bluuebunny/crossref_metadata_2025 huggingface dataset:
A Global Set of Subduction Zone Earthquake Scenarios and Recurrence Intervals Inferred From Geodetically Constrained Block Models of Interseismic Coupling Distributions
Authors: Graham Shannon E. , Loveless John P. , Meade Brendan J.
Published: October 2021

The past 100 years have seen the occurrence of five earthquakes and 94 earthquakes. Here we assess the potential for future great earthquakes using inferences of interseismic subduction zone coupling from a global block model incorporating both tectonic plate motions and earthquake cycle effects. Interseismic earthquake cycle effects are represented using a first‐order quasistatic elastic approximation and include of interacting fault system area across the globe. We use estimated spatial variations in decadal‐duration coupling at 15 subduction zones and the Himalayan range front to estimate the locations and magnitudes of potential seismic events using empirical scaling relationships relating coupled area to moment magnitude. As threshold coupling values increase, estimates of potential earthquake magnitudes decrease, but the total number of large earthquakes varies non‐monotonically. These rupture scenarios include as many as 14 recent or potential earthquakes globally and up to 18 distinct events associated with a single subduction zone (South America). We also combine estimated slip deficit rates and potential event magnitudes to calculate recurrence intervals for large earthquake scenarios, finding that almost all potential earthquakes would have a recurrence time of less than 1,000 years.
Seawater Chemistry and Hydrothermal Controls on the Cenozoic Osmium Cycle
Authors: Katchinoff Joachim A. R. , Syverson Drew D. , Planavsky Noah J. , Evans Erica S. J. , Rooney Alan D.
Published: October 2021

Osmium isotope ratios are a key tool to track changes in global weathering and carbon cycle evolution through time. Long‐term changes in seawater Os isotope records over the Cenozoic have been used to argue for changes in weathering from increased uplift, leading to long‐term global cooling. Sulfide mineral precipitation during hydrothermal circulation traps the majority of mantle‐derived Os within mid‐ocean ridge (MOR) hydrothermal systems. Building from evidence that the amount of sulfide mineral precipitation in the subseafloor of MOR systems is related to the amount of sulfate and calcium in seawater, we show that as seawater chemistry changed through time, so too has the extent of hydrothermal sulfide formation and the global Os cycle. With currently estimated changes in seawater Ca/SO4 ratios, the observed progressive increase in seawater Os isotope values through the Cenozoic can be linked to changes in seawater chemistry—instead of a major shift in continental weathering processes.
Large‐Scale Forcing Impact on the Development of Shallow Convective Clouds Revealed From LASSO Large‐Eddy Simulations
Authors: Shin Hyeyum Hailey , Xue Lulin , Li Weiwei , Firl Grant , D’Amico Daniel F. , Muñoz‐Esparza Domingo , Ek Michael B. , Chu Yufei , Wang Zhien , Gustafson William I. , Vogelmann Andrew M.
Published: October 2021

Real‐world large‐eddy simulations (LES) are driven by time‐varying large‐scale forcings (LSF)—e.g., temperature advection, moisture advection, and subsidence—derived from large‐scale weather models. This study investigates the impact of the uncertainty in LSF on real‐world LES in terms of the development of shallow convection at the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) atmospheric observatory for the June 11, 2016 case using LES provided by the U.S. Department of Energy's LES ARM Symbiotic Simulation and Observation (LASSO) activity. The LASSO data set provides an ensemble of LES for the selected case, which consists of LES runs that were driven by different LSF. The two contrasting LES runs investigated here generate different types of convective clouds, i.e., nonprecipitating shallow clouds and precipitating cumulus congestus, mainly due to the difference of LSF in temperature advection in the free troposphere. The temperature advection modulates the strength of the capping inversion and therefore the buoyancy of the air parcels rising from the atmospheric boundary layer (ABL). The inversion, together with large‐scale updrafts, controls the penetration of the ABL thermals into the free troposphere, leading to cumulus congestus in the case of a weaker inversion. In contrast, clouds remain shallow in the case of a strong inversion. Differences between the two simulations are amplified over time, as mixed‐phase clouds are formed near the top of the congestus in the weaker inversion case. This high dependency of LES results to LSF stresses the importance of accurate LSF by large‐scale models to real‐world LES simulations.
Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy
Authors: Tang Jinyun , Riley William J. , Marschmann Gianna L. , Brodie Eoin L.
Published: October 2021

In studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.
Systematic review and meta-analysis determining the benefits of in vivo genetic therapy in spinal muscular atrophy rodent models
Authors: Chilcott Ellie M. , Muiruri Evalyne W. , Hirst Theodore C. , Yáñez-Muñoz Rafael J.
Published: October 2021

