bluuebunny/crossref_metadata_2025 huggingface dataset:
Production optimization of green coffee extracts from Jember robusta (Coffeacanephora) coffee using foam mat drying method
Authors: Pranowo D , Adiatmi A Y , Dewi I A
Published: May 2021

Robusta coffee contains around 10% polyphenol compounds. The roasting process could change the chemical composition and biological activity ofcoffee thusreduced polyphenols and antioxidant activity. Production of the green coffee extract was performed by foam mat drying method, whichrequiresencapsulating materials such as maltodextrin and foaming agent tween 80. This study aimed to determine the optimal concentration of maltodextrin and tween 80 to obtain high phenol content and strong antioxidant activity of green coffee extract powder. This research used Response Surface Methodology with Central Composite Design using two factors namely maltodextrin concentration (12%; 17%; 22%) and tween 80 (0.4%, 0.9%; 1.4%). The optimum solution results were obtained in the treatment of maltodextrin and tween 80 concentrations of 14.78% and tween 80 of 0.93% which produced green coffee extract powder with a total phenol content of 183.639 mg GAE/g and IC50 values of 25.187 ppm.
Bioentrepreneurship approach as a pillar to accelerate the integrated farming system implementation
Authors: Wulandari S
Published: May 2021

The Integrated Farming System (IFS), as one of the bioeconomy models, operates with a variety of agricultural activities interaction to optimize benefits through the synergistic transfer of resources. In IFS, implementation of Integrated Crop Livestock Systems (ICLS) is more complicated than Mixed Crops System (MCS). The ICLS need to be operated by individuals who aspire to generate values through the creation or expansion of economic activity, by identifying and exploring new products, processes or markets. It has specific characteristics in strategy, competencies and management. It aligns with the entrepreneurship aspect, which in agriculture is known as bioentrepreneurship. One strategy to achieve it is by implementing bioentrepreneurship approach. This study is intended to identify the aspects and elements of bioentrepreneurship and analysis in a case study. The analysis used radar charts that map the value of each element of the aspect of bioentrepreneurship based on its important values and real score. Analysis of bioentrepreneurship is divided into entrepreneurial orientation, entrepreneurial learning abilities, and entrepreneurial network capabilities. Entrepreneurial orientation generally refers to autonomy, competitive aggressiveness, innovativeness, proactiveness, and risk-taking. Entrepreneurial learning capacity is related to knowledge and skills, collaboration, and culture of sustainable improvement, while entrepreneurial networking capability is about constructing bonding, bridging, and linking capability.
Siwak (Salvadora persica) extract as a natural anti-halitosis mouth spray
Authors: Resmisari R S , Wicaksono S T , Alfiani N , Effendi S R N
Published: May 2021

Bad breath or halitosis is a pathologist that often experienced in the community. Bacteria that play a specific role in halitosis are anaerobic. To overcome bad breath due to the development of bacteria in the oral cavity is using Siwak spray. Siwak solution is obtained through maceration. The maceration results went through several stages of testing, namely, organoleptic, pH, and antibacterial testing through Nutrient Agar (NA). Analysis of the quantitative data obtained using the Friedman method. The organoleptic results show that the concentration of 1% that was most accepted by 76.66% of the panellists. The optimal bacterial inhibition was at a concentration of 2%. The pH for the 1% Siwak concentration was the best matches.
Techno-economic analysis of mung bean-based (Vigna radiata L.) synbiotic beverage production
Authors: Andriana Y , Iwansyah A C , Minh T N , Indriati A , Mayasti N K I , Anggara C E W , Astro H M , Rahman N
Published: May 2021

The demand for healthy drinks produced by combining bioactive carbohydrates and probiotic microorganisms increases during the rising of customer awareness related to digestive health issues. In this study, a techno-economic analysis was conducted for establishing a mini-plant to produce a synbiotic fermented drink from mung bean (Vigna radiata L.). From the technological analysis, inulin and Lactobacillus bulgaricus were the most suitable ingredients for mung bean-based synbiotic beverage production. With a total investment of 3,112,000,000, - IDR and a total production capacity of 10,800 kL/year, based on financial analysis, this mini-plant was feasible to be established. This was indicated by some feasibility criteria such as B/C ratio, net present value (NPV), break event point (BEP), internal rate of return (IRR), and pay-back period (PBP) that presented of 1.70, 12.079 billion, 2.8 million packs (@125 mL), 21.78%, 3.46 years, respectively. From location selection analysis, by an analytical hierarchy process (AHP), Kebumen regency was the most suitable location to build this plant due to the availabilities of raw material and water. This study revealed that mung bean-based synbiotic beverage was prospective to be developed and techno-economically feasible.
Microbial biomass and phospholipid fatty acid (PLFA) profile changes in bioconversion of wheat straw
Authors: Nurika I
Published: May 2021

