bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of upland cotton micronaire accounting for the effects of environment and crop demand from fruit growth
Authors: Bange Michael P. , Long Robert L. , Caton Sarah J. , Finger Nicolas 
Published: December 2021

AbstractEnvironment and crop management can play an important role in determining upland cotton (Gossypium hirsutumL.) fiber quality. An important quality parameter is fiber micronaire, which is an indirect measure of fiber linear density (fineness) and maturity, and it is affected by crop supply and partitioning of assimilates to cotton fruit. High micronaire occurs when there is an excess of assimilates because of good growing conditions and fruit number is low. Conversely low micronaire occurs when growing conditions are poor and fruit number is high. Little research has established the degree of impact of these variables in combination influencing micronaire. Two field experiments were conducted to generate variability in micronaire by changing planting time, cultivars, canopy size, and fruit load (boll number). From these experiments, a significant relationship (r2= 0.79) to predict micronaire was generated using temperature during crop fiber filling, leaf area index (LAI) at the start of crop fiber thickening, and the mass of individual bolls at harvest. Subsequent experiments in different seasons (included variations in planting time, fruit load, and water deficit during fiber thickening) successfully validated the relationship. Reasonable success was attained in predicting fiber linear density and maturity ratio independently and then used to calculate estimates of micronaire. Prediction of these quality attributes may offer more detailed information on the effects of environment and management influencing fiber quality affecting yarn quality. Overall, the ability to predict micronaire (and potentially its components) could be used to refine management decisions to improve fiber quality management prior to or at harvest time.
From traits to typologies: Piloting new approaches to profiling trait preferences along the cassava value chain in Nigeria
Authors: Balogun Ireti , Garner Elisabeth , Amer Peter , Fennessy Peter , Teeken Béla , Olaosebikan Olamide , Abolore Bello , Madu Tessy , Okoye Benjamin , Santos Bruno , Byrne Tim , Martin‐Collado Daniel , Egesi Chiedozie , Kulakow Peter , Tufan Hale Ann 
Published: December 2021

AbstractBreeding programs are increasing efforts towards demand‐led breeding approaches to ensure that cultivars released meet the needs of end users including processors, traders, and consumers, and that they are adopted by farmers. To effectively deploy these approaches, new tools are required to better understand and quantify the degree of preference differences among alternative trait changes competing for measurement and selection effort. The purpose of this study was to present a method of quantifying preferences and developing typologies according to breeding priorities by applying an online trait preference survey approach to cassava (Manihot esculenta Crantz). This paper presents a conjoint analysis based on Potentially All Pairwise RanKings of all possible Alternatives (PAPRIKA) to help guide breeding programs in understanding trait preferences across value chain roles and social contexts and set breeding priorities that represent diverse interests. Trait preferences were assessed using a comprehensive survey and analysis package incorporating a core adaptive conjoint method (1000minds, 2020). Trait selection was based on a trade‐off of 11 cassava traits carried out with 792 cassava value chain actors in four geopolitical regions in Nigeria. Principal component and cluster analyses revealed three clusters (typologies) of respondents according to their trait preferences. The results demonstrate the usefulness of this methodology that innovates on previous trait preference approaches to address the expanding needs of plant breeding programs within smallholder contexts.
Dose‐dependent mathematical modeling of interferon‐α‐treatment for personalized treatment of myeloproliferative neoplasms
Authors: Pedersen Rasmus K. , Andersen Morten , Knudsen Trine A. , Skov Vibe , Kjær Lasse , Hasselbalch Hans C. , Ottesen Johnny T. 
Published: December 2021