Spinal muscular atrophy (SMA) is a severe childhood neuromuscular disease for which two genetic therapies, Nusinersen (Spinraza, an antisense oligonucleotide), and AVXS-101 (Zolgensma, an adeno-associated viral vector of serotype 9 AAV9), have recently been approved. We investigated the pre-clinical development of SMA genetic therapies in rodent models and whether this can predict clinical efficacy. We have performed a systematic review of relevant publications and extracted median survival and details of experimental design. A random effects meta-analysis was used to estimate and compare efficacy. We stratified by experimental design (type of genetic therapy, mouse model, route and time of administration) and sought any evidence of publication bias. 51 publications were identified containing 155 individual comparisons, comprising 2573 animals in total. Genetic therapies prolonged survival in SMA mouse models by 3.23-fold (95% CI 2.75–3.79) compared to controls. Study design characteristics accounted for significant heterogeneity between studies and greatly affected observed median survival ratios. Some evidence of publication bias was found. These data are consistent with the extended average lifespan of Spinraza- and Zolgensma-treated children in the clinic. Together, these results support that SMA has been particularly amenable to genetic therapy approaches and highlight SMA as a trailblazer for therapeutic development.
Decreased frontotemporal connectivity in patients with parkinson’s disease experiencing face pareidolia
Authors: Kajiyama Yuta , Hattori Noriaki , Nakano Tomohito , Revankar Gajanan S. , Otomune Hironori , Hashimoto Ryota , Mori Etsuro , Ikeda Manabu , Mihara Masahito , Mochizuki Hideki
Published: October 2021

The precise neural underpinnings of face pareidolia in patients with Parkinson’s disease (PD) remain unclear. We aimed to clarify face recognition network abnormalities associated with face pareidolia in such patients. Eighty-three patients with PD and 40 healthy controls were recruited in this study. Patients with PD were classified into pareidolia and nonpareidolia groups. Volumetric analyses revealed no significant differences between the pareidolia (n = 39) and nonpareidolia (n = 44) patient groups. We further observed decreased functional connectivity among regions of interest in the bilateral frontotemporal lobes in patients with pareidolia. Seed-based analysis using bilateral temporal fusiform cortices as seeds revealed significantly decreased connectivity with the bilateral inferior medial prefrontal cortices in the pareidolia group. Post hoc regression analysis further demonstrated that the severity of face pareidolia was negatively correlated with functional connectivity between the bilateral temporal fusiform and medial prefrontal cortices. Our findings suggest that top-down modulation of the face recognition network is impaired in patients with PD experiencing face pareidolia.
DNA methylation atlas of the mouse brain at single-cell resolution
Authors: Liu Hanqing , Zhou Jingtian , Tian Wei , Luo Chongyuan , Bartlett Anna , Aldridge Andrew , Lucero Jacinta , Osteen Julia K. , Nery Joseph R. , Chen Huaming , Rivkin Angeline , Castanon Rosa G. , Clock Ben , Li Yang Eric , Hou Xiaomeng , Poirion Olivier B. , Preissl Sebastian , Pinto-Duarte Antonio , O’Connor Carolyn , Boggeman Lara , Fitzpatrick Conor , Nunn Michael , Mukamel Eran A. , Zhang Zhuzhu , Callaway Edward M. , Ren Bing , Dixon Jesse R. , Behrens M. Margarita , Ecker Joseph R.
Published: October 2021

Mammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing1,2 to profile 103,982 nuclei (including 95,815 neurons and 8,167 non-neuronal cells) from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, we constructed an artificial neural network model that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data3 enabled prediction of high-confidence enhancer–gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments4. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse cerebrum.
An atlas of cortical arealization identifies dynamic molecular signatures
Authors: Bhaduri Aparna , Sandoval-Espinosa Carmen , Otero-Garcia Marcos , Oh Irene , Yin Raymund , Eze Ugomma C. , Nowakowski Tomasz J. , Kriegstein Arnold R.
Published: October 2021

The human brain is subdivided into distinct anatomical structures, including the neocortex, which in turn encompasses dozens of distinct specialized cortical areas. Early morphogenetic gradients are known to establish early brain regions and cortical areas, but how early patterns result in finer and more discrete spatial differences remains poorly understood1. Here we use single-cell RNA sequencing to profile ten major brain structures and six neocortical areas during peak neurogenesis and early gliogenesis. Within the neocortex, we find that early in the second trimester, a large number of genes are differentially expressed across distinct cortical areas in all cell types, including radial glia, the neural progenitors of the cortex. However, the abundance of areal transcriptomic signatures increases as radial glia differentiate into intermediate progenitor cells and ultimately give rise to excitatory neurons. Using an automated, multiplexed single-molecule fluorescent in situ hybridization approach, we find that laminar gene-expression patterns are highly dynamic across cortical regions. Together, our data suggest that early cortical areal patterning is defined by strong, mutually exclusive frontal and occipital gene-expression signatures, with resulting gradients giving rise to the specification of areas between these two poles throughout successive developmental timepoints.
The mouse cortico–basal ganglia–thalamic network
Authors: Foster Nicholas N. , Barry Joshua , Korobkova Laura , Garcia Luis , Gao Lei , Becerra Marlene , Sherafat Yasmine , Peng Bo , Li Xiangning , Choi Jun-Hyeok , Gou Lin , Zingg Brian , Azam Sana , Lo Darrick , Khanjani Neda , Zhang Bin , Stanis Jim , Bowman Ian , Cotter Kaelan , Cao Chunru , Yamashita Seita , Tugangui Amanda , Li Anan , Jiang Tao , Jia Xueyan , Feng Zhao , Aquino Sarvia , Mun Hyun-Seung , Zhu Muye , Santarelli Anthony , Benavidez Nora L. , Song Monica , Dan Gordon , Fayzullina Marina , Ustrell Sarah , Boesen Tyler , Johnson David L. , Xu Hanpeng , Bienkowski Michael S. , Yang X. William , Gong Hui , Levine Michael S. , Wickersham Ian , Luo Qingming , Hahn Joel D. , Lim Byung Kook , Zhang Li I. , Cepeda Carlos , Hintiryan Houri , Dong Hong-Wei
Published: October 2021

