bluuebunny/crossref_metadata_2025 huggingface dataset:
Data-driven quantification of nitrogen enrichment impact on Northern Hemisphere plant biomass
Authors: Liu Yongwen , Piao Shilong , Makowski David , Ciais Philippe , Gasser Thomas , Song Jian , Wan Shiqiang , Peñuelas Josep , Janssens Ivan A
Published: June 2022

The production of anthropogenic reactive nitrogen (N) has grown so much in the last century that quantifying the effect of N enrichment on plant growth has become a central question for carbon (C) cycle research. Numerous field experiments generally found that N enrichment increased site-scale plant biomass, although the magnitude of the response and sign varied across experiments. We quantified the response of terrestrial natural vegetation biomass to N enrichment in the Northern Hemisphere (>30° N) by scaling up data from 773 field observations (142 sites) of the response of biomass to N enrichment using machine-learning algorithms. N enrichment had a significant and nonlinear effect on aboveground biomass (AGB), but a marginal effect on belowground biomass. The most influential variables on the AGB response were the amount of N applied, mean biomass before the experiment, the treatment duration and soil phosphorus availability. From the machine learning models, we found that N enrichment due to increased atmospheric N deposition during 1993–2010 has enhanced total biomass by 1.1 ± 0.3 Pg C, in absence of losses from harvest and disturbances. The largest effect of N enrichment on plant growth occurred in northeastern Asia, where N deposition markedly increased. These estimates were similar to the range of values provided by state-of-the-art C–N ecosystem process models. This work provides data-driven insights into hemisphere-scale N enrichment effect on plant biomass growth, which allows to constrain the terrestrial ecosystem process model used to predict future terrestrial C storage.
Power-law Lévy processes, power-law vector random fields, and some extensions
Authors: Ma Chunsheng
Published: June 2022

This paper introduces a power-law subordinator and a power-law Lévy process whose Laplace transform and characteristic function are simply made up of power functions or the ratio of power functions, respectively, and proposes a power-law vector random field whose finite-dimensional characteristic functions consist merely of a power function or the ratio of two power functions. They may or may not have first-order moment, and contain Linnik, variance Gamma, and Laplace Lévy processes (vector random fields) as special cases. For a second-order power-law vector random field, it is fully characterized by its mean vector function and its covariance matrix function, just like a Gaussian vector random field. An important feature of the power-law Lévy processes (random fields) is that they can be used as the building blocks to construct other Lévy processes (random fields), such as hyperbolic secant, cosine ratio, and sine ratio Lévy processes (random fields).
Smooth rigidity for codimension one Anosov flows
Authors: Gogolev Andrey , Hertz Federico
Published: June 2022

We introduce the matching functions technique in the setting of Anosov flows. Then we observe that simple periodic cycle functionals (also known as temporal distances) provide a source of matching functions for conjugate Anosov flows. For conservative codimension one Anosov flows

φ
t

:
M
→
M

\varphi ^t\colon M\to M

,

dim
⁡
M
≥
4

\dim M\ge 4

, these simple periodic cycle functionals are

C
1

C^1

regular and, hence, can be used to improve regularity of the conjugacy. Specifically, we prove that a continuous conjugacy must, in fact, be a

C
1

C^1

diffeomorphism for an open and dense set of codimension one conservative Anosov flows.
On explicit abstract neutral differential equations with state-dependent delay
Authors: Hernández Eduardo
Published: June 2022

We introduce and study a class of abstract neutral differential equations with state-dependent delay at the temporal derivative. We study the local and global existence and uniqueness of mild solution and the existence of strict solution. Some examples concerning partial neutral integro-differential equations are presented.
Bacteria: A Very Short Introduction
Authors: Amyes Sebastian G. B.
Published: June 2022

Bacteria: A Very Short Introduction explores the nature of bacteria, which are the most abundant form of life on the planet. The first organisms to evolve, they include forms that can survive the toughest environments, from deep rocks to frozen wastes. No other organisms are as adaptable. We are most familiar with them as agents of disease, but benign bacteria are critical to ecosystems, as well as to human health. Bacteria play a significant role in the environment and in disease. We cannot ignore the growing resistance of bacteria to antibiotics.
1. Origins
Authors: Amyes Sebastian G. B.
Published: June 2022

‘Origins’ traces the origins of bacteria. The early bacteria emerged approximately 1.5 billion years after the creation of the planet. This was before the Cambrian explosion of half a billion years ago, when the diversity of life forms increased rapidly. The common view is that prokaryotic cells, such as bacteria, and eukaryotic cells, such as those that comprise our bodies, had a common ancestor: the last universal common ancestor (LUCA) or cenancestor. The first bacteria were anaerobic, then photosynthetic bacteria and cyanobacteria emerged creating oxygen allowing the development of aerobic bacteria, which then flourished about 2.5 billion years ago. We categorise bacteria according to their response to the Gram strain.
5. Environment and civilization
Authors: Amyes Sebastian G. B.
Published: June 2022