Serpula lacrymans was shown to grow rapidly on wheat straw solid state fermentation (SSF). This study aimed to determine the pattern of ergosterol and the relative composition of phospholipid fatty acid (PLFA) produced during fungal growth. The PLFA analysis was carried out on the upper layer of the solvent extraction and was performed on the incubation from 0 up to 35 days. Relative abundant (%) of each fatty acid methyl ester (FAME) produced during the fungal growth was measured by comparing the amount of an individual FAME with the total FAME detected. The dominant PLFA released by the fungi were: 18:2n6c (linoleic acid) 24:1n9 (nervonic acid), 18:1n9c (oleic acid), and 16:0 (palmitic acid). The highest amount of fatty acid produced during the fungal growth is linoleic acid ranged from 186.92-345.78 μg g-1.
Quantum photonics in triangular-cross-section nanodevices in silicon carbide
Authors: Majety Sridhar , Norman Victoria A , Li Liang , Bell Miranda , Saha Pranta , Radulaski Marina
Published: May 2021

Silicon carbide is evolving as a prominent solid-state platform for the realization of quantum information processing hardware. Angle-etched nanodevices are emerging as a solution to photonic integration in bulk substrates where color centers are best defined. We model triangular cross-section waveguides and photonic crystal cavities using Finite-Difference Time-Domain and Finite-Difference Eigensolver approaches. We analyze optimal color center positioning within the modes of these devices and provide estimates on achievable Purcell enhancement in nanocavities with applications in quantum communications. Using open quantum system modeling, we explore emitter-cavity interactions of multiple non-identical color centers coupled to both a single cavity and a photonic crystal molecule in SiC. We observe polariton and subradiant state formation in the cavity-protected regime of cavity quantum electrodynamics applicable in quantum simulation.
Estimation of Lorentz force detuning and its compensation on 650 MHz βg = 0.92 single cell SCRF cavity
Authors: Rathore M , Jain V K , Singh K K , Puntambekar A M. , Porwal R K. , Atulkar A
Published: May 2021

Superconducting technologies are widely used in modern radiofrequency (RF) cavities for particle accelerators in various fields of applications. The Superconducting radiofrequency (SCRF) cavities are highly sensitive to small perturbation on cavity dimensions. The operation of the superconducting cavity becomes challenging due to narrow resonance bandwidth on account of a very high-quality factor. The main perturbing source is Lorentz Force acting on the cavity wall, which detunes the cavity from resonance. Finite element (FE) analysis has an important role in Lorentz force detuning (LFD) estimation, which requires coupled-field FE analysis between the structural and RF domains of the cavity. The LFD effect can be mitigated up to a certain extent by using a proper fast tuning methodology. This paper represents the methodology for structural-high frequency electromagnetic coupled field simulation for LFD calculation of 650MHz, βg = 0.92 single-cell SCRF cavity. First, the static LFD is calculated for various voltage gradients of SCRF cavity structure and then dynamic behavior of cavity due to LFD pressure pulse is studied at different pulse widths (PW) and pulse repetition rates (PRR). A comparison of transient FE analysis of the single-cell cavity with one end fixed and another end free and cantilever beam for similar loading is done for benchmarking. To counter the detuning effect, the SCRF cavity employs a piezo tuning device. The dynamic behavior of piezo pulse response on the cavity is also studied. An experimental test of the piezo tuner system has been performed at room temperature to validate the FE coupled simulation. Further, dynamic analysis has been carried for the combined effect of LFD pressure and piezo load pulse to compensate for the LFD effect. Optimizing the piezo load for compensating the frequency shift is also discussed and based on optimum load, LFD has been mitigated for different acceleration gradients.
In-flight sensing of pollen grains via laser scattering and deep learning
Authors: Grant-Jacob James A , Praeger Matthew , Eason Robert W , Mills Ben
Published: May 2021

The identification and imaging of pollen grains in-flight was performed via illumination of the pollen grains with three collinear laser beams that had central wavelengths of 450 nm, 520 nm and 635 nm. Two neural networks are reported here; the first neural network was able to categorise pollen grain species from their scattering patterns with ∼86% accuracy, while the second neural network generated images of the pollen grains from their scattering patterns. This work demonstrates the potential application of laser scattering and deep learning for real-world in-flight pollen identification.
Change in Dysfunctional Sleep-Related Beliefs is Associated with Changes in Sleep and Other Health Outcomes Among Older Veterans With Insomnia: Findings From a Randomized Controlled Trial
Authors: Song Yeonsu , Kelly Monica R , Fung Constance H , Dzierzewski Joseph M , Grinberg Austin M , Mitchell Michael N , Josephson Karen , Martin Jennifer L , Alessi Cathy A
Published: May 2021

Background

Cognitive behavioral therapy for insomnia (CBTI) targets changing dysfunctional sleep-related beliefs. The impact of these changes on daytime functioning in older adults is unknown.

Purpose

We examined whether changes in sleep-related beliefs from pre- to post-CBTI predicted changes in sleep and other outcomes in older adults.

Method

Data included 144 older veterans with insomnia from a randomized controlled trial testing CBTI. Sleep-related beliefs were assessed with the Dysfunctional Beliefs and Attitudes about Sleep-16 (DBAS-16, subscales: Consequences, Worry/Helplessness, Sleep Expectations, Medication). Outcomes included sleep diary variables, actigraphy-measured sleep efficiency, Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), Epworth Sleepiness Scale (ESS), Flinders Fatigue Scale (FFS), Patient Health Questionnaire-9, and health-related quality of life. Analyses compared slope of change in DBAS subscales from baseline to posttreatment between CBTI and control, and assessed the relationship between DBAS change and the slope of change in outcomes from baseline to 6 months.

