bluuebunny/crossref_metadata_2025_split huggingface dataset:
The RNA-binding protein HuR is required for maintenance of the germinal centre response
Authors: Osma-Garcia Ines C. , Capitan-Sobrino Dunja , Mouysset Mailys , Bell Sarah E. , Lebeurrier Manuel , Turner Martin , Diaz-Muñoz Manuel D. 
Published: November 2021

AbstractThe germinal centre (GC) is required for the generation of high affinity antibodies and immunological memory. Here we show that the RNA binding protein HuR has an essential function in GC B cells to sustain the GC response. In its absence, the GC reaction and production of high-affinity antibody is severely impaired. Mechanistically, HuR affects the transcriptome qualitatively and quantitatively. The expression and splicing patterns of hundreds of genes are altered in the absence of HuR. Among these genes, HuR is required for the expression of Myc and a Myc-dependent transcriptional program that controls GC B cell proliferation and Ig somatic hypermutation. Additionally, HuR regulates the splicing and abundance of mRNAs required for entry into and transition through the S phase of the cell cycle, and it modulates a gene signature associated with DNA deamination protecting GC B cells from DNA damage and cell death.
Computational redesign of Fab CC12.3 with substantially better predicted binding affinity to SARS-CoV-2 than human ACE2 receptor
Authors: Treewattanawong Wantanee , Sitthiyotha Thassanai , Chunsrivirot Surasak 
Published: November 2021

AbstractSARS-CoV-2 is responsible for COVID-19 pandemic, causing large numbers of cases and deaths. It initiates entry into human cells by binding to the peptidase domain of angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain of S1 subunit of spike protein (SARS-CoV-2-RBD). Employing neutralizing antibodies to prevent binding between SARS-CoV-2-RBD and ACE2 is an effective COVID-19 therapeutic solution. Previous studies found that CC12.3 is a highly potent neutralizing antibody that was isolated from a SARS-CoV-2 infected patient, and its Fab fragment (Fab CC12.3) bound to SARS-CoV-2-RBD with comparable binding affinity to ACE2. To enhance its binding affinity, we employed computational protein design to redesign all CDRs of Fab CC12.3 and molecular dynamics (MD) to validate their predicted binding affinities by the MM-GBSA method. MD results show that the predicted binding affinities of the three best designed Fabs CC12.3 (CC12.3-D02, CC12.3-D05, and CC12.3-D08) are better than those of Fab CC12.3 and ACE2. Additionally, our results suggest that enhanced binding affinities of CC12.3-D02, CC12.3-D05, and CC12.3-D08 are caused by increased SARS-CoV-2-RBD binding interactions of CDRs L1 and L3. This study redesigned neutralizing antibodies with better predicted binding affinities to SARS-CoV-2-RBD than Fab CC12.3 and ACE2. They are promising candidates as neutralizing antibodies against SARS-CoV-2.
Collapse dynamics and Hilbert-space stochastic processes
Authors: Bajoni Daniele , Nicrosini Oreste , Rimini Alberto , Rodini Simone 
Published: November 2021

AbstractSpontaneous collapse models of state vector reduction represent a possible solution to the quantum measurement problem. In the present paper we focus our attention on the Ghirardi–Rimini–Weber (GRW) theory and the corresponding continuous localisation models in the form of a Brownian-driven motion in Hilbert space. We consider experimental setups in which a single photon hits a beam splitter and is subsequently detected by photon detector(s), generating a superposition of photon-detector quantum states. Through a numerical approach we study the dependence of collapse times on the physical features of the superposition generated, including also the effect of a finite reaction time of the measuring apparatus. We find that collapse dynamics is sensitive to the number of detectors and the physical properties of the photon-detector quantum states superposition.
Prevalence and characteristics of thoracic diffuse idiopathic skeletal hyperostosis in 3299 black patients
Authors: Yoshihara Hiroyuki , Nadarajah Vidushan , Horowitz Evan 
Published: November 2021

