bluuebunny/crossref_metadata_2025_split huggingface dataset:
An experimental Stommel Retention Zone facility with an application to oil droplet dispersion
Authors: Gurung Sanjib , Smith Carlowen Andrew , Zeidi Seyedmohammadjavad , Tejada‐Martinez Andres E. , Murphy David W. 
Published: September 2022

AbstractStommel Retention Zones (SRZs) associated with wind‐driven Langmuir circulation (LC) facilitate the subsurface retention of particles and thus affect processes such as oil spill dispersion, sediment suspension, oil–particle aggregation, and plankton distribution. Since the effect of SRZs on these processes is difficult to study in the field, we present a novel laboratory facility designed to recreate the counterrotating vortex pair flow pattern associated with small‐scale SRZs of various strengths in two dimensions (2D). We then inject an oil jet into this facility to study buoyant oil droplet retention in these SRZs. 2D particle image velocimetry and hybrid Reynolds‐averaged Navier–Stokes/large eddy simulation are used to characterize the flow. Large‐scale oil droplet trajectories in the SRZs are visualized, and oil droplet statistics in the downwelling region and vortex core are measured using high‐magnification brightfield imaging and a droplet detection algorithm. Values of maximum velocity (7.7–32.2 mm s−1), turbulent kinetic energy (10−6 to 10−4 m2 s−2), and turbulent kinetic energy dissipation rate (10−7 to 10−5 m2 s−3) in the downwelling region of the facility fall within the range of values observed in the field. Flow field strength strongly influences oil droplet trajectories, the shape and size of the SRZ, and oil droplet statistics over time, with stronger flows retaining larger oil droplets in the downwelling region over longer periods of time. Indeed, droplets of almost 400 μm diameter are observed in the downwelling region after almost 10 min for the strongest flow. The facility may be used to study the behavior of microplastics, sediments, and zooplankton in LC in the future.
Increasing the scope of the resazurin‐resorufin smart tracer system in hydrologic and biogeochemical sciences: The effects of storage duration and temperature on preservation
Authors: Howard Ben Christopher , Baker Ian , Kettridge Nicholas , Ullah Sami , Krause Stefan 
Published: September 2022

AbstractThe resazurin (raz)‐resorufin (rru) smart tracer system has led to significant advances in hydrologic and biogeochemical sciences but its application has been limited in scope and geography by the short duration that it has been assumed samples can be reliably stored before analysis. For the first time, we quantify the effects of sample storage duration and temperature on measured raz and rru concentrations in order to identify robust storage protocols. Raz/rru concentrations equivalent to those typically used in field and laboratory applications were prepared in three different mediums (deionized water, groundwater, and surface water). Samples were stored at 20°C, 5°C, and −20°C, representing average room, refrigerator, and freezer temperatures. Analysis of raz/rru concentration changes were conducted systematically during an 84‐day period, with higher frequency of analysis in the first 7 d. For samples stored at room temperature, changes of up to 22.6% were observed over the initial 24 h. In contrast, for samples stored in the refrigerator and freezer, changes of up to 8.4% and 6.9% were observed in the same period, respectively. Freezing samples provided the best preservation, yielding a maximum of ~ 10% change after 14 d compared to a maximum of ~ 30% change when cooled. It is generally recommended that raz/rru samples be stored cooled for up to 48 h and frozen for up to 14 d. This offers exciting opportunities to broaden the application of the raz‐rru system to undertake measurements in wider geographical (remote) locations and at increased sampling frequencies.
Comparing methods for measuring egestion in aquatic animals
Authors: May Emily M. , El‐Sabaawi Rana W. 
Published: September 2022

AbstractMost aquatic research on animal waste production evaluates excretion and not egestion, as it is difficult both to collect feces and to accurately analyze its nutrient content. This limits our understanding of how individuals process their dietary nutrients and how animal waste production impacts ecosystems. In this study, we systematically analyzed whether incubation experiments effectively quantify egestion (at high and low temperatures), estimated fecal phosphorus (P) leaching, and evaluated foregut‐hindgut analyses as a complementary method. Incubations were superficially effective but were flawed. Although 82% of fish in high‐temperature incubations and 75% of fish in low‐temperature incubations egested in 24 h, a minority of fish cleared their guts (38% at high temperatures and 6% at low temperatures), making analyzing full nutrient input and output impossible. Furthermore, feces leached P rapidly and variably; a field population's and an experimental population's feces leached 41% and 75% of their initial P respectively. This suggests that previous egestion research that does not measure leaching underestimates fecal nutrient content. Foregut‐hindgut analyses are unaffected by leaching and so effectively complemented incubations. These analyses provided enough hindgut material to estimate fecal %P and allowed us to estimate both dietary nutrient intake (when unknown) and the relative quantity of P in the diet and in the feces. Overall, we suggest that future researchers combine incubations and foregut‐hindgut analyses to estimate aquatic animal waste production.
Thiol‐Click Based Polyglycerol Hydrogels as Biosensing Platform with In Situ Encapsulated Streptavidin Probes
Authors: Thongrom Boonya , Dimde Mathias , Schedler Uwe , Haag Rainer 
Published: September 2022

