bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of BiOBr/graphene oxide photocatalyst assisted by sodium dodecyl sulfate for efficient degradation of organic pollutants
Authors: Yang Jiayan , Liu Yuanyuan , Wu Jing , Lang Tian , Chen Jie , Liu Yao , Qiu Qingqing , Liang Tongxiang , Zeng Jinming
Published: August 2024

Surfactant‐assisted synthesis of photocatalysts for water treatment has received extensive attention from researchers. In this paper, a novel and efficient BiOBr/graphene oxide (BiOBr/GO) photocatalyst assisted by sodium dodecyl sulfate (SDS) was synthesized by a simple solvothermal method. Compared with use of other surfactants, like polyvinylpyrrolidone (PVP) and cetyltrimethylammonium bromide (CTAB), BiOBr/GO (SDS) shows outstanding photocatalytic degradation activity under optimal conditions: The degradation rate constants of BiOBr/GO (SDS) for oxytetracycline (OTC), tetracycline hydrochloride (TCH), brilliant blue (BB), and Rhodamine B (RhB) are 0.073, 0.057, 0.166, and 0.626 min−1, which are 2.8, 1.8, 9, and 1.5 times larger than pure BiOBr, respectively. In addition, after five cycles, BiOBr/GO (SDS) exhibits superior cycling stability. The enhanced photocatalytic performance can benefit from the introduction of SDS and GO. With the assistance of SDS in the preparation process, BiOBr/GO (SDS) nanosheets have good adsorption performance and dispersion effect, which is favorable for raising their specific surface area. Meanwhile, the electron capture effect of GO improves the transfer and separation efficiency of photogenerated carriers. Moreover, the possible degradation pathway for TCH is identified through liquid chromatography–mass spectrometry (LC–MS). This research can become a valuable reference for synthesizing photocatalysts with visible light response to degrading organic pollutants such as antibiotics and dyes.
Anthropogenic stressors and rocky shore communities along Atlantic Patagonia: The need of including coastal biodiversity in marine protected areas planning
Authors: Mendez María M. , Schwindt Evangelina
Published: August 2024

The conservation of marine ecosystems depends on the establishment and functioning of marine protected areas (MPAs). These areas are not exempt from the effects generated by a variety of anthropogenic stressors. Coastal biodiversity can provide key information of MPAs health; however, it is not usually considered in MPAs planning process, particularly in the Southwestern Atlantic.

In this work, we provide an analysis and discussion of the anthropogenic stressors and the rocky intertidal biodiversity parameters occurring along 10 latitudinal degrees within the major MPAs of the continental Patagonia (Argentina). Specifically, we studied the intensity of 10 social, economic and environmental marine‐related anthropogenic stressors and characterized the intertidal biodiversity (biomass, density and size of scorched mussels and its associated communities) in the mid intertidal rocky shore.

We found that most of the anthropogenic stressors studied had some level of intensity at all MPAs in Patagonia. In addition, each MPA has unique biodiversity assemblages. Total anthropogenic stress was not directly correlated with the mussel bed parameters or the richness of the associated fauna. Artisanal fisheries, tourism, invasive species and trampling were found to have the highest intensity on the MPAs. Moreover, a negative relation between artisanal fisheries, tourism and invasive species and the biomass and size of mussels was found, along with a negative relation between tourism and density. Furthermore, three MPAs registered the greatest anthropogenic pressure.

Our study evidence that although Argentina has significantly advanced in the creation of MPAs in the last decades, the objectives for the conservation of the ecosystems are still narrow. Our results highlight that globally, MPAs need to include the perspective of coastal intertidal biodiversity and their stressors in their management strategies. By doing this, it will contribute to have a more holistic approach and thus it will improve MPAs conservation efforts.
Trends in information behavior research, 2016–2022: An Annual Review of Information Science and Technology (ARIST) paper
Authors: Huvila Isto , Gorichanaz Tim
Published: August 2024

Research on how people look for and interact with information has a long history in the information field. The current literature has been repeatedly reviewed in earlier volumes of Annual Review of Information Science and Technology. In this review, we offer an overview of the research published in this area in the years 2016–2022 with a focus on the trends that have emerged in this period. We use the term “information behavior” as an umbrella for the research area interested in how people become informed and engage with information in diverse manners acknowledging that different researchers and subfields prefer other terms and frameworks, including information practices, information experience, and health information seeking, to name a few. We reviewed 1270 articles in the field published in the years 2016–2022 and identified seven emerging trends: The CoVID‐19 Pandemic, Diversity and Inclusion, Embodiment, Misinformation and Trust, Social Q&A Websites, Collaboration, and Information Creation. The reviewed literature and trends are discussed in relation to their significance for information, earlier review of information behavior research, and the long‐debated issue of theory‐driven versus atheoretical research in the field.
Long‐term oncological outcomes after multimodal treatment for locally advanced prostate cancer
Authors: Roldan Fiorella L. , Falagario Ugo Giovanni , Olsson Mats , Salas Rodolfo Sánchez , Aly Markus , Egevad Lars , Lantz Anna , Grönberg Henrik , Akre Olof , Hosseini Abolfazl , Wiklund N. Peter
Published: August 2024

Objective

The aim of this study is to evaluate treatment patterns and long‐term oncological outcomes of patients with locally advanced prostate cancer (LAPCa).

Patients and methods

This is a population‐based study including LAPC (cT3‐4, M0) patients from the Stockholm region (Sweden). A sub‐analysis was performed in men treated with primary cystoprostatectomy or total pelvic exenteration (TPE) for cT4 prostate cancer (PCa).