‘Environment and civilization’ evaluates the role of bacteria in the environment and in civilization. From the rise of prehistoric man to the end of the 19th century, the main involvement of humans with bacteria had been as a result of their ability to spoil food and liquids. Cooking, food preservation, alcohol production, cheese and yogurt manufacturing, and probiotics are all developments that are important within this topic. Bacteria have always been an essential component of the disposal of human waste and have played a considerable role in body decomposition after death.
9. The future
Authors: Amyes Sebastian G. B.
Published: June 2022

‘The future’ reflects on the future of bacteria. The genomic sequencing of bacteria is still in its infancy when one considers the vast number of bacterial species on the planet. The more genomic sequences of each species that are completed, the more comprehensive a map of their evolution will be obtained.
This will, however, require very detailed molecular analysis and the use of molecular biological techniques. We have to consider the possible emergence of new bacterial pathogens that have as devastating an effect as the Black Death. Bacteria have the capacity to survive within the modern world and we mustn't forget the importance of genetically modified and synthetic bacteria.
4. Dimensions
Authors: Lauga Eric
Published: June 2022

‘Dimensions’ begins by evaluating the role that physical dimensions and dimensional analysis play in physics and it then explains the differences between dimensions and units and introduces the concept of dimensional homogeneity. Dimensional homogeneity has had a huge impact on physical sciences, including the pioneering scientists who proposed it. The chapter then explains how to reduce a given physics problem to a simpler one involving numbers with no dimensions, termed dimensionless numbers. Dimensionless numbers have a role in our understanding of fluid mechanics. The Reynolds number (quantifying the relative impact of inertial vs. viscous forces in flows), the Womersley number (unsteady inertia vs. viscous forces), the Froude number (gravitational potential vs. kinetic energy), the Bond number (gravitational potential vs. surface energy), the Weber (inertia vs. surface tension) and capillary numbers (viscous forces vs. surface tension), the Mach number (flow speeds vs. sound speed), and the Rossby number (flow time scale vs. Coriolis frequency) are all worth considering here.
8. Researching fluids and flows
Authors: Lauga Eric
Published: June 2022

‘Researching fluids and flows’ summarizes current research in fluid mechanics by starting with environmental flows, motivated by climate change, and the active fluid dynamics of our changing environment. Examples include atmospheric flows, ocean transport, ice dynamics, flow of rivers and lakes, and the role of stratification. The fluid mechanics of energy is motivated by the desire to build a greener world. Examples include wind farms, natural ventilation, biofuels, pollution transport, and remediation. Complex fluids and materials, including non-Newtonian fluids, can behave as a combination of both fluids and solids. Examples include cosmetic products, granular materials, suspensions, and liquid crystals. It is worth looking at flows on small scales, where a new fundamental understanding of flows at the limit of the continuum scale is now possible. Flows are relevant to the biological world. Examples include locomotion, vascular plants, blood flow, and the fluid dynamics of disease transmission. there are two fundamental mysteries at the heart of fluid
mechanics: the nature of turbulence and the mathematical structure of the equations for fluid flows (Navier–Stokes equations).
1. In the beginning
Authors: Leather Simon
Published: June 2022

‘In the beginning’ introduces arthropods, which are described as the most diverse and successful group of animals in the world. Arthropods include the insects, spiders, millipedes, scorpions, shrimps, crabs, woodlice, and the barnacles. The word arthropod means hardened appendages with rings of soft unsclerotized cuticle in between. This word can be translated as jointed foot. Arthropods are characterized by tagmata. The body of an arthropod is covered by a chitinous exoskeleton to which the body parts and muscles are attached internally. The success of arthropods can be attributed to their very adaptable body plan.
8. The good, the bad, and the ugly
Authors: Leather Simon
Published: June 2022

‘The good, the bad, and the ugly’ points out how most people think of insects as good or bad: honeybees and other pollinators versus mosquitoes and crop pests, like the ubiquitous greenfly. Insects are not just pests and pollinators. Most insects do not harm humans. Pollinators, such as honeybees, flies, beetles, moths, butterflies, and other Hymenoptera are important in that they play their part in making sure that food crops are fruitful. There are also the largely unseen, overlooked insects busy helping with the recycling processes, improving soil quality, and acting to reduce the numbers of insects that would threaten human existence.
Ruling Party Patronage, Brokerage, and Contestations at Urban Markets in Harare
Authors: Oosterom Marjoke , Gukurume Simbarashe
Published: June 2022