AbstractLong‐term treatment with interferon‐alfa (IFN) can reduce the disease burden of patients diagnosed with myeloproliferative neoplasms (MPNs). Determining individual patient responses to IFN therapy may allow for efficient personalized treatment, reducing both drop‐out and disease burden. A mathematical model describing hematopoietic stem cells and the immune system is suggested. Considering the bone marrow and the blood allows for modeling disease dynamics both in the absence and presence of IFN treatment. Through comprehensive modeling of the effects of IFN, the model was related to individualized patient‐data consisting of longitudinal hematologic and molecular measurements. Treatment responses were modeled on a population level, allowing for personalized predictions from a single pretreatment data point. Personalized fits were found to agree well with data for individual patients. This allowed for a quantitative description of the treatment response, yielding a mechanistic interpretation of differences from patient to patient. The treatment responses of individual patients were combined and a formulation of treatment responses on the population level was described and simulated. Based on pretreatment data and the actual treatment scheduling, the population‐level response was found to predict the treatment response of particular patients accurately over a five‐year period. Mechanism‐based modeling of treatment effects demonstrates that hematologic and molecular observable quantities can be predicted on the level of individual patients. Personalized patient‐fits suggest that the effect of IFN treatment can be quantified and interpreted through mathematical modeling, despite variation in hematologic and molecular responses between patients. Mathematical modeling suggests that in general both hematologic and molecular markers must be considered to avoid early relapse. Furthermore, personalized model‐fits provide quantitative measures of the hematologic and molecular responses, determining when treatment‐cessation is appropriate. Proof‐of‐concept population‐level modeling of treatment responses from pretreatment data successfully predicted clinical measures for a 5‐year period. We believe that this approach could have direct clinical relevance, offering expert guidance for clinical decisions about IFN treatment of MPN patients.
Circuit theory model‐based analysis of triple‐band stub and notches loaded epoxy substrate patch antenna for wireless applications
Authors: Verma Ramesh Kumar , Srivastava Dinesh Kumar , Mishra Brijesh 
Published: December 2021

SummaryThe research presented in this paper is intended to design and analyze of a triple‐band stub and notches loaded antenna for wireless applications. The optimized and proposed antenna (Antenna‐4: 0.235λ0 × 0.238λ0 × 0.013λ0 mm3) is decided after systematic investigation of Antennas‐1 to ‐4 at design frequency of 2.45 GHz. One orthogonal and two parallel notches and one stub are used on the radiating patch of the substrate to obtain the desired specifications. Theoretical analysis based on circuit theory model has been performed to obtain the equivalent circuit of the proposed antenna. Antenna parameters are analyzed by means of IE3D electromagnetic solver and circuit theory model, and results are validated with experimental results. The impedance bandwidths (S11 < –10 dB) of the proposed antenna are 41.3% between 1.42 and 2.16 GHz (theoretical), 21.6% between 1.61 and 2 GHz (simulated), and 41.4% between 1.40 and 2.13 GHz (measured) at lower resonant frequency (
); 4.1% between 2.61 and 2.72 GHz (theoretical), 17.4% between 2.36 and 2.81 GHz (simulated), and 8.8% between 2.50 and 2.73 GHz (measured) at middle resonant frequency (
); and 42.3% between 3.32 and 5.10 GHz (theoretical), 49.9% between 3.04 and 5.06 GHz (simulated), and 44.4% between 2.98 and 4.68 GHz (measured) at higher resonant frequency (
) observed, respectively. The measured stable peak gain of 2.6 dB at 1.9 GHz, 3.8 dB at 2.6 GHz, and 5.4 dB at 3.6GHz is observed in lower, middle, and higher bands, respectively.
Biopsy diagnosis of type 1 autoimmune pancreatitis: Does it bring a conclusion or confusion?
Authors: Notohara Kenji 
Published: December 2021