AbstractThe purpose of this study was to examine the prevalence and characteristics of thoracic diffuse idiopathic skeletal hyperostosis (T-DISH) in the Black patients using the computed tomography (CT) analysis. This study is a cross-sectional study. All patients who underwent chest CT for the trauma screening and whose race was categorized as “Black” on the questionnaire were recruited in the study from Mar 2019 to Mar 2020. Demographic data, including age, sex, body mass index (BMI), and presence of diabetes mellitus (DM), were recorded. A total of 3299 Black patients (1507 women and 1792 men) were included for the analysis. The prevalence of T-DISH was 7.7% (255 patients), with 8.6% for females and 7.0% for males. The highest prevalence was observed in patients at the age of 70 years (11.7%), followed by the age of 80 years (10.5%). The highest prevalence level of T-DISH segment was at T8, followed by T9, and T7. The most frequent number of contiguous vertebrae was seven (21%). BMI was not associated with T-DISH. The presence of DM was significantly higher in male patients with T-DISH than those without T-DISH (P = 0.02).
The first report of iron-rich population of adapted medicinal spinach (Blitum virgatum L.) compared with cultivated spinach (Spinacia oleracea L.)
Authors: Ammarellou Ali , Mozaffarian Valiollah 
Published: November 2021

AbstractFolk medicine such as herbal and natural products have been used for centuries in every culture throughout the world. The Chenopodiaceae family with more than 1500 species is dispersed worldwide. The Iranian wild spinach (Blitum virgatum L.) is an important traditional medicinal plant used for antiviral diseases such as pneumonia and other respiratory track infections. This plant is a mountainous herb and is growing upper than 3000 m. We performed a mass selection plant breeding program on wild populations of this Iranian wild spinach during 2013–2020. Based on experimental and field characteristics this plant was identified as B. virgatum, |abbaricum|, and related characteristics were prepared with reference to the International Union for the Protection of New Varieties of Plants (UPOV). Mass selection program resulted from an adapted population named as medicinal spinach (MSP) population. To compare the mineral content of the mass-selected population with cultivated spinach (Spinacia oleracea L. |Varamin 88|), both plants were planted in pots and fields under similar conditions. In five leaves stage, plant samples were taken from both leaf and crown sections and used for experimental analysis. Atomic absorption spectroscopy was used to determine the mineral content including iron (Fe), zinc (Z), manganese (Mn), and copper (Cu). Our results showed the selected medicinal spinach population (MSP) with about 509 ppm iron was an important iron-rich population with about 3.5–4 times more than the amount of iron in cultivated spinach in the same conditions. Because iron is an important essential element for blood production, respiration process, energy metabolisms, synthesis of collagen, and some neurotransmitters are needed for proper immune function, so the supply of absorbable adequate iron is very important. The reasons such as the prevalence of the COVID-19 pandemic, which affects the amount of exchangeable oxygen in the lungs and historical local evidences of the use of this plant (MSP) for pneumonia, could open new horizons for focusing on studies related to the use of ancestral human experiences in addition to scientifically modern research.
Comparative analysis of dielectric, shear mechanical and light scattering response functions in polar supercooled liquids
Authors: Ngai K. L. , Wojnarowska Z. , Paluch M. 
Published: November 2021

AbstractThe studies of molecular dynamics in the vicinity of liquid–glass transition are an essential part of condensed matter physics. Various experimental techniques are usually applied to understand different aspects of molecular motions, i.e., nuclear magnetic resonance (NMR), photon correlation spectroscopy (PCS), mechanical shear relaxation (MR), and dielectric spectroscopy (DS). Universal behavior of molecular dynamics, reflected in the invariant distribution of relaxation times for different polar and weekly polar glass-formers, has been recently found when probed by NMR, PCS, and MR techniques. On the other hand, the narrow dielectric permittivity function ε*(f) of polar materials has been rationalized by postulating that it is a superposition of a Debye-like peak and a broader structural relaxation found in NMR, PCS, and MR. Herein, we show that dielectric permittivity representation ε*(f) reveals details of molecular motions being undetectable in the other experimental methods. Herein we propose a way to resolve this problem. First, we point out an unresolved Johari–Goldstein (JG) β-relaxation is present nearby the α-relaxation in these polar glass-formers. The dielectric relaxation strength of the JG β-relaxation is sufficiently weak compared to the α-relaxation so that the narrow dielectric frequency dispersion faithfully represents the dynamic heterogeneity and cooperativity of the α-relaxation. However, when the other techniques are used to probe the same polar glass-former, there is reduction of relaxation strength of α-relaxation relative to that of the JG β relaxation as well as their separation. Consequently the α relaxation appears broader in frequency dispersion when observed by PCS, NMR and MR instead of DS. The explanation is supported by showing that the quasi-universal broadened α relaxation in PCS, NMR and MR is captured by the electric modulus M*(f) = 1/ε*(f) representation of the dielectric measurements of polar and weakly polar glass-formers, and also M*(f) compares favorably with the mechanical shear modulus data G*(f).
Key factors of the functional ability of older people to self-manage medications
Authors: Advinha Ana Margarida , Nunes Carla , de Barros Carla Teixeira , Lopes Manuel José , de Oliveira-Martins Sofia 
Published: November 2021