This study contributes to debates on varieties of clientelism through an analysis of brokerage and ruling party patronage at urban markets in Harare, Zimbabwe. Urban markets are sites of contestation between the opposition-dominated city council and actors aligned with the ruling party, the Zimbabwe African National Union—Patriotic Front (ZANU-PF). Based on qualitative case study research at two designated markets, the article demonstrates how ruling party brokers are central to organizing patronage and political mobilization, thus sustaining authoritarian politics. While ruling party patronage is a deliberate strategy to control urban spaces, the article demonstrates how it is being negotiated. Factionalism within ZANU-PF shifted the power of brokers, and the lockdown enforced in response to the coronavirus disease 2019 pandemic in 2020 caused a rupture, offering the city council and opposition-aligned youth the opportunity to (re)claim control over vending spaces. This article contributes to debates on clientelism in authoritarian regime settings, by showing the imbrication of coercion and patronage in the role of the broker and demonstrating how patronage is organized vertically through brokerage. This study extends the study of clientelism beyond electoral politics, since brokers are not always politicians, but nonetheless are part of the systems of ruling party patronage.
Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana
Authors: Morales Alejandro , de Boer Hugo J , Douma Jacob C , Elsen Saskia , Engels Sophie , Glimmerveen Tobias , Sajeev Nikita , Huber Martina , Luimes Mathijs , Luitjens Emma , Raatjes Kevin , Hsieh Chenyun , Teapal Juliane , Wildenbeest Tessa , Jiang Zhang , Pareek Ashwani , Singla-Pareek Sneh , Yin Xinyou , Evers Jochem , Anten Niels P R , van Zanten Martijn , Sasidharan Rashmi
Published: June 2022

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.
riboCleaner: a pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants
Authors: Huang Pu , Davis Erin , Cao Xia , Cameron Hunter J
Published: June 2022

Motivation

Analysis of gene expression data can be crucial for elucidating biological relationships within living organisms. However, accurate quantification of gene expression relies directly upon the accuracy of the reference genome or transcriptome to which the expression data are mapped. Errors in gene annotation can lead to errors in the quantification of gene expression. One source of gene annotation error in eukaryotes arises from incorrect predictions of messenger RNA gene models within ribosomal DNA (rDNA) regions.

Results

Here, we provide examples of how the presence of false gene models in rDNA regions can result in a handful of genes appearing to contribute to >50% of the total transcripts per million values of entire RNA-seq datasets. To this end, we have created riboCleaner, a bioinformatics pipeline designed to identify misannotated gene models in rDNA regions and quantify rRNA-derived reads in RNA-seq data. We also show the applicability of riboCleaner in several plant genome assemblies.

Availability and implementation

We have implemented riboCleaner as a containerized Snakemake workflow. The workflow, instructions for building the container and other documentation are available at https://github.com/basf. The data underlying this article are available in GitHub at https://github.com/basf/riboCleaner. For convenience, a prebuilt Docker image containing riboCleaner is available at https://hub.docker.com/u/basfcontainers.

Supplementary information

Supplementary data are available at Bioinformatics online.
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression
Authors: Christensen Niels Johan , Demharter Samuel , Machado Meera , Pedersen Lykke , Salvatore Marco , Stentoft-Hansen Valdemar , Iglesias Miquel Triana
Published: June 2022

Motivation

The identification of predictive biomarker signatures from omics and multi-omics data for clinical applications is an active area of research. Recent developments in assay technologies and machine learning (ML) methods have led to significant improvements in predictive performance. However, most high-performing ML methods suffer from complex architectures and lack interpretability.

Results

We present the application of a novel symbolic-regression-based algorithm, the QLattice, on a selection of clinical omics datasets. This approach generates parsimonious high-performing models that can both predict disease outcomes and reveal putative disease mechanisms, demonstrating the importance of selecting maximally relevant and minimally redundant features in omics-based machine-learning applications. The simplicity and high-predictive power of these biomarker signatures make them attractive tools for high-stakes applications in areas such as primary care, clinical decision-making and patient stratification.

Availability and implementation

The QLattice is available as part of a python package (feyn), which is available at the Python Package Index (https://pypi.org/project/feyn/) and can be installed via pip. The documentation provides guides, tutorials and the API reference (https://docs.abzu.ai/). All code and data used to generate the models and plots discussed in this work can be found in https://github.com/abzu-ai/QLattice-clinical-omics.

Supplementary information

Supplementary material is available at Bioinformatics online.
Functional characterization of co-phosphorylation networks
Authors: Ayati Marzieh , Yılmaz Serhan , Chance Mark R , Koyuturk Mehmet
Published: June 2022

Motivation

Protein phosphorylation is a ubiquitous regulatory mechanism that plays a central role in cellular signaling. According to recent estimates, up to 70% of human proteins can be phosphorylated. Therefore, the characterization of phosphorylation dynamics is critical for understanding a broad range of biological and biochemical processes. Technologies based on mass spectrometry are rapidly advancing to meet the needs for high-throughput screening of phosphorylation. These technologies enable untargeted quantification of thousands of phosphorylation sites in a given sample. Many labs are already utilizing these technologies to comprehensively characterize signaling landscapes by examining perturbations with drugs and knockdown approaches, or by assessing diverse phenotypes in cancers, neuro-degerenational diseases, infectious diseases and normal development.