Cox regression was used to identify predictors of overall mortality (OM) and cancer‐specific mortality (CSM). Biochemical progression‐free survival (BPFS) and 90 days complications were reported for the radical surgery subgroup.

Results

We included 2921 patients with cT3(N = 2713) or cT4(N = 208), M0 PCa diagnosed between 2003 and 2019. Out of these, 249(9%), 1497(51%) and 1175(40%) underwent radical prostatectomy, RT + ADT and androgen deprivation therapy (ADT), respectively. Survival rates were 76% (IQR: 68, 83), 47% (IQR: 44, 50) and 23% (IQR: 20, 27), respectively at 10 years. Irrespective of treatment modalities, cT4 patients had worse survival compared to cT3 patients (OM: HR1.44, IQR:1.17,1.77; PCSM: HR1.39, IQR:1.06,1.82). Twenty‐seven patients with cT4, N0‐1, M0 were treated with cystoprostatectomy or TPE. Twenty‐two patients (81.5%) received neoadjuvant ADT. The 5‐year BPFS, CSS and OS rates were 39.6%, 68.8% and 63.8%, respectively. Nine patients (33.3%) had Clavien‐Dindo grade III and 1 (3.7%) grade IV complication within 90 days after surgery.

Conclusions

Pelvic surgery with radical intent as part of a multidisciplinary management may be an effective alternative for selected patients with locally advanced PCa leading to local tumour control and an acceptable morbidity.
Permeable TAD boundaries and their impact on genome‐associated functions
Authors: Chang Li‐Hsin , Noordermeer Daan
Published: August 2024

TAD boundaries are genomic elements that separate biological processes in neighboring domains by blocking DNA loops that are formed through Cohesin‐mediated loop extrusion. Most TAD boundaries consist of arrays of binding sites for the CTCF protein, whose interaction with the Cohesin complex blocks loop extrusion. TAD boundaries are not fully impermeable though and allow a limited amount of inter‐TAD loop formation. Based on the reanalysis of Nano‐C data, a multicontact Chromosome Conformation Capture assay, we propose a model whereby clustered CTCF binding sites promote the successive stalling of Cohesin and subsequent dissociation from the chromatin. A fraction of Cohesin nonetheless achieves boundary read‐through. Due to a constant rate of Cohesin dissociation elsewhere in the genome, the maximum length of inter‐TAD loops is restricted though. We speculate that the DNA‐encoded organization of stalling sites regulates TAD boundary permeability and discuss implications for enhancer–promoter loop formation and other genomic processes.
Screening and characterization of cosmetic efficacy components of Terminalia chebula based on biological activity‐guided methodology
Authors: Liang Cai‐Cai , Zhang Feng‐Qin , Chen Juan
Published: August 2024

Terminalia chebula exhibits a high level of antioxidant capacity and is highly valued in medicine and cosmetics. However, its main efficacy and active ingredients related to antioxidant, whitening, and anti‐aging are still unclear. In this study, the active site responsible for its cosmetic efficacy was specified by the biological activity‐guided method and further characterized by using ultra‐high‐performance liquid chromatography coupled with quadrupole time‐of‐flight mass spectrometry (UHPLC‐QTOF‐MS/MS). T. chebula was ultrasonically extracted by five solvents, and 30% ethanol extract was screened out for subsequent purification by 1,1‐D‐iphenyl‐2‐picrylhydrazyl radical (DPPH), 2,2′‐Azinobis‐(3‐ethylbenzothiazoline‐6‐sulphonate) (ABTS), hydroxyl, and superoxide anion free radical scavenging assays. Five elution fractions were obtained by column chromatography on D101 macroporous adsorbent resin eluted by an increased proportion of ethanol. The 30% ethanol elution fraction was specified as the enrichment site of active ingredients showing good antioxidant capacity and potent inhibitory activity against tyrosinase and elastase. A total of 30 compounds were identified by UHPLC‐QTOF‐MS/MS in the 30% ethanol elution fraction, including 11 gallotannins, 14 ellagitannins, and 5 other compounds, and these compounds may be the key ingredients in cosmetics beneficial for the skin. Such a biological activity‐guided method has provided a simple and rapid venue for specifying the components of medicinal herbs responsible for cosmetic efficacy.
The interaction between cannabinoids and long‐term synaptic plasticity: A survey on memory formation and underlying mechanisms
Authors: Azarfarin Maryam , Ghadiri Tahereh , Dadkhah Masoomeh , Sahab‐Negah Sajad
Published: August 2024

Synaptic plasticity, including long‐term potentiation (LTP) and long‐term depression (LTD), is an essential phenomenon in memory formation as well as maintenance along with many other cognitive functions, such as those needed for coping with external stimuli. Synaptic plasticity consists of gradual changes in the biochemistry and morphology of pre‐ and postsynaptic neurons, particularly in the hippocampus. Consuming marijuana as a primary source of exocannabinoids immediately impairs attention and working memory‐related tasks. Evidence regarding the effects of cannabinoids on LTP and memory is contradictory. While cannabinoids can affect a variety of specific cannabinoid receptors (CBRs) and nonspecific receptors throughout the body and brain, they exert miscellaneous systemic and local cerebral effects. Given the increasing use of cannabis, mainly among the young population, plus its potential adverse long‐term effects on learning and memory processes, it could be a future global health challenge. Indeed, the impact of cannabinoids on memory is multifactorial and depends on the dosage, timing, formula, and route of consumption, plus the background complex interaction of the endocannabinoids system with other cerebral networks. Herein, we review how exogenously administrated organic cannabinoids, CBRs agonists or antagonists, and endocannabinoids can affect LTP and synaptic plasticity through various receptors in interaction with other cerebral pathways and primary neurotransmitters.
DEAD/H‐box helicase 11 is transcriptionally activated by Yin Yang‐1 and accelerates oral squamous cell carcinoma progression
Authors: Yang Guang , Shi Xin , Zhang Meixia , Wang Kaiwen , Tian Xin , Wang Xiaofeng
Published: August 2024