The cortico–basal ganglia–thalamo–cortical loop is one of the fundamental network motifs in the brain. Revealing its structural and functional organization is critical to understanding cognition, sensorimotor behaviour, and the natural history of many neurological and neuropsychiatric disorders. Classically, this network is conceptualized to contain three information channels: motor, limbic and associative1–4. Yet this three-channel view cannot explain the myriad functions of the basal ganglia. We previously subdivided the dorsal striatum into 29 functional domains on the basis of the topography of inputs from the entire cortex5. Here we map the multi-synaptic output pathways of these striatal domains through the globus pallidus external part (GPe), substantia nigra reticular part (SNr), thalamic nuclei and cortex. Accordingly, we identify 14 SNr and 36 GPe domains and a direct cortico-SNr projection. The striatonigral direct pathway displays a greater convergence of striatal inputs than the more parallel striatopallidal indirect pathway, although direct and indirect pathways originating from the same striatal domain ultimately converge onto the same postsynaptic SNr neurons. Following the SNr outputs, we delineate six domains in the parafascicular and ventromedial thalamic nuclei. Subsequently, we identify six parallel cortico–basal ganglia–thalamic subnetworks that sequentially transduce specific subsets of cortical information through every elemental node of the cortico–﻿basal ganglia–thalamic loop. Thalamic domains relay this output back to the originating corticostriatal neurons of each subnetwork in a bona fide closed loop.
Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease
Authors: Karvelis Tautvydas , Druteika Gytis , Bigelyte Greta , Budre Karolina , Zedaveinyte Rimante , Silanskas Arunas , Kazlauskas Darius , Venclovas Česlovas , Siksnys Virginijus
Published: October 2021

Transposition has a key role in reshaping genomes of all living organisms1. Insertion sequences of IS200/IS605 and IS607 families2 are among the simplest mobile genetic elements and contain only the genes that are required for their transposition and its regulation. These elements encode tnpA transposase, which is essential for mobilization, and often carry an accessory tnpB gene, which is dispensable for transposition. Although the role of TnpA in transposon mobilization of IS200/IS605 is well documented, the function of TnpB has remained largely unknown. It had been suggested that TnpB has a role in the regulation of transposition, although no mechanism for this has been established3–5. A bioinformatic analysis indicated that TnpB might be a predecessor of the CRISPR–Cas9/Cas12 nucleases6–8. However, no biochemical activities have been ascribed to TnpB. Here we show that TnpB of Deinococcus radiodurans ISDra2 is an RNA-directed nuclease that is guided by an RNA, derived from the right-end element of a transposon, to cleave DNA next to the 5′-TTGAT transposon-associated motif. We also show that TnpB could be reprogrammed to cleave DNA target sites in human cells. Together, this study expands our understanding of transposition mechanisms by highlighting the role of TnpB in transposition, experimentally confirms that TnpB is a functional progenitor of CRISPR–Cas nucleases and establishes TnpB as a prototype of a new system for genome editing.
Wild meat consumption in tropical forests spares a significant carbon footprint from the livestock production sector
Authors: Nunes André Valle , Peres Carlos A. , Constantino Pedro de Araujo Lima , Fischer Erich , Nielsen Martin Reinhardt
Published: October 2021