Results

We comprehensively investigate the concept of ‘co-phosphorylation’ (Co-P), defined as the correlated phosphorylation of a pair of phosphosites across various biological states. We integrate nine publicly available phosphoproteomics datasets for various diseases (including breast cancer, ovarian cancer and Alzheimer’s disease) and utilize functional data related to sequence, evolutionary histories, kinase annotations and pathway annotations to investigate the functional relevance of Co-P. Our results across a broad range of studies consistently show that functionally associated sites tend to exhibit significant positive or negative Co-P. Specifically, we show that Co-P can be used to predict with high precision the sites that are on the same pathway or that are targeted by the same kinase. Overall, these results establish Co-P as a useful resource for analyzing phosphoproteins in a network context, which can help extend our knowledge on cellular signaling and its dysregulation.

Availability and implementation

github.com/msayati/Cophosphorylation. This research used the publicly available datasets published by other researchers as cited in the manuscript.

Supplementary information

Supplementary data are available at Bioinformatics online.
FMRP-dependent production of large dosage-sensitive proteins is highly conserved
Authors: Flanagan Keegan , Baradaran-Heravi Alireza , Yin Qi , Dao Duc Khanh , Spradling Allan C , Greenblatt Ethan J
Published: June 2022

Mutations in FMR1 are the most common heritable cause of autism spectrum disorder. FMR1 encodes an RNA-binding protein, FMRP, which binds to long, autism-relevant transcripts and is essential for normal neuronal and ovarian development. In contrast to the prevailing model that FMRP acts to block translation elongation, we previously found that FMRP activates the translation initiation of large proteins in Drosophila oocytes. We now provide evidence that FMRP-dependent translation is conserved and occurs in the mammalian brain. Our comparisons of the mammalian cortex and Drosophila oocyte ribosome profiling data show that translation of FMRP-bound mRNAs decreases to a similar magnitude in FMRP-deficient tissues from both species. The steady-state levels of several FMRP targets were reduced in the Fmr1 KO mouse cortex, including a ∼50% reduction of Auts2, a gene implicated in an autosomal dominant autism spectrum disorder. To distinguish between effects on elongation and initiation, we used a novel metric to detect the rate-limiting ribosome stalling. We found no evidence that FMRP target protein production is governed by translation elongation rates. FMRP translational activation of large proteins may be critical for normal human development, as more than 20 FMRP targets including Auts2 are dosage sensitive and are associated with neurodevelopmental disorders caused by haploinsufficiency.
Range Expansion of Native and Invasive Ticks: A Looming Public Health Threat
Authors: Molaei Goudarz , Eisen Lars M , Price Keith J , Eisen Rebecca J
Published: June 2022

Native and invasive tick species pose a serious public health concern in the United States. Range expansion of several medically important tick species has resulted in an increasing number of communities at risk for exposure to ticks and tick-borne pathogens.
Evaluation of Recombinant Live-Attenuated Respiratory Syncytial Virus (RSV) Vaccines RSV/ΔNS2/Δ1313/I1314L and RSV/276 in RSV-Seronegative Children
Authors: Cunningham Coleen K , Karron Ruth A , Muresan Petronella , Kelly Matthew S , McFarland Elizabeth J , Perlowski Charlotte , Libous Jennifer , Oliva Jennifer , Jean-Philippe Patrick , Moye Jack , Schappell Elizabeth , Barr Emily , Rexroad Vivian , Johnston Benjamin , Chadwick Ellen G , Cielo Mikhaela , Paul Mary , Deville Jaime G , Aziz Mariam , Yang Lijuan , Luongo Cindy , Collins Peter L , Buchholz Ursula J ,   the International Maternal Pediatric Adolescent AIDS Clinical Trials (IMPAACT) 2018 Study Team
Published: June 2022

Background

This United States-based study compared 2 candidate vaccines: RSV/ΔNS2/Δ1313/I1314L, attenuated by NS2 gene-deletion and temperature-sensitivity mutation in the polymerase gene; and RSV/276, attenuated by M2-2 deletion.

Methods

RSV-seronegative children aged 6–24 months received RSV/ΔNS2/Δ1313/I1314L (106 plaque-forming units [PFU]), RSV/276 (105 PFU), or placebo intranasally. Participants were monitored for vaccine shedding, reactogenicity, and RSV serum antibodies, and followed over the subsequent RSV season.

Results

Enrollment occurred September 2017 to October 2019. During 28 days postinoculation, upper respiratory illness and/or fever occurred in 64% of RSV/ΔNS2/Δ1313/I1314L, 84% of RSV/276, and 58% of placebo recipients. Symptoms were generally mild. Cough was more common in RSV/276 recipients than RSV/ΔNS2/Δ1313/I1314L (48% vs 12%; P = .012) or placebo recipients (17%; P = .084). There were no lower respiratory illness or serious adverse events. Eighty-eight and 96% of RSV/ΔNS2/Δ1313/I1314L and RSV/276 recipients were infected with vaccine (shed vaccine and/or had ≥4-fold rises in RSV antibodies). Serum RSV-neutralizing titers and anti-RSV F IgG titers increased ≥4-fold in 60% and 92% of RSV/ΔNS2/Δ1313/I1314L and RSV/276 vaccinees, respectively. Exposure to community RSV during the subsequent winter was associated with strong anamnestic RSV-antibody responses.