Oral squamous cell carcinoma (OSCC) is the most common oral malignancy. DEAD/H‐box helicase 11 (DDX11), a DNA helicase, has been implicated in the progression of several cancers. Yet, the precise function of DDX11 in OSCC is poorly understood. The DDX11 expression in OSCC cells and normal oral keratinocytes was evaluated in the Gene Expression Omnibus database (GSE146483 and GSE31853). SCC‐4 and CAL‐27 cells expressing doxycycline‐inducible DDX11 or DDX11 shRNA were generated by lentiviral infection. The role of DDX11 in OSCC cells was determined by 3‐(4, 5‐Dimethylthiazol‐2‐yl)‐2, 5‐diphenyltetrazolium bromide assay, colony formation assay, flow cytometry assay, TUNEL staining, and western blot. The effects of DDX11 on tumor growth were explored in a xenograft nude mouse model. The relationship between DDX11 and transcription factor Yin Yang‐1 (YY1) was researched using the dual luciferase report assay and chromatin immunoprecipitation assay. DDX11 expression was significantly upregulated in OSCC cells. Knockdown of DDX11 inhibited cell proliferation, induced cell cycle arrest, and suppressed PI3K‐AKT pathway, while DDX11 overexpression showed opposite effects. The number of apoptotic cells was increased in DDX11 silenced cells. DDX11 upregulation or knockdown accelerated or suppressed tumor growth in vivo, respectively. Moreover, the YY1 bound and activated the DDX11 promoter, resulting in increasing DDX11 expression. Forced expression DDX11 reversed the anticancer effects of YY1 silencing on OSCC cells. DDX11 has tumor‐promoting function in OSCC and is transcriptionally regulated by YY1, indicating that DDX11 may serve as a potential target for the OSCC treatment.
Development of machine learning models for fractional flow reserve prediction in angiographically intermediate coronary lesions
Authors: Lombardi Marco , Vergallo Rocco , Costantino Andrea , Bianchini Francesco , Kakuta Tsunekazu , Pawlowski Tomasz , Leone Antonio M. , Sardella Gennaro , Agostoni Pierfrancesco , Hill Jonathan M. , De Maria Giovanni L. , Banning Adrian P. , Roleder Tomasz , Belkacemi Anouar , Trani Carlo , Burzotta Francesco
Published: August 2024

Background

Fractional flow reserve (FFR) represents the gold standard in guiding the decision to proceed or not with coronary revascularization of angiographically intermediate coronary lesion (AICL). Optical coherence tomography (OCT) allows to carefully characterize coronary plaque morphology and lumen dimensions.

Objectives

We sought to develop machine learning (ML) models based on clinical, angiographic and OCT variables for predicting FFR.

Methods

Data from a multicenter, international, pooled analysis of individual patient's level data from published studies assessing FFR and OCT on the same target AICL were collected through a dedicated database to train (n = 351) and validate (n = 151) six two‐class supervised ML models employing 25 clinical, angiographic and OCT variables.

Results

A total of 502 coronary lesions in 489 patients were included. The AUC of the six ML models ranged from 0.71 to 0.78, whereas the measured F1 score was from 0.70 to 0.75. The ML algorithms showed moderate sensitivity (range: 0.68–0.77) and specificity (range: 0.59–0.69) in detecting patients with a positive or negative FFR. In the sensitivity analysis, using 0.75 as FFR cut‐off, we found a higher AUC (0.78–0.86) and a similar F1 score (range: 0.63–0.76). Specifically, the six ML models showed a higher specificity (0.71–0.84), with a similar sensitivity (0.58–0.80) with respect to 0.80 cut‐off.

Conclusions

ML algorithms derived from clinical, angiographic, and OCT parameters can identify patients with a positive or negative FFR.
Selenium‐Centered Cascade Exchangers and Conformational Control Unlock Unique Patterns of Thiol‐Mediated Cellular Uptake
Authors: Coelho Filipe , Zeisel Lukas , Thorn‐Seshold Oliver , Matile Stefan
Published: August 2024