Whether sustainable or not, wild meat consumption is a reality for millions of tropical forest dwellers. Yet estimates of spared greenhouse gas (GHG) emissions from consuming wild meat, rather than protein from the livestock sector, have not been quantified. We show that a mean per capita wild meat consumption of 41.7 kg yr−1 for a population of ~ 150,000 residents at 49 Amazonian and Afrotropical forest sites can spare ~ 71 MtCO2-eq annually under a bovine beef substitution scenario, but only ~ 3 MtCO2-eq yr−1 if this demand is replaced by poultry. Wild meat offtake by these communities could generate US$3M or US$185K in carbon credit revenues under an optimistic scenario (full compliance with the Paris Agreement by 2030; based on a carbon price of US$50/tCO2-eq) and US$1M or US$77K under a conservative scenario (conservative carbon price of US$20.81/tCO2-eq), representing considerable incentives for forest conservation and potential revenues for local communities. However, the wild animal protein consumption of ~ 43% of all consumers in our sample was below the annual minimum per capita rate required to prevent human malnutrition. We argue that managing wild meat consumption can serve the interests of climate change mitigation efforts in REDD + accords through avoided GHG emissions from the livestock sector, but this requires wildlife management that can be defined as verifiably sustainable.
Impact of children born with low birth weight on stunting and wasting in Sindh province of Pakistan: a propensity score matching approach
Authors: Abbas Faisal , Kumar Ramesh , Mahmood Tahir , Somrongthong Ratana
Published: October 2021

Low Birth Weight (LBW) is considered as a major public health issue and leading cause of neonatal death. Almost one in four newborns are reported as underweight in Pakistan. Children born with low birth weight are highly vulnerable to develop diseases and death and/or remain undernourished (i.e., stunted and wasted). This study determines the LBW newborns are more prone to develop stunting and wasting in province of Sindh, Pakistan. Moreover, regression-based estimation of the impact of LBW on the child health outcomes of under five years of age, may be prone to selection bias because of the nature of non-experimental data set, thus, propensity score matching methods are used in this study. Data for this study was used from Multiple Indicators Cluster Survey (MICS-2014). MICS is a two-stage, stratified cluster sampling household level data covering urban and rural areas and consists of 19,500 households from five administrative divisions and 28 districts of Sindh province of Pakistan. The total sample size of children less than five years of age after cleaning the data are 7781, of which 2095 are LBW having birth weight categorized as “smaller than average and very small” and 5686 are normal birth weight (NBW) having birth weight very large, larger than average, and average. This study employed propensity score matching (PSM) regression methods to understand whether the children born as low birth weight are more prone to stunting and wasting and/or both. In province of Sindh, moderate wasting children under five years were 21%, severe wasting 6% and both wasting and stunting 10%. The propensity score results are shown significant in all groups. Specifically, all four types of PSM methods confirm a significant difference in the potential outcome variables—meaning that a child born with LBW has a significant adverse effect on the potential child health outcome variables (stunting, wasting and both). Thus, the propensity score matching findings confirm a significant and adverse effect of LBW on potential health outcomes of under five children. Similarly, low birth weight children are significantly more likely to be moderately wasted (OR = 1.5, CI = 1.3–1.6) and severely wasted (OR = 1.6, CI = 1.3–2.0) and both (stunted and wasted, OR = 2.0, CI = 1.7–2.3) as compared to children with normal birth weight. Male children, if born with low birth weight, are significantly more likely to be moderately wasted (OR = 1.3, CI = 1.1–1.5) and both (wasted and stunted, OR = 1.3, CI = 1.1–1.5) than girls. This large data analysis finding proved that the LBW newborns are on higher risk to develop wasting and stunting in Pakistan.
Cytokine response in cerebrospinal fluid of meningitis patients and outcome associated with pneumococcal serotype
Authors: Müller Annelies , Schramm Diana B. , Kleynhans Jackie , de Gouveia Linda , Meiring Susan , Ramette Alban , von Gottberg Anne , Hathaway Lucy Jane
Published: October 2021

Streptococcus pneumoniae causes life-threatening meningitis. Its capsular polysaccharide determines the serotype and influences disease severity but the mechanism is largely unknown. Due to evidence of elevated cytokines levels in the meningeal inflammatory response, we measured 41 cytokines/chemokines and growth factors in cerebrospinal fluid (CSF) samples from 57 South African meningitis patients (collected in the period 2018–2019), with confirmed S. pneumoniae serotypes, using a multiplexed bead-based immunoassay. Based on multivariable Bayesian regression, using serotype 10A as a reference and after adjusting for HIV and age, we found IL-6 concentrations significantly lower in patients infected with serotypes 6D (undetectable) and 23A (1601 pg/ml), IL-8 concentrations significantly higher in those infected with 22A (40,459 pg/ml), 7F (32,400 pg/ml) and 15B/C (6845 pg/ml), and TNFα concentration significantly higher in those infected with serotype 18A (33,097 pg/ml). Although a relatively small number of clinical samples were available for this study and 28% of samples could not be assigned to a definitive serotype, our data suggests 15B/C worthy of monitoring during surveillance as it is associated with in-hospital case fatality and not included in the 13-valent polysaccharide conjugate vaccine, PCV13. Our data provides average CSF concentrations of a range of cytokines and growth factors for 18 different serotypes (14, 19F, 3, 6A, 7F, 19A, 8, 9N, 10A, 12F, 15B/C, 22F, 16F, 23A, 31, 18A, 6D, 22A) to serve as a basis for future studies investigating host–pathogen interaction during pneumococcal meningitis. We note that differences in induction of IL-8 between serotypes may be particularly worthy of future study.
Evaluation of head posture using an inertial measurement unit
Authors: Al-Yassary Mustafa , Billiaert Kelly , Antonarakis Gregory S. , Kiliaridis Stavros
Published: October 2021