Results

Compared to controls, the CBTI group demonstrated stronger associations between improvement in DBAS-Consequences and subsequent improvement in PSQI, ISI, ESS, and FFS. The CBTI group also demonstrated stronger associations between improvement in DBAS-Worry/Helplessness and subsequent improvements in PSQI, ISI, and FFS; improvements in DBAS-Medication and PSQI; and improvements in DBAS-Sleep Expectations and wake after sleep onset (sleep diary) and FFS (all p < .05).

Conclusions

Significant reduction in dysfunctional sleep-related beliefs following CBTI in older adults predicted improvement in several outcomes of sleep and daytime functioning. This suggests the importance of addressing sleep-related beliefs for sustained improvement with CBTI in older veterans.

Trial Registration

ClinicalTrials.gov Identifier: NCT00781963.
The First of Two One-Year, Multicenter, Open-Label, Repeat-Dose, Phase II Safety Studies of PrabotulinumtoxinA for the Treatment of Moderate to Severe Glabellar Lines in Adult Patients
Authors: Kaufman-Janette Joely , Avelar Rui L , Biesman Brian S , Draelos Zoe Diana , Gross John E , Jones Derek H , Lupo Mary P , Maas Corey S , Schlessinger Joel , Shamban Ava Teresa , Sundaram Hema , Weinkle Susan H , Young Vernon L
Published: May 2021

Background

PrabotulinumtoxinA is a 900-kDa botulinum toxin type A produced by Clostridium botulinum.

Objectives

The authors sought to investigate the safety of prabotulinumtoxinA for treatment of glabellar lines.

Methods

This was a multicenter, open-label, repeat-dose, 1-year phase II safety study. Adults with moderate to severe glabellar lines at maximum frown, as assessed by the investigator on the validated 4-point photonumeric Glabellar Line Scale (0 = no lines, 1 = mild, 2 = moderate, 3 = severe), were enrolled. On day 0, patients received an initial treatment of 20 U prabotulinumtoxinA (4 U/0.1 mL freeze-dried formulation injected into 5 target glabellar sites). On and after day 90, patients received a repeat treatment (RT) if their Glabellar Line Scale score was ≥2 at maximum frown by investigator assessment. Safety was evaluated throughout the study.

Results

The 352 study patients received a median total dose of 60 U, that is, 3 treatments per year. Fifty-one patients (14.5%) experienced adverse events (AEs) assessed as possibly study drug related; 11.1% experienced study drug-related AEs after the initial treatment. With each RT, progressively lower percentages of patients experienced study drug-related AEs. Six patients (1.7%) experienced study drug-related AEs of special interest: 3 eyelid ptosis (0.9%), 2 speech disorder (0.6%), and 1 blepharospasm (0.3%). Seven patients (2.0%) experienced serious AEs; none were study drug related. Of the 2393 samples tested, 2 patients (0.6%) tested positive for antibotulinum toxin antibodies at a single postbaseline visit.

Conclusions

The safety of RTs of 20 U of prabotulinumtoxinA for moderate to severe glabellar lines was first established in this early phase II study based on a broad range of outcomes.

Level of Evidence: 2
Applications of Medical Tattooing: A Systematic Review of Patient Satisfaction Outcomes and Emerging Trends
Authors: Becker Stacie J , Cassisi Jeffrey E
Published: May 2021

Background

Medical tattooing is often applied in the context of plastic, aesthetic, and reconstructive surgery to help achieve the best cosmetic outcome.

Objectives

This article reviews various conditions that medical tattooing has been empirically studied in terms of patient satisfaction outcomes, makes practice recommendations, and suggests future directions for research.

Methods

This review was performed following the PRISMA guidelines. Studies were included if the tattooing application was associated with a medical condition and if outcome data were provided using at least a case series methodology. Where no cohort or clinical series exist, case examples are used from the literature and the author’s practice to illustrate emerging medical tattooing applications that need further evaluation.

Results

Eighteen studies met the inclusion criteria and addressed the following conditions: baldness, vitiligo, scars from incisions, lacerations or burns, and nipple-areola complex reconstruction.

Conclusions

The application of medical tattooing has shown high levels of patient satisfaction across conditions. The practice recommendation grade is “B” or recommend since the level of evidence for these interventions ranged from III to IV according to the American Society of Plastic Surgeons guidelines. This means clinicians can consider this treatment alternative, but they should be alert to new information and be sensitive to patient preferences. Recommendations are made for reporting future research including clearly describing procedural details, identifying the professional performing the procedure, increased use of standardized outcome measures, and that satisfaction ratings be assessed by someone independent of the health service provider. Further research using randomized controlled trial methodology with waitlist controls is needed.