Conclusions

Both vaccines had excellent infectivity and were well tolerated. RSV/276 induced an excess of mild cough. Both vaccines were immunogenic and primed for strong anamnestic responses.

Clinical Trials Registration

NCT03227029 and NCT03422237.
Mobile Burn Disaster Response Teams: A Scoping Review
Authors: Fuchko Danielle , King-Shier Kathryn , Gabriel Vincent
Published: June 2022

The resources needed to deliver modern burn care may be overwhelmed by mass casualty disasters. In 2021, the World Health Organization (WHO) recommended that countries prepare teams of deployable burn experts to assist with responding to a mass casualty disaster. The aim of this scoping review was to identify existing literature regarding burn mobile response team organization, describe the reported effectiveness of these teams, identify challenges in adopting the WHO recommendations, and consider how the recommendations may be reconsidered. We conducted a scoping review of all literature types published up to January 2022. Searches of MEDLINE, EMBASE, Scopus, and CINAHL databases were conducted to identify reports informing or reporting the use of mobile burn care specialty teams that respond to events resulting in multiple burn-injured victims, including pediatric victims and military response to civilian events. Of 6132 identified reports, 26 publications were reviewed. Three types of mobile burn response teams were identified: (1) teams organized by burn care networks, (2) government-organized medical disaster teams with burn-specific experts, and (3) the U.S. Army Burn Flight Team. Teams have responded to events such as terrorist attacks by providing specialized burn supplies and personnel. These teams have demonstrated expert triage and stabilization advantages but are limited by the number of deployable specialists. Although the WHO recommends increasing the number of mobile burn response teams available around the world, few countries have implemented this recommendation. A hybrid model where responders on scene communicate with burn center experts to manage triage may address these challenges.
The Transposition Rate Has Little Influence on the Plateauing Level of the P-element
Authors: Kofler Robert , Nolte Viola , Schlötterer Christian
Published: June 2022

The popular trap model assumes that the invasions of transposable elements (TEs) in mammals and invertebrates are stopped by piRNAs that emerge after insertion of the TE into a piRNA cluster. It remains, however, still unclear which factors influence the dynamics of TE invasions. The activity of the TE (i.e., transposition rate) is one frequently discussed key factor. Here we take advantage of the temperature-dependent activity of the P-element, a widely studied eukaryotic TE, to test how TE activity affects the dynamics of a TE invasion. We monitored P-element invasion dynamics in experimental Drosophila simulans populations at hot and cold culture conditions. Despite marked differences in transposition rates, the P-element reached very similar copy numbers at both temperatures. The reduction of the insertion rate upon approaching the copy number plateau was accompanied by similar amounts of piRNAs against the P-element at both temperatures. Nevertheless, we also observed fewer P-element insertions in piRNA clusters than expected, which is not compatible with a simple trap model. The ping-pong cycle, which degrades TE transcripts, becomes typically active after the copy number plateaued. We generated a model, with few parameters, that largely captures the observed invasion dynamics. We conclude that the transposition rate has at the most only a minor influence on TE abundance, but other factors, such as paramutations or selection against TE insertions are shaping the TE composition.
Cellular-level distribution of manganese in Macadamia integrifolia, M. ternifolia, and M. tetraphylla from Australia
Authors: Abubakari Farida , Fernando Denise R , Nkrumah Philip Nti , Harris Hugh H , Erskine Peter D , van der Ent Antony
Published: June 2022

Macadamia integrifolia and M. tetraphylla, unlike M. ternifolia, are known for their edible nuts. All three species over-accumulate the trace metal nutrient manganese (Mn) in their shoots. This study seeks to examine tissue- and cellular-level distribution of Mn and other plant nutrients in the three Macadamia species. The distribution of Mn, calcium, iron, and potassium were investigated in whole leaves and cross-sections of roots, petioles, and leaves using synchrotron-based X-ray fluorescence microscopy (XFM) in M. integrifolia, M. tetraphylla, and M. ternifolia. The results show Mn sequestration primarily in the leaf and midrib palisade mesophyll cells of all three species. Leaf interveinal regions, root cortical cells, and phloem cells were also found to be Mn loaded. The current study confirms earlier findings but further reveals that Mn is concentrated in the vacuoles of mesophyll cells owing to the exceptional resolution of the synchrotron XFM data, and the fact that fresh hydrated samples were used. New insights gained here into Mn compartmentalization in these highly Mn-tolerant Macadamias expand knowledge about potentially toxic over-accumulation of an essential micronutrient, which ultimately stands to inform strategies around farming edible species in particular.
Prediction of measured GFR after living kidney donation from pre-donation parameters
Authors: van Londen Marco , van der Weijden Jessica , Niznik Robert S , Mullan Aidan F , Bakker Stephan J L , Berger Stefan P , Nolte Ilja M , Sanders Jan-Stephan F , Navis Gerjan , Rule Andrew D , de Borst Martin H
Published: June 2022

Background

One of the challenges in living kidney donor screening is to estimate remaining kidney function after donation. Here we developed a new model to predict post-donation measured glomerular filtration rate (mGFR) from pre-donation serum creatinine, age and sex.

