bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural network reconstruction of late-time cosmology and null tests
Authors: Dialektopoulos Konstantinos , Said Jackson Levi , Mifsud Jurgen , Sultana Joseph , Zarb Adami Kristian
Published: February 2022

The prospect of nonparametric reconstructions of cosmological parameters from observational data sets has been a popular topic in the literature for a number of years. This has mainly taken the form of a technique based on Gaussian processes but this approach is exposed to several foundational issues ranging from overfitting to kernel consistency problems. In this work, we explore the possibility of using artificial neural networks (ANN) to reconstruct late-time expansion and large scale structure cosmological parameters. We first show how mock data can be used to design an optimal ANN for both parameters, which we then use with real data to infer their respective redshift profiles. We further consider cosmological null tests with the reconstructed data in order to confirm the validity of the concordance model of cosmology, in which we observe a mild deviation with cosmic growth data.
Power law scaling and country-level centralization of global agricultural production and trade
Authors: Dupas Marie-Cécile , Halloy José , Chatzimpiros Petros
Published: February 2022

Global food production and international trade are rapidly expanding and drive increasing agricultural globalization and specialization. Following production patterns, network properties and added-value chains, exportable surpluses of countries can offset food and feed deficits in other countries. However, production and trade patterns are barely addressed in the scientific literature as two interactive components of global agriculture. Integrated analysis of the temporal dynamics and distribution patterns of production and trade among countries can help addressing future food security challenges in view of ongoing trends. Here, we analyse the interdependent patterns of global agricultural production and trade from 1986 to 2016. We classify total production and trade mass into six product categories—cereals, oilcrops, meat, fruits and vegetables, coffee and cocoa. We estimate reexports in global trade by assessing mass balances of production, imports and exports per country. We show that global trade and reexports increase exponentially faster than production and that production and trade are highly centralized among a small number of countries. For most agricultural categories, the centralization of flows has increased in time for production and net exports, and has decreased for net imports and reexports. Accordingly, a growing number of deficient countries are sustained by a decreasing number of top-producing countries. In parallel, reexport routes are increasingly dominated by long-industrialized countries besides the increase in time in the number of reexporting countries. We discuss the interdependencies between global agricultural production and trade patterns. We highlight the drivers and implications of the observed trends for food security challenges.
Quantum phase transition of a modified spin-boson model
Authors: Qin Yan , Li Sheng-Chang
Published: February 2022

We adopt a modified spin-boson model to investigate the quantum phase transition in an ultracold atom-molecule conversion system involving molecule–molecule interaction. We explore the properties of ground state, entanglement entropy, and many-body dynamics, which confirm that the system exhibits a second-order phase transition from a pure atom phase to a mixed atom-molecule phase when the energy detuning is below a critical value. We obtain three scaling laws and the corresponding two critical exponents to characterize the phase transition. In particular, we discuss the effects of both the speed of ground-state dynamical evolution and the strength of molecular interaction on the phase transition. The adiabatic evolution condition is obtained as well. Our results show that the molecular interaction can greatly reduce the upper bound of the adiabatic condition, which provides a theoretical basis for easier observation of the phase transition in experiments.
Resistance law dependence on radius ratios for turbulent Taylor-Couette flow from extended local balance model
Authors: Balonishnikov Alexander , Kruchkova Julia
Published: February 2022

Turbulent Couette-Taylor flow is the most interesting kind of flow for theoreticians and experimenters. There are a great number of theories and experiments for larger and larger Reynolds numbers. The picture becomes more complex if we consider the case of independently rotating cylinders. The most simple quantity is a torque, acting on the lateral surface of inner cylinder by rotating fluid. How can we deduce theoretically the torque from Navier-Stokes equation? Unfortunately we have only bounds on this variable yet. So we cause use models of turbulence to predict the torque dependence on Reynolds numbers or Taylor number and on radius ration. Here we present the results of simple calculations, based on extended local balance model. The study compares the theory with experiments.
Choosing technical components of the physical protection system of objects
Authors: Fedorov S Yu , Khalizev V N , Tarasov E S
Published: February 2022

This article presents a method for solving the urgent problem of choosing a combination of technical systems of physical protection of objects of informatization of an organization, on the example of an integrated security system using methods of system analysis. The article proposes a new approach that combines the methods of the theory of antagonistic games and methods of fuzzy logic. On the basis of this mathematical model, a program and a database have been developed, including interconnected tables of physical protection systems, capabilities of protection systems, tables of threats and ways of implementing threats. As a result of the application of this method, with the help of the program, a specialist can quickly solve the complex problem of choosing the optimal combination of physical protection systems to counter probable threats for a specific object of the organization’s informatization. Based on the results of the program’s work, the developer receives a report with recommendations.
Development of a bi-fuel power supply system for a diesel engine
Authors: Buzikov Sh V , Matushkin O P , Matushkina Yu N
Published: February 2022