Level of Evidence: 4
Triterpenes induced by young apple fruits in response to herbivore attack
Authors: Ohata Yuto , Tetsumoto Yuuki , Morita Sayo , Mori Naoki , Ishiguri Yoichi , Yoshinaga Naoko
Published: May 2021

Apples Malus domestica, known as a rich source of triterpene acids, induced more variety and quantity of triterpene acids in response to herbivory or mechanical damage. There were 3 major induced compounds: pomaceic acid and euscaphic acid, both of which are known apple triterpene acids, and 2α,19α-dihydroxy-3-oxours-12-en-28-oic acid (named eriobotoric acid), which was first identified in apples. In this study, the 3 compounds’ induction curves after damage, varietal differences in induction amounts, and physiological roles against pest insects were further investigated. Eriobotoric acid showed clear antifeedant activity against lepidopteran insect Spodoptera litura but not against apple pests.
Social insect colonies are more likely to accept unrelated queens when they come with workers
Authors: De Gasperin Ornela , Blacher Pierre , Chapuisat Michel
Published: May 2021

Relatedness underlies the evolution of reproductive altruism, yet eusocial insect colonies occasionally accept unrelated reproductive queens. Why would workers living in colonies with related queens accept unrelated ones, when they do not gain indirect fitness through their reproduction? To understand this seemingly paradox, we investigated whether acceptance of unrelated queens by workers is an incidental phenomenon resulting from failure to recognize non-nestmate queens, or whether it is adaptively favored in contexts where cooperation is preferable to rejection. Our study system is the socially polymorphic Alpine silver ant, Formica selysi. Within populations, some colonies have a single queen, and others have multiple, sometimes unrelated, breeding queens. Social organization is determined by a supergene with two haplotypes. In a first experiment, we investigated whether the number of reproductive queens living in colonies affects the ability of workers at rejecting alien queens, as multiple matrilines within colonies could increase colony odor diversity and reduce workers’ recognition abilities. As workers rejected all alien queens, independently of the number of queens heading their colony, we then investigated whether their acceptance is flexible and favored in specific conditions. We found that workers frequently accepted alien queens when these queens came with a workforce. Our results show that workers flexibly adjust their acceptance of alien queens according to the situation. We discuss how this conditional acceptance of unrelated queens may be adaptive by providing benefits through increased colony size and/or genetic diversity, and by avoiding rejection costs linked to fighting.
Interacting Epidemics in Amazonian Brazil: Prior Dengue Infection Associated With Increased Coronavirus Disease 2019 (COVID-19) Risk in a Population-Based Cohort Study
Authors: Nicolete Vanessa C , Rodrigues Priscila T , Johansen Igor C , Corder Rodrigo M , Tonini Juliana , Cardoso Marly A , de Jesus Jaqueline G , Claro Ingra M , Faria Nuno R , Sabino Ester C , Castro Marcia C , Ferreira Marcelo U
Published: May 2021

Background

Immunity after dengue virus (DENV) infection has been suggested to cross-protect from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and mortality.

Methods

We tested whether serologically proven prior DENV infection diagnosed in September–October 2019, before the coronavirus disease 2019 (COVID-19) pandemic, reduced the risk of SARS-CoV-2 infection and clinically apparent COVID-19 over the next 13 months in a population-based cohort in Amazonian Brazil. Mixed-effects multiple logistic regression analysis was used to identify predictors of infection and disease, adjusting for potential individual and household-level confounders. Virus genomes from 14 local SARS-CoV-2 isolates were obtained using whole-genome sequencing.

Results

Anti-DENV immunoglobulin G (IgG) was found in 37.0% of 1285 cohort participants (95% confidence interval [CI]: 34.3% to 39.7%) in 2019, with 10.4 (95% CI: 6.7–15.5) seroconversion events per 100 person-years during the follow-up. In 2020, 35.2% of the participants (95% CI: 32.6% to 37.8%) had anti-SARS-CoV-2 IgG and 57.1% of the 448 SARS-CoV-2 seropositives (95% CI: 52.4% to 61.8%) reported clinical manifestations at the time of infection. Participants aged >60 years were twice more likely to have symptomatic COVID-19 than children under 5 years. Locally circulating SARS-CoV-2 isolates were assigned to the B.1.1.33 lineage. Contrary to the cross-protection hypothesis, prior DENV infection was associated with twice the risk of clinically apparent COVID-19 upon SARS-CoV-2 infection, with P values between .025 and .039 after adjustment for identified confounders.

Conclusions

Higher risk of clinically apparent COVID-19 among individuals with prior dengue has important public health implications for communities sequentially exposed to DENV and SARS-CoV-2 epidemics.
Patient-specific iPSC-derived cardiomyocytes reveal abnormal regulation of FGF16 in a familial atrial septal defect
Authors: Ye Lingqun , Yu You , Zhao Zhen-Ao , Zhao Dandan , Ni Xuan , Wang Yong , Fang Xing , Yu Miao , Wang Yongming , Tang Jun-Ming , Chen Ying , Shen Zhenya , Lei Wei , Hu Shijun
Published: May 2021

Aims

Congenital heart disease (CHD) frequently occurs in newborns due to abnormal formation of the heart or major blood vessels. Mutations in the GATA4 gene, which encodes GATA binding protein 4, are responsible for atrial septal defect (ASD), a common CHD. This study aims to gain insights into the molecular mechanisms of CHD using human-induced pluripotent stem cells (iPSCs) from a family cohort with ASD.