AbstractA biopsy‐based diagnosis of type 1 autoimmune pancreatitis (AIP) is now feasible via an endoscopic ultrasound‐guided fine‐needle biopsy, but there are potential issues to address. The benefits of acquiring large tissue samples include more successful immunostaining for Immunoglobulin G4 and more identifications of storiform fibrosis, obliterative phlebitis, and the ductal lesions of type 1 AIP. However, storiform fibrosis may not be present in all the type 1 AIP lesions. An interobserver agreement study revealed only slight‐to‐moderate agreement among pathologists diagnosing the histological findings of type 1 AIP. Potential reasons for disagreement are the different time phases of the inflammation (which result in heterogeneous histological pictures), a focal appearance of the typical histological findings, and the different definitions used by pathologists. We have thus devised guidance for diagnosing type 1 AIP based on biopsy tissues. In this guidance, we define each histological finding of type 1 AIP, for example, storiform fibrosis as a swirling arrangement of inflammatory cells, spindle‐shaped cells, and delicate collagens as a unit. The necessity of elastic stains for identifying obliterative phlebitis is explained, with examples of mimickers. Another important purpose of a biopsy in type 1 AIP cases is differentiation from pancreatic ductal adenocarcinoma (PDAC). In this situation, acinar‐ductal metaplasia observed in type 1 AIP is a mimicker of PDAC and should not be confused. For the resolution of potential disagreements among pathologists, a multi‐disciplinary approach with the collaboration of clinicians, radiologists, and pathologists is necessary to avoid confusion.
Pressure‐correction projection methods for the time‐dependent micropolar fluids
Authors: Maimaiti Halimang , Liu Demin 
Published: December 2021

AbstractThe unsteady micropolar Navier–Stokes equations (MNSE) is a system which describes the evolution of an incompressible fluid whose material particles possess both translational and rotational degrees of freedom. In this article, both the first order and second order pressure‐correction (PC) projection method for the MNSE are proposed. The unconditionally stability analysis corresponding to the temporal semidiscrete version and the fully discrete version of the PC projection method are proved, and the first order error estimation for the temporal semidiscrete version is deduced. Some numerical simulation results are presented to show the effect of PC projection method.
Catalytic C−H Activation via Four‐Membered Metallacycle Intermediate
Authors: Bhagat Kanhaiya Kumar , Biswas Jyoti Prasad , Dutta Subhabrata , Maiti Debabrata 
Published: December 2021

AbstractC−H Activation by transition metals has revolutionized the field of modern synthetic organic chemistry thereby enabling efficient and atom‐economical construction of complex organic frameworks in reduced number of steps. Various ways are being explored in order to maximize efficiency of the approach and construct previously unknown molecules. The major challenge in this aspect is the ubiquitous presence of C−H bond in an organic molecule that demands sophistication to achieve site‐selective functionalization. Directing group approach provided the most viable solution which operates through formation of a thermodynamically preferred metallacycle. Although, five and six membered metallacycles are known to be thermodynamically most favorable, there exists ingenious methodologies that operates through a four‐membered metallacycle in order to achieve site‐selectivity. In this review article, we summarize the C−H activation reactions evidenced to proceed via four‐membered metallacycle intermediate to achieve synthetically relevant transformations.
Effect of inactivated nature‐derived microbial composition on mouse immune system
Authors: González‐Rodríguez Martín Ignacio , Nurminen Noora , Kummola Laura , Laitinen Olli H. , Oikarinen Sami , Parajuli Anirudra , Salomaa Tanja , Mäkelä Iida , Roslund Marja I. , Sinkkonen Aki , Hyöty Heikki , Junttila Ilkka S. ,   for the ADELE Research Group
Published: December 2021