AbstractDaily medication use can be affected by the gradual loss of functional ability. Thus, elderly patients are at risk for nonadherence due to functional decline, namely, decreases in cognitive skills and visual and manual dexterity. The main objective was to assess the ability of older people to self-manage their medication and to identify the main predictors for unintentional nonadherence. A cross-sectional study was conducted (2014–2017) in community centers and pharmacies. Functional assessment was performed with the Portuguese versions of the Drug Regimen Unassisted Grading Scale (DRUGS-PT) and the Self-Medication Assessment Tool (SMAT-PT). A purposive sample including 207 elderly patients was obtained. To identify the main predictors, binary logistic regression was performed. The average DRUGS-PT score was slightly lower than that in other studies. On the SMAT-PT, the greatest challenge for patients was identifying medications by reading labels/prescriptions. The main difficulties identified were medication memorization and correct schedule identification. The scores were higher with the real regimen than with the simulated regimen, underlining the difficulties for patients in receiving new information. Regarding the predictors of an older individual’s ability to self-manage medications, two explanatory models were obtained, with very high areas under the curve (> 90%). The main predictors identified were cognitive ability, level of schooling and daily medication consumption.
Mathematical modeling and thermodynamics of Prandtl–Eyring fluid with radiation effect: a numerical approach
Authors: Ullah Zakir , Ullah Ikram , Zaman Gul , Khan Hamda , Muhammad Taseer 
Published: November 2021

AbstractMain concern of current research is to develop a novel mathematical model for stagnation-point flow of magnetohydrodynamic (MHD) Prandtl–Eyring fluid over a stretchable cylinder. The thermal radiation and convective boundary condition are also incorporated. The modeled partial differential equations (PDEs) with associative boundary conditions are deduced into coupled non-linear ordinary differential equations (ODEs) by utilizing proper similarity transformations. The deduced dimensionless set of ODEs are solved numerically via shooting method. Behavior of controlling parameters on the fluid velocity, temperature fields as well as skin friction and Nusselt number are highlighted through graphs. Outcome declared that dimensionless fluid temperature boosts up for both the radiation parameter and Biot number. It is also revealed that the magnitude of both heat transfer rate and skin friction enhance for higher estimation of curvature parameter. Furthermore, comparative analysis between present and previous reports are provided for some specific cases to verify the obtained results.
Past, present, and future climate space of the only endemic vertebrate genus of the Italian peninsula
Authors: Macaluso Loredana , Villa Andrea , Carnevale Giorgio , Delfino Massimo 
Published: November 2021

AbstractThe two extant Salamandrina species represent a unique case of morphology, ecology, and ethology among urodeles. The range of this genus is currently limited to Italy, where it represents the only endemic vertebrate genus, but its past range extended over a much broader area of Europe, including the Iberian and Balkan peninsulas. ENM analyses using modern occurrences of Salamandrina demonstrate that the current climate of the majority of Europe, and especially areas where fossils of this genus were found, is currently not suitable for this genus, neither was it suitable during the last 3.3 million years. This result allows possible assumptions about the climatic influence on the former extirpation of this salamander from several areas of Europe. Furthermore, it shows that, during Pliocene–Pleistocene climatic oscillations, Mediterranean peninsulas, despite being generally considered together because of similar latitude, had different potential to effectively become glacial refugia for this salamander, and possibly for other species as well. Future projections using different CO2 emission scenarios predict that climatic suitability will be even more drastically reduced during the next 50 years, underlining once more the importance of conservation strategies and emission-reducing policies.
Resonant X-ray photo-oxidation of light-harvesting iron (II/III) N-heterocyclic carbene complexes
Authors: Temperton Robert H. , Guo Meiyuan , D’Acunto Giulio , Johansson Niclas , Rosemann Nils W. , Prakash Om , Wärnmark Kenneth , Schnadt Joachim , Uhlig Jens , Persson Petter 
Published: November 2021