An inertial measurement unit (IMU) is an electronic device that measures and track the orientation of a body. We conducted this study in accordance with the STARD guidelines to evaluate the accuracy of IMU (index test) for measuring head posture compared to the current gold standard using a cervical range of motion (CROM) device. The reproducibility of the hunter and mirror-guided head posture was also evaluated. In vitro and in vivo tests were carried out to assess the validity of the IMU. To assess reproducibility, thirty healthy young adults were asked to look at four different locations in two different sessions while the head posture was recorded. Excellent correlation (r = 0.99; p < 0.001) was found between the IMU and CROM device with an absolute mean difference of 0.45° ± 0.58° (p = 0.85) for the in vitro test and 0.88° ± 1.20° (p = 0.99) for the in vivo test. For the reproducibility test, moderate to good correlation coefficients were found (r = 0.55 to 0.89; all p < 0.05) between the two sessions. The intraclass correlation coefficient ranged from moderate to excellent reliability (ICC from 0.74 to 0.96). These results suggest that the IMU sensors, when calibrated correctly, can be adequate to analyze head posture.
Functional characterization of a bioengineered liver after heterotopic implantation in pigs
Authors: Anderson Brett D. , Nelson Erek D. , Joo DongJin , Amiot Bruce P. , Katane Aleksandr A. , Mendenhall Alyssa , Steiner Benjamin G. , Stumbras Aron R. , Nelson Victoria L. , Palumbo R. Noelle , Gilbert Thomas W. , Davidow Dominique S. , Ross Jeffrey J. , Nyberg Scott L.
Published: October 2021

Organ bioengineering offers a promising solution to the persistent shortage of donor organs. However, the progression of this technology toward clinical use has been hindered by the challenges of reconstituting a functional vascular network, directing the engraftment of specific functional cell types, and defining appropriate culture conditions to concurrently support the health and phenotypic stability of diverse cell lineages. We previously demonstrated the ability to functionally reendothelialize the vasculature of a clinically scaled decellularized liver scaffold with human umbilical vein endothelial cells (HUVECs) and to sustain continuous perfusion in a large animal recovery model. We now report a method for seeding and engrafting primary porcine hepatocytes into a bioengineered liver (BEL) scaffold previously reendothelialized with HUVECs. The resulting BELs were competent for albumin production, ammonia detoxification and urea synthesis, indicating the presence of a functional hepatocyte compartment. BELs additionally slowed ammonia accumulation during in vivo perfusion in a porcine model of surgically induced acute liver failure. Following explant of the graft, BEL parenchyma showed maintenance of canonical endothelial and hepatocyte markers. Taken together, these results support the feasibility of engineering a clinically scaled functional BEL and establish a platform for optimizing the seeding and engraftment of additional liver specific cells.
The enpp4 ectonucleotidase regulates kidney patterning signalling networks in Xenopus embryos
Authors: Massé Karine , Bhamra Surinder , Paroissin Christian , Maneta-Peyret Lilly , Boué-Grabot Eric , Jones Elizabeth A.
Published: October 2021

The enpp ectonucleotidases regulate lipidic and purinergic signalling pathways by controlling the extracellular concentrations of purines and bioactive lipids. Although both pathways are key regulators of kidney physiology and linked to human renal pathologies, their roles during nephrogenesis remain poorly understood. We previously showed that the pronephros was a major site of enpp expression and now demonstrate an unsuspected role for the conserved vertebrate enpp4 protein during kidney formation in Xenopus. Enpp4 over-expression results in ectopic renal tissues and, on rare occasion, complete mini-duplication of the entire kidney. Enpp4 is required and sufficient for pronephric markers expression and regulates the expression of RA, Notch and Wnt pathway members. Enpp4 is a membrane protein that binds, without hydrolyzing, phosphatidylserine and its effects are mediated by the receptor s1pr5, although not via the generation of S1P. Finally, we propose a novel and non-catalytic mechanism by which lipidic signalling regulates nephrogenesis.
ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces
Authors: Al-ramahi Yamal , Nyerges Akos , Margolles Yago , Cerdán Lidia , Ferenc Gyorgyi , Pál Csaba , Fernández Luis Ángel , de Lorenzo Víctor
Published: October 2021