Methods and results

Patient-specific iPSCs possess the same genetic information as the donor and can differentiate into various cell types from all three germ layers in vitro, thus presenting a promising approach for disease modelling and molecular mechanism research. Here, we generated a patient-specific iPSC line (iPSC-G4T280M) from a family cohort carrying a hereditary ASD mutation in GATA4 gene (T280M), as well as a human embryonic stem cell line (ESC-G4T280M) carrying the isogenic T280M mutation using the CRISPR/Cas9 genome editing method. The GATA4-mutant iPSCs and ESCs were then differentiated into cardiomyocytes (CMs) to model GATA4 mutation-associated ASD. We observed an obvious defect in cell proliferation in cardiomyocytes derived from both GATA4T280M-mutant iPSCs (iPSC-G4T280M-CMs) and ESCs (ESC-G4T280M-CMs), while the impaired proliferation ability of iPSC-G4T280M-CMs could be restored by gene correction. Integrated analysis of RNA-Seq and ChIP-Seq data indicated that FGF16 is a direct target of wild-type GATA4. However, the T280M mutation obstructed GATA4 occupancy at the FGF16 promoter region, leading to impaired activation of FGF16 transcription. Overexpression of FGF16 in GATA4-mutant cardiomyocytes rescued the cell proliferation defect. The direct relationship between GATA4T280M and ASD was demonstrated in a human iPSC model for the first time.

Conclusions

In summary, our study revealed the molecular mechanism of the GATA4T280M mutation in ASD. Understanding the roles of the GATA4-FGF16 axis in iPSC-CMs will shed light on heart development and provide novel insights for the treatment of ASD and other CHD disorders.
A non-parametric framework to estimate fertilization response in loblolly pine plantations using environmental covariates
Authors: Kinane Stephen M , Montes Cristian R , Bullock Bronson P
Published: May 2021

Fertilization is a common practice to increase the productivity and the stand value in the southeastern US. The decision to fertilize a given site is driven by site characteristics and the expected magnitude of response. To determine the magnitude, forest researchers typically rely on fertilization trials established throughout the region of interest and derive growth equations to reflect an increase in either site index or volume. Such equations lack an explicit spatial prediction component. To bridge this gap, we developed a modeling framework that explicitly evaluates the likelihood of a fertilization response as a binary process and the magnitude of such response as a separate model. The methodology relies on the non-parametric interpolator thin plate spines. To test the efficacy of this framework, both percent volume and dominant height response to repeated fertilizer treatments were estimated using data from long-term research trials in Georgia. Several environmental covariates were evaluated on their ability to reduce the models’ root mean square error and account for more of the variation in percent gain from fertilization regimes. Results showed that the inclusion of such covariates improved the model performance and reduced errors associated with interpolation. Thresholding expected responses from fertilization treatments allows practitioners to evaluate the probability of achieving a given response.
An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi
Authors: Mead Matthew E , Steenwyk Jacob L , Silva Lilian P , de Castro Patrícia A , Saeed Nauman , Hillmann Falk , Goldman Gustavo H , Rokas Antonis
Published: May 2021

Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to nonpathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and nonpathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1700 genes whose evolutionary rate differed between pathogens and nonpathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and nonpathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.
Constraint and Function in the Predefinitive Plumages of Manakins (Aves: Pipridae)
Authors: Schaedler Laura M , Taylor Liam U , Prum Richard O , Anciães Marina
Published: May 2021

Synopsis

Birds with delayed plumage maturation exhibit a drab predefinitive plumage, often despite gonad maturation, before developing the definitive plumage associated with increased reproductive success. Manakins are a diverse clade of neotropical lekking birds with extreme sexual dichromatism, radical sexual displays, and a unique diversity in the predefinitive plumages of males across species. Here, we provide the first full review of the natural history of manakin predefinitive plumages as the basis for qualitatively addressing the six major hypotheses about the production and function of predefinitive plumages. We find little evidence to support the possibilities that manakin predefinitive plumages are directly constrained by inflexible molt schedules, resource limitations to definitive coloration, or hormonal ties to reproductive behaviors. There is little evidence that could support a crypsis function, although direct experimentation is needed, and mimicry is refuted except for one unusual species in which predefinitive males sire young. Instead, evidence from a handful of well-studied species suggests that predefinitive plumages help young males explicitly signal their social status, and thereby gain entry to the social hierarchies which dictate future reproductive success. Our conclusions are especially influenced by the unique fact that males of at least 11 species throughout the family exhibit multiple predefinitive plumage stages with distinctively male patches. For each hypothesis, we highlight ways in which a better knowledge of female and young male birds offers critical opportunities for the use of manakins as a model clade.
Error estimates for the Cahn–Hilliard equation with dynamic boundary conditions
Authors: Harder Paula , Kovács Balázs
Published: May 2021