The relevance of the study is due to the lack of systems in which the proportions of the used fuels in the mixture and the values of the cycle supply are simultaneously controlled depending on the load-speed mode of the diesel engine. The aim of the research is to develop a design for a bi-fuel power supply system for a diesel engine, which allows for the simultaneous regulation of the proportions of the components of a mixture consisting of alternative and diesel fuels, as well as the values of the cyclic supply of this mixture to the diesel cylinders. As a result of the research, an algorithm was calculated for the simultaneous control of the proportions of the components of a mixture consisting of alternative and diesel fuels, as well as the values of the cyclic supply of this mixture to the diesel cylinders. As a result of the operation of the fuel supply system on mixtures of diesel and alternative fuels according to the developed algorithm, it made it possible to achieve the identical operation of a diesel engine on pure diesel fuel at all load-speed modes of diesel operation. Also, in the course of the research carried out, a bi-fuel power supply system for a diesel engine was developed, which makes it possible to simultaneously regulate the amount (cycle supply) and the composition of a mixture consisting of diesel and alternative fuel supplied to the diesel cylinders, depending on the speed and load modes of operation.
Plant responses to heterogeneous salinity: agronomic relevance and research priorities
Authors: Valenzuela Francisco Jose , Reineke Daniela , Leventini Dante , Chen Christopher Cody Lee , Barrett-Lennard Edward G , Colmer Timothy D , Dodd Ian C , Shabala Sergey , Brown Patrick , Bazihizina Nadia
Published: February 2022

Background

Soil salinity, in both natural and managed environments, is highly heterogeneous, and understanding how plants respond to this spatiotemporal heterogeneity is increasingly important for sustainable agriculture in the era of global climate change. While the vast majority of research on crop response to salinity utilizes homogeneous saline conditions, a much smaller, but important, effort has been made in the past decade to understand plant molecular and physiological responses to heterogeneous salinity mainly by using split-root studies. These studies have begun to unravel how plants compensate for water/nutrient deprivation and limit salt stress by optimizing root-foraging in the most favourable parts of the soil.

Scope

This paper provides an overview of the patterns of salinity heterogeneity in rain-fed and irrigated systems. We then discuss results from split-root studies and the recent progress in understanding the physiological and molecular mechanisms regulating plant responses to heterogeneous root-zone salinity and nutrient conditions. We focus on mechanisms by which plants (salt/nutrient sensing, root-shoot signalling and water uptake) could optimize the use of less-saline patches within the root-zone, thereby enhancing growth under heterogeneous soil salinity conditions. Finally, we place these findings in the context of defining future research priorities, possible irrigation management and crop breeding opportunities to improve productivity from salt-affected lands.
POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability
Authors: Li Fengcheng , Zhou Ying , Zhang Ying , Yin Jiayi , Qiu Yunqing , Gao Jianqing , Zhu Feng
Published: February 2022

Mass spectrometry-based proteomic technique has become indispensable in current exploration of complex and dynamic biological processes. Instrument development has largely ensured the effective production of proteomic data, which necessitates commensurate advances in statistical framework to discover the optimal proteomic signature. Current framework mainly emphasizes the generalizability of the identified signature in predicting the independent data but neglects the reproducibility among signatures identified from independently repeated trials on different sub-dataset. These problems seriously restricted the wide application of the proteomic technique in molecular biology and other related directions. Thus, it is crucial to enable the generalizable and reproducible discovery of the proteomic signature with the subsequent indication of phenotype association. However, no such tool has been developed and available yet. Herein, an online tool, POSREG, was therefore constructed to identify the optimal signature for a set of proteomic data. It works by (i) identifying the proteomic signature of good reproducibility and aggregating them to ensemble feature ranking by ensemble learning, (ii) assessing the generalizability of ensemble feature ranking to acquire the optimal signature and (iii) indicating the phenotype association of discovered signature. POSREG is unique in its capacity of discovering the proteomic signature by simultaneously optimizing its reproducibility and generalizability. It is now accessible free of charge without any registration or login requirement at https://idrblab.org/posreg/
CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications
Authors: Rapti Melivoia , Zouaghi Yassine , Meylan Jenny , Ranza Emmanuelle , Antonarakis Stylianos E , Santoni Federico A
Published: February 2022

CoverageMaster (CoM) is a copy number variation (CNV) calling algorithm based on depth-of-coverage maps designed to detect CNVs of any size in exome [whole exome sequencing (WES)] and genome [whole genome sequencing (WGS)] data. The core of the algorithm is the compression of sequencing coverage data in a multiscale Wavelet space and the analysis through an iterative Hidden Markov Model. CoM processes WES and WGS data at nucleotide scale resolution and accurately detects and visualizes full size range CNVs, including single or partial exon deletions and duplications. The results obtained with this approach support the possibility for coverage-based CNV callers to replace probe-based methods such as array comparative genomic hybridization and multiplex ligation-dependent probe amplification in the near future.
Loss of Nobox prevents ovarian differentiation from juvenile ovaries in zebrafish
Authors: Qin Mingming , Xie Qingping , Wu Kun , Zhou Xianqing , Ge Wei
Published: February 2022