ssDNA recombineering has been exploited to hyperdiversify genomically-encoded nanobodies displayed on the surface of Escherichia coli for originating new binding properties. As a proof-of-principle a nanobody recognizing the antigen TirM from enterohaemorrhagic E. coli (EHEC) was evolved towards the otherwise not recognized TirM antigen from enteropathogenic E. coli (EPEC). To this end, E. coli cells displaying this nanobody fused to the intimin outer membrane-bound domain were subjected to multiple rounds of mutagenic oligonucleotide recombineering targeting the complementarity determining regions (CDRs) of the cognate VHH gene sequence. Binders to the EPEC-TirM were selected upon immunomagnetic capture of bacteria bearing active variants and nanobodies identified with a new ability to strongly bind the new antigen. The results highlight the power of combining evolutionary properties of bacteria in vivo with oligonucleotide synthesis in vitro for the sake of focusing diversification to specific segments of a gene (or protein thereof) of interest.
Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus)
Authors: Weldenegodguad Melak , Pokharel Kisun , Niiranen Laura , Soppela Päivi , Ammosov Innokentyi , Honkatukia Mervi , Lindeberg Heli , Peippo Jaana , Reilas Tiina , Mazzullo Nuccio , Mäkelä Kari A. , Nyman Tommi , Tervahauta Arja , Herzig Karl-Heinz , Stammler Florian , Kantanen Juha
Published: October 2021

Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions.
Experimental demonstration of coherence flow in PT- and anti-PT-symmetric systems
Authors: Fang Yu-Liang , Zhao Jun-Long , Zhang Yu , Chen Dong-Xu , Wu Qi-Cheng , Zhou Yan-Hui , Yang Chui-Ping , Nori Franco
Published: October 2021

Non-Hermitian parity-time ($${{{{{{{\mathcal{P}}}}}}}}{{{{{{{\mathcal{T}}}}}}}}$$
P
T
) and anti-parity-time ($${{{{{{{\mathcal{APT}}}}}}}}$$
APT
)-symmetric systems exhibit novel quantum properties and have attracted increasing interest. Although many counterintuitive phenomena in $${{{{{{{\mathcal{P}}}}}}}}{{{{{{{\mathcal{T}}}}}}}}$$
P
T
- and $${{{{{{{\mathcal{APT}}}}}}}}$$
APT
-symmetric systems were previously studied, coherence flow has been rarely investigated. Here, we experimentally demonstrate single-qubit coherence flow in $${{{{{{{\mathcal{P}}}}}}}}{{{{{{{\mathcal{T}}}}}}}}$$
P
T
- and $${{{{{{{\mathcal{APT}}}}}}}}$$
APT
-symmetric systems using an optical setup. In the symmetry unbroken regime, we observe different periodic oscillations of coherence. Particularly, we observe two complete coherence backflows in one period in the $${{{{{{{\mathcal{P}}}}}}}}{{{{{{{\mathcal{T}}}}}}}}$$
P
T
-symmetric system, while only one backflow in the $${{{{{{{\mathcal{APT}}}}}}}}$$
APT
-symmetric system. Moreover, in the symmetry broken regime, we observe the phenomenon of stable value of coherence flow. We derive the analytic proofs of these phenomena and show that most experimental data agree with theoretical results within one standard deviation. This work opens avenues for future study on the dynamics of coherence in $${{{{{{{\mathcal{P}}}}}}}}{{{{{{{\mathcal{T}}}}}}}}$$
P
T
- and $${{{{{{{\mathcal{APT}}}}}}}}$$
APT
-symmetric systems.
A high dimensional oxysulfide built from large iron-based clusters with partial charge-ordering
Authors: Almoussawi Batoul , Arevalo-Lopez Angel M. , Simon Pardis , Kabbour Houria
Published: October 2021

We report the original non-centrosymmetric Ba10Fe7.75Zn5.25S18Si3O12 oxysulfide which crystallizes in a new structural type. Contrary to usual oxychalcogenides, it crystallizes with a 3D spatial network structure built from large magnetic clusters.
A metal–polyphenolic nanosystem with NIR-II fluorescence-guided combined photothermal therapy and radiotherapy
Authors: Li Jie , Li Wenxi , Xie Lisi , Sang Wei , Wang Guohao , Zhang Zhan , Li Bei , Tian Hao , Yan Jie , Tian Ye , Li Zhenhua , Fan Quli , Yu Lin , Dai Yunlu
Published: October 2021

A polyphenolic semiconducting polymer was prepared to chelate the high-Z Hf ions, followed by coating of the amphiphilic polymers to form a nanostructure (CPPDA–Hf@Poloxamer nanoparticles) for precise lesion imaging and photothermal therapy.
Suppressing barite crystallization with organophosphorus compounds
Authors: Sosa Ricardo D. , Conrad Jacinta C. , Reynolds Michael A. , Rimer Jeffrey D.
Published: October 2021

A naturally derived phosphorous-containing molecule, phytate, functions as a dual inhibitor of barium sulfate (barite) nucleation and growth, making it a potentially viable environmentally-friendly alternative to current barite scale treatments.
What can we learn from transition path time distributions for protein folding and unfolding?
Authors: Dutta Rajesh , Pollak Eli
Published: October 2021

