bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Transmission Mitigation Impact of Testing for Infectious Diseases
Authors: Middleton Casey , Larremore Daniel B. 
Published: September 2023

AbstractA fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE)—the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale—and a model that incorporates test specifications and usage, within-host pathogen dynamics, and human behaviors to estimate TE. Using TE to guide recommendations, we show that today’s rapid diagnostics should be used immediately upon symptom onset to control influenza A and respiratory syncytial virus (RSV), but delayed by up to 2d to control omicron-era SARS-CoV-2. Furthermore, while rapid tests are superior to RT-qPCR for control of founder-strain SARS-CoV-2, omicron-era changes in viral kinetics and rapid test sensitivity cause a reversal, with higher TE for RT-qPCR despite longer turnaround times. Finally, we illustrate the model’s flexibility by quantifying tradeoffs in the use of post-diagnosis testing to shorten isolation times.
Bi-directional communication between monocytes and trophoblasts under hypoxia and hypoxia-reperfusion conditions
Authors: Yankello Hannah , Lee Yerim , Megli Christina , Wayne Elizabeth 
Published: September 2023

AbstractIntroductionPregnancy-related disorders such as preeclampsia are associated with syncytiotrophoblast (STB) stress and monocyte dysregulation. It remains unclear whether this stress derives from prolonged placental hypoxia or a hypoxia-reperfusion-type injury. Thus, this study investigated how these two models of STB stress impact trophoblast-monocyte interactions.MethodCobalt chloride chemically induced hypoxia in BeWo b30 cells. A transwell coculture system was used to examine trophoblast-monocyte signaling. qPCR quantified gene expression changes following coculture. Monocyte phagocytosis ofE. Colior adhesion to placental cells was determined via flow cytometry. Monocyte migration to placental signals was quantified using a cell counter.ResultsCobalt chloride induced a hypoxic state in BeWo b30s. Reperfusion restored the expression of indirect hypoxia genes and ER stress genes. Coculturing THP-1 monocytes with normoxic, hypoxic, and hypoxic-reperfused BeWo b30s promoted b30 survival but not wound-healing capacity. Compared to hypoxic-reperfused BeWos, hypoxic cells increased monocyte adhesion and inflammatory gene expression, decreased monocyte phagocytosis, and did not change monocyte migration. Finally, placental signaling in early-onset PE decreased monocyte chemotaxis, but monocyte precondition more strongly influenced migration compared to placental state.DiscussionOverall, hypoxic placental signals most effectively recapitulate monocyte functional behavior observed in preeclampsia. Further research is needed to understand spatial and temporal changes in monocyte-trophoblast interactions and pregnancy outcomes. Monocyte chemotaxis to primary placental signals varied by gestational age, maternal diagnosis, and monocyte condition, implying monocytes could be used as functional biomarkers to predict their behavior at the maternal-fetal interface as well as the onset of disease.Abstract Figure
Recurrent activity within microcircuits of macaque dorsolateral prefrontal cortex tracks cognitive flexibility
Authors: Nolan Suzanne O , Melugin Patrick R , Erickson Kirsty R , Adams Wilson R , Farahbakhsh Zahra Z , Mcgonigle Colleen E , Kwon Michelle H , Costa Vincent D , Lapish Christopher C , Hackett Troy A , Cuzon Carlson Verginia C , Constantinidis Christos , Grant Kathleen A , Siciliano Cody A 
Published: September 2023

SummaryHuman and non-human primate data clearly implicate the dorsolateral prefrontal cortex (dlPFC) as critical for advanced cognitive functions1,2. It is thought that intracortical synaptic architectures within dlPFC are the integral neurobiological substrate that gives rise to these processes, including working memory, inferential reasoning, and decision-making3–7. In the prevailing model, each cortical column makes up one fundamental processing unit composed of dense intrinsic connectivity, conceptualized as the ‘canonical’ cortical microcircuit3,8. Each cortical microcircuit receives sensory and cognitive information from a variety of sources which are represented by sustained activity within the microcircuit, referred to as persistent or recurrent activity4,9. Via recurrent connections within the microcircuit, activity can propagate for a variable length of time, thereby allowing temporary storage and computations to occur locally before ultimately passing a transformed representation to a downstream output4,5,10. Competing theories regarding how microcircuit activity is coordinated have proven difficult to reconcilein vivowhere intercortical and intracortical computations cannot be fully dissociated5,9,11,12. Here, we interrogated the intrinsic features of isolated microcircuit networks using high-density calcium imaging of macaque dlPFCex vivo. We found that spontaneous activity is intrinsically maintained by microcircuit architecture, persisting at a high rate in the absence of extrinsic connections. Further, using perisulcal stimulation to evoke persistent activity in deep layers, we found that activity propagates through stochastically assembled intracortical networks, creating predictable population-level events from largely non-overlapping ensembles. Microcircuit excitability covaried with individual cognitive performance, thus anchoring heuristic models of abstract cortical functions within quantifiable constraints imposed by the underlying synaptic architecture.
Neuroplasticity of speech-in-noise processing in older adults assessed by functional near-infrared spectroscopy (fNIRS)
Authors: Mai Guangting , Jiang Zhizhao , Wang Xinran , Tachtsidis Ilias , Howell Peter 
Published: September 2023

