bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences.
Authors: Lascaris R F , Mager W H , Planta R J 
Published: July 2002

Abstract
MOTIVATION: High-level transcriptional activation of most ribosomal protein (rp) genes in Saccharomyces cerevisiae is promoted by the global DNA-binding factor Rap1p. The creation of the complete database of yeast rp gene promoter sequences enabled us to develop a computational selection strategy aimed at acquiring detailed information concerning the DNA-binding specificity of Rap1p. RESULTS: Rap1p sites in rp gene promoters are often found in duplicate, exhibiting strong preferences in both spacing and orientation. Using these preferences, a weight matrix was selected that represents the in vivo binding requirements of Rap1p. The resulting matrix renders the identification of functional Rap1p binding sites more accurate and allowed us to re-evaluate previous in vitro data. Tandemly arranged Rap1p binding sites appear to be typical for rp gene promoters and differ in preferred spacing from sites occurring in (sub)telomeric repeats. The preferred spacing that is found in duplicate Rap1p binding sites of rp gene promoters is restricted to a small window between 15 and 26 bp. This is proposed to reflect the borders within which binding co-operativity operates. The data presented clearly illustrate that computational selection strategies provide information that reaches beyond experimental data. AVAILABILITY: The rp database is available at the url: http://www. chem.vu.nl/BMB/Database.html.
Improved performance in protein secondary structure prediction by inhomogeneous score combination.
Authors: Guermeur Y , Geourjon C , Gallinari P , Del√©age G 
Published: July 2002

Abstract
MOTIVATION: In many fields of pattern recognition, combination has proved efficient to increase the generalization performance of individual prediction methods. Numerous systems have been developed for protein secondary structure prediction, based on different principles. Finding better ensemble methods for this task may thus become crucial. Furthermore, efforts need to be made to help the biologist in the post-processing of the outputs. RESULTS: An ensemble method has been designed to post-process the outputs of discriminant models, in order to obtain an improvement in prediction accuracy while generating class posterior probability estimates. Experimental results establish that it can increase the recognition rate of protein secondary structure prediction methods that provide inhomogeneous scores, even though their individual prediction successes are largely different. This combination thus constitutes a help for the biologist, who can use it confidently on top of any set of prediction methods. Moreover, the resulting estimates can be used in various ways, for instance to determine which areas in the sequence are predicted with a given level of reliability. AVAILABILITY: The prediction is freely available over the Internet on the Network Protein Sequence Analysis (NPS@) WWW server at http://pbil.ibcp.fr/NPSA/npsa_server.ht ml. The source code of the combiner can be obtained on request for academic use.
Food Insecurity Among Individuals With Cardiovascular Disease and Cardiometabolic Risk Factors Across Race and Ethnicity in 1999-2018
Authors: Brandt Eric J. , Chang Tammy , Leung Cindy , Ayanian John Z. , Nallamothu Brahmajee K. 
Published: September 2022