Methods

In the prospective development cohort (TransplantLines, n = 511), several prediction models were constructed and tested for accuracy, precision and predictive capacity for short- and long-term post-donation 125I-iothalamate mGFR. The model with optimal performance was further tested in specific high-risk subgroups (pre-donation eGFR <90 mL/min/1.73 m2, a declining 5-year post-donation mGFR slope or age >65 years) and validated in internal (n = 509) and external (Mayo Clinic, n = 1087) cohorts.

Results

In the development cohort, pre-donation estimated GFR (eGFR) was 86 ± 14 mL/min/1.73 m2 and post-donation mGFR was 64 ± 11 mL/min/1.73 m2. Donors with a pre-donation eGFR ≥90 mL/min/1.73 m2 (present in 43%) had a mean post-donation mGFR of 69 ± 10 mL/min/1.73 m2 and 5% of these donors reached an mGFR <55 mL/min/1.73 m2. A model using pre-donation serum creatinine, age and sex performed optimally, predicting mGFR with good accuracy (mean bias 2.56 mL/min/1.73 m2, R2 = 0.29, root mean square error = 11.61) and precision [bias interquartile range (IQR) 14 mL/min/1.73 m2] in the external validation cohort. This model also performed well in donors with pre-donation eGFR <90 mL/min/1.73 m2 [bias 0.35 mL/min/1.73 m2 (IQR 10)], in donors with a negative post-donation mGFR slope [bias 4.75 mL/min/1.73 m2 (IQR 13)] and in donors >65 years of age [bias 0.003 mL/min/1.73 m2 (IQR 9)].

Conclusions

We developed a novel post-donation mGFR prediction model based on pre-donation serum creatinine, age and sex.
Introduction
Authors: Dove Guy
Published: June 2022

This chapter introduces the theoretical notion of a concept. Concepts are bodies of knowledge that are quickly accessed in various situations. Sorting the world into categories enables us to recall and use information that we have gathered over time. We use concepts to recognize patterns, draw inferences, make decisions, and understand word meanings. In this chapter, the author explains why researchers think that our concepts might be grounded in action, emotion, and perception systems and why abstract concepts threaten this proposal. A road map for the arguments contained in the book is provided. The author contends that researchers need to explore the diverse sources of grounding, the influence of higher-level representations, and the ways in which concepts are shaped by social factors and situations.
Introduction
Authors: Godrej Farah
Published: June 2022

This chapter introduces the central themes of the book and summarizes its main arguments. It describes the deeply unjust phenomenon known as mass incarceration, and explains the structural and systemic inequities of the American carceral state. It outlines the central questions motivating the project, and briefly summarizes the key findings, showing how yoga and meditation can produce both compliance and docility toward unjust systems, as well as a posture of ethical defiance and opposition, whether implicitly (through beliefs and conversations) or explicitly (through actions). The chapter presents a contrast between these two models, while also offering the caveat that this binary does not explain everything. The chapter briefly describes the various interpretive methods—such as interviews and ethnography—used to investigate these issues, interweaving academic research with personal narratives of volunteer work and collaboration.
“Rescued by Prison” or “Drinking the Kool-Aid?”
Authors: Godrej Farah
Published: June 2022

Chapter 5 introduces us to the two narratives about the purpose of yoga and meditation in prisons, through interviews with formerly incarcerated practitioners. One narrative is characterized by a focus on individual improvement and personal responsibility, while the other offers a version of self-improvement that includes discussions of the collective and systemic causes of suffering. These narratives often overlap, and are not mutually exclusive. But this chapter ultimately takes us beyond the binary, to an important common theme: how incarcerated persons can assert internal freedom and control in the face of routine dehumanization. These interviews show how they can preserve a more capacious, expansive sense of self, without needing to undertake explicit resistance against the system. In so doing, they reveal that “resistance” need not entail grappling publicly with social or political issues, but instead can lie in the realm of one’s interior life.
Contesting the Last Frontier
Authors: Lien Pei-te , Filler Nicole
Published: June 2022