As a species without master sex-determining genes, zebrafish displays high plasticity in sex differentiation, making it an excellent model for studying the regulatory mechanisms underlying gonadal differentiation and gametogenesis. Despite being a gonochorist, zebrafish is a juvenile hermaphrodite that undergoes a special phase of juvenile ovary before further differentiation into functional testis and ovary. The mechanisms underlying juvenile ovary formation and subsequent gonadal differentiation remain largely unknown. In this study, we explored the role of Nobox/nobox (new born ovary homeobox protein), another oocyte-specific transcription factor in females, in early zebrafish gonadogenesis using CRISPR/Cas9 technology. As in mammals, nobox is specifically expressed in zebrafish gonads with a dimorphic pattern at juvenile stage. In contrast to the mutant of figla (factor in the germline alpha, another oocyte-specific transcription factor), the nobox mutants showed formation of typical perinucleolar (PN) follicles at primary growth (PG) stage in juvenile gonads, suggesting occurrence of follicle assembly from cystic oocytes (chromatin nucleolar stage, CN). These follicles, however, failed to develop further to form functional ovaries, resulting in all-male phenotype. Despite its expression in adult testis, the loss of nobox did not seem to affect testis development, spermatogenesis and male spawning. In summary, our results indicate an important role for Nobox in zebrafish ovarian differentiation and early folliculogenesis.
Authoritarian Legality and Legal Instrumentalism in China
Authors: Wang Shucheng
Published: February 2022

Law has become increasingly important for authoritarian regimes. This article analyzes the dynamics of authoritarian legality by delineating two pure types of authoritarian politics, i.e. normal politics and exceptional politics. It explains the institutionalization of authoritarian legality – from law-making to final adjudication – through a politically controllable congress and court system. It further identifies three pure types of instantiations of legal instrumentalism, based on the variance of political ideologies: liberal, apolitical, and illiberal. Taking China as an example, the instantiation of legal instrumentalism in illiberal regimes has been different from those in liberal regimes. It further argues that legal instrumentalism as instantiated in an illiberal context provides a more explanatory framework than either Marxist or Confucian legal theories to reveal the law’s nature and function as a crucial instrument for developing the enterprise of legality grounded on illiberal principles in China.
Specialize or diversify? And in What? Trade composition, quality of specialization, and persistent growth
Authors: Dosi Giovanni , Riccio Federico , Virgillito Maria Enrica
Published: February 2022

This paper, using a long-term, product-level, cross-country dataset, analyzes the trade–growth nexus by introducing two novel indicators able to capture demand and supply attributes of countries’ quality of specialization. The Keynesian efficiency index measures demand attractiveness of the export baskets, estimating product-level demand elasticities and weighting them by diversification; the Schumpeterian efficiency index tracks the export baskets’ technological dynamism proxied by product-level patent intensities. These two dimensions of quality of specialization are effective in explaining the rate and volatility of growth and the duration of growth episodes, identified as periods longer than 8 years of 2% average growth and, even more, of exceptional growth episodes ($\geq\,5\%$). Our results, robust to a wide range of control variables, suggest that specialization per sé is detrimental for growth resilience while countries with a diversified export structure specialized either in demand-elastic and technological-dynamic productions are likely to experience longer growth episodes.
Mosquito Repellent Potential ofCarpesium abrotanoidesEssential Oil and Its Main Components Against a Dengue Vector,Aedes aegypti(Diptera: Culicidae)
Authors: Haris Abdullah , Azeem Muhammad , Binyameen Muhammad
Published: February 2022

Disease vectoring mosquitoes are a serious threat to humans. However, till today only few mosquito repellents have been identified. The current study was conducted to evaluate the repellent potential of Carpesium abrotanoides essential oil against Aedes aegypti females by human bait technique. Essential oil was extracted by steam distillation process while the identification of chemical constituents was carried out by gas chromatography–mass spectrometry. Time span repellent bioassays of C. abrotanoides essential oil in comparison to DEET were performed at three different doses (33 μg/cm2, 165 μg/cm2, and 330 μg/cm2) under laboratory conditions. Highest repellency periods for essential oil and DEET were observed at the tested dose of 330 μg/cm2 with 315 min and 720 min, respectively. Lowest repellency period of 45 min for essential oil and 105 min for DEET was recorded at the tested dose of 33 μg/cm2. Major constituents caryophyllene (24.3%) and trans-nerolidol (12.0%) of C. abrotanoides essential oil were also evaluated as repellents at three different doses (330 μg/cm2, 165 μg/cm2, and 33 μg/cm2) against Ae. aegypti. Surprisingly, trans-nerolidol completely inhibited Ae. aegypti landings for 45 min when tested at 330 μg/cm2. However, caryophyllene did not completely inhibit Ae. aegypti landing even after immediate application at the tested dose of 330 μg/cm2. At the tested dose of 330 μg/cm2, the mixture (trans-nerolidol + caryophyllene) completely inhibited Ae. aegypti landing for 60 min indicating the synergistic effect of caryophyllene. Hence, C. abrotanoides as well as its major constituent, especially trans-nerolidol, have potential to formulate as mosquito repellent comparable of DEET.
Molecular phylogenetics reveals the common species ofTrochus(Vetigastropoda: Trochidae) found on Japanese temperate subtidal reefs
Authors: Sawayama Shuhei , Yanagimoto Takashi , Chow Seinen , Onitsuka Toshihiro , Shirafuji Norio , Hayakawa Jun , Kurogi Hiroaki
Published: February 2022