ImportanceFood insecurity is a risk factor for poor cardiovascular outcomes that occur disproportionately among individuals from racial and ethnic minority backgrounds who have cardiovascular disease (CVD) or cardiometabolic risk factors.ObjectiveTo assess long-term prevalence of food insecurity among those with CVD or cardiometabolic risk factors in the United States.Design, Setting, and ParticipantsThis serial cross-sectional study includes data for noninstitutionalized US adults from the National Health and Nutrition Examination Survey (1999-2018).Main Outcomes and MeasuresFood insecurity was assessed using the US Department of Agriculture Adult Food Security Survey Module. We estimated prevalence of food insecurity among adults with prior CVD (myocardial infarction, stroke, heart failure) and cardiometabolic risk factors (hypertension, diabetes, obesity, hyperlipidemia) across racial and ethnic groups and prevalence of Supplemental Nutrition Assistance Program (SNAP) participation among those reporting food insecurity.ResultsIn the analytic sample of 57 517 adults, 6770 individuals (11.8%) reported food insecurity, which was more prevalent among Hispanic (1938 [24.0%]) and non-Hispanic Black (1202 [18.2%]) than non-Hispanic Asian (100 [8.0%]) and non-Hispanic White adults (3221 [8.5%]). Among 57 517 adults, 4527 (7.9%) had any CVD, 2933 (5.1%) coronary artery disease, 1536 (2.7%) stroke, 1363 (2.4%) heart failure, 28 528 (49.6%) hypertension, 17 979 (33.2%) obesity, 6418 (11.2%) diabetes, and 19 178 (30.8%) dyslipidemia. All CVD and cardiometabolic diseases except coronary artery disease were more prevalent among those with food insecurity. Food insecurity increased over time and was more frequent for patients with CVD but not for cardiometabolic risk factors. From 2011 to 2018, non-Hispanic Black adults with CVD had a decrease in food insecurity prevalence (36.6%; 95% CI, 23.9%-49.4%, to 25.4%; 95% CI, 21.4%-29.3%; P = .04 for trend), whereas adults of other races and ethnicities or data based on cardiometabolic risk factors had no significant change. For individuals who had food insecurity, SNAP participation was higher among those with CVD vs without CVD (54.2%; 95% CI, 46.6%-61.8%, vs 44.3%; 95% CI, 40.5%-48.1%; P = .01).Conclusions and RelevanceThe prevalence of food insecurity among patients with CVD increased over time. Although members of non-Hispanic Black and Hispanic groups had the highest food insecurity, non-Hispanic Black individuals with CVD were the only group to have a significant decrease in food insecurity since 2011. Increased recognition of food insecurity and resources for treating it are needed to address the negative consequences of food insecurity on CVD outcomes.
Contrasting Case-Control and Normative Reference Approaches to Capture Clinically Relevant Structural Brain Abnormalities in Patients With First-Episode Psychosis Who Are Antipsychotic Naive
Authors: Remiszewski Natalie , Bryant James Edward , Rutherford Saige E. , Marquand Andre F. , Nelson Eric , Askar Ibrahim , Lahti Adrienne Carol , Kraguljac Nina Vanessa 
Published: September 2022

ImportanceTo make progress toward precision psychiatry, it is crucial to move beyond case-control studies and instead capture individual variations and interpret them in the context of a normal range of biological systems.ObjectiveTo evaluate whether baseline deviations from a normative reference range in subcortical volumes are better predictors of antipsychotic treatment response than raw volumes in patients with first-episode psychosis (FEP) who were naive to antipsychotic medication.Design, Setting, and ParticipantsIn this prospective longitudinal study, patients with first-episode psychosis who were referred from different clinical settings (emergency department, inpatient units, and outpatient clinics) at the University of Alabama at Birmingham were included. A total of 286 patients were screened, 114 consented, 104 enrolled in the treatment trial, and 85 completed the trial. Patients were observed for 16 weeks. Controls were matched by age and sex. Data were collected between June 2016 and July 2021, and data were analyzed from August 2021 to June 2022.InterventionsRisperidone on a flexible dosing scheme for 16 weeks. There was an option to switch to aripiprazole for excessive adverse effects.Main Outcomes and MeasuresThe main outcome of this study was to evaluate, in patients with FEP who were naive to antipsychotic medication, the association of baseline raw volumes and volume deviations in subcortical brain regions with response to antipsychotic medication. Raw brain volumes or volume deviation changes after treatment were not examined.ResultsOf 190 included participants, 111 (58.4%) were male, and the mean (SD) age was 23.7 (5.5) years. Volumes and deviations were quantified in 98 patients with FEP, and data from 92 controls were used as comparison for case-control contrasts and reference curve calibration. In case-control contrasts, patients with FEP had lower raw thalamus (P = .002; F = 9.63; df = 1), hippocampus (P = .009; F = 17.23; df = 1), amygdala (P = .01; F = 6.55; df = 1), ventral diencephalon (P = .03; F = 4.84; df = 1), and brainstem volumes (P = .004; F = 8.39; df = 1). Of 98 patients, 36 patients with FEP (36%) displayed extreme deviations. Associations with treatment response significantly differed between raw volume and deviation measures in the caudate (z = −2.17; P = .03) and putamen (z = −2.15; P = .03).Conclusions and RelevanceThese data suggest that normative modeling allows capture of interindividual heterogeneity of regional brain volumes in patients with FEP and characterize structural pathology in a clinically relevant fashion. This holds promise for progress in precision medicine in psychiatry, where group-level studies have failed to derive reliable maps of structural pathology.
Iron‐Catalyzed Cross‐Dehydrogenative Coupling
Authors: Jia Fan , Li Zhiping 
Published: September 2022