This book examines the scope and significance of the rise of Asian (and Pacific Islander) Americans in US elective office over the past half-century. By scrutinizing the political trajectory of pioneering figures and their significant followers in each of the major Asian ethnic communities, this book provides unprecedentedly broad and detailed coverage of the development of the electoral landscape of the relatively unknown community in American politics. This book aims not only to fill a missing piece of American electoral history but to challenge the “model minority” and “perpetual foreigner” tropes of Asians in American society and politics. To help interpret the complex experiences of these political women and men situated at the intersection of race, gender, and other dimensions of marginalization, this book adopts an intersectionality framework that puts women of color at the center of storytelling and analysis. Our account includes their trajectories to office, their divergent patterns of political socialization, the barriers and opportunities they faced on the campaign trail, and how these elected officials enacted their roles as representatives at local, state, and federal levels of government. This book documents how Asian immigrants of various origins and those born on US soil strived to serve the interests of the rapidly expanding and majority-immigrant population, especially those disadvantaged by the intersections of gender, ethnicity, and nativity. Our research demonstrates the intrinsic values of the feminist/womanist leadership praxis in illuminating the meanings and significance of political representation and leadership for Asians and other nonwhite American women and men in elective office.
Introduction
Authors: Lien Pei-te , Filler Nicole
Published: June 2022

This introductory chapter begins by laying out the complexity and inherent contradictions in studying the political experiences of the Asian American community. It justifies the need for employing intersectionality as a framework for the analysis and womanist leadership praxis as a model of social justice-focused political representation rooted in the Asian American movement and other social movements and grassroots activism of Black and other women of color. It also argues for the need to identify an Asian American version of the womanist leadership praxis for advancing social justice and uses it as a filter to screen elected officials for inclusion and focused interpretation in our narration. In addition, it defines the notion of political incorporation for Asian Americans and discusses how their political representation needs to be assessed both quantitatively and qualitatively with different indicators and over time.
Evolution of the Electoral Landscape
Authors: Lien Pei-te , Filler Nicole
Published: June 2022

This chapter provides an aggregate-level view of the evolution of the electoral landscape that began in the territory and state of Hawaii. It analyzes the growth and transformation of the population structure of the APA community since 1965 to help contextualize continuities and changes in the contours and makeup of the population of APA elected officials (APAEOs) between 1980 and 2020. The chapter appraises the various gaps in descriptive representation by gender, ethnicity, and nativity among APAEOs across levels of offices nationwide and between Hawaii and California, the top two states in the number of APAs elected to offices. Then, focusing on Asian city council members in California and using data collected over eight time points, the chapter appraises sustainability issues in their political incorporation and the relationship between demography and representation over time. It also examines the significance of local officeholding in political ascension and assesses the facilitating role of term limits.
The Meaning of If
Authors: Khoo Justin
Published: June 2022

Conditional sentences remain a puzzling source of philosophical speculation in large part because there seems to be nothing they could possibly mean that would vindicate the roles they play in language and thought. Bringing together work from philosophy and linguistics, Justin Khoo articulates a theory of what conditionals mean that captures their varied and complex behavior. According to the theory, conditionals form a unified class of expressions that share a common semantic core that encodes inferential dispositions. Thus, rather than represent the world, conditionals are devices used to communicate how we are disposed to infer. Khoo shows that this core theory can be extended to predict the correct probabilities of conditionals, as well as the semantic and pragmatic between different kinds of conditionals. The resulting theory has broad implications beyond debates about the meaning of conditionals, including upshots about the nature of metaphysical and epistemic possibility, the cognitive roles of non-factual contents, and the relationship between counterfactuals and causation.
Temporal Past
Authors: Khoo Justin
Published: June 2022

This chapter articulates and argues for a novel version of the temporal past view—this is the view that subjunctive conditionals are distinguished from indicative conditionals by having an extra layer of past tense that shifts their evaluation time to the past. This version of the theory makes several surprising predictions—in particular, that we should expect epistemic subjunctive conditionals and metaphysical indicative conditionals—which are argued to be correct. The chapter concludes by showing how the theory can also predict the counterfactuality implicature of subjunctive conditionals.
Sufficiency Networks
Authors: Khoo Justin
Published: June 2022

This chapter refines the temporal past theory of subjunctive conditionals to predict more plausible truth conditions for such conditionals, arguing that (metaphysical) subjunctive conditionals express facts about sufficiency networks that encode objective relations between propositions. The chapter argues that a simple interventionist theory of subjunctive conditionals fails, and instead that the past time at which subjunctive conditionals are evaluated is flexible, resulting in the phenomena of backtracking interpretations.
Subjunctive Probabilities
Authors: Khoo Justin
Published: June 2022

This chapter brings together the main results of the book, showing how we can predict the correct probabilities of (metaphysical) subjunctive conditionals. I argue that the resulting theory avoids some recent triviality results that have seemed to threaten the possibility of predicting plausible probabilities for subjunctive conditionals, and I prove that the resulting theory is tenable.
Large Stones—Big Challenge?
Authors: Rheidt Klaus
Published: June 2022