Dynamic‐covalent electrophiles called cascade exchangers (CAXs) can reversibly engage cell‐surface thiols. Conjugates between CAXs and molecular or even protein‐sized cargos can deliver these cargos into cells by thiol‐mediated uptake (TMU); free CAXs can also hinder TMU presumably by competing for thiol exchange sites. So far, three orthogonal networks of cellular thiol exchange partners have been identified to participate in TMU, centering on the transferrin receptor, integrins, and protein disulfide isomerases. This study introduces cyclic selenenylsulfides as a new CAX type, with polarised reactivity that brings important differences from the known disulfide and diselenide CAXs. Additionally, this study introduces methods to modulate CAX activity by employing remote functional groups to tune ring re‐closure rates, e. g. via thiolate de/stabilization by hydrogen bonding and ion pairing. Differently to all CAXs known, Se‐centred CAXs participate in two different TMU networks (integrins preferred, PDIA3 tolerated). When free, the remotely tuned Se‐centred CAXs were strong inhibitors of most TMU systems, but again brought a novel feature: they increased the uptake of tetrel‐centred Michael acceptor CAXs, making them the first free CAX we know of that can accelerate TMU. We conclude that Se‐ and tetrel‐centred CAXs share a cellular thiol exchange partner that hinders TMU, which may be a target for improving the delivery of Michael acceptor drugs. The unique thiol exchange partner patterns generated by Se‐centered CAXs with remotely tuned ring closure motifs support that they will prove a valuable tool to help decode TMU and achieve chemical control over cellular entry on the molecular level.
Flow reduction due to arterial catheterization during stroke treatment – A computational study using a distributed compartment model
Authors: Pradhan Aseem , Mut Fernando , Sosale Medhini , Cebral Juan
Published: August 2024

The effectiveness of various stroke treatments depends on the anatomical variability of the cerebral vasculature, particularly the collateral blood vessel network. Collaterals at the level of the Circle of Willis and distal collaterals, such as the leptomeningeal arteries, serve as alternative avenues of flow when the primary pathway is obstructed during an ischemic stroke. Stroke treatment typically involves catheterization of the primary pathway, and the potential risk of further flow reduction to the affected brain area during this treatment has not been previously investigated. To address this clinical question, we derived the lumped parameters for catheterized blood vessels and implemented a corresponding distributed compartment (0D) model. This 0D model was validated against an experimental model and benchmark test cases solved using a 1D model. Additionally, we compared various off‐center catheter trajectories modeled using a 3D solver to this 0D model. The differences between them were minimal, validating the simplifying assumption of the central catheter placement in the 0D model. The 0D model was then used to simulate blood flows in realistic cerebral arterial networks with different collateralization characteristics. Ischemic strokes were modeled by occlusion of the M1 segment of the middle cerebral artery in these networks. Catheters of different diameters were inserted up to the obstructed segment and flow alterations in the network were calculated. Results showed up to 45% maximum blood flow reduction in the affected brain region. These findings suggest that catheterization during stroke treatment may have a further detrimental effect for some patients with poor collateralization.
Nutritional Composition of Post‐Catastrophic Foods
Authors: Mather Tara , Siva Niroshan , Jauregui Marjorie , Poudel Pradip , de Lima Brossi Maria Julia , Lambert Joshua D. , Di Gioia Francesco , Connolly Erin L. , Anderson Charles T.
Published: August 2024

In addition to current challenges in food production arising from climate change, soil salinization, drought, flooding, and human‐caused disruption, abrupt sunlight reduction scenarios (ASRS), e.g., a nuclear winter, supervolcano eruption, or large asteroid or comet strike, are catastrophes that would severely disrupt the global food supply and decimate normal agricultural practices. In such global catastrophes, teragrams of particulate matter, such as aerosols of soot, dust, and sulfates, would be injected into the stratosphere and block sunlight for multiple years. The reduction of incident sunlight would cause a decrease in temperature and precipitation and major shifts to climate patterns leading to devastating reductions in agricultural production of traditional food crops. To survive a catastrophic ASRS or endure current and future disasters and famines, humans might need to rely on post‐catastrophic foods, or those that could be foraged, grown, or produced under the new climate conditions to supplement reduced availability of traditional foods. These foods have sometimes been referred to as emergency, alternate, or resilient foods in the literature. While there is a growing body of work that summarizes potential post‐catastrophic foods and their nutritional profiles based on existing data in the literature, this article documents a list of protocols to experimentally determine fundamental nutritional properties of post‐catastrophic foods that can be used to assess the relative contributions of those foods to a balanced human diet that meets established nutritional requirements while avoiding toxic levels of nutrients. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Total digestible glucans

Basic Protocol 2: Apparent protein digestibility

Basic Protocol 3: Vitamins B1, B3, B9, C, and D2 by HPLC

Basic Protocol 4: Total antioxidant activity (DPPH‐scavenging activity)

Basic Protocol 5: Total phenolic compounds (Folin–Ciocalteu reagent method)

Basic Protocol 6: Mineral content by ICP‐OES
Ultra‐Dilute SnCl4‐Catalyzed Conversion of Concentrated Glucose to 5‐Hydroxymethylfurfural in Aqueous Deep Eutectic Solvent
Authors: Xusheng Guo , Chuan Qin , Yuxi Si , Xilei Lyu , Youwei Cheng
Published: August 2024