Abstract
The sustainable construction of carbon–carbon bonds or carbon–heteroatom bonds is critical for future green chemical synthesis. Cross‐dehydrogenative coupling (CDC) reactions have thus been widely developed as one of the most sustainable and efficient synthetic strategies for such a philosophy. A number of obvious merits of iron catalysts make this reaction model more potential for industrial production and manufacturing applications. Iron‐catalyzed CDC reactions have emerged as a greener strategy for the direct formation of CC and C–heteroatom bonds from easily available compounds. The use of simple, low toxicity, and cheap iron‐based catalysts meets the criteria for the basis of chemical synthesis compared to those high price, toxic, and precious metal catalysts. In this article, we present the development of iron‐catalyzed CDC reactions by some selected results.
Ni‐Catalyzed C(sp
3
)H Bond Functionalization: Arylation and Aminoxylation
Authors: Sivakumar Ganesan , Subaramanian Murugan , Balaraman Ekambaram 
Published: September 2022

Abstract

Catalytic functionalization of challenging C(sp
3
)H bonds is a readily growing field in chemical synthesis. Significant progress in this field is primarily based on precious transition metal (4d or 5d) catalysts. Recently, the design and development of a new catalytic system based on less‐toxic and inexpensive 3d‐transition metals is emerging as an environmentally benign and sustainable alternative. Especially nickel catalysts have shown tremendous activity in the field of CH bond functionalization. In this article, we briefly describe the recent advances and prospects in the Ni‐catalyzed direct arylation and selective aminoxylation reactions via the C(sp
3
)H bond‐functionalization strategy.
(Hetero)Aryl CH Amination via Organic Electrochemistry
Authors: Shah Jagrut A. , Ngai Ming‐Yu 
Published: September 2022

Abstract
Aromatic amines are essential compounds found in various natural products, drugs, and materials. Their widespread presence has motivated scientists worldwide to explore new avenues for the development of aromatic CN bond formation methodologies. Since the turn of the century, there has been a growing impetus to develop sustainable molecular syntheses. Having been recognized as an effective tool to control the redox events and flow of electrons between reactive species, organic electrocatalysis has been revived after being somewhat dormant for decades in industry and academia. This article provides an overview of electrocatalyzed aromatic CN bond formation reactions, which involve dehydrogenative coupling between aromatic CH bonds and amines through electrocatalysis. We present mechanistic insights and the scope of the methodology in terms of various substrates. We also have provided an outlook for future synthetic applications and different technologies that can merge with electrosynthesis.
Rare‐Earth Metal‐Catalyzed CH Functionalization
Authors: Pan Ying‐Ming , Ye Bo‐Chao , Tang Hai‐Tao 
Published: September 2022

Abstract
CH bond activation has always been attractive research in that it brings the most rapid and atom‐economic transformation approach to synthesize and further utilize the existing chemicals. As what has been published, due to its special and unique structural and electronic properties, rare‐earth metal complexes have been used as the efficient catalyst for CH functionalization in organic synthesis, electrocatalysis, and photocatalysis. This article describes a few examples of the high‐efficiency rare‐earth metal catalysts and the CH functionalization by rare‐earth metal catalysis in organic synthesis.
Free‐Blockage Mesoporous Silica Nanoparticles Loaded with Cerium Oxide as ROS‐Responsive and ROS‐Scavenging Nanomedicine
Authors: Purikova Olha , Tkachenko Ihor , Šmíd Břetislav , Veltruská Kateřina , Dinhová Thu Ngan , Vorokhta Maryna , Kopecký Vladimír , Hanyková Lenka , Ju Xiaohui 
Published: September 2022