Five species of the marine gastropod genus Trochus are found on the Japanese coast. It was considered that Trochus rota was the most northerly species, whereas subtropical species, including T. histrio, were limited to the southern region. In recent years, however, several researchers have reported shells of T. histrio at higher latitudes than the previously assumed northern limit of this species. For the identification of the Japanese Trochus species, traditional shell morphological characters are insufficient. To provide better identification criteria, we performed a detailed morphological investigation and molecular analysis for Trochus individuals (n = 55) collected from a subtidal reef in Nagai, on the temperate Pacific coast of Japan. Our phylogenetic analysis, which was based on the mitochondrial DNA genes cytochrome c oxidase subunit I and 16S ribosomal RNA, shows that T. histrio, despite its relatively low genetic diversity, exhibits substantial variation in the morphology of the shell base (i.e. in the extent of red spotting on the inner part of the aperture and in the prominence of the knobs protruding along the base of the shell periphery). A shell size comparison indicates that the variation in the shell base reflects growth-associated morphological change. We found significant differences between T. histrio and T. rota in two shell characters (the number of knobs along the base of the shell periphery and shell height/width ratio) with size as a covariate. We conclude that these two species can usually be distinguished from each other by the combination of two characters: presence/absence of red spots on the inner aperture and the extent (i.e. number and prominence) of knob-like structures on the shell base. In addition, field sampling in Nagai shows that T. histrio is currently much more common than T. rota at two sites having contrasting kelp forest conditions. The diagnostic criteria presented here provide a useful basis for research on the ecology of Japanese Trochus species.
Preoperative [11C]methionine PET to personalize treatment decisions in patients with lower-grade gliomas
Authors: Ninatti Gaia , Sollini Martina , Bono Beatrice , Gozzi Noemi , Fedorov Daniil , Antunovic Lidija , Gelardi Fabrizia , Navarria Pierina , Politi Letterio S , Pessina Federico , Chiti Arturo
Published: February 2022

Background

PET with radiolabeled amino acids is used in the preoperative evaluation of patients with glial neoplasms. This study aimed to assess the role of [11C]methionine (MET) PET in assessing molecular features, tumor extent, and prognosis in newly diagnosed lower-grade gliomas (LGGs) surgically treated.

Methods

One hundred and fifty-three patients with a new diagnosis of grade 2/3 glioma who underwent surgery at our Institution and were imaged preoperatively using [11C]MET PET/CT were retrospectively included. [11C]MET PET images were qualitatively and semi-quantitatively analyzed using tumor-to-background ratio (TBR). Progression-free survival (PFS) rates were estimated using the Kaplan-Meier method and Cox proportional-hazards regression was used to test the association of clinicopathological and imaging data to PFS.

Results

Overall, 111 lesions (73%) were positive, while thirty-two (21%) and ten (6%) were isometabolic and hypometabolic at [11C]MET PET, respectively. [11C]MET uptake was more common in oligodendrogliomas than IDH-mutant astrocytomas (87% vs 50% of cases, respectively). Among [11C]MET-positive gliomas, grade 3 oligodendrogliomas had the highest median TBRmax (3.22). In 25% of patients, PET helped to better delineate tumor margins compared to MRI only. In IDH-mutant astrocytomas, higher TBRmax values at [11C]MET PET were independent predictors of shorter PFS.

Conclusions

This work highlights the role of preoperative [11C]MET PET in estimating the type of suspected LGGs, assessing tumor extent, and predicting biological behavior and prognosis of histologically confirmed LGGs. Our findings support the implementation of [11C]MET PET in routine clinical practice to better manage these neoplasms.
An Evaluation of Five Models of Arc Volcanism
Authors: Turner Stephen J , Langmuir Charles H
Published: February 2022

A first-order observation of convergent margin volcanism is that continental arc stratovolcanoes have substantially elevated incompatible element abundances and notable fractionations of certain incompatible element ratios compared to oceanic arc stratovolcanoes. Models to account for these differences include (1) a greater influence of differentiation and contamination due to thicker crust, (2) a variable slab flux controlled by the slab thermal structure, (3) heterogeneity of the ambient mantle wedge, (4) variations in extents of melting caused by wedge thermal structure, and (5) slab diapirs and subduction erosion that provide different source materials to the melting regime. An evaluation of these models using arc geochemistry, experimental results, physical models, and tectonic constraints shows that models 1, 2, and 5 are inconsistent with a variety of observations. While a slab component is always present along the arc front, variations in the slab component are not the primary cause of the continental/oceanic arc dichotomy. There is compelling evidence for models 3 and 4, wedge heterogeneity and variations in extents of melting, which in combination provide straightforward explanations for the first-order features of arc geochemistry. Oceanic arcs with back-arc basins are formed by large extents of melting of an ambient mantle that is more depleted than the normal ocean ridge basalt mantle source. Continental arcs are formed by smaller extents of melting of an ambient mantle that is usually more enriched. The apparent greater influence of slab components in oceanic arcs can be understood by the greater leverage that the slab component has on depleted mantle compositions. These conclusions apply to the first-order global and regional systematics, which is not to say that individual volcanoes or samples may be more influenced by crustal processes, slab temperature, or a sediment diapir intermittently incorporated into the mantle wedge.
Transcriptomic and functional analysis provides molecular insights into multicellular trichome development
Authors: Dong Mingming , Xue Shudan , Bartholomew Ezra S , Zhai Xuling , Sun Lei , Xu Shuo , Zhang Yaqi , Yin Shuai , Ma Wenyue , Chen Shuying , Feng Zhongxuan , Geng Chao , Li Xiangdong , Liu Xingwang , Ren Huazhong
Published: February 2022

