bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing teacher noticing on paper and pencil and technology tasks
Authors: Chandler Kayla 
Published: October 2023

AbstractWork in teacher noticing has captured to what extent teachers notice students' thinking on paper and pencil tasks and technology tasks, yet no one study has considered how the same group of teachers notices across task types. This study used Jacobs et al.'s (Journal for Research in Mathematics Education, 2010, 41(2), pp: 169–202.) professional noticing of students' thinking framework to guide the design and analysis of prospective secondary mathematics teachers' (PSMTs) noticing of high school students' thinking on two geometry tasks: a paper and pencil task and a technology task. High school students' written work and a video clip were shared as the artifacts from which to notice for each task. PSMTs responded to a set of noticing prompts to capture how they were attending, interpreting, and deciding to respond to students' thinking for each task. Their written responses to these questions were then open coded for each noticing component and codes from each task were compared to reveal any differences in the content of PSMTs' noticing across task types. Results revealed differences between tasks for each component skill of noticing. Implications of these findings for mathematics teacher educators and future research are discussed.
The relationship between site history and human health risks: Lessons from 13 years of contaminated land risk assessments in Victoria, Australia
Authors: Kabay Victor Gabriel , Papaleo Clare Boni , Reichman Suzie M. 
Published: October 2023

AbstractSite history is widely recognized as one of the key determinants of the nature and scale of contamination that is likely to be present at a location. While there is vast anecdotal and empirical evidence on the relationship between site history and risk of exposure to pollution, few attempts have been made to systematically collate data across sites to rigorously identify such trends. This study presents an analysis of human health risk metrics extracted from all 1732 contaminated land environmental audits published in Victoria, Australia between 2006 and 2018. The contaminating activities found to be most likely associated with elevated risks to human health were service stations, fuel depots, dry cleaners, gasworks, mechanical parts manufacturers, imported fill and unknown offsite sources generating regional groundwater pollution (usually polluted with trichloroethene). The ten chemical contaminants most frequently assessed in human health risk assessment reports included (in order): benzene, C>10–16 petroleum hydrocarbons, naphthalene, C6–10 petroleum hydrocarbons, xylenes, trichloroethene, toluene, ethylbenzene, benzo(a)pyrene, and tetrachloroethene. The findings of this report include recommendations to develop regulatory guideline values in Australia for trimethylbenzenes, heavy fraction petroleum hydrocarbons (C>16), and trans‐1,2‐dicholoethene, and to strengthen the evidence base informing risks associated with light fraction petroleum hydrocarbons (C6–16) and trichloroethene. To the author's knowledge, this study is the first to extract risk metrics from environmental audit reports and provides a strong evidence base to help regulators, academics and commercial practitioners rank and prioritize sites based on their site history and associated risks.
A rigidity result for holomorphic quadratic differentials of finite norm in the unit disk
Authors: Gao Qiang 
Published: October 2023

AbstractLet be a holomorphic quadratic differential of finite norm in the unit disk . Let be equipped with the metric . In this paper, we prove that a geodesic‐preserving map of the unit disk into itself is affine. A map is called geodesic‐preserving if the image of each geodesic is a geodesic. We make no assumptions on the continuity of such a map.
Analysis of Shear Wave Propagation in Soft Biomaterials Using a Finite Element Model
Authors: Wang Jianing , Li Runze , Zhou Qifa , Gu Linxia , Dong Pengfei 
Published: October 2023