AbstractFunctional near-infrared spectroscopy (fNIRS), a non-invasive optical neuroimaging technique that is portable and acoustically silent, has become a promising tool for evaluating auditory brain functions in hearing- vulnerable individuals. This study, for the first time, used fNIRS to evaluate neuroplasticity of speech-in-noise processing in older adults. Ten older adults, most of whom had moderate-to-mild hearing loss, participated in a 4-week speech-in-noise training. Their speech-in-noise performances and fNIRS brain responses to speech (auditory sentences in noise), non-speech (spectrally-rotated speech in noise) and visual (flashing chequerboards) stimuli were evaluated pre- (T0) and post-training (immediately after training, T1; and after a 4-week retention, T2). Behaviourally, speech-in-noise performances were improved after retention (T2 vs. T0) but not immediately after training (T1 vs. T0). Neurally, we intriguingly found brain responses to speech vs. non-speech decreased significantly in the left auditory cortex after retention (T2 vs. T0 and T2 vs. T1) for which we interpret as suppressed processing of background noise during speech listening alongside the significant behavioural improvements. Meanwhile, functional connectivity within and between multiple regions of temporal, parietal and frontal lobes was significantly enhanced in the speech condition after retention (T2 vs. T0). We also found neural changes before the emergence significant behavioural improvements. Compared to pre-training, responses to speech vs. non-speech in the left frontal/prefrontal cortex were decreased significantly both immediately after training (T1 vs. T0) and retention (T2 vs. T0), reflecting possible alleviation of listening efforts. Finally, connectivity was significantly decreased between auditory and higher-level non-auditory (parietal and frontal) cortices in response to visual stimuli immediately after training (T1 vs. T0), indicating decreased cross-modal takeover of speech-related regions during visual processing. The results thus showed that neuroplasticity can be observed not only at the same time, but alsobeforebehavioural changes in speech-in- noise perception. To our knowledge, this is the first fNIRS study to evaluate speech-based auditory neuroplasticity in older adults. It thus provides important implications for current research by illustrating the promises of detecting neuroplasticity using fNIRS in hearing-vulnerable individuals.
Bio-inspired mineralization collagen induce fibrocartilage regeneration after tendon-bone injury by activating Gli1+Dkk3+ progenitor cells
Authors: Zhang Tao , Lei Tingyun , Han Jie , Zhang Ru , Shen Weiliang , Liu Yi , Liao Youguo , Zhao Yanyan , Zhang Xianzhu , Yan Ruojin , He Qiulin , Chen Yangwu , Pan Haihua , Hongwei Ouyang , Wang Lingting , Yin Wei , Yin Zi , Xiao Chen 
Published: September 2023

SummaryA fibrocartilaginous connection between the tendon and bone, plays a critical role in transferring force from muscle to bone to enable joint movement. However, due to the high mechanical stress it experiences, the enthesis is vulnerable to injury and incapable of regenerating. The spatial relationship and functional basis of the principal components of the fibrocartilage - mineral and collagen - have not been clearly elucidated, which is a significant remaining gap in reconstructing complex architectures for promoting interface tissue regeneration. Here, using three-dimensional electron tomography imaging and high-resolution two-dimensional electron microscopy, we discover that mineral particles form a continuous cross-fibrillar phase within the fibrocartilage region. By developing a “floating mineralization” system, we fabricate a three-layer hydrogel that mimics the hierarchical nano- to micro-scale structure of tendon-bone interface (TBI). The middle layer is noteworthy for its resemblance to the nanostructure of fibrocartilage and its superior ability to induce mineralized fibrochondrogenesisin vitro. Based on motor function analysis, imaging diagnosis, histological staining, immunofluorescence staining, and biomechanics performance, we demonstrate that in situ transplantation of the gradient hydrogel achieved tendon-fibrocartilage-bone synchronous regeneration and result in 68% maximum mechanical recovery at 8-week postoperation. Single-cell RNA sequencing analysis reveals that a unique atlas of in situ stem/progenitor cells is generated during the TBI healingin vivo. Notably, the bio-inspired hydrogel microenvironment drived endogenous Gli1+Dkk3+progenitor cells, playing a key role in TBI regeneration. Therefore, we have successfully decoded and reconstructed the nanostructure of fibrocartilage, which has great potential in TBI regeneration.
Graph-Dynamo: Learning stochastic cellular state transition dynamics from single cell data
Authors: Zhang Yan , Qiu Xiaojie , Ni Ke , Weissman Jonathan , Bahar Ivet , Xing Jianhua 
Published: September 2023