Trichomes, the hair-like structures located on aerial parts of most vascular plants, are associated with a wide array of biological processes and affect the economic value of certain species. The processes involved in unicellular trichome formation have been well-studied in Arabidopsis (Arabidopsis thaliana). However, our understanding of the morphological changes and the underlying molecular processes involved in multicellular trichome development is limited. Here, we studied the dynamic developmental processes involved in glandular and nonglandular multicellular trichome formation in cucumber (Cucumis sativus L.) and divided these processes into five sequential stages. To gain insights into the underlying mechanisms of multicellular trichome formation, we performed a time-course transcriptome analysis using RNA-sequencing analysis. A total of 711 multicellular trichome-related genes were screened and a model for multicellular trichome formation was developed. The transcriptome and co-expression datasets were validated by reverse transcription-quantitative PCR and in situ hybridization. In addition, virus-induced gene silencing analysis revealed that CsHOMEOBOX3 (CsHOX3) and CsbHLH1 are involved in nonglandular trichome elongation and glandular trichome formation, respectively, which corresponds with the transcriptome data. This study presents a transcriptome atlas that provides insights into the molecular processes involved in multicellular trichome formation in cucumber and can be an important resource for future functional studies.
INFLUENCE OF SAMPLING FLOW RATE ON THORON EXHALATION RATE MEASUREMENTS BY THE CIRCULATION METHOD
Authors: Hosoda Masahiro , Yamada Ryohei , Kobyashi Hiromu , Tamakuma Yuki , Nugraha Eka Djatnika , Hashimoto Hiroki , Negami Ryoju , Kranrod Chutima , Omori Yasutaka , Tazoe Hirofumi , Akata Naofumi , Tokonami Shinji
Published: February 2022

Researchers have used various methods to obtain the exhalation rates of radon and thoron from soil and building materials. One of the typical methods for radon exhalation rate is the circulation method using an accumulation container, an external or internal sampling pump and a continuous radon monitor. However, it is necessary to consider sampling flow rate if this method is applied to exhalation rate measurement for thoron due to its short half-life. Based on a calibration experiment, the measured thoron concentrations obtained by an electrostatic collection type radon and thoron monitor (RAD7) were found to be influenced strongly by the sampling flow rate. It was also found that the thoron exhalation rate from a soil sample depended on the pressure difference which was proportional to the increasing sampling flow rate. The thoron exhalation rate measured at the generally used sampling flow rate of the internal sampling pump of the RAD7 was overestimated compared with the value at 0 L min−1.
Mycobacterium Species on the Cutaneous Microbiome of Very Preterm Neonates
Authors: Shah Pritik A , Govindarajan Varun , Rangaiah Ambica , Diggikar Shivashankar , Devadas Sahana , Chunchanur Sneha K , Shankar Sathyanarayan Muthur , Das Subhadeep , Kariyappa Mallesh
Published: February 2022

The neonatal skin microbiome consists of all the genomes and genetic products of microorganisms harboring on an infant’s skin. Host and the microbiota develop a harmonious environment resulting in symbiosis. Any disruption of this environment could lead to pathological disease. This study was conducted to understand the neonatal skin microbiome of very preterm neonates (under 32 weeks) admitted to the Neonatal Intensive Care Unit(NICU) at a tertiary healthcare setting before and after kangaroo mother care (KMC), using next-generation sequencing (NGS). Skin swabs were collected on two different occasions and analyzed using the NGS technique after amplification via polymerase chain reaction. The results showed relative abundance for Mycobacterium tuberculosis in 83.33% and 66.67% (p = 0.29) and Mycobacteroides abscessus in 100% and 93.33% (p = 0.30) of the very preterm neonates on the skin microbiome before and after KMC, respectively as an incidental finding. The mere presence of these bacilli as commensals or as potential pathogens is alarming due to the risk of early exposure and incidence of tuberculosis from birth. These findings, in our view, are the first findings to be established in such a setting.
Plant-Growth-Promoting Traits of Bacillus Species Associated with Quinoa (Chenopodium quinoa) and Lambsquarters (Chenopodium album)
Authors: Testen Anna L. , Magnus Mayra Claros , Backman Paul A.
Published: February 2022