AbstractIntroductionThe hygiene hypothesis suggests that decrease in early life infections due to increased societal‐level hygiene standards subjects one to allergic and autoimmune diseases. In this report, we have studied the effect of sterilized forest soil and plant‐based material on mouse immune system and gut microbiome.MethodsInbred C57Bl/6 mice maintained in normal sterile environment were subjected to autoclaved forest soil‐derived powder in their bedding for 1 h a day for 3 weeks. Immune response was measured by immune cell flow cytometry, serum cytokine enzyme‐linked immunoassay (ELISA) and quantitative polymerase chain reaction (qPCR) analysis. Furthermore, the mouse gut microbiome was analyzed by sequencing.ResultsWhen compared to control mice, mice treated with soil‐derived powder had decreased level of pro‐inflammatory cytokines namely interleukin (IL)−17F and IL‐21 in the serum. Furthermore, splenocytes from mice treated with soil‐derived powder expressed less IL‐1b, IL‐5, IL‐6, IL‐13, and tumor necrosis factor (TNF) upon cell activation. Gut microbiome appeared to be stabilized by the treatment.ConclusionsThese results provide insights on the effect of biodiversity on murine immune system in sterile environment. Subjecting mice to soil‐based plant and microbe structures appears to elicit immune response that could be beneficial, for example, in type 2 inflammation‐related diseases, that is, allergic diseases.
Quantum Crystallography:N‐Representability Big and Small**
Authors: Matta Chérif F. , Huang Lulu , Massa Lou 
Published: December 2021

AbstractLinus Pauling contributions span structural biology, chemistry in its broadest definition, quantum mechanical theory, valence bond theory, and even nuclear physics. A principal tool developed and used by Pauling is X‐ray (and electron) diffraction. One possible extension of Pauling's oeuvre could be the “marriage” of crystallography and quantum mechanics. Such an effort dates back to the sixties and has now flourished into an entire subfield termed “Quantum Crystallography”. Quantum Crystallography could be achieved through the application of Clinton equations to yieldN‐representable density matrices consistent with experimental data. The implementation of the Clinton equations is qualitatively different for small and for large systems. For a small system, quantum mechanics isextractedfrom X‐ray data while for a large system, the quantum mechanics isinjectedinto the system. In both cases,N‐representability is imposed by the use of the Clinton equations.
The use of in vitro methods in assessing human health risks associated with short‐chain perfluoroalkyl and polyfluoroalkyl substances (PFAS)
Authors: Solan Megan E. , Lavado Ramon 
Published: December 2021

AbstractPerfluoroalkyl and polyfluoroalkyl substances (PFAS) are a large class of industrial chemicals with a ubiquitous and persistent presence in the environment. Of the thousands of PFAS used by consumers and industry, very few have been thoroughly characterized for potential adverse effects. This is especially true for the novel short‐chain (C < 8) alternatives that replaced legacy PFAS. Perfluoroalkyl and polyfluoroalkyl substances have revealed inconsistencies in the toxicokinetics predicted by animal models and empirical findings in humans. To adequately assess the possible health effects of short‐chain PFAS, there is a need for robust aggregated data sets on the mechanistic underpinnings and physiochemical properties of these alternatives. Acquiring relevant data on the health effects of short‐chain PFAS can be achieved through high‐throughput methods supported by in vitro human cell‐based models. This review briefly summarizes some of the toxicity data obtained using human cells in vitro, discusses the advantages and limitations of cell‐based models, and provides insights on potential solutions to challenges presented with the use of these methods for use in safety assessments.
Effects of a novel self‐assembling peptide scaffold on bone regeneration and controlled release of two growth factors
Authors: Tian Hongchuan , Guo Ai , Li Kai , Tao Bailong , Lei Dengliang , Deng Zhongliang 
Published: December 2021