A proof of convergence is given for a bulk–surface finite element semidiscretisation of the Cahn–Hilliard equation with Cahn–Hilliard-type dynamic boundary conditions in a smooth domain. The semidiscretisation is studied in an abstract weak formulation as a second-order system. Optimal-order uniform-in-time error estimates are shown in the $L^2$- and $H^1$-norms. The error estimates are based on a consistency and stability analysis. The proof of stability is performed in an abstract framework, based on energy estimates exploiting the anti-symmetric structure of the second-order system. Numerical experiments illustrate the theoretical results.
The role of microRNAs on doxorubicin drug resistance in breast cancer
Authors: Jamialahmadi Khadijeh , Zahedipour Fatemeh , Karimi Gholamreza
Published: May 2021

Objectives

Resistance to chemotherapeutic drugs is a serious challenge for effective therapy of cancers. Doxorubicin is a drug which is typically used for breast cancer treatment. Several mechanisms are involved in resistance to doxorubicin including overexpression of ATP-binding cassette (ABC) transporters, altering apoptosis, autophagy and cell cycle arrest. In this review, we focus on the potential effects of microRNAs on doxorubicin resistance in breast cancer.

Methods

Literature review focusing on the ‘microRNAs and doxorubicin drug resistance in breast cancer’ was conducted comprehensively. The search was performed in PubMed, Scopus, Google and Google Scholar databases and reference lists of relevant articles were also included.

Key ﬁndings

MicroRNAs play essential role in resistance of breast cancer to doxorubicin by affecting several key cellular pathways, including overexpression of ABC transporters, altering apoptosis, autophagy and cell signaling pathways, cell cycle arrest, epithelial to mesenchymal transition (EMT) and cancer stem cells (CSCs).

Conclusions

Cancer treatment methods are moving from conventional therapies to targeted therapies such as using microRNAs. MiRNAs can act as regulatory molecules to overcome breast cancer doxorubicin resistance by controlling the expression levels of genes involved in different cellular pathways. Thus, exact elucidation of their role in different cellular processes can help overcome the breast cancer development and drug resistance.
Survey on utilization of flattening filter-free photon beams in Japan
Authors: Kodama Takumi , Yasui Keisuke , Nishioka Shie , Miyaura Kazunori , Takakura Toru , Katayose Tetsurou , Nakamura Mitsuhiro
Published: May 2021

To understand the current state of flattening filter-free (FFF) beam implementation in C-arm linear accelerators (LINAC) in Japan, the quality assurance (QA)/quality control (QC) 2018–2019 Committee of the Japan Society of Medical Physics (JSMP) conducted a 37-question survey, designed to investigate facility information and specifications regarding FFF beam adoption and usage. The survey comprised six sections: facility information, devices, clinical usage, standard calibration protocols, modeling for treatment planning (TPS) systems and commissioning and QA/QC. A web-based questionnaire was developed. Responses were collected between 18 June and 18 September 2019. Of the 846 institutions implementing external radiotherapy, 323 replied. Of these institutions, 92 had adopted FFF beams and 66 had treated patients using them. FFF beams were used in stereotactic radiation therapy (SRT) for almost all disease sites, especially for the lungs using 6 MV and liver using 10 MV in 51 and 32 institutions, respectively. The number of institutions using FFF beams for treatment increased yearly, from eight before 2015 to 60 in 2018. Farmer-type ionization chambers were used as the standard calibration protocol in 66 (72%) institutions. In 73 (80%) institutions, the beam-quality conversion factor for FFF beams was calculated from TPR20,10, via the same protocol used for beams with flattening filter (WFF). Commissioning, periodic QA and patient-specific QA for FFF beams also followed the procedures used for WFF beams. FFF beams were primarily used in high-volume centers for SRT. In most institutions, measurement and QA was conducted via the procedures used for WFF beams.
The Pop-Gen Pipeline Platform: A Software Platform for Population Genomic Analyses
Authors: Webb Andrew , Knoblauch Jared , Sabankar Nitesh , Kallur Apeksha Sukesh , Hey Jody , Sethuraman Arun
Published: May 2021

The Pop-Gen Pipeline Platform (PPP) is a software platform for population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including input preparation, file format conversion, various population genomic analyses, and output generation. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html.
Evolutionary Dynamics of the OR Gene Repertoire in Teleost Fishes: Evidence of an Association with Changes in Olfactory Epithelium Shape
Authors: Policarpo Maxime , Bemis Katherine E , Tyler James C , Metcalfe Cushla J , Laurenti Patrick , Sandoz Jean-Christophe , Rétaux Sylvie , Casane Didier
Published: May 2021