As quinoa (Chenopodium quinoa Willd.) production expands globally, methods to mitigate abiotic and biotic production constraints are needed. One potential method to improve quinoa productivity is through the use of plant-growth-promoting microbes. In this study, we examined Chenopodium-associated Bacillus populations from Bolivia, Ecuador, and the United States for their ability to solubilize phosphate, antagonize Fusarium oxysporum, and produce phytase, indole acetic acid (IAA), and chitinase. The majority (99%) of isolates screened (n = 496) exhibited one or more traits related to plant growth promotion. Phosphate solubilization was observed in 75%, phytase production in 89%, IAA production in 44%, chitinase production in 13%, and antagonism to F. oxysporum in 8% of screened isolates. Some species or species groups screened were more likely than others to exhibit certain traits, such as B. megaterium, B. pumilus group, and B. subtilis group for phosphate solubilization and B. cereus group for chitinase production. This study indicates that many Chenopodium-associated Bacillus isolates exhibit plant-growth-promoting traits and could be studied further to promote quinoa production.
A Person-Centered Approach Understanding Stroke Survivor and Family Caregiver Emotional Health
Authors: Varughese Tina , Casameni Montiel Tahani , Engebretson Joan , Savitz Sean I. , Sharrief Anjail , Beauchamp Jennifer E. S.
Published: February 2022

BACKGROUND: The purpose of this study was to incorporate a person-centered approach to understand the emotional health needs and perspectives of stroke survivors (SSs) and their caregivers. METHODS: In collaboration with 4 SSs and caregivers as research partners, quantitative data were collected to assess poststroke emotional health needs, and qualitative data were collected to gain insight into SS and caregiver emotional health perspectives after stroke. RESULTS: Forty surveys (n = 26 SSs, n = 14 caregivers) were collected. The predominate emotional health needs were frustration (65%), anxiety (54%), and stress (50%) for SSs and stress (71%), worry (57%), and frustration (57%) for caregivers. Two group interviews (n = 7 SSs, n = 3 caregivers) were completed. Four emerging themes were identified: receiving support from those in similar situations, poststroke emotional responses, situations experienced in healthcare settings, and a hypervigilance for sudden and unexpected events. CONCLUSION: Emotional healthcare services for SSs and their caregivers may consider providing reoccurring mental health education and multifaceted treatment approaches, including provision of peer support, and addressing the unique emotional stressors SSs and caregivers may be experiencing. The small sample size precludes generalizing the results into the broader stroke population. However, by leveraging the lived experience of SSs and their caregivers, the results may help find ways to support SSs' and caregivers' emotional health.
Parent Protector
Authors: Waldron Mia K.
Published: February 2022

Black infants have twice the incidence of infant mortality (IM), death before the first birthday, and preterm birth in comparison to other US racial/ethnic groups; these factors make Black infants a high-risk group. The literature on the factors impacting caregivers and home environments for these infants is sparse. The purpose of this descriptive qualitative study was to explore perceived parental readiness to care for their Black preterm infants at home after discharge from a neonatal intensive care unit (NICU). Ten NICU parents of Black preterm infants completed a structured interview and self-report questionnaires before hospital discharge; data were analyzed using descriptive and semantic content methods. Coded parent responses were categorized as Parent Protector of Infants' Health (n = 94, 29.2%); Hindrances to Parental Readiness for Transition to Home (n = 97, 30.1%), and Parent as Partner in NICU to Home Transition (n = 131, 40.6%). All parents rated themselves “confident” (n = 6) or “very confident” (n = 4) in their ability to care for their infant after NICU discharge. Partnership with the healthcare team was described as involving health information resources, effective communication, and, most importantly, support for the parental role as infant protector for transition to home for their high-risk infant after NICU discharge.
The Burden of Vaccine-preventable Diseases in Patients With Inflammatory Bowel Disease
Authors: Kröner Paul T. , Picco Michael F. , Cangemi John R. , Hayney Mary S. , Farraye Francis A. , Caldera Freddy
Published: February 2022

Background:

Patients with inflammatory bowel disease (IBD) are at an increased risk of infections, including vaccine-preventable diseases (VPDs). The aim of this study was to explore the inpatient prevalence of VPD in patients with IBD, as well as inpatient outcomes.

Methods:

Retrospective study using the 2013-2017 Nationwide Inpatient Sample databases. All patients 18 years of age or older with International Classification of Diseases, Ninth and 10th Revisions, Clinical Modification (ICD-9/10 CM) codes for IBD were included, as well as patients with VPDs as a principal diagnostic code. The primary outcome was the occurrence and odds of VPD in patients with IBD compared with patients with no IBD. Secondary outcomes were inpatient mortality, morbidity, and economic burden compared with patients with IBD and non–vaccine-preventable infections (VPIs). Multivariate regression yielded adjusted odds ratios.

Results:

Of 1,622,245 (0.9%) patients with a diagnosis of IBD, 3560 (0.2%) had associated VPDs, while 131,150 patients had non-VPI (8.1%). The most common VPDs were influenza, herpes zoster (HZ), pneumococcal pneumonia, and varicella. Only HZ and varicella had increased odds of occurrence in patients with IBD of all ages. Patients with IBD 65 years of age or older had increased odds of VPD compared with patients under 65 years. Patients with IBD and associated VPD had higher odds of intensive care unit stay, systemic inflammatory response syndrome, and multiorgan failure compared with patients with IBD and non-VPI.