AbstractTwo photoactive iron N-heterocyclic carbene complexes $${[\hbox {Fe}^{{{\rm{II}}}}(\hbox {btz})_2(\hbox {bpy})]^{2+}}$$

[

Fe
II

(
btz
)

2

(
bpy
)

]

2
+

and $${[\hbox {Fe}^{{\rm{III}}}(\hbox {btz})_3]^{3+}}$$

[

Fe
III

(
btz
)

3

]

3
+

, where btz is 3,3’-dimethyl-1,1’-bis(p-tolyl)-4,4’-bis(1,2,3-triazol-5-ylidene) and bpy is 2,2’-bipyridine, have been investigated by Resonant Photoelectron Spectroscopy (RPES). Tuning the incident X-ray photon energy to match core-valence excitations provides a site specific probe of the electronic structure properties and ligand-field interactions, as well as information about the resonantly photo-oxidised final states. Comparing measurements of the Fe centre and the surrounding ligands demonstrate strong mixing of the Fe $${\hbox {t}_{{\rm{2g}}}}$$

t

2
g

levels with occupied ligand $$\pi$$
π
orbitals but weak mixing with the corresponding unoccupied ligand orbitals. This highlights the importance of $$\pi$$
π
-accepting and -donating considerations in ligand design strategies for photofunctional iron carbene complexes. Spin-propensity is also observed as a final-state effect in the RPES measurements of the open-shell $$\hbox {Fe}^{{\rm{III}}}$$

Fe
III

complex. Vibronic coupling is evident in both complexes, where the energy dispersion hints at a vibrationally hot final state. The results demonstrate the significant impact of the iron oxidation state on the frontier electronic structure and highlights the differences between the emerging class of $$\hbox {Fe}^{{\rm{III}}}$$

Fe
III

photosensitizers from those of more traditional $$\hbox {Fe}^{{\rm{II}}}$$

Fe
II

complexes.
Systems pharmacology to reveal multi-scale mechanisms of traditional Chinese medicine for gastric cancer
Authors: Zhang Lulu , Xiao Yue , Yang Ruijie , Wang Siyi , Ma ShuangXin , Liu Jianling , Xiao Wei , Wang Yonghua 
Published: November 2021

AbstractBecause of the complex etiology, the treatment of gastric cancer is a formidable challenge for contemporary medical. The current treatment method focuses on traditional surgical procedures, supplemented by other treatments. Among these other treatments, Traditional Chinese Medicine (TCM) plays an important role. Here, we used the systems pharmacology approach to reveal the potential molecular mechanism of PRGRC on gastric cancer which composes of Pinellia ternata(Thunb.) Breit., Rheum palmatumL., Gentiana scabraBunge, Radix Aucklandiae and Citrus aurantium L. This approach combines pharmacokinetics analysis with pharmacodynamics evaluation for the active compounds screening, targets prediction and pathways assessing. Firstly, through pharmacokinetic evaluation and target prediction models, 83 potential compounds and 184 gastric cancer-related targets were screened out. Then, the results of network analysis suggested that the targets of PRGRC were mainly involved two aspects: apoptosis and inflammation. Finally, we verified the reliability of the above analysis at the cellular level by using naringenin and luteolin with good pharmacokinetic activity as representative compounds. Overall, we found that PRGRC could influence the development of gastric cancer from a multi-scale perspective. This study provided a new direction for analyzing the mechanism of TCM.
Incorporating the field border effect to reduce the predicted uncertainty of pollen dispersal model in Asia
Authors: Su Yuan-Chih , Lee Cheng-Bin , Yiu Tien-Joung , Kuo Bo-Jein 
Published: November 2021

