peiqi , Ren Chaoxiang , Dong Shuai , Chen Chao , Chen Shilin , Xu Jiang , Pei Jin
Published: September 2023

Safflower (Carthamus tinctorius) is widely cultivated around the world for its seeds and flowers. The presence of linoleic acid (LA) in its seeds and hydroxysafflor yellow A (HSYA) in its flowers are the crucial traits that enable safflower to be used for industrial and medicinal purposes. Understanding the genetic control of these traits is essential for optimizing the quality of safflower and its breeding. To further this research, we present a chromosome-scale assembly of the genome of the safflower variety ‘Chuanhonghua 1’, which was achieved using an integrated strategy combining Illumina, Oxford Nanopore, and Hi-C sequencing. We obtained a 1.17-Gb assembly with a contig N50 of 1.08 Mb, and all assembled sequences were assigned to 12 pseudochromosomes. Safflower’s evolution involved the core eudicot γ-triplication event and a whole-genome duplication event, which led to large-scale genomic rearrangements. Extensive genomic shuffling has occurred since the divergence of the ancestor of dicotyledons. We conducted metabolite and transcriptome profiles with time- and part-dependent changes and screened candidate genes that significantly contribute to seed lipid biosynthesis. We also analyzed key gene families that participate in LA and HSYA biosynthesis. Additionally, we re-sequenced 220 safflower lines and carried out a genome-wide association study using high-quality SNP data for eight agronomic traits. We identified SNPs related to important traits in safflower. Besides, the candidate gene HH_034464 (CtCGT1) was shown to be involved in the biosynthesis of HSYA. Overall, we provide a high-quality reference genome and elucidate the genetic basis of LA and HSYA biosynthesis in safflower. This vast amount of data will benefit further research for functional gene mining and breeding in safflower.
International Criminal Court Standards in a Context of Transitional Justice
Authors: Gutiérrez-Rodríguez Carlos
Published: September 2023

On October 2021, Colombia and the Office of the Prosecutor (OTP) of the International Criminal Court (ICC) signed a Cooperation Agreement that closed the preliminary examination opened in 2004. This is the first agreement of its kind. This article analyses the evolution of the OTP’s reasoning in considering whether a state has genuinely administered justice in a transitional context. To do so, it chronologically analyses the Colombian case, which is the first peace process in the world developed entirely under the continued scrutiny of the ICC. Furthermore, the Colombian situation was the ICC’s most extended preliminary examination, influencing in turn, the transitional justice outcomes as well as the position of the OTP. The Cooperation Agreement offers, therefore, an outstanding opportunity to analyse from a practical point of view, debates that have been predominantly theoretical and will have future consequences elsewhere.
Carbohydrate or Electrolyte Rehydration Recovers Plasma Volume but Not Post-immersion Performance Compared to Water After Immersion Diuresis
Authors: Wheelock Courtney E , Lavoie Elizabeth M , Stooks Jocelyn , Schwob Jacqueline , Hess Hayden W , Pryor Riana R , Hostler David
Published: September 2023

Introduction

We tested the hypothesis that a carbohydrate (CHO: 6.5%) or carbohydrate–electrolyte (CHO + E: 6.5% + 50 mmol/L NaCl) drink would better recover plasma volume (PV) and exercise performance compared to water (H2O) after immersion diuresis.

Methods

Twelve men (24 ± 2 years; 82.4 ± 15.5 kg; and V̇O2max: 49.8 ± 5.1 mL · kg−1 · min−1) completed four experimental visits: a no-immersion control (CON) and three 4-h cold-water (18.0 °C) immersion trials (H2O, CHO, and CHO + E) followed by exercise in a warm environment (30 °C, 50% relative humidity). The exercise was a 60-minute loaded march (20.4 kg; 55% VO2max) followed by a 10-minute intermittent running protocol. After immersion, subjects were rehydrated with 100% of body mass loss from immersion diuresis during the ruck march. PV is reported as a percent change after immersion, after the ruck march, and after the intermittent running protocol. The intermittent running protocol distance provided an index of exercise performance. Data are reported as mean ± SD.

Results

After immersion, body mass loss was 2.3 ± 0.7%, 2.3 ± 0.5%, and 2.3 ± 0.6% for H2O, CHO, and CHO + E. PV loss after immersion was 19.8 ± 8.5% in H2O, 18.2 ± 7.0% in CHO, and 13.9 ± 9.3% in CHO + E, which was reduced after the ruck march to 14.7 ± 4.7% (P = .13) in H2O, 8.8 ± 8.3% (P < .01) in CHO, and 4.4 ± 10.9% (P = .02) in CHO + E. The intermittent running protocol distance was 1.4 ± 0.1 km in CON, 1.4 ± 0.2 km in H2O, 1.4 ± 0.1 km in CHO, and 1.4 ± 0.2 km in CHO + E (P = .28).