5‐Hydroxymethylfurfural(HMF) is a versatile chemical synthesized from glucose dehydration catalyzed by metal chloride (MClx) in deep eutectic solvents (DESs). However, the low glucose concentration and high catalyst dosage hinder large‐scale HMF production. Herein, we report an aqueous DES of tetraethylammonium bromide(TEAB)‐glucose for converting concentrated glucose (40 wt %, relative to TEAB) using ultra‐dilute SnCl4 (0.25 mol %), achieving a 62 % yield of HMF. Ultra‐dilute MClx‐catalyzed selective conversion of glucose is feasible only when combining SnCl4 with Br‐based DES, which is elucidated by density functional theory and molecular dynamic calculations. Using SnCl4 is essential due to its higher glucose isomerization activity than AlCl3 and CrCl3, which can be attributed to its low‐barrier coordination with glucose and its barrier‐free separation from fructose. Halide anions in DESs strongly interact with glucose, hindering the MClx‐glucose coordination and thereby reducing MClx’s activity for glucose isomerization. Consequently, Br‐based DESs facilitate higher activity of MClx than Cl‐based DESs, due to the weaker interaction between halide anion and glucose. In addition, we elucidated the side reactions including condensation, polymerization, and isomerization, and proposed a reaction network. Our findings clarify the differential activity of MClx and the impact of halide anions in DESs on MClx’s activity.
CPT1A‐IL‐10‐mediated macrophage metabolic and phenotypic alterations ameliorate acute lung injury
Authors: Wang Muyun , Wu Di , Liao Ximing , Hu Haiyang , Gao Jing , Meng Linlin , Wang Feilong , Xu Wujian , Gao Shaoyong , Hua Jing , Wang Yuanyuan , Li Qiang , Wang Kun , Gao Wei
Published: August 2024

Background

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) is a common acute respiratory failure due to diffuse pulmonary inflammation and oedema. Elaborate regulation of macrophage activation is essential for managing this inflammatory process and maintaining tissue homeostasis. In the past decades, metabolic reprogramming of macrophages has emerged as a predominant role in modulating their biology and function. Here, we observed reduced expression of carnitine palmitoyltransferase 1A (CPT1A), a key rate‐limiting enzyme of fatty acid oxidation (FAO), in macrophages of lipopolysaccharide (LPS)‐induced ALI mouse model. We assume that CPT1A and its regulated FAO is involved in the regulation of macrophage polarization, which could be positive regulated by interleukin‐10 (IL‐10).

Methods

After nasal inhalation rIL‐10 and/or LPS, wild type (WT), IL‐10‐/‐, Cre‐CPT1Afl/fl and Cre+CPT1Afl/fl mice were sacrificed to harvest bronchoalveolar lavage fluid, blood serum and lungs to examine cell infiltration, cytokine production, lung injury severity and IHC. Bone marrow‐derived macrophages (BMDMs) were extracted from mice and stimulated by exogenous rIL‐10 and/or LPS. The qRT‐PCR, Seahorse XFe96 and FAO metabolite related kits were used to test the glycolysis and FAO level in BMDMs. Immunoblotting assay, confocal microscopy and fluorescence microplate were used to test macrophage polarization as well as mitochondrial structure and function damage.

Results

In in vivo experiments, we found that mice lacking CPT1A or IL‐10 produced an aggravate inflammatory response to LPS stimulation. However, the addition of rIL‐10 could alleviate the pulmonary inflammation in mice effectively. IHC results showed that IL‐10 expression in lung macrophage decreased dramatically in Cre+CPT1Afl/fl mice. The in vitro experiments showed Cre+CPT1Afl/fl and IL‐10‐/‐ BMDMs became more “glycolytic”, but less “FAO” when subjected to external attacks. However, the supplementation of rIL‐10 into macrophages showed reverse effect. CPT1A and IL‐10 can drive the polarization of BMDM from M1 phenotype to M2 phenotype, and CPT1A‐IL‐10 axis is also involved in the process of maintaining mitochondrial homeostasis.

Conclusions

CPT1A modulated metabolic reprogramming and polarisation of macrophage under LPS stimulation. The protective effects of CPT1A may be partly attributed to the induction of IL‐10/IL‐10 receptor expression.
Artificial intelligence in fusion protein three‐dimensional structure prediction: Review and perspective
Authors: Kumar Himansu , Kim Pora
Published: August 2024

Recent advancements in artificial intelligence (AI) have accelerated the prediction of unknown protein structures. However, accurately predicting the three‐dimensional (3D) structures of fusion proteins remains a difficult task because the current AI‐based protein structure predictions are focused on the WT proteins rather than on the newly fused proteins in nature. Following the central dogma of biology, fusion proteins are translated from fusion transcripts, which are made by transcribing the fusion genes between two different loci through the chromosomal rearrangements in cancer. Accurately predicting the 3D structures of fusion proteins is important for understanding the functional roles and mechanisms of action of new chimeric proteins. However, predicting their 3D structure using a template‐based model is challenging because known template structures are often unavailable in databases. Deep learning (DL) models that utilize multi‐level protein information have revolutionized the prediction of protein 3D structures. In this review paper, we highlighted the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using DL models. We aim to explore both the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr‐Rosetta and D‐I‐TASSER for modelling the 3D structures.

Highlights

This review provides the overall pipeline and landscape of the prediction of the 3D structure of fusion protein.

This review provides the factors that should be considered in predicting the 3D structures of fusion proteins using AI approaches in each step.

This review highlights the latest advancements and ongoing challenges in predicting the 3D structure of fusion proteins using deep learning models.