Conclusions:

VPDs represent a clinically relevant cause of infectious disease-related hospital admissions in patients with IBD. Patients with IBD are at increased risk for hospitalization due to HZ and varicella. Those hospitalized for VPD have higher morbidity compared with patients with IBD and non-VPI. These findings echo the importance of instituting optimal immunization schedules in patients with IBD, particularly in patients 65 years or older.
Effect of antiretroviral therapy care interruptions on mortality in children living with HIV
Authors: Davies Claire , Johnson Leigh , Sawry Shobna , Chimbetete Cleophas , Eley Brian , Vinikoor Michael , Technau Karl-Günter , Ehmer Jochen , Rabie Helena , Phiri Sam , Tanser Frank , Malisita Kennedy , Fatti Geoffrey , Osler Meg , Wood Robin , Newton Sam , Haas Andreas , Davies Mary-Ann
Published: February 2022

Objective:

To evaluate the characteristics and outcomes of HIV-infected children that have care interruptions, during which the child's health status and use of medication is unknown.

Design:

We included data on children initiating ART between 2004 and 2016 at less than 16 years old at 16 International Epidemiologic Databases to Evaluate AIDS Southern Africa cohorts. Children were classified as loss to follow up (LTFU) if they had not attended clinic for more than 180 days. Children had a care interruption if they were classified as LTFU, and subsequently returned to care. Children who died within 180 days of ART start were excluded.

Methods:

The main outcome was all cause mortality. Two exposed groups were considered: those with a first care interruption within the first 6 months on ART, and those with a first care interruption after 6 months on ART. Adjusted hazard ratios were determined using a Cox regression model.

Results:

Among 53 674 children included, 23 437 (44%) had a care interruption, of which 10 629 (20%) had a first care interruption within 6 months on ART and 12 808 (24%) had a first care interruption after 6 months on ART. Increased mortality was associated with a care interruption within 6 months on ART [adjusted hazard ratio (AHR) = 1.52, 95% CI 1.12–2.04] but not with a care interruption after 6 months on ART (AHR = 1.05, 95% CI 0.77–1.44).

Conclusion:

The findings suggest that strengthening retention of children in care in the early period after ART initiation is critical to improving paediatric ART outcomes.
Posttreatment monitoring by ASCL1/LHX8 methylation analysis in women with HIV treated for cervical intraepithelial neoplasia grade 2/3
Authors: Vink Frederique J. , Steenbergen Renske D.M. , Kremer Wieke W. , Lissenberg-Witte Birgit I. , Heideman Daniëlle A.M. , Bleeker Maaike C.G. , van Zummeren Marjolein , Breytenbach Erika , Visser Cathy , Lukhwareni Azwidowi , Meijer Chris J.L.M. , Dreyer Greta
Published: February 2022

Objective:

Women with HIV (WWH) have an increased risk to develop recurrent cervical intraepithelial neoplasia grade 2/3 (rCIN2/3) after treatment compared with HIV-negative women. Therefore, appropriate posttreatment monitoring of WWH is important. This study evaluates the performance of ASCL1 and LHX8 methylation analysis as posttreatment monitoring test in WWH treated for CIN2/3, as alternative to cytology or human papillomavirus (HPV) as follow-up test.

Design:

Prospective observational cohort study.

Methods:

WWH treated for CIN2/3 by large loop excision of the transformation zone (LLETZ) (n 
= 61) were invited for follow-up study visits at 1, 2.5 and 4 years after baseline. Baseline and follow-up cervical scrapes were tested for cytology, HPV and DNA methylation of ASCL1 and LHX8 genes. The performance of these strategies for the detection of rCIN2/3 was evaluated in the first follow-up cervical scrape.

Results:

Thirteen (21.3%) rCIN2/3 lesions were detected within 4 years of follow-up. In women without rCIN2/3 in follow-up, methylation levels of ASCL1 and LHX8 decreased significantly after LLETZ treatment (P 
= 0.02 and 0.007, respectively). In women with rCIN2/3, methylation levels remained high after LLETZ treatment. The 4-year rCIN2/3 risk was 4.9% (95% CI: 0.6–16.5) for ASCL1/LHX8-negative women, 8.1% (95% CI: 1.7–21.9) for HPV-negative women and 7.7% (95% CI: 2.1–18.5) for cytology-negative women.

Conclusion:

A negative ASCL1/LHX8 methylation test in follow-up is associated with a low rCIN2/3 risk and could serve as an objective test of cure and well tolerated alternative for HPV and/or cytology screening in the posttreatment monitoring of WWH.
Rescue therapies in epilepsy
Authors: Sharma Sonali , Detyniecki Kamil
Published: February 2022

Purpose of review

The purpose of this review is to provide a succinct evaluation of the current rescue medications and action plans available to our patients with seizure clusters in the outpatient setting.

Recent findings

The main themes of the recent findings are that rescue medications and seizure action plans (SAPs) are underutilized, particularly in the adult population. The safety and efficacy of intranasal midazolam and intranasal diazepam is comparable with rectal diazepam for the treatment of seizure clusters. Additionally, this intranasal formulation has the benefit of a more socially acceptable route of administration and ease of use.