Abstract
The elastography method has been widely used to estimate the stiffness of biomaterials based on the shear wave speed. The wave propagation excited by a single indent on the surface of the biomaterials is not always an ideal shear wave. The distance from the interested region to the indent or different algorithms for elastography may affect the calculation of stiffness. This paper aims to analyze the shear wave propagation in soft biomaterials using a finite element model. A finite element model was constructed based on the setup of our previous in vitro experiments on the elastography of gelatin. Briefly, a shear wave propagation was induced by a single indent with a frequency of 1 kHz. Following simulation, the displacements along a path line, at three depths, were extracted for analyzing the shear wave propagation. The influence of the damping behavior and three different elastography algorithms were investigated. Results have shown that finite element simulation agreed well with the previous in vitro experiments. The estimated stiffness increased by more than 10% as the depth increased from 1 mm to 7 mm. This increase was even larger for the material with a larger damping behavior (viscoelasticity). The precise estimation was related to the distance between the interested region and the indent for the material with a larger damping behavior after the distance of 4 mm. The feasibility of three algorithms, i.e., wavefront slope, cross-correlation algorithm, and finite differencing method (FDM), were investigated. The FDM proposed in this work can determine the shear wave speed based on local spatial and temporal data, while it demands high-frequency data. The understanding from this work may provide valuable information for optimizing the performance of elastography.
An Integrated Kinematic Mapping and Fourier Method to Design Spherical Coupled Serial Chain Mechanisms for Single-Joint Rehabilitation
Authors: Li Xiangyun , Lv Hao , Yu Xi , Chen Peng , Li Kang 
Published: October 2023

Abstract
Robotic devices are capable of reducing the physical burden on rehabilitation therapists and providing training programs of good repeatability, high efficiency, and high precision. When designing the kinematic structure for rehabilitation robots, there has been a growing interest toward one-degree-of-freedom (DOF) end-effector mechanisms due to their simpler structure and less complicated control algorithms. Compared with current one-DOF mechanism designs that are mainly customized for multi-joint robotic training, spherical coupled serial chain (SCSC) mechanisms are proposed in this paper to specifically deliver the single-joint robotic training, which is of equal importance to the effective physical recovery. Using kinematic mapping theory, the end-effector motion of SCSC mechanisms can be naturally transformed to two trigonometric curves composed of finite Fourier series in two separate planes of the image space. This novel formulation helps to establish an analytical and direct relationship between the design parameters of the SCSC mechanism and the harmonic parameters of the image-space representation of the task rehabilitation motion. The result is a simple and effective method for kinematic synthesis of SCSC mechanisms for generation of single-joint motion with an arbitrary number of spherical poses. An example of designing SCSC mechanisms for shoulder-joint rehabilitation is presented at the end of this paper to illustrate the feasibility of the proposed method.
Correlating the Influence of the Purity of Hydrogen Produced by a Surplus Power on the Production of Green Ammonia
Authors: Kim Byungjun , Lee Young Duk 
Published: October 2023

Abstract
Carbon dioxide is the primary greenhouse gas contributing to climate change. Furthermore, due to the surplus power generated by renewable energy resources, various approaches have been developed to handle this overproduction. This study verifies via a correlation analysis the influence of the purity of hydrogen produced by a continuous surplus power on sustainable ammonia production. The influence of the temperature and pressure of the hydrogen treatment system on the purity of the hydrogen gas produced in the alkaline water electrolysis system was investigated, where the purity increased with a decrease in temperature and an increase in pressure. The purity of the produced ammonia was positively correlated with the purity of hydrogen. Furthermore, the energy consumption of the ammonia production process increased when the purity of hydrogen was low. In the case of storing the surplus power as ammonia, the effect of hydrogen purity was less affected by the hydrogen production system than by the ammonia production system, and it was thus concluded that it is more desirable to determine the hydrogen purity in the hydrogen production system prior to employing it in the ammonia production system.
A broadly immunogenic polyvalent
Shigella
multiepitope fusion antigen protein protects against
Shigella sonnei
and
Shigella flexneri
lethal pulmonary challenges in mice
Authors: Li Siqi , Anvari Shaghayegh , Ptacek Galen , Upadhyay Ipshita , Kaminski Robert W. , Sack David A. , Zhang Weiping 
Published: October 2023