Teleost fishes perceive their environment through a range of sensory modalities, among which olfaction often plays an important role. Richness of the olfactory repertoire depends on the diversity of receptors coded by homologous genes classified into four families: OR, TAAR, VR1, and VR2. Herein, we focus on the OR gene repertoire. While independent large contractions of the OR gene repertoire associated with ecological transitions have been found in mammals, little is known about the diversity of the OR gene repertoire and its evolution in teleost fishes, a group that includes more than 34,000 living species. We analyzed genomes of 163 species representing diversity in this large group. We found a large range of variation in the number of functional OR genes, from 15 in the Broad-nose Pipefish Syngnathus typhle and the Ocean Sunfish Mola mola, to 429 in the Zig-zag Eel Mastacembelus armatus. The number of OR genes was higher in species when a multilamellar olfactory rosette was present. Moreover, the number of lamellae was correlated with the richness of the OR gene repertoire. While a slow and balanced birth-and-death process generally drives the evolution of the OR gene repertoire, we inferred several episodes of high rates of gene loss, sometimes followed by large gains in the number of OR genes. These gains coincide with morphological changes of the olfactory organ and suggest a strong functional association between changes in the morphology and the evolution of the OR gene repertoire.
A forgotten subspecies of the land snail speciesArianta arbustorumfrom a Pleistocene refuge in the Western Alps
Authors: Hausdorf Bernhard , Walther Frank
Published: May 2021

Alpine Arianta populations from the Biellese Alps in Italy are characterized by imperforate, thin-shelled, dark brown shells without or with sparse light spots that resemble widespread phenotypes of Arianta arbustorum arbustorum found in calcium-deficient areas. Therefore, they were not considered a distinct taxon. However, molecular phylogenetic analyses show that they belong to a group of subspecies of A. arbustorum from the Western Alps and the Pyrenees. We classify them as a distinct subspecies, Arianta a. doriae (Paulucci, 1878), which reduces the geographical gap between the western group of subspecies of A. arbustorum and the Eastern Alps where Arianta originated. This subspecies survived the glacials in a peripheral mountain refuge at the southern margin of the Biellese Alps.
Insight into the adaptive evolution of mitochondrial genomes in intertidal chitons
Authors: Dhar Dipanjana , Dey Debayan , Basu Soumalee , Fortunato Helena
Published: May 2021

The intertidal zone is one of the most stressful environments, with extreme shifts in temperature, salinity, pH and oxygen concentration. Marine molluscs, particularly chitons that belong to the category of ecologically significant organisms, survive in this extreme environment, and are ideal systems for studying stress adaptation. Mitochondria are known to be critical for energy homeostasis, and changes in environmental factors result in their dysfunction and consequent injury to the organism. Intertidal organisms are exception in this respect because they are capable of maintaining mitochondrial integrity. Here, we used mitochondrial genetic components from seven chitons of the intertidal zone to infer phylogenetic relationships. Selection analyses on individual protein-coding genes (PCGs) were performed to identify and map potentially adaptive residues in the modelled structures of the mitochondrial respiratory chain complexes. The results showed significant amino acid changes in sites under diversifying selection for all the PCGs, indicating that the mitochondrial genome in chitons is undergoing adaptive evolution. Such sites were observed in the proton pump as well as in the translocation channel of the transmembrane helices and the surrounding loop regions, thus implying functional modification of the mitochondrial proteins essential for survival in the dynamic environment of the intertidal zone.
Graphery: interactive tutorials for biological network algorithms
Authors: Zeng Heyuan , Zhang Jinbiao , Preising Gabriel A , Rubel Tobias , Singh Pramesh , Ritz Anna
Published: May 2021

Networks have been an excellent framework for modeling complex biological information, but the methodological details of network-based tools are often described for a technical audience. We have developed Graphery, an interactive tutorial webserver that illustrates foundational graph concepts frequently used in network-based methods. Each tutorial describes a graph concept along with executable Python code that can be interactively run on a graph. Users navigate each tutorial using their choice of real-world biological networks that highlight the diverse applications of network algorithms. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Graphery is available at https://graphery.reedcompbio.org/.
Single-cell image analysis reveals a protective role for microglia in glioblastoma
Authors: Woolf Zoe , Swanson Molly E V , Smyth Leon C , Mee Edward W , Schweder Patrick , Heppner Peter , Kim Bernard J H , Turner Clinton , Oldfield Robyn L , Curtis Maurice A , Faull Richard L M , Scotter Emma L , Park Thomas I-H , Dragunow Michael
Published: May 2021

Background

Microglia and tumor-associated macrophages (TAMs) constitute up to half of the total tumor mass of glioblastomas. Despite these myeloid populations being ontogenetically distinct, they have been largely conflated. Recent single-cell transcriptomic studies have identified genes that distinguish microglia from TAMs. Here we investigated whether the translated proteins of genes enriched in microglial or TAM populations can be used to differentiate these myeloid cells in immunohistochemically stained human glioblastoma tissue.

Methods

Tissue sections from resected low-grade, meningioma, and glioblastoma (grade IV) tumors and epilepsy tissues were immunofluorescently triple-labeled for Iba1 (pan-myeloid marker), CD14 or CD163 (preferential TAM markers), and either P2RY12 or TMEM119 (microglial-specific markers). Using a single-cell-based image analysis pipeline, we quantified the abundance of each marker within single myeloid cells, allowing the identification and analysis of myeloid populations.

Results

P2RY12 and TMEM119 successfully discriminated microglia from TAMs in glioblastoma. In contrast, CD14 and CD163 expression were not restricted to invading TAMs and were upregulated by tumor microglia. Notably, a higher ratio of microglia to TAMs significantly correlated with increased patient survival.