AbstractAn in situ streptavidin‐encapsulated hydrogel based on dendritic polyglycerol (dPG) which is functionalized with either an acrylate, allyl or acrylamide group and dithiolated polyethylene glycol (PEG) is constructed via a thiol‐click chemistry approach and is investigated for biosensing applications. The hydrogel platform is screened for the encapsulation and release efficiencies of the model protein streptavidin under varying physicochemical conditions, for example, crosslinking chemistry reactions, the molar ratio between the two gel components, macromonomer concentrations or pH‐values. By that, tailor‐made hydrogels can be developed, which are able to encapsulate or release the model protein for several days based on its modality. Furthermore, the accessible binding site of encapsulated streptavidin or in other words, the biotin‐binding performance is quantified, and the stability of the various hydrogel types is studied by rheology measurements, 1H NMR, gel permeation chromatography (GPC), and mass loss experiments.
Uncommon posttranslational modifications in proteomics: ADP‐ribosylation, tyrosine nitration, and tyrosine sulfation
Authors: Bashyal Aarti , Brodbelt Jennifer S. 
Published: September 2022

AbstractPosttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry‐based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography‐tandem mass spectrometry (LC‐MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate‐ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
Quantitative nuclear magnetic resonance of chloride by an accurate internal standard approach
Authors: Wood Jared S. , Dal Poggetto Guilherme , Wang Xiao , Reibarkh Mikhail , Williamson R. Thomas , Cohen Ryan D. 
Published: September 2022

AbstractChloride is the most common counterion used to improve aqueous solubility and enhance stability of small molecule active pharmaceutical ingredients. While several analytical techniques, such as titration, HPLC with charged aerosol detection, and ion chromatography, are currently utilized to assay the level of chloride, they have notable limitations, and these instruments may not be readily available. Here, we present a generally applicable 35Cl solution NMR method to assay the level of chloride in pharmaceutical compounds. The method uses KClO4 as an internal standard for improved accuracy in comparison with external standard methods, and it was found to be robust, linear over three orders of magnitude, precise (<3% RSD), and accurate (<0.5% absolute error).
Convective thermal conditions and the thermophoretic effect's impacts on a hybrid nanofluid over a moving thin needle
Authors: Madhukesh Javali Kotresh , Ramesh Gosikere Kenchappa , Prasannakumara Ballajja Chandrappa 
Published: September 2022

AbstractThis research focuses on the heat source/sink, chemical reaction, and thermophoretic particle deposition in the influence of hybrid nanofluid over a moving thin needle subjected to a magnetic field. Using the appropriate transformations, a group of nonlinear partial differential equations may be converted to ordinary differential equations. Additionally, with the aid of computational software, the RKF‐45 approach is used for the numerical assessment, as well as the shooting operation. It should be mentioned that the results' approval demonstrates a strong association with the previous findings. The resulting graphs mainly explain the fundamental characteristics of hybrid nanofluids and nanofluids, as well as the consequences of different restrictions. An increase in needle size enhances the velocity profile, temperature profile, and concentration profile. The radial and axial velocity profiles are reduced when the magnetic constraint is increased, whereas the thermal and concentration patterns are reversed. Improved heat source‐sink as well as Biot number values will enhance the thermal profile. The concentration profiles will decrease due to reaction rate restrictions and thermophoretic limits. The inclusion of solid volume fraction reduces surface drag forces while increasing the rate of mass transfer. In most circumstances, hybrid nanofluid plays a prominent role than nanofluid.
Optimal control for Hilfer fractional neutral integrodifferential evolution equations with infinite delay
Authors: Kavitha Krishnan , Vijayakumar Velusamy 
Published: September 2022

AbstractThe optimal control solutions for Hilfer fractional neutral integrodifferential evolution equations with infinite delay in Banach space are investigated in this study. To begin, we use fractional computations, Holder inequality, and Banach fixed point approaches to examine conclusions for fractional integrodifferential evolution equations. Following that, we created the fractional integrodifferential evolution system's continuous dependency. We also looked at optimal controls for the Lagrange problem. Finally, an application is given to extract the primary theory.
Crystal structure and reaction mechanism of a bacterial Mg‐dechelatase homolog from the Chloroflexi Anaerolineae
Authors: Dey Debayan , Nishijima Masayoshi , Tanaka Ryouichi , Kurisu Genji , Tanaka Hideaki , Ito Hisashi 
Published: September 2022

AbstractChlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg‐dechelatase enzyme encoded by Stay‐Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues—H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.
Structural basis for the interaction between the first SURP domain of the SF3A1 subunit in U2 snRNP and the human splicing factor SF1
Authors: Nameki Nobukazu , Takizawa Masayuki , Suzuki Takayuki , Tani Shoko , Kobayashi Naohiro , Sakamoto Taiichi , Muto Yutaka , Kuwasako Kanako 
Published: September 2022

AbstractSURP domains are exclusively found in splicing‐related proteins in all eukaryotes. SF3A1, a component of the U2 snRNP, has two tandem SURP domains, SURP1, and SURP2. SURP2 is permanently associated with a specific short region of SF3A3 within the SF3A protein complex whereas, SURP1 binds to the splicing factor SF1 for recruitment of U2 snRNP to the early spliceosomal complex, from which SF1 is dissociated during complex conversion. Here, we determined the solution structure of the complex of SURP1 and the human SF1 fragment using nuclear magnetic resonance (NMR) methods. SURP1 adopts the canonical topology of α1–α2–310–α3, in which α1 and α2 are connected by a single glycine residue in a particular backbone conformation, allowing the two α‐helices to be fixed at an acute angle. A hydrophobic patch, which is part of the characteristic surface formed by α1 and α2, specifically contacts a hydrophobic cluster on a 16‐residue α‐helix of the SF1 fragment. Furthermore, whereas only hydrophobic interactions occurred between SURP2 and the SF3A3 fragment, several salt bridges and hydrogen bonds were found between the residues of SURP1 and the SF1 fragment. This finding was confirmed through mutational studies using bio‐layer interferometry. The study also revealed that the dissociation constant between SURP1 and the SF1 fragment peptide was approximately 20 μM, indicating a weak or transient interaction. Collectively, these results indicate that the interplay between U2 snRNP and SF1 involves a transient interaction of SURP1, and this transient interaction appears to be common to most SURP domains, except for SURP2.
Population pharmacokinetic‐pharmacodynamic analyses of amyloid positron emission tomography and plasma biomarkers for lecanemab in subjects with early Alzheimer's disease
Authors: Hayato Seiichi , Takenaka Osamu , Sreerama Reddy Sree Harsha , Landry Ishani , Reyderman Larisa , Koyama Akihiko , Swanson Chad , Yasuda Sanae , Hussein Ziad 
Published: September 2022

AbstractLecanemab is a humanized immunoglobulin G1 monoclonal antibody that selectively binds to soluble Aβ aggregate species, while demonstrating low affinity for Aβ monomer. This article describes the population pharmacokinetic (PK) and PK/pharmacodynamic (PD) analyses for amyloid plaques, as measured using positron emission tomography (PET), and biomarkers of amyloid pathology as evidenced by Aβ42/40 ratio and plasma p‐tau181 following i.v. administration of lecanemab in subjects with early Alzheimer's disease. Lecanemab PKs were well‐characterized with a two‐compartment model with first‐order elimination. Final PK model contained covariate effects of anti‐drug antibody positive status, sex, body weight, and albumin on clearance. The time course of amyloid PET standard uptake ratio (SUVr), plasma Aβ42/40 ratio, and p‐tau181 were described using indirect response models with lecanemab exposure as a maximum effect function stimulating the reduction of SUVr, and as a linear function increasing Aβ42/40 ratio and decreasing p‐tau181 formation rates. PK/PD simulations show that 10 mg/kg biweekly dosing results in larger and faster decrease in SUVr and p‐tau181 and increase in Aβ42/40 ratio as compared to 10 mg/kg monthly dose. Furthermore, the PK/PD simulations showed that after treatment discontinuation the brain amyloid re‐accumulation to baseline levels is slow with a recovery half‐life of ~4 years, whereas plasma Aβ42/40 ratio and p‐tau181 return to baseline levels faster than amyloid. Given the relationship between changes in amyloid PET SUVr and soluble biomarkers, the developed PK/PD models can be used to inform lecanemab dose regimens in future clinical studies.
Hydrophilic, dual amino acid–functionalized zinc sulfide quantum dot for specific identification of N‐glycopeptides from biological samples
Authors: Feng Quanshou , Xie Zehu , Liang Hongze , Zhang Zhenbin , Yan Yinghua , Ding Chuan‐Fan 
Published: September 2022