Conclusions

Although CHO and CHO + E better restored PV after immersion, post-immersion exercise performance was not augmented compared to H2O, highlighting that fluid replacement following immersion diuresis should focus on restoring volume lost rather than fluid constituents.
Star clusters in tidal debris
Authors: Rodruck Michael , Charlton Jane , Borthakur Sanchayeeta , Chitre Aparna , Durrell Patrick R , Elmegreen Debra , English Jayanne , Gallagher Sarah C , Gronwall Caryl , Knierman Karen , Konstantopoulos Iraklis , Li Yuexing , Maji Moupiya , Mullan Brendan , Trancho Gelys , Vacca William
Published: September 2023

We present results of a Hubble Space Telescope (HST) UBVI-band study of star clusters in tidal tails, using new WFC3 and ACS imaging to complement existing WFPC2 data. We survey 12 tidal tails across seven merging systems, deriving ages and masses for 425 star cluster candidates (SCCs). The stacked mass distribution across all systems follows a power law of the form dN/dM ∝ Mβ, with β = −2.02 ± 0.15, consistent with what is seen in other star-forming environments. GALEX and Swift UV imaging provide star formation rates (SFRs) for our tidal tails, which when compared with ages and masses of our SCCs, allows for a determination of the cluster formation efficiency (CFE). We find the CFE increases with increasing SFR surface density, matching the theoretical model. We confirm this fit down at SFR densities lower than previously measured (log ΣSFR (M⊙ yr−1 kpc−2) ≈ −4.2), as related to the CFE. We determine the half-light radii for a refined sample of 57 SCCs with our HST WFC3 and ACS imaging, and calculate their dynamical age, finding the majority of them to be gravitationally bound. We also provide evidence of only low-mass (<104 M⊙) cluster formation in our nearest galaxy, NGC 1487, consistent with the theory that this system is a dwarf merger.
Thermal self-similar disc winds: transonic nature
Authors: Fukue J
Published: September 2023

Thermally driven two-dimensional disc winds are examined under the fully self-similar treatment, focusing the attention on the transonic nature. In the spherical potential, such as point-mass and logarithmic ones, the usual transonic solutions cannot be constructed, because the critical conditions themselves do not exist. That is, the flow can reach the sonic point in the polar direction, while there is no gravitational force in the polar direction, and the regularity condition does not hold. In the non-spherical potential, such as the Mestel self-gravitating one, the gravity works in the polar direction, and therefore, there are critical points in the flow. However, the usual transonic solutions do not exist, since the topology of the critical points is always centre (O-type). Hence, in the fully self-similar disc winds, the usual transonic solutions passing through the critical points do not exist, at least for typical cases. Instead, the new-type wind solutions are found in the point-mass case. In contrast to the usual transonic flows, the new-type solutions are continuously accelerated along the streamline by the thermal pressure, and eventually become supersonic in the streamline direction without passing through the critical points. These new-type solutions are possible, when the density distribution is centrally concentrated, and when the initial subsonic velocity is not so large to avoid singularities.
Uric acid and diabetes mellitus: an update
Authors: Singh Shailendra K , Singh Rina , Singh Santosh K , Iquebal Mir A , Jaiswal Sarika , Rai Pradeep K
Published: September 2023

The relationship between diabetes mellitus (DM) and high serum uric acid is complex and controversial. Many epidemiological studies have reported a positive association, whereas others have reported an inverse association or none. In the pathogenesis of DM it is the intracellular urate that is more important than the extracellular and dissociation between the two is possible. Evidence suggests that high serum uric acid induces insulin resistance and beta cell failure in animal models. Reduction of intracellular uric acid can be achieved by dietary measures such as reducing fructose and salt intake, and uric acid–lowering drugs. We suggest that in the Western diet, these elements play a crucial role in pathogenesis of DM. To determine the precise and exact interrelationship between intracellular and extracellular uric acid, well-designed studies are required. Besides this, clinical trials are needed to determine whether intracellular and extracellular urate reduction will provide benefit in prevention and treatment of DM and complications associated with it.
Hispanic Men’s Earnings Mobility Across Immigrant Generations: Estimates Using Tax Records
Authors: Villarreal Andrés , Tamborini Christopher R
Published: September 2023

Whether immigrants and their descendants are catching up socioeconomically with the rest of society is a fundamental question in the study of immigrant assimilation. In this paper, we examine the progress that Hispanic immigrant men make catching up with the earnings of later-generation Whites across generations. We rely on data from multiple years of the Current Population Survey linked with individuals’ tax earnings. This unique dataset allows us to overcome some important limitations of previous studies that employ a synthetic generation approach in which individuals born approximately one generation earlier are used as proxies for actual parents. Our matching strategy also enables us to identify the exact third generation and evaluate the contribution of ethnic attrition to estimates of intergenerational mobility. Second-generation Hispanic men are found to experience lower mobility than later-generation Whites for most values of parental earnings. However, their lower mobility can be explained by their immigrant parents’ lower education levels. In contrast, third-generation Hispanic men experience lower mobility even after accounting for parental education and ethnic attrition. This finding is consistent with a stalling or reversal in the socioeconomic progress of Hispanics beyond the second generation.