This review explores the advantages and challenges of employing AlphaFold2, RoseTTAFold, tr-Rosetta, and D-I-TASSER to model 3D structures.
Compact planar 28/60‐GHz wideband MIMO antenna for 5G‐enabled IoT devices
Authors: Farooq Umar , Lokam Anjaneyulu , Mallavarapu Sandhya
Published: August 2024

This work presents a compact two‐element multi‐input‐multi‐output (MIMO) antenna for 5G‐enabled IoT devices. The antenna operates over a wide frequency range of 24.6 to 31.4 GHz (28‐GHz band) and 57.6 to 60.2 GHz (60‐GHz band). Each MIMO element consists of an inverted L‐shaped slotted radiator with a partial ground plane. The antenna offers a peak gain of 5.45 and 5.56 dBi across two operating bands. The minimum isolation between the two ports is −26.5 dB, reaching a maximum value of over −45 dB. The investigation of MIMO metrics like “envelope correlation coefficient (ECC),” “diversity gain (DG),” “mean effective gain (MEG),” “channel capacity loss (CCL),” and “total active reflection coefficient (TARC)” also show favorable characteristics. The antenna is fabricated on a 10 × 22 × 0.503 mm3 Rogers 5880 substrate. The experimental results are in close agreement with that of the simulation results. The distinguishing features of the proposed antenna such as its compact design, simple geometrical configuration, wide operating bandwidth, low ECC, and high isolation make it a strong candidate for 5G‐enabled IoT devices.
Dynamics of a goshawk population across half a century is driven by the variation of first‐year survival
Authors: Schaub Michael , Looft Volkher , Plard Floriane , von Rönn Jan A. C.
Published: August 2024

Population dynamics are driven by stochastic and density‐dependent processes acting on demographic rates. Individuals differ demographically, and to capture these differences, models of population dynamics are usually structured by age and stage, rarely by sex. An effect of sex on population dynamics is expected if the dynamics of males and females differ, requiring an unequal sex ratio at birth and/or sex‐specific survival probabilities. Goshawks (Accipiter gentilis) show large sexual size dimorphism and differential survival, but it is unknown whether males and females contribute differently to population dynamics. We studied a goshawk population in northern Germany over 47 years using brood monitoring data, collected feathers and nestling ringing data. We jointly analyzed the data using a two‐sex integrated population model and performed retrospective and prospective population analyses to understand whether the demographic drivers of population change differ between the sexes. The population showed large fluctuations, during which the number of breeding pairs doubled, but the long‐term trend of the population was slightly negative. Female survival exceeded male survival during the first year of life. Females started to reproduce at a younger age than males, productivity increased with female age, the sex ratio of nestlings was male biased and there was moderate male immigration. Despite these differences, temporal variation in sex ratio did not contribute to population dynamics and the contribution of temporal variation in survival was similar for both sexes. Variation in first‐year survival was the strongest driver in this population, regulated by a weak density‐dependent feedback acting through female first‐year survival. Overall, the contributions of the two sexes to population dynamics were similar in this monogamous species with strong sexual size dimorphism.
Climate change and C4 and C3 grasses in a midlatitude dryland steppe
Authors: Anderson Robert C. , Martyn Trace E. , Renne Rachel R. , Burke Ingrid C. , Lauenroth William K.
Published: August 2024

Climate change is projected to alter the structure of plant communities due to increasing temperatures and changes to precipitation patterns, particularly in midlatitude dryland ecosystems. Modifications to climatic suitability may lead to major community changes such as altered dominant plant functional types. Previous studies have indicated that climatic suitability is likely to increase for C4 grasses and decrease for C3 grasses in the Western United States. However, if no C4 grass species currently exist to serve as a propagule source, expansion into areas of increased suitability will be limited. We conducted a field and modeling study in the Upper Green River Basin (UGRB) of Western Wyoming to determine if (1) C4 grasses are present to provide a propagule source and (2) C4 grasses are likely to increase in importance relative to C3 grasses due to climatic changes. We searched 44 sites for C4 grasses to establish presence, and modeled suitability at 35 sites using 17 Global Climate Models, two greenhouse gas Representative Concentration Pathways (RCPs; 4.5 and 8.5), and two time periods (mid‐ and late century; 2030–2060 and 2070–2099, respectively). We found C4 grasses at 10 of the 44 sites, indicating that there is a present propagule source. Our model projected increases in suitability for both C3 and C4 grasses across sites for all RCPs and time periods. In the mid‐century RCP 4.5 scenario, the C3 functional type increased in projected biomass in 29 of 35 sites, and the C4 type increased in 31 sites. In this scenario, C3 grasses increased in projected biomass by a median 4 g m−2 (5% change), and C4 grass biomass increased by a median 8 g m−2 (21% change). Our study suggests that climate change will increase climatic suitability for grasses across the UGRB, and that all requirements are in place for C4 grasses to increase in abundance.
Unlocking rivers' hidden diversity and ecological status using DNA metabarcoding in Northwest Spain
Authors: Fueyo Álvaro , Sánchez Omar , Carleos Carlos , Escudero Amando , Cordón Javier , Granero‐Castro Javier , Borrell Yaisel Juan
Published: August 2024

Rivers are crucial ecosystems supporting biodiversity and human well‐being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms of taxonomic resolution and scalability. This study explores the application of DNA metabarcoding analysis in both bulk and environmental DNA (eDNA) samples for comprehensive assessment of macrozoobenthic biodiversity, detection of invasive and endangered species, and evaluation of river ecological status in northwestern Spain. DNA metabarcoding of homogenized bulk samples and water eDNA revealed a mean of 100 and 87 macrozoobenthos species per sample respectively. However, the specific composition was significantly different with only 27.3% of the total species being shared. It was not possible to identify all the OTUs to species level; only 17.43% and 49.4% of the OTUs generated could be identified to species level in the bulk and eDNA samples, respectively. Additionally, a total of 11 exotic species (two first records for the Iberian Peninsula and another three first records for Asturias region) and one endangered species were detected by molecular tools. Molecular methods showed significant correlations with morphological identification for EQR values (Ecological Quality Ratio) of IBMWP index, yet differences in inferred river ecological status were noted, with bulk samples tending to indicate higher status. Overall, DNA metabarcoding offers a promising approach for river biomonitoring, providing insights into biodiversity, invasive species, and ecological status within a single analysis. Further optimization and intercalibration are required for its implementation in routine biomonitoring programmes, but its scalability and multi‐tasking capabilities position it as a valuable tool for integrated monitoring of river ecosystems.
Wearable defibrillator to improve accuracy in selecting candidates to implantable defibrillator: A real‐world experience
Authors: Dell'Era Gabriele , Caimmi Philippe , Spinoni Enrico Guido , Battistini Eleonora , Porcellini Stefano , De Vecchi Federica , Santagostino Matteo , Ghiglieno Chiara , Degiovanni Anna , Leigheb Fabrizio , Kozel Daniela , Capponi Andrea , Patti Giuseppe
Published: August 2024