The implication of these findings is a greater variety and awareness in the rescue medications available to our patients suffering from seizure clusters.
An attempt of using public ambient temperature data in swine genetic evaluation for litter size traits at birth in Japan
Authors: Hara Hitomi , Ogawa Shinichiro , Ohnishi Chika , Ishii Kazuo , Uemoto Yoshinobu , Satoh Masahiro
Published: February 2022

To obtain the fundamental information on using ambient temperature information in developing the model for routine swine genetic evaluation in Japan, we analyzed total number born (TNB), number born alive (NBA), and number stillborn (NSB) collected at a Japanese farm, together with off-farm ambient temperature measured at a nearest Automated Meteorological Data Acquisition System station. Five repeatability animal models were exploited, considering the effects of farrowing season (model 1), farrowing month (model 2), quadratic regressions of daily maximum ambient temperature of farrowing day (model 3), season and temperature (model 4), or month and temperature (model 5). Patterns of the effects of daily maximum temperature of farrowing day estimated using model 3 was similar to those of farrowing season by model 1 and those of farrowing month by model 2. Adding the effect of daily maximum temperature of farrowing day (models 4 and 5) could explain phenotypic variability greater than only considering either of farrowing season and month (models 1 and 2). Estimated heritability was stable among the models and the rank correlation of predicted breeding values between models was >0.98 for all traits. The results indicate the possibility that using public ambient temperature can capture a large part of the phenotypic variability in litter size traits at birth caused by the seasonality in Japan and do not harm, at least, the performance of genetic evaluation. This study could support the availability of public meteorological data in flexible developing operational models for future swine genetic evaluation in Japan.
Historical contingency drives compensatory evolution and rare reversal of phage resistance
Authors: Debray Reena , De Luna Nina , Koskella Britt
Published: February 2022

Bacteria and lytic viruses (phages) engage in highly dynamic coevolutionary interactions over time, yet we have little idea of how transient selection by phages might shape the future evolutionary trajectories of their host populations. To explore this question, we generated genetically diverse phage-resistant mutants of the bacterium Pseudomonas syringae. We subjected the panel of mutants to prolonged experimental evolution in the absence of phages. Some populations re-evolved phage sensitivity, while others acquired compensatory mutations that reduced the costs of resistance without altering resistance levels. To ask whether these outcomes were driven by the initial genetic mechanisms of resistance, we next evolved independent replicates of each mutant lineage in the absence of phages. We found a strong signature of historical contingency: some mutations were highly reversible across replicate populations, while others were highly entrenched. Through whole-genome sequencing of bacteria over time, we also found that populations with resistance mutations in the same gene acquired more parallel sets of mutations than populations with resistance mutations in different genes, suggesting that compensatory adaptation is also contingent on how resistance initially evolved. Our study identifies an evolutionary ratchet in bacteria-phage coevolution, and may explain previous observations that resistance persists over time in some bacterial populations but is lost in others. We add to a growing body of work describing the key role of phages in the ecological and evolutionary dynamics of their host communities. Beyond this specific trait, our study provides new insight into the genetic architecture of historical contingency, a crucial component of interpreting and predicting evolution.
Conserved basal lamina proteins, laminin and nidogen, are repurposed to organize mechanosensory complexes responsible for touch sensation
Authors: Das Alakananda , Franco Joy A. , Mulcahy Ben , Wang Lingxin , Chapman Dail , Jaisinghani Chandni , Pruitt Beth L. , Zhen Mei , Goodman Miriam B.
Published: February 2022

The sense of touch is conferred by the conjoint function of somatosensory neurons and skin cells. These cells meet across a gap filled by a basal lamina, an ancient structure found in metazoans. UsingCaenorhabditis elegans, we show that membrane-matrix complexes containing laminin, nidogen, and the MEC-4 mechano-electrical transduction channel reside at this interface and are instrumental for proper touch sensation. These complexes fail to coalesce in touch-insensitive extracellular matrix mutants and in dissociated neurons. MEC-4, but not laminin or nidogen, is destabilized by point mutations in the C-terminal Kunitz domain of the extracellular matrix component, MEC-1. Thus, neuron-epithelial cell interfaces are instrumental in mechanosensory complex assembly and function. Loss of nidogen reduces the density of mechanoreceptor complexes and the amplitude of the touch-evoked currents they carry. These findings imply that somatosensory neurons secrete proteins that actively repurpose the basal lamina to generate special-purpose mechanosensory complexes responsible for vibrotactile sensing.
Control of protein-based pattern formation via guiding cues
Authors: Burkart Tom , Wigbers Manon C. , Würthner Laeschkir , Frey Erwin
Published: February 2022

Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about the cell’s geometry and the cell-cycle stage. Such protein patterns arise from protein transport and reaction kinetics, and they can be controlled by various guiding cues within the cell. Here, we review how protein patterns are guided by cell size and shape, by other protein patterns that act as templates, and by the mechanical properties of the cell. The basic mechanisms of guided pattern formation are elucidated with reference to recent observations in various biological model organisms. We posit that understanding the controlled formation of protein patterns in cells will be an essential part of understanding information processing in living systems.