AbstractMesoporous silica nanoparticles (MSNs) with reactive oxygen species (ROS)‐responsive “nanogate” as drug delivery platforms are extensively investigated for biomedical applications. However, the physical blockages used to control the cargo release are often limited by their poor sealing ability and low biocompatibility. Herein, a design of free‐blockage MSNs with methylthiopropyl units is proposed as the ROS‐responsive switch. Four synthetic routes are compared with different precursors through either co‐condensation or grafting methods to achieve the methylthio‐functionalized MSNs. The quantity, localization, and chemical structure of the functional units, as well as the mesoporous structure of the silica can be tuned by optimizing the synthetic pathways to obtain desired final products. The ROS‐responsive methylthiopropyl groups can be oxidized to sulfoxides in response to the presence of H2O2, leading to the hydrophobic/hydrophilic conversion of the MSNs. As a proof‐of‐concept design, ultrasmall cerium oxide nanoparticles are encapsulated into the functionalized MSNs and released out within 10 min scavenging more than 80% of the H2O2 in an ROS‐rich environment. This study provides a novel design of a free‐blockage ROS‐controlled release system loaded with ROS‐scavenging nanoparticles for the future application of targeted drug delivery systems combined with antioxidant therapy.
Multifunctional Alendronate‐PEI Carbon Dots for the Treatment of Bone‐Destructive Diseases via Bidirectional Regulation of Osteoblast‐Osteoclast Function
Authors: Zhang Kai , Da Junlong , Wang Jianqun , Liu Lixue , Liu Xinpeng , Yuan Haoze , Jiang Lili , Geng Yawei , Liu Xiaoyao , Jiang Zhuling , Jin Han , Li Ying , Zhang Bin 
Published: September 2022

AbstractBone damage results from the imbalance of bone homeostasis maintained by osteoblast‐regulated bone formation and osteoclast‐mediated bone resorption. Conventional drug therapy and gene therapy may not optimally regulate the bone remodeling process due to the unitary pharmacological mechanism of drug and the safety and targeting of gene vectors. In the present study, multifunctional fluorescent alendronate‐polyethyleneimine carbon dots (Alen‐PEI CDs) are innovatively synthesized, which have excellent biocompatibility, selective bone targeting, gene carrying capacity, and anti‐bone absorption effect. As gene vectors, bone morphogenic protein 2 (BMP2) gene‐loaded Alen‐PEI CDs greatly enhance osteoblast differentiation and bone regeneration. Notably, Alen‐PEI CDs are found to directly inhibit the formation and function of osteoclasts, effectively attenuating the LPS‐induced skull osteolysis in mice. Furthermore, their cumulative toxicity is lower than that of Alen, indicating their potential as an anti‐bone resorptive nanodrug. These results show that the bone‐targeting Alen‐PEI CDs significantly reverse the imbalance of bone homeostasis through a dual‐directional mechanism—directly suppressing bone resorption and indirectly inducing bone formation by transfection of osteogenic therapeutic genes. Overall, the study expands the application for carbon dots in biomedicine, providing new insights for the further development of novel selectively targeted multifunctional nanodrugs for the treatment of bone‐destructive diseases.
Unstated impacts of the green energy industry on the habitat of a coastal delphinid: Turbid‐turbulent wakes induced by offshore wind turbine foundations
Authors: Huang Shiang‐Lin 
Published: September 2022

Abstract

Offshore wind farms (OWFs) are a green energy solution to reducing CO2 emissions, but often encroach on major habitats of coastal delphinids. Clustered OWF construction in shallow waters may have cumulative negative impacts on coastal delphinids and marine ecosystems. Although the impacts of piling noise have been discussed extensively, the potential impacts of oceanographic alterations induced by wind turbine foundations are rarely discussed.
Two OWFs were constructed near the core habitat of a critically endangered subspecies of humpback dolphin (Sousa chinensis taiwanensis) in the eastern Taiwan Strait. Turbid‐turbulent wakes induced by wind turbine foundations were inspected using Landsat images. Sighting rates of the humpback dolphin that were obtained from boat‐based line‐transect surveys near the northern OWF (OWFn) since the late 2000s were examined.
Indicators of surface turbidity were used to highlight turbid‐turbulent wakes extending in the direction of the main current. Sighting rates of the humpback dolphins near the OWFn have been declining since the 2000s, but decreased significantly after the OWFn was constructed and began operating.
The long‐term decline in sighting rates implies an alarming decline in the population size of humpback dolphins. Decreased sighting rates after the OWFn installation indicate the reduced utilization of a once‐important habitat. Offshore wind farm construction may influence prey abundance and composition and cause acute stress from piling noise; operational noise may mask the chorus of prey fish and turbid‐turbulent wakes may disturb the benthic ecosystem.
Site selection committees for future OWFs should avoid the habitats of coastal delphinids and areas subject to strong ocean currents. Ecological impact assessments for OWF projects should examine the impacts of turbulent wakes on benthic ecosystems and of acoustic disturbance on marine mammals. Long‐term environmental monitoring programmes are recommended, which can be funded by wind energy companies as a compensatory measure.
An interrupted time series approach to assess Marine Protected Area impacts on recreational fishing licence sales
Authors: Fox Haley K. , Molina Allen C. , Swearingen Thomas C. 
Published: September 2022