ABSTRACT

There are no licensed vaccines for
Shigella
, a leading cause of children’s diarrhea and a common etiology of travelers’ diarrhea. To develop a cross-protective
Shigella
vaccine, in this study, we constructed a polyvalent protein immunogen to present conserved immunodominant epitopes of
Shigella
invasion plasmid antigens B (IpaB) and D (IpaD), VirG, GuaB, and Shiga toxins on backbone protein IpaD, by applying an epitope- and structure-based multiepitope-fusion-antigen (MEFA) vaccinology platform, examined protein (
Shigella
MEFA) broad immunogenicity, and evaluated antibody function against
Shigella
invasion and Shiga toxin cytotoxicity but also protection against
Shigella
lethal challenge. Mice intramuscularly immunized with
Shigella
MEFA protein developed IgG responses to IpaB, IpaD, VirG, GuaB, and Shiga toxins 1 and 2; mouse sera significantly reduced invasion of
Shigella sonnei
,
Shigella flexneri
serotype 2a, 3a, or 6,
Shigella boydii,
and
Shigella dysenteriae
type 1 and neutralized cytotoxicity of Shiga toxins of
Shigella
and Shiga toxin-producing
Escherichia coli in vitro
. Moreover, mice intranasally immunized with
Shigella
MEFA protein (adjuvanted with dmLT) developed antigen-specific serum IgG, lung IgG and IgA, and fecal IgA antibodies, and survived from lethal pulmonary challenge with
S. sonnei
or
S. flexneri
serotype 2a, 3a, or 6. In contrast, the control mice died, became unresponsive, or lost 20% of body weight in 48 h. These results indicated that this
Shigella
MEFA protein is broadly immunogenic, induces broadly functional antibodies, and cross-protects against lethal pulmonary challenges with
S. sonnei
or
S. flexneri
serotypes, suggesting a potential application of this polyvalent MEFA protein in
Shigella
vaccine development.
N-terminal domain of classical swine fever virus N
pro
induces proteasomal degradation of specificity protein 1 with reduced HDAC1 expression to evade from innate immune responses
Authors: Chen Rong , Han Xiao , Xu Hankun , Xu Jidong , Cao Tong , Shan Ying , He Fang , Fang Weihuan , Li Xiaoliang 
Published: October 2023

ABSTRACT

Classical swine fever virus (CSFV) poses a major threat to the pig industry. The mechanisms that CSFV uses to evade host innate immunity are not fully understood. Acetylation of histones and non-histone proteins is involved in modulating innate immune responses. Histone deacetylase 1 (HDAC1) could be proviral or antiviral by modulating the acetylation status of histones, viral proteins or non-histone host proteins, depending on the type of viruses involved. First, we found that CSFV infection in IPEC-J2 cells resulted in reduced expression of HDAC1. By chemical inhibition, gene silencing, and overexpression, we revealed that HDAC1 acts as a negative regulator of CSFV replication in IPEC-J2 cells probably through activation of poly(I:C) and IFN-λ3-induced IFN-I/III innate immunity. Mechanistically, CSFV N
pro
downregulated HDAC1 and its transcriptional regulator specificity protein 1 (Sp1). N
pro
interacted with Sp1 to facilitate its degradation through the ubiquitin-proteasome pathway via its N-terminal domain, a region that does not have significant effect on IRF3 stability. Thus, it is clear that CSFV deploys the two domains of its N
pro
to counteract the innate immune responses, the C-terminal one targeting the IRF3 pathway as previously reported, and the N-terminal one targeting the Sp1-HDAC1 axis.

IMPORTANCE

Of the flaviviruses, only CSFV and bovine viral diarrhea virus express N
pro
as the non-structural protein which is not essential for viral replication but functions to dampen host innate immunity. We have deciphered a novel mechanism with which CSFV uses to evade the host antiviral immunity by the N-terminal domain of its N
pro
to facilitate proteasomal degradation of Sp1 with subsequent reduction of HDAC1 and ISG15 expression. This is distinct from earlier findings involving N
pro
-mediated IRF3 degradation via the C-terminal domain. This study provides insights for further studies on how HDAC1 plays its role in antiviral immunity, and if and how other viral proteins, such as the core protein of CSFV, the nucleocapsid protein of porcine epidemic diarrhea virus, or even other coronaviruses, exert antiviral immune responses via the Sp1-HDAC1 axis. Such research may lead to a deeper understanding of viral immune evasion strategies as part of their pathogenetic mechanisms.
The SET and ankyrin domains of the secreted
Legionella pneumophila
histone methyltransferase work together to modify host chromatin
Authors: Rolando Monica , Wah Chung Ivy Yeuk , Xu Caishuang , Gomez-Valero Laura , England Patrick , Cygler Miroslaw , Buchrieser Carmen 
Published: October 2023