AbstractThe presence of the field border (FB), such as roadways or unplanted areas, between two fields is common in Asian farming system. This study evaluated the effect of the FB on the cross-pollination (CP) and predicted the CP rate in the field considering and not considering FB. Three experiments including 0, 6.75, and 7.5 m width of the FB respectively were conducted to investigate the effect of distance and the FB on the CP rate. The dispersal models combined kernel and observation model by calculating the parameter of observation model from the output of kernel. These models were employed to predict the CP rate at different distances. The Bayesian method was used to estimate parameters and provided a good prediction with uncertainty. The highest average CP rates in the field with and without FB were 74.29% and 36.12%, respectively. It was found that two dispersal models with the FB effect displayed a higher ability to predict average CP rates. The correlation coefficients between actual CP rates and CP rates predicted by the dispersal model combined zero-inflated Poisson observation model with compound exponential kernel and modified Cauchy kernel were 0.834 and 0.833, respectively. Furthermore, the predictive uncertainty was reducing using the dispersal models with the FB effect.
Dependency of active pressure and equation of state on stiffness of wall
Authors: Pirhadi Emad , Cheng Xiang , Yong Xin 
Published: November 2021

AbstractAutonomous motion and motility are hallmarks of active matter. Active agents, such as biological cells and synthetic colloidal particles, consume internal energy or extract energy from the environment to generate self-propulsion and locomotion. These systems are persistently out of equilibrium due to continuous energy consumption. It is known that pressure is not always a state function for generic active matter. Torque interaction between active constituents and confinement renders the pressure of the system a boundary-dependent property. The mechanical pressure of anisotropic active particles depends on their microscopic interactions with a solid wall. Using self-propelled dumbbells confined by solid walls as a model system, we perform numerical simulations to explore how variations in the wall stiffness influence the mechanical pressure of dry active matter. In contrast to previous findings, we find that mechanical pressure can be independent of the interaction of anisotropic active particles with walls, even in the presence of intrinsic torque interaction. Particularly, the dependency of pressure on the wall stiffness vanishes when the stiffness is above a critical level. In such a limit, the dynamics of dumbbells near the walls are randomized due to the large torque experienced by the dumbbells, leading to the recovery of pressure as a state variable of density.
Connectivity dynamics in Irish mudflats between microorganisms including Vibrio spp., common cockles Cerastoderma edule, and shorebirds
Authors: Albuixech-Martí Sara , Lynch Sharon A. , Culloty Sarah C. 
Published: November 2021

AbstractShellfish, including the key species the common cockle Cerastoderma edule, living and feeding in waters contaminated by infectious agents can accumulate them within their tissues. It is unknown if microbial pathogens and microparasites can subsequently be transmitted via concomitant predation to their consumers, including shorebirds. The objective of this study was to assess if pathogens associated with C. edule could be detected seasonally in the faeces of shorebirds that feed on C. edule and in the physical environment (sediment) in which C. edule reside, along the Irish and Celtic Seas. Two potentially pathogenic global groups, Vibrio and Haplosporidia, were detected in C. edule. Although Haplosporidia were not detected in the bird faeces nor in the sediment, identical strains of Vibrio splendidus were detected in C. edule and bird faecal samples at sites where the oystercatcher Haematopus ostralegus and other waders were observed to be feeding on cockles. Vibrio spp. prevalence was seasonal and increased in C. edule and bird faecal samples during the warmer months, possibly due to higher seawater temperatures that promote the replication of this bacteria. The sediment samples showed an overall higher prevalence of Vibrio spp. than the bird faecal and C. edule samples, and its detection remained consistently high through the sites and throughout the seasons, which further supports the role of the sediment as a Vibrio reservoir. Our findings shed light on the fact that not all pathogen groups are transmitted from prey to predator via feeding but bacteria such as V. splendidus can be. As most of the wading birds observed in this study are migratory, the results also indicate the potential for this bacterium to be dispersed over greater geographic distances, which will have consequences for areas where it may be introduced.