Aims

The indication for implantable cardioverter defibrillator (ICD) for sudden cardiac death (SCD) prevention relies mostly on left ventricular ejection fraction (LVEF) ≤ 35%. The use of a wearable cardioverter defibrillator (WCD) in the case of dynamic alterations of LVEF may help avoid an improper early ICD implant when a favourable evolution in the post‐acute phase is observed and may help reduce costs.

Methods

This parallel cohort retrospective study included patients with heart failure with reduced ejection fraction (HFrEF) at high risk of arrhythmias recruited in the acute phase and divided into an early ICD cohort and a WCD cohort for primary prevention during the waiting period established by European Society of Cardiology guidelines.

Results

A total of 41 consecutive patients were enrolled: 26 in the WCD group and 15 in the early ICD group. Age, LVEF at baseline, causes of HFrEF and drug therapy in the two cohorts were similar. During the waiting period after the inclusion, three patients (11.5%) in the WCD cohort and four (26.7%) in the early ICD cohort developed relevant ventricular arrhythmias (P = 0.22); none of them had subsequent LVEF recovery. At the end of the waiting period, 13 patients (50%) in the WCD group and 7 (46.7%) in the early ICD group experienced LVEF recovery (P = 0.84). The average cost per patient at the end of the waiting period was €23 934 in the early ICD cohort versus €19 167 in the WCD cohort (−19.9%). This cost savings from WCD use appears even higher when projected over a 10 year period (−41.2%).

Conclusions

WCD may represent a cost‐effective strategy to more accurately select candidates for the primary prevention ICD implant among high‐risk patients with HFrEF. ICD use provides effective protection from SCD and reduces costs compared with an extensive early ICD implant.
Interactive effects of elevation difference, slope variation, and terrain formation on road traffic crashes occurrences using triangular irregular network
Authors: Jima Debela , Sipos Tibor
Published: August 2024

Numerous factors contribute to traffic crashes, which result in fatalities and injuries. Road traffic crashes and their severity level are likely caused by variations in elevation, slope, and terrain formation. As far as our knowledge is concerned, the triangular irregular network (TIN) was not used to analyze dangerous zones of the road network with respect to traffic crashes' location. The main purpose of this study was to investigate a dangerous road network that was affected by traffic crashes using TIN. To address the goal, this study used elevation differences slope variation, and terrain between road traffic crash locations. The study used the intersection zone road network coordinates of traffic crashes in the city of Budapest that were recorded from 2017 to 2021. Using tools like ArcGIS and MS Excel, the study organized, modeled, and analyzed the data. Geometrical interval classification was used to classify the data in accordance with the characteristics of elevation deference and slope variation. Both inferential and descriptive statistics were engaged to explain, analyze, and summarize the findings. The results of this study demonstrated that the majority of traffic crashes occurred in locations with lower elevations and their differences, steeper/cliff slopes between points, and flat terrain. The finding was in contrast to what was observed in other studies. This study advocates that TIN is the optimal method and substitute for analyzing the risky zone of the road network at macroscopic level.
An improved Harris hawks optimizer with enhanced logarithmic spiral and dynamic factor and its application for predicting molten iron temperature in the blast furnace
Authors: Liu Zhendong , Fang Yiming , Liu Le , Ma Shuidong
Published: August 2024

In response to the problem of poor search performance and difficulty in escaping from the local optimum in the Harris hawks optimizer, an improved Harris hawks optimizer with enhanced logarithmic spiral and dynamic factor (IHHO‐ELSDF) is proposed in this paper. The enhanced logarithmic spiral mechanism is adopted in the exploration phase, and its main feature is the use of an improved opposite‐learning hybrid logarithmic spiral mechanism to search for more promising regions. The dynamic factor is used to replace the escaping energy to improve the global search capability of the algorithm, and it can better balance exploration and exploitation. In addition, a random distribution strategy is proposed for the exploitation phase to avoid falling into the local optimum. Based on 23 classical test functions, the influence of the distribution probability, the three improved mechanisms, and the exploration–exploitation ratio in IHHO‐ELSDF are analyzed. Subsequently, IHHO‐ELSDF is subjected to a comparative analysis with 17 algorithms on the IEEE CEC2022 benchmark suite. These tests show that IHHO‐ELSDF outperforms most competitors in numerical optimization. Furthermore, to assess its applicability in real‐world problems, IHHO‐ELSDF is employed to optimize parameters in the wavelet neural network used for molten iron temperature prediction. The simulation results based on real production data show that the proposed prediction model achieves a high prediction precision with , , and .
A Quantitative Adverse Outcome Pathway for Embryonic Activation of the Aryl Hydrocarbon Receptor of Fishes by Polycyclic Aromatic Hydrocarbons Leading to Decreased Fecundity at Adulthood
Authors: Doering Jon A. , Dubiel Justin , Stock Eric , Collins Cameron H. , Frick Ian , Johnson Hunter M. , Lowrey-Dufour Christopher M. , Miller Justin G. P. , Xia Zhe , Tomy Gregg T. , Wiseman Steve
Published: August 2024