The production and, most especially, the transportation of very large stones were always opportunities for spectacle in preindustrial times. The Egyptian obelisks in Rome as well as the Thunder Stone of St. Petersburg are outstanding examples of phenomenal efforts against gravity undertaken by Roman emperors or by Catherine the Great to demonstrate that imperial power and skilled engineering were at an apex. The largest ashlar blocks ever placed into a wall were set up in Baalbek, Lebanon. To move those megaliths, some 500 to 1,000 tons in weight, and to put them into place required highly experienced stone masons and complex machinery—a considerable technical challenge accompanied by spectacular scenes of transportation. Are the Baalbek megaliths, as well, witnesses of Roman power in the Levant? Or does the use of very large stones merely follow a structural rationale? This chapter aims to position the megalithism of Baalbek between design and construction and between skilled workmanship, architectural expression, and imperial power.
Creating “Hanging Gardens”
Authors: Wulf-Rheidt Ulrike
Published: June 2022

Though famous as one of the Seven Wonders of the Ancient World, the Hanging Gardens have yet to be securely located. Undaunted, many artists, architects, and scholars have suggested reconstructions with the help of descriptions in Greco-Roman literature, such as the illustration by the Dutch artist Maerten van Heemskerck. In his depiction, the gardens are very similar in appearance to the so-called Domus Severiana, one part of the imperial palace in Rome along the Circus Maximus, which clearly inspired van Heemskerck’s reconstruction. The idea of a flourishing artificial garden, rich with water, situated within a metropolis simmering in the desert heat has proven fascinating, not only in recent times but already in antiquity, when it had an enduring influence on both landscape architecture and on Roman palace architecture. The main floor of the Domus Aurea, and subsequently also of the palaces on the Palatine, stood atop high substructures and thus dominated the surrounding city while offering those within a privileged view. Integrating a variety of water installations into these large platforms increased the sense of an artificial landscape in the form of a “hanging garden.” Thus, vague and often fantastic ideas like those about the design of the Hanging Garden of Babylon inspired Roman builders and their architects and led the art of building Roman villas and imperial palaces to new heights.
Reconstructions of Roman Polychrome Architecture
Authors: Zink Stephan
Published: June 2022

Efforts to understand polychromy in Roman architecture must address two inherent challenges: first, documenting surface finishes for Roman monuments is difficult when that evidence is scarce and scientific methods of evaluation are continually developing. Second, interpreting and presenting that evidence is far from straightforward. This chapter examines how the presentation of evidence for polychromy was deeply shaped by both the ideology and ideals of the 19th and early 20th centuries. Scholars today still hew to paradigms set decades earlier, often without any awareness of the cultural and historic forces that lie behind their choices. To address these issues, the careful study of architectural polychromy needs to be reintegrated into Roman Bauforschung.
Introduction
Authors: Richmond Oliver P.
Published: June 2022

Introduces the concept of the IPA
Stages One and Two
Authors: Richmond Oliver P.
Published: June 2022

This chapter examines the dynamics of the geopolitical order and the first stage or layer of the international peace architecture, aimed at state-centric and imperial balancing behaviour and very negative forms of peace.
The Derailment of the Transition to Stage Five
Authors: Richmond Oliver P.
Published: June 2022

This chapter outlines how counter-revolutionary international and domestic forces, both from within the liberal order and connected to the geopolitical layer, attempted a neoliberal retrenchment entangled with geopolitics as liberal internationalism began to lose political legitimacy.
From Nonverbal Communication to Co-speech Gesture
Authors: Bavelas Janet Beavin
Published: June 2022

Face-to-face dialogue is both audible and visible, combining speech and co-speech gestures. Co-speech hand gestures include hands, arms, or shoulders. Co-speech facial gestures include facial configurations as well as movements or positions of the head and gaze. It is essential to distinguish between co-speech gestures and nonverbal communication. Nonverbal communication is by definition any behavior or state that is independent of speech; it is often characterized as a separate channel of information. In contrast, co-speech gestures are by definition closely synchronized with speech in both their timing and their meaning. The meaning of a nonverbal communication relies on expert inference or ratings by other observers and is usually about attitudes, feelings, personality, and other characteristics of an individual. The meaning of a co-speech act is what it explicitly portrays to the person to whom it is addressed in the context of the immediately accompanying words and ongoing conversation.
Dialogue Favors Demonstrations
Authors: Bavelas Janet Beavin
Published: June 2022

Demonstrations are communicative acts that resemble or create an image of what they represent; they are iconic or analogic. Our research group studied five different demonstrations: hand gestures, facial portrayals, motor mimicry, figurative language, and direct quotations. These experiments separated the effects of visibility and of dialogue on demonstrations by creating and comparing three formats: face-to-face dialogues, telephone dialogues, and monologues to a tape recorder. The results showed that all five demonstrations occur at higher rates in dialogue than in monologue (where they almost disappear). There was no effect of visibility on hand gestures or figurative language, but visibility did increase the rates of motor mimicry, facial portrayals, and direct quotations. There are several possible explanations for the dialogue-demonstration link, testable in future research.