AbstractRADA16 is a self‐assembling peptide material with good bioactivity. To improve the bioactivity of a material, some specific functional motifs can be added to its peptide sequence. Here, we report a self‐assembling peptide nanogel, RADA16‐RGD, that has better bioactivity than RADA16 and can simultaneously carry and control the release of two growth factors, VEGF and BMP‐2, which have synergistic effects on bone formation. The peptide materials were characterized by transmission electron microscopy and scanning electron microscopy. The mechanical properties of the peptides were evaluated by the rheology test. The biocompatibility of the materials was evaluated via the use of the CCK‐8 test, live/dead staining and confocal laser scanning microscopy. Osteogenesis capability in vitro was evaluated by means of ALP staining, extracellular matrix mineralization and detection of osteogenic markers. The controlled release of growth factors was examined by ELISA. The results showed that RADA16‐RGD exhibited a better ability than RADA16 to promote cell proliferation, adhesion and bone formation. In addition, RADA16‐RGD had good biocompatibility and exhibited effective controlled release of VEGF and BMP‐2. More importantly, compared with RADA16‐RGD loaded with single growth factor or without growth factors, RADA16‐RGD loaded with two growth factors exhibited a stronger ability to promote cell proliferation and osteogenesis. This study provides a promising strategy for the application of self‐assembling peptides to promote osteogenesis and controlled release of proteins.
In vivo evaluation of 3D printed polycaprolactone composite scaffold and recombinant human bone morphogenetic protein‐2 for vertical bone augmentation with simultaneous implant placement on rabbit calvaria
Authors: Chang Yun‐Young , Lee SaYa , Jeong Hun‐Jin , Cho Young‐Sam , Lee Seung‐Jae , Yun Jeong‐Ho 
Published: December 2021

AbstractThis study evaluated 3D printed polycaprolactone (PCL) composite scaffold and recombinant human bone morphogenetic protein‐2 (rhBMP‐2), loaded either onto a PCL composite scaffold or implant surface, for vertical bone augmentation with implant placement. Three‐dimensional printed PCL frames were filled with powdered PCL, hydroxyapatite, and β‐tricalcium phosphate. RhBMP‐2 was loaded to the PCL composite scaffolds and implant surfaces, and rhBMP‐2 release was quantified for 21 days. Experimental implants were placed bilaterally on 20 rabbit calvaria, and the PCL composite scaffolds were vertically augmented. The randomly allocated experimental groups were divided by carrier and rhBMP‐2 dosage as no rhBMP‐2 (control), 5 μg rhBMP‐2 loaded to PCL composite (Scaffold/rhBMP‐2[5 μg]), 5 μg rhBMP‐2 loaded to implant (Implant/rhBMP‐2[5 μg]), 30 μg rhBMP‐2 loaded to PCL composite (Scaffold/rhBMP‐2[30 μg]), and 30 μg rhBMP‐2 loaded to implant (Implant/rhBMP‐2[30 μg]). Histologic and histometric analyses were conducted after 8 weeks. In both scaffold‐loading and implant‐loading, rhBMP‐2 released initially rapidly, then slowly and constantly. Released rhBMP‐2 totaled 23.02 ± 1.03% and 24.69 ± 1.14% in the scaffold‐loaded and implant‐loaded groups, respectively. There were no significant differences in histologic bone‐implant contact (%). Peri‐implant bone density (%) was significantly higher in the Scaffold/rhBMP‐2(30 μg) and Implant/rhBMP‐2(30 μg) groups. Total bone density (%) was not significantly different between the Scaffold/rhBMP‐2(5 μg), Implant/rhBMP‐2(5 μg), and control groups, or between the Scaffold/rhBMP‐2(30 μg) and Implant/rhBMP‐2(30 μg) groups, but was significantly higher in the Scaffold/rhBMP‐2(30 μg) and Implant/rhBMP‐2(30 μg) groups than in the controls. Three‐dimensional printed PCL composite scaffold with rhBMP‐2 produced vertical osteogenesis and osseointegration, regardless of rhBMP‐2 loading to the PCL composite scaffold or implant surface.
CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field
Authors: Kognole Abhishek A. , Lee Jumin , Park Sang‐Jun , Jo Sunhwan , Chatterjee Payal , Lemkul Justin A. , Huang Jing , MacKerell Alexander D. , Im Wonpil 
Published: December 2021

AbstractExplicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM‐GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre‐equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF‐based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. In addition, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. The capabilities and availability of Drude Prepper in CHARMM‐GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.