Conclusions

We demonstrate the validity of previously defined microglial-specific genes P2RY12 and TMEM119 as robust discriminators of microglia and TAMs at the protein level in human tissue. Moreover, our data suggest that a higher proportion of microglia may be beneficial for patient survival in glioblastoma. Accordingly, this tissue-based method for myeloid population differentiation could serve as a useful prognostic tool.
2021 update on ATP-binding cassette (ABC) transporters: how they meet the needs of plants
Authors: Do Thanh Ha Thi , Martinoia Enrico , Lee Youngsook , Hwang Jae-Ung
Published: May 2021

Recent developments in the field of ABC proteins including newly identified functions and regulatory mechanisms expand the understanding of how they function in the development and physiology of plants.
THREE-POINT AREA METHOD FOR THERMOLUMINESCENCE GLOW CURVE ANALYSIS AND ITS APPLICATION TO THE GLOW PEAK OF K2SRP2O7:PR
Authors: Kundu M , Bhattacharyya S , Karmakar M , Majumdar P S
Published: May 2021

A method has been proposed to evaluate the kinetic parameters, viz. activation energy ($E$) and order of kinetics ($b$) from a single or isolated thermoluminescence (TL) glow peak. Along with the area under the entire curve, this method uses a set of three arbitrary data points and calculates the partial area under the curve from each point to the endpoint. In this way, the entire information associated with the curve is used and the method is named as ‘Three-Point Area’ (TPA) method. We have applied it successfully on a number of theoretically simulated TL curves generated in One Trap One Recombination centre (OTOR) model and General-Order Kinetics (GOK) model under quasi-equilibrium approximations with linear heating scheme. The activation energies are found in good agreement with input values for both the models. For OTOR model, temperature average of order of kinetics is estimated to compare with the present result. Systematic analysis is carried out for estimation of errors inherent in the method in the purview of GOK model. A closer look on the results reveals that any set of three points, preferably chosen from the rising side of the curve, can yield activation energy and order of kinetics. The validity of the method to extract $E$ and $b$ from experimental glow curves is exemplified by considering experimental TL data reported in literature. Finally, a complete study starting from the synthesis of a new phosphor $\mathrm{K_2SrP_2O_7:Pr} $ and analysis of the recorded TL data to estimate $E$ and $b$ employing the TPA method has been reported.
Sexual function in patients with idiopathic inflammatory myopathies: a cross-sectional study
Authors: Heřmánková Barbora , Špiritović Maja , Oreská Sabína , Štorkánová Hana , Komarc Martin , Klein Martin , Mann Heřman , Pavelka Karel , Šenolt Ladislav , Vencovský Jiří , Tomčík Michal
Published: May 2021

Objectives

To date, there is almost no information concerning the sexual health of patients with idiopathic inflammatory myopathies (IIM). This cross-sectional study aimed to compare sexual function in patients with IIM to age-/sex-matched healthy controls (HC) and determine the potential impact of clinical features on sexual function.

Methods

In total, 122 women (61 with IIM, 61 age-matched HC) and 22 men (11 with IIM, 11 age-matched HC) aged 18–80 years completed gender-specific selection of 7 well-established and validated questionnaires assessing sexual health and function (Female Sexual Function Index, Brief Index of Sexual Function for Women, Sexual Function Questionnaire, Sexual Quality of Life Questionnaire–Female, International Index of Erectile Function, Male Sexual Health Questionnaire, Sexual Quality of Life Questionnaire–Male). Results were compared between patients and HC and correlated with selected disease-related features.

Results

The prevalence of sexual dysfunction in IIM was 59% in women (vs 40% in HC), and 64% (vs 9% in HC) in men. Men and women with IIM reported significantly impaired sexual function compared with sex-/age-matched HC. Decreased sexual function was associated with muscle weakness, disability, physical inactivity, fatigue, depression and decreased quality of life.

Conclusions

Our results suggest that sexual dysfunction is common among IIM patients and more attention should be paid to this aspect of the disease.
Shimizu Ikutarō and the Precarious Coexistence of Progressivism and Conservatism
Authors: LEE Seok-Won
Published: May 2021

Shimizu Ikutarō (1907–1988) is one of the most controversial postwar Japanese intellectuals. His transition from the icon of the Anpo protests to an advocate of a nuclear Japan has been considered an intellectual conversion (tenkō). Instead of revisiting the notion of conversion, this study shows that his wartime thoughts—bottom-up nationalism in particular—continued to influence Shimizu’s postwar writings and activism on both conservative and liberal sides. Shimizu delineated his historical concept of how ordinary people in Meiji and Taisho Japan had contributed to the development of a modern society and called for the construction of a new system. Endorsing Japan’s wartime efforts, Shimizu strove to center nationalist energies by ordinary Japanese on his concept of a new Japan. However, Shimizu’s adherence to bottom-up movements in wartime and postwar Japan reflects his problematic interpretation of Japanese history. Neglecting Japan’s nationalistic path to colonial violence, his writings on the society and culture of wartime and postwar Japan affirm grass-root nationalism as Japan’s key to modern development. This line of thinking was later associated with anti-American nationalist movements in the 1950s. His notion of civil society movements soon encountered a highly nationalistic project of a nuclear Japan in the 1970s.