Quantitative adverse outcome pathways (qAOPs) describe the response–response relationships that link the magnitude and/or duration of chemical interaction with a specific molecular target to the probability and/or severity of the resulting apical-level toxicity of regulatory relevance. The present study developed the first qAOP for latent toxicities showing that early life exposure adversely affects health at adulthood. Specifically, a qAOP for embryonic activation of the aryl hydrocarbon receptor 2 (AHR2) of fishes by polycyclic aromatic hydrocarbons (PAHs) leading to decreased fecundity of females at adulthood was developed by building on existing qAOPs for (1) activation of the AHR leading to early life mortality in birds and fishes, and (2) inhibition of cytochrome P450 aromatase activity leading to decreased fecundity in fishes. Using zebrafish (Danio rerio) as a model species and benzo[a]pyrene as a model PAH, three linked quantitative relationships were developed: (1) plasma estrogen in adult females as a function of embryonic exposure, (2) plasma vitellogenin in adult females as a function of plasma estrogen, and (3) fecundity of adult females as a function of plasma vitellogenin. A fourth quantitative relationship was developed for early life mortality as a function of sensitivity to activation of the AHR2 in a standardized in vitro AHR transactivation assay to integrate toxic equivalence calculations that would allow prediction of effects of exposure to untested PAHs. The accuracy of the predictions from the resulting qAOP were evaluated using experimental data from zebrafish exposed as embryos to another PAH, benzo[k]fluoranthene. The qAOP developed in the present study demonstrates the potential of the AOP framework in enabling consideration of latent toxicities in quantitative ecological risk assessments and regulatory decision-making. Environ Toxicol Chem 2024;43:2145–2156. © 2024 SETAC
Nogo‐A‐mediated constraints on activity‐dependent synaptic plasticity and associativity in rat hippocampal CA2 synapses
Authors: Pavon Maria Vazquez , Navakkode Sheeja , Sajikumar Sreedharan
Published: August 2024

Hippocampal area CA2 has garnered attention in recent times owing to its significant involvement in social memory and distinctive plasticity characteristics. Research has revealed that the CA2 region demonstrates a remarkable resistance to plasticity, particularly in the Schaffer Collateral (SC)‐CA2 pathway. In this study we investigated the role of Nogo‐A, a well‐known axon growth inhibitor and more recently discovered plasticity regulator, in modulating plasticity within the CA2 region. The findings demonstrate that blocking Nogo‐A in male rat hippocampal slices facilitates the establishment of both short‐term and long‐term plasticity in the SC‐CA2 pathway, while having no impact on the Entorhinal Cortical (EC)‐CA2 pathway. Additionally, the study reveals that inhibiting Nogo‐A enables association between the SC and EC pathways. Mechanistically, we confirm that Nogo‐A operates through its well‐known co‐receptor, p75 neurotrophin receptor (p75NTR), and its downstream signaling factor such as Rho‐associated protein kinase (ROCK), as their inhibition also allows plasticity induction in the SC‐CA2 pathway. Additionally, the induction of long‐term depression (LTD) in both the EC and SC‐CA2 pathways led to persistent LTD, which was not affected by Nogo‐A inhibition. Our study demonstrates the involvement of Nogo‐A mediated signaling mechanisms in limiting synaptic plasticity within the CA2 region.
Susceptibility weighted imaging for detection of thrombus in acute ischemic stroke: A cross‐sectional study
Authors: Phuyal Subash , Paudel Sushanta , Chhetri Suchit Thapa , Phuyal Prakash , Shrestha Sadina , Maharjan Anzil Man Singh
Published: August 2024

Background and Aims

Susceptibility‐weighted imaging (SWI) can help in the diagnosis of thrombus within the vessel in acute ischemic stroke, known as susceptibility vessel sign (SVS), and detection of SVS within the vessel can predict treatment modality and outcome. In this study, the purpose is to correlate the SVS on SWI with different parameters of stroke.

Methods

This prospective cross‐sectional study enrolled consecutive stroke patients with vessel occlusion on magnetic resonance angiography (MRA) over 1 year. The relationship between SVS on SWI with risk factors, territory involved, and length of thrombus was correlated with the National Institutes of Health Stroke Scale (NIHSS).

Results

A total of 105 patients were enrolled in this study. Sixty‐two percent (66 out of 105) of patients showed SVS on SWI with MRA‐positive occlusion. A positive correlation was observed between SVS on SWI and the risk factor (p = 0.003, chi‐square test), with 86% of patients with heart disease and 47% with hypertension exhibiting SVS. Additionally, a positive correlation was observed between SVS on SWI and territorial occlusion (p = 0.000, chi‐square test). A moderate positive correlation was observed between the NIHSS and thrombus length (p = 0.002, Pearson's correlation coefficient), with a Pearson's coefficient of 0.367.

Conclusions

SWI can be useful in identifying the location of the thrombus, and NIHSS can determine the thrombus length in acute stroke. A higher incidence of SVS can be associated with risk factors, and it also depends upon the site of occlusion of the vessel.