bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

AbstractResearch 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

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

AbstractTAD 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

AbstractTerminalia 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

AbstractSynaptic 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

AbstractOral 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

AbstractBackgroundFractional 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.ObjectivesWe sought to develop machine learning (ML) models based on clinical, angiographic and OCT variables for predicting FFR.MethodsData 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.ResultsA 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.ConclusionsML 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

AbstractDynamic‐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

AbstractThe 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

AbstractIn 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 glucansBasic Protocol 2: Apparent protein digestibilityBasic Protocol 3: Vitamins B1, B3, B9, C, and D2 by HPLCBasic 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

Abstract5‐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.