Theoretical analysis of measured transition path time distributions in protein folding and unfolding reactions reveals a long time tail which may indicate the existence of an intermediate trap in the transition free energy surface.
Theoretical study of the stability, structure, and optical spectra of small silver clusters and their formation using density functional theory
Authors: Farshad Mohsen , Perera Duwage C. , Rasaiah Jayendran C.
Published: October 2021

An understanding of the mechanism of formation of small clusters would help to identify efficient routes to their synthesis.
A high-performance, durable and low-cost proton exchange membrane electrolyser with stainless steel components
Authors: Stiber S. , Sata N. , Morawietz T. , Ansar S. A. , Jahnke T. , Lee J. K. , Bazylak A. , Fallisch A. , Gago A. S. , Friedrich K. A.
Published: October 2021

A high-performance, durable and low-cost PEM electrolyser that can be produced almost entirely with coated stainless steel parts.
Quantitative analysis of Cr in soil based on variable selection coupled with multivariate regression using laser-induced breakdown spectroscopy
Authors: Huang Yutao , Lin Jingjun , Lin Xiaomei , Zheng Weinan
Published: October 2021

Compared with LASSO, ALASSO can better select the variables of soil LIBS spectra.
Retraction: Pt NPs@GO as a highly efficient and reusable catalyst for one-pot synthesis of acridinedione derivatives
Authors: Kaya Muharrem , Aday Burak
Published: October 2021

Retraction for ‘Pt NPs@GO as a highly efficient and reusable catalyst for one-pot synthesis of acridinedione derivatives’ by Handan Pamuk et al., RSC Adv., 2015, 5, 49295–49300, DOI: 10.1039/C5RA06441D.
Moderate conformational transition promotes the formation of a self-reinforced highly oriented silk fibroin network structure
Authors: Shu Ting , Cui Jing , Lv Zhuochen , Cao Leitao , Ren Jing , Ling Shengjie
Published: October 2021

Moderate conformation transition promotes the formation of low-density crosslinking molecular network and further rearrangement of amorphous proteins to form the highly oriented molecular network structure, which paved the way for achieving mechanical-enhanced silk fibroin materials.
Predictors of Aspiration and Silent Aspiration in Patients With New Tracheostomy
Authors: Marvin Stevie , Thibeault Susan L.
Published: October 2021

Purpose

Hospitalized, medically complex patients with new tracheostomy are at risk for aspiration. This study reports incidence of aspiration in these patients with new tracheostomy and investigates possible risk factors for aspiration and silent aspiration in this patient population.

Method

Retrospective review of instrumental swallowing evaluations from hospitalized inpatients with new tracheostomy tubes to determine frequency of aspiration and silent aspiration and patient factors associated with aspiration. Patient variables including sex, age, reason for hospital admission, reason for tracheostomy, duration of intubation, time since tracheostomy placement, and tracheostomy cuff and cap status were examined as possible risk factors for aspiration and silent aspiration.

Results

Of the 272 patients with new tracheostomies who underwent instrumental swallowing evaluation, 59% aspirated on at least one consistency. Odds of aspiration were twice as high in patients with uncapped tracheostomy compared to closed (i.e., cap or speaking valve in place). Odds of aspiration were 3.4 times greater with patients who underwent tracheostomy for an oropharyngeal etiology (oropharyngeal or laryngeal tumor, surgery, or infection). Of the patients who aspirated, 81% aspirated silently on at least one consistency. Odds of silent aspiration was 4.5 greater with an uncapped tracheostomy.

Conclusions

Medically complex patients with new tracheostomy are at risk for aspiration and benefit from instrumental swallowing evaluations. Future prospective research is warranted to determine contributing factors responsible for this risk. Lastly, speech pathologists play an important role in the patient’s recovery.
Comparing the Informativeness of Single-Word Samples and Connected Speech Samples in Assessing Speech Sound Disorders
Authors: Yeh Li-Li , Liu Chia-Chi
Published: October 2021

Purpose

Speech-language pathologists (SLPs) are faced with the challenge of quickly and accurately identifying children who present with speech sound disorders (SSD) compared to typically developing (TD) children. The goal of this study was to compare the clinical relevance of two speech sampling methods (single-word vs. connected speech samples) in how sensitive they are in detecting atypical speech sound development in children, and to know whether the information obtained from single-word samples is representative enough of children's overall speech sound performance.

Method

We compared the speech sound performance of 37 preschool children with SSD (Mage= 4;11 years) and 37 age-sex-matched typically developing children (Mage= 5;0 years) by eliciting their speech in two ways: (a) a picture-naming task to elicit single words, and (b) a story-retelling task to elicit connected speech. Four speech measures were compared across sample type (single words vs. connected speech) and across groups (SSD vs. TD): intelligibility, speech accuracy, phonemic inventory, and phonological patterns.

Results

Interaction effects were found between sample type and group on several speech sound performance measures. Single-word speech samples were found to differentiate the SSD group from the TD group, and were more sensitive than connected speech samples across various measures. The effect size of single-word samples was consistently higher than connected speech samples for three measures: intelligibility, speech accuracy, and phonemic inventory. The gap in sample type informativeness may be attributed to salience and avoidance effects, given that children tend to avoid producing unfamiliar phonemes in connected speech. The number of phonological patterns produced was the only measure that revealed no gap between two sampling types for both groups.