ABSTRACT

Legionella pneumophila
is a bacterial pathogen ubiquitous in natural and man-made aquatic environments, where it replicates in protozoa. Its intracellular life cycle depends on the establishment of a
Legionella
-containing vacuole (LCV) where the bacteria replicate. To form the LCV,
L. pneumophila
depends on a type-4 secretion system that secretes more than 300 proteins in the host cell. Among these is RomA that encodes an N-terminal catalytic methyltransferase domain with a SET fold and a C-terminal domain containing six ankyrin repeats. We have reported that the SET domain has histone methyltransferase activity and specifically methylates lysine 14 of histone H3 during infection; however, the role of the ankyrin repeats is unknown. Here, we report the structure of RomA co-crystallized with a 15-mer peptide corresponding to the N-terminal tail of histone H3 at 2.2 Å. This structure revealed that the N-terminal arm of the peptide from Thr3-Ala7 binds to the ankyrin repeat domain and the C-terminal arm from Gly13-Arg17 and interacts with the SET domain, inserting Lys14 into the active site for methylation. Importantly, the interactions of the five N-terminal residues of the H3-peptide with the ankyrin domains account for ~50% of the peptide-RomA contacts, predicting that the ankyrin domains of RomA are essential for histone H3 binding and subsequent lysine methylation.
In vitro
enzymatic activity and binding assays confirmed these predictions. Thus, the six ankyrin domains are essential for chromatin binding, thereby allowing the SET domain to fulfill its histone transferase activity and to modify the host chromatin to the advantage of the pathogen.

IMPORTANCE

Legionella pneumophila
is an intracellular bacterium responsible of Legionnaires’ disease, a severe pneumonia that is often fatal when not treated promptly. The pathogen’s ability to efficiently colonize the host resides in its ability to replicate intracellularly. Essential for intracellular replication is translocation of many different protein effectors
via
a specialized secretion system. One of them, called RomA, binds and directly modifies the host chromatin at a unique site (tri-methylation of lysine 14 of histone H3 [H3K14me]). However, the molecular mechanisms of binding are not known. Here, we resolve this question through structural characterization of RomA together with the H3 peptide. We specifically reveal an active role of the ankyrin repeats located in its C-terminal in the interaction with the histone H3 tail. Indeed, without the ankyrin domains, RomA loses its ability to act as histone methyltransferase. These results discover the molecular mechanisms by which a bacterial histone methyltransferase that is conserved in
L. pneumophila
strains acts to modify chromatin.
Mycobacteriales
taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation
Authors: Val-Calvo Jorge , Vázquez-Boland José A. 
Published: October 2023

ABSTRACT

Genomics allows accurately pinpointing microbial ancestry for taxonomic purposes, yet there is currently no consensus to genus definition based on genome data. Different metrics and criteria are used, with an increasing trend toward genera over-splitting. Here, we report a method for prokaryotic genus assignment that combines normalized tree clustering and network analysis of several genomic relatedness indices. Objectivity is maximized by linear application of the same partitioning thresholds across an entire middle/high taxonomic rank context (order level), with the classical (“pre-genomic”) genera as demarcation reference, ensuring continuity in taxonomy and nomenclature. We tested the method with the
Mycobacteriales
, where recent examples of genus fragmentation divided
Mycobacterium
into five genera, or made
Rhodococcus
paraphyletic by creating the genus
Prescottella
for the sublineage containing the animal and human pathogen,
Rhodococcus equi
. Our approach did not support the mycobacterial five-genus split or the
Prescottella
nested genus, but identified a basal branch in each of the mycobacterial and rhodococcal radiations warranting genus status (
Mycobacteroides
, and novel genus
Rhodococcoides
for the
Rhodococcus fascians
clade, respectively). The median average amino acid identity (AAI) between the demarcated genera was 56% to 59%, consistent with the <65% AAI genus boundary standard. Shifting the demarcation threshold to the
Prescottella
/mycobacterial five-genus level systematically elevated the intrageneric sublineages to genus rank, leading to taxonomic atomization (≈threefold increase in potential
Mycobacteriales
genera). The proposed approach provides a standardizable methodological framework for non-subjective prokaryotic genus delineation.