RationaleGlycosylation of proteins is one of the most significant and complex post‐translational modifications, and N‐glycosylation plays a crucial role in life activities. Mass spectrometry (MS) has been a powerful technique in the analysis of protein glycosylation. However, the direct detection of glycoproteins in biological samples based on MS still suffers from huge challenges. Therefore, enrichment and purification of samples before MS analysis is an essential prerequisite.MethodsHydrophilic interaction liquid chromatography (HILIC) has significantly developed for selective enrichment of glycopeptides due to its simple operation process and unbiased enrichment. Herein, hydrophilic, dual amino acid–functionalized zinc sulfide quantum dots (ZnS QDs) were prepared to enrich glycopeptides using an easy procedure. The enriched glycopeptides were detected using matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS).ResultsThe obtained material exhibited high selectivity (1:2000), low detection limit (0.1 fmol/μl), good repeatability (10 times), and excellent recovery (89.8%) in glycopeptide enrichment. In the actual application in biological samples, 71 N‐glycopeptides and 161 N‐glycopeptides were detected from human saliva and serum, respectively.ConclusionsZnS‐Au‐GC was successfully prepared using an easy method. The results showed that the obtained material exhibited excellent performance in glycopeptide enrichment. Furthermore, it had showed great potential for glycopeptide enrichment in complex biological samples.
When it starts in the skin and goes to the lungs, where does it stop?
Authors: Catarino Ferro Ana Rita , Ferreira Campos Ana Margarida 
Published: September 2022

Key messageThis clinical case reports a rare disease—Birt‐Hogg‐Dubé Syndrome—characterized by skin lesions and multiple lung cysts. Because of its rarity, BHDS is likely undiagnosed and mistaken for primary spontaneous pneumothorax or emphysema. An early diagnosis is important to set up screening for renal cancer in patients and affected relatives.
A flexible‐hazards cure model with application to patients with soft tissue sarcoma
Authors: Xie Can , Huang Xuelin , Li Ruosha , Pisters Peter W. T. 
Published: September 2022

In medical research, it is often of great interest to have an accurate estimation of cure rates by different treatment options and for different patient groups. If the follow‐up time is sufficiently long and the sample size is large, the proportion of cured patients will make the Kaplan‐Meier estimator of survival function have a flat plateau at its tail, whose value indicates the overall cure rate. However, it may be difficult to estimate and compare the cure rates for all the subsets of interest in this way, due to the limit of sample sizes and curse of dimensionality. In the current literature, most regression models for estimating cure rates assume proportional hazards (PH) between different subgroups. It turns out that the estimation of cure rates for subgroups is highly sensitive to this assumption, so more flexible models are needed, especially when this PH assumption is clearly violated. We propose a new cure model to simultaneously incorporate both PH and non‐PH scenarios for different covariates. We develop a stable and easily implementable iterative procedure for parameter estimation through maximization of the nonparametric likelihood function. The covariance matrix is estimated by adding perturbation weights to the estimation procedure. In simulation studies, the proposed method provides unbiased estimation for the regression coefficients, survival curves, and cure rates given covariates, while existing models are biased. Our model is applied to a study of stage III soft tissue sarcoma and provides trustworthy estimation of cure rates for different treatment and demographic groups.
The effectiveness of self‐distanced versus self‐immersed reflections among adults: Systematic review and meta‐analysis of experimental studies
Authors: Murdoch Elizabeth M. , Chapman Michael T. , Crane Monique , Gucciardi Daniel F. 
Published: September 2022

AbstractStressor events can be highly emotional and disruptive to our functioning, yet they also present opportunities for learning and growth via self‐reflections. Self‐distanced reflections in which one reasons about target events in ways that maximise their removal of the current self from the experiential reality are said to facilitate this reflective process. We tested the expectation that self‐distanced reflections offer an advantage over self‐immersed vistas via a pre‐registered systematic review of seven electronic databases (Scopus, Medline, Web of Science, PsycInfo, CINAHL Plus, Embase, and ProQuest Dissertations and Theses Global) to identify experimental tests with adults aged 18–65 years where the focus of the reflection was a stressor or adverse event that participants had already experienced. A three‐level, random effects meta‐analysis of 25 experiments (N = 2,397, 68 effects) revealed a small‐to‐moderate advantage of self‐distanced reflections (g = 0.19, SE = 0.07, 95% CI [0.05, 0.33]) and were most effective when they targeted a stressor experience that emphasised one's emotional state or lifetime. Nevertheless, our assessment of the overall quality of evidence including risk of bias suggested uncertainty regarding the benefit of this pragmatic self‐regulatory tactic and therefore the need for future high‐powered, high‐quality experiments.