Conclusions

On measures of intelligibility, speech accuracy, and phonemic inventory, obtaining a single-word sample proved to be a more informative method of differentiating children with SSD from TD children than connected speech samples. This finding may guide SLPs in their choice of sampling type when they are under time pressure. We discuss how children's performance on the connected speech sample may be biased by salience and avoidance effects and/or task design, and may, therefore, not necessarily reveal a poorer performance than single-word samples, particularly in intelligibility, speech accuracy, and the number of phonological patterns, if these task limitations are circumvented. Our findings show that the performance gap, typically observed between the two sampling types, largely depends on which performance measures are evaluated with the speech sample. Our study is the first to address sampling type differences in SSD versus TD children and has significant clinical implications for SLPs looking for sampling types and measures that reliably identify SSD in preschool-aged children.
Assessing Language in Unstructured Conversation in People With Aphasia: Methods, Psychometric Integrity, Normative Data, and Comparison to a Structured Narrative Task
Authors: Leaman Marion C. , Edmonds Lisa A.
Published: October 2021

Purpose

This study evaluated interrater reliability (IRR) and test–retest stability (TRTS) of seven linguistic measures (percent correct information units, relevance, subject–verb–[object], complete utterance, grammaticality, referential cohesion, global coherence), and communicative success in unstructured conversation and in a story narrative monologue (SNM) in persons with aphasia (PWAs) and matched participants without aphasia (M-PWoAs). Furthermore, the relationship of language in unstructured conversation and SNM was investigated for these measures.

Methods

Twenty PWAs and 20 M-PWoAs participated in two unstructured conversations on different days with different speech-language pathologists trained as social conversation partners. An 8- to 12-min segment of each conversation was analyzed. Additionally, a wordless picture book was used to elicit an SNM sample at each visit. Correlational analyses were conducted to address the primary research questions. Normative range and minimal detectable change data were also calculated for the measures in both conditions.

Results

IRR and TRTS were moderate to good for parametric measures and moderate to excellent for nonparametric measures for both groups, except for TRTS for referential cohesion for the PWAs in conversation. Furthermore, in PWAs, a strong correlation was demonstrated for three of eight measures across conditions. Moderate or weaker correlations were demonstrated for three of eight measures, and correlations for two of eight measures were not significant. An ancillary finding was no significant differences occurred for sample-to-sample variability between the two conditions for any measure.

Conclusions

This study replicates previous research demonstrating the feasibility to reliably measure language in unstructured conversation in PWAs. Furthermore, this study provides preliminary evidence that language production varies for some measures between unstructured conversation and SNM, contributing to a literature base that demonstrates language variation between different types of monologue. Thus, these findings suggest that inclusion of the specific types of discourse of interest to the PWA may be important for comprehensive assessment of aphasia.

Supplemental Material

https://doi.org/10.23641/asha.16569360
A Concise Study on Shearing Operation in Metal Forming
Authors: Omolayo M. Ikumapayi , Sunday A. Afolalu , Olawale S. Fatoba , Rasaq A. Kazeem , Adedotun A. Adetunla , Samuel O. Ongbali
Published: October 2021

This study outlines the recent developments in metal forming processes, focusing mainly on the shearing process. A summary of the background of the shearing process is given to give perspective on how such a process has changed over time. It explains what shearing operations are and how the shearing process is operated in metal forming. While also outlining the difference between shearing, slitting, punching, notching, and blanking processes, and the advantages and disadvantages of the shearing process are detailed. Different types of modern shearing machines are documented. The ways of ensuring the optimal functionality of the shearing machine and how the shearing operation has improved the manufacturing products were scripted. Three cases were given on the recent advancement in the use of shearing operation. Recommendations on how to improve efficiency in shearing metal forming are specified with relevance to the theory and a conclusion is drawn.
Application of ANN in prediction of response parameters in CNC Turning
Authors: Kumar Raman , Singh Chohan Jasgurpreet , Singh Sandeep , Kaur Jatinder
Published: October 2021

Product surface quality material removal rate play a great role in the current manufacturing industry. The use of artificial intelligence becomes immensely important component in research work. . In today advanced technology era, the use of CNC in lathe is common and essential to enhance the productivity of manufacturing industry. In this research work, the application of artificial neural network has been shown to predict the values of surface finish and MRR during turning operation on a CNC lathe machine. The association between process variables and response variables through hidden layers has been presented. The experimental data set was used for training (70%), testing (15%) and validation (15%) of neural network. The measured values are compared with the predicted values and percentage of predicated errors are computed. In present work, a neural network is developed and trained, tested and validated with the help of MATLAB. The study can be beneficial for estimation of surface finish of products during commercialization which would reduce the manufacturing coat and time.