Abstract

Marine Protected Areas (MPAs) are increasingly used as a management and conservation strategy. However, the effects of MPA implementation (i.e. restrictions on extractive use) on recreational fishers' spatial behaviour are often not considered. Spatial shifts in fishing pressure and which port fishers choose to fish from can have ecological and economic impacts. Therefore, it is critical that MPA impacts on recreational fishers are adequately investigated and weighed against potential conservation benefits from MPA designation.
The State of Oregon, USA, has a system of five no‐take marine reserves (MRs) with adjacent limited‐take MPAs. This study used an interrupted time series approach to investigate how fishing licence sales were impacted by MR implementation.
This study found that recreational fishers near only one MR were potentially adversely impacted by MR implementation. The proportion of coastal licence sales near Redfish Rocks MR displayed an immediate sustained 47.1% proportional decrease following reserve implementation. Conversely, there was a 0.5% proportional increase in monthly demand for licence sales near Otter Rock and Cascade Head MRs.
This study suggests that most MRs in Oregon were designated in a manner that limited significant adverse impacts to some ocean users, a specified MR objective. The process of MR planning in Oregon, which involved considerable public input, could be used as an example for MR designation in other similar settings. However, when a potential MR site and adjacent town's conditions match those at Redfish Rocks MR, there may be adverse socio‐economic impacts that should be weighed against potential ecological benefits.
This study also demonstrates the application of an interrupted time series approach. When sufficient data are available, this is a robust approach that addresses numerous shortfalls of traditional MPA impact evaluations.
Behavior analysis in college classrooms: A scoping review
Authors: Curiel Emily S. L. , Kranak Michael P. , Fielding Cheryl , Curiel Hugo , Miller Megan M. 
Published: September 2022

AbstractWe conducted a scoping review of interventions that have been implemented classroom‐wide in college classroom settings. We searched nine behavior‐analytic journals from 2000 through 2020. We identified 59 studies that met our inclusion criteria and organized them into 13 categories: acceptance and commitment therapy (n = 1), equivalence‐based instruction (n = 1), SAFMEDS (n = 4), guided notes (n = 4), response cards (n = 5), group contingencies (n = 5), interteaching (n = 6), programmed instruction, PSI, computer‐aided (CA)PSI (n = 7), contingency arrangements (n = 15), feedback (n = 4), online delivery techniques (n = 4), game study sessions (n = 2), and peer‐generated examples (n = 1). The interventions have been used with undergraduate and graduate students across various course topics and modalities. Most interventions produced positive results, commonly assessed via quiz and exam scores. This review presents the scope of interventions, their characteristics, and recommendations for future research.
Activity of a hypochlorous acid‐producing electrochemical bandage as assessed with a porcine explant biofilm model
Authors: Tibbits Gretchen , Mohamed Abdelrhman , Gelston Suzanne , Flurin Laure , Raval Yash S. , Greenwood‐Quaintance Kerryl E. , Patel Robin , Beyenal Haluk 
Published: September 2022

AbstractThe activity of a hypochlorous acid‐producing electrochemical bandage (e‐bandage) in preventing methicillin‐resistant Staphylococcus aureus infection (MRSA) infection and removing biofilms formed by MRSA was assessed using a porcine explant biofilm model. e‐Bandages inhibited S. aureus infection (p = 0.029) after 12 h (h) of exposure and reduced 3‐day biofilm viable cell counts after 6, 12, and 24 h exposures (p = 0.029). Needle‐type microelectrodes were used to assess HOCl concentrations in explant tissue as a result of e‐bandage treatment; toxicity associated with e‐bandage treatment was evaluated. HOCl concentrations in infected and uninfected explant tissue varied between 30 and 80 µM, decreasing with increasing distance from the e‐bandage. Eukaryotic cell viability was reduced by an average of 71% and 65% in fresh and day 3‐old explants, respectively, when compared to explants exposed to nonpolarized e‐bandages. HOCl e‐bandages are a promising technology that can be further developed as an antibiotic‐free treatment for wound biofilm infections.