IMPORTANCE

A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order
Mycobacteriales
. Formal descriptions of proposed taxonomic changes based on our study are included.
Deciphering the molecular components of the
quorum sensing
system in the fungus
Ophiostoma piceae
Authors: Santos-Pascual Rodrigo , Campoy Iván , Sanz Mata David , Martínez María Jesús , Prieto Alicia , Barriuso Jorge 
Published: October 2023

ABSTRACT

Quorum sensing
(QS) is a complex cell-cell communication mechanism that coordinates population-level behaviors in microbes. In eukaryotes, this phenomenon has been extensively described in the dimorphic yeast
Candida albicans
as its main QS molecule, the sesquiterpene alcohol farnesol, is responsible for various phenotypic (i.e., inhibition of yeast-to-hyphae transition, biofilm formation, and, hence, pathogenesis) and metabolic (i.e., induction of oxidative stress and apoptosis) changes.
Ophiostoma piceae
CECT 20416 is a dimorphic saprotrophic ascomycete with biotechnological interest that also produces farnesol as QS molecule, but in this case, the alcohol promotes the morphological transition to the mycelial form, biofilm formation, enzyme secretion, and melanin production. Here, we characterized the physiological response of
Ophiostoma piceae
to farnesol, the molecular components of the QS system of this fungus have been investigated using a “multiomics” approach that involved genomic, transcriptomic, and proteomic analyses. Some genes identified in this work are proposed as key factors in farnesol transport and signaling. We have also cataloged the genes undergoing major transcriptional changes triggered by the presence of the autoinducer, such as cell-wall remodeling, reactive oxygen species (ROS) protection, and melanin biosynthesis, using self-organizing maps. This analysis could be useful for applications in the forestry industry, for enzymes production, and for the valorization of residues. Furthermore, it might as well help to investigate the QS mechanisms of clinically relevant fungi phylogenetically related to
Ophiostoma
.

IMPORTANCE

This manuscript presents a comprehensive study on the molecular mechanisms triggered by the
quorum sensing
(QS) molecule farnesol in the biotechnologically relevant fungus
Ophiostoma piceae
. We present for the first time, using a multiomics approach, an in-depth analysis of the QS response in a saprotroph fungus, detailing the molecular components involved in the response and their possible mechanisms of action. We think that these results are particularly relevant in the knowledge of the functioning of the QS in eukaryotes, as well as for the exploitation of these mechanisms.
Atypical case of acute posterior multifocal placoid pigment epitheliopathy with intraretinal fluid
Authors: Barbosa Renato Correia , Gonçalves Rita , Vieira Bruna 
Published: October 2023

Acute posterior multifocal placoid pigment epitheliopathy is a rare inflammatory chorioretinopathy, classified as a white dot syndrome, in which ischaemia of the choriocapillaris leads to atrophy of the external retinal layers, including the retinal pigment epithelium.A male patient in his 20s presented with sudden severe loss of vision in the left eye. Funduscopy revealed with yellow placoid lesions in the macula and near periphery. Spectral-domain optical coherence tomography and fluorescein angiography revealed the presence of central intraretinal fluid in the left eye and multiple areas of macular ischaemia bilaterally. Treatment with oral corticosteroids was initiated, and the anatomical changes, including the intraretinal fluid, improved steadily over the following weeks.Although rare, the presence of subretinal or intraretinal fluid should not decrease the suspicion of acute posterior multifocal placoid pigment epitheliopathy. Reabsorption of the fluid is usually accompanied by the improvement of the remaining anatomical changes and the visual function.