AbstractModeling cellular processes in the framework of dynamical systems theories is a focused area in systems and mathematical biology, but a bottleneck to extend the efforts to genome-wide modeling is lack of quantitative data to constrain model parameters. With advances of single cell techniques, learning dynamical information from high throughput snapshot single cell data emerges as an exciting direction in single cell studies. Our previously developed dynamo framework reconstructs generally nonlinear genome-wide gene regulation relations from single cell expression state and either splicing- or metabolic labeling-based RNA velocity data. In this work, we first developed a graph-based machine learning procedure that imposes a mathematical constraint that the RNA velocity vectors lie in the tangent space of the low-dimensional manifold formed by the single cell expression data. Unlike a popular cosine correlation kernel used in literature, this tangent space projection (TSP) preserves the magnitude information of a vector when one transforms between different representations of the data manifold. Next, we formulated a data-driven graph Fokker-Planck (FPE) equation formalism that models the full cellular state transition dynamics as a convection-diffusion process on a data-formed graph network. The formalism is invariant under representation transformation and preserves the topological and dynamical properties of the system dynamics. Numerical tests on synthetic data and experimental scRNA-seq data demonstrate that the graph TSP/FPE formalism built from snapshot single cell data can recapitulate system dynamics.Significance StatementA cell is a dynamical system, which responds to extracellular and intracellular cues and changes its internal state. In practice the internal state of a cell is often characterized by its gene expression profile such as its transcriptome measured through destructive single cell techniques. Just like one can use Newton’s equations to describe motions of the celestial bodies in the solar system, the state change of a cell in principle can also be described by a set of mathematical equations. Determining the form and associated parameters of such equations, however, is challenging. This work presented a general framework of reconstructing dynamical equations from snapshot single cell data.
Longitudinal study ofChlamydia pecorumin a healthy Swiss cattle population
Authors: Loehrer Samuel , Hagenbuch Fabian , Marti Hanna , Pesch Theresa , Hässig Michael , Borel Nicole 
Published: September 2023

AbstractChlamydia pecorumis a globally endemic livestock pathogen but prevalence data from Switzerland has so far been limited. The present longitudinal study aimed to get an insight into theC. pecorumprevalence in Swiss cattle and investigated infection dynamics. The study population consisted of a bovine herd (n = 308) located on a farm in the north-eastern part of Switzerland. The herd comprised dairy cows, beef cattle and calves all sampled up to five times over a one-year period. At each sampling timepoint, rectal and conjunctival swabs were collected resulting in 782 samples per localization (total n = 1564).Chlamydiaceaescreening was performed initially, followed byC. pecorum-specific real-time qPCR on all samples. ForC. pecorum-positive samples, bacterial loads were determined. During this study,C. pecorumwas the only chlamydial species found. Animal prevalences included 5.2%-11.4%, 38.1%-61.5% and 55%-100% in dairy cows, beef cattle and calves, respectively. In all categories, the number ofC. pecorum-positive samples was higher in conjunctival (n = 151) compared to rectal samples (n = 65), however, the average rectal load was higher. At a younger age, the chlamydial prevalence and the mean bacterial loads were significantly higher. Of all sampled bovines, only 9.4% (29/308) were high shedders (number of copies per µl >1000). Calves, which tested positive multiple times, either failed to eliminate the pathogen between sampling timepoints or were reinfected, whereas dairy cows were mostly only positive at one timepoint. In conclusion,C. pecorumwas found in healthy Swiss cattle. Our observations suggested that infection takes place at an early age and immunity might develop over time. Although the gastrointestinal tract is supposed to be the main infection site,C. pecorumwas not present in rectal samples from dairy cows.
Class A capsid assembly modulator apoptotic elimination of hepatocytes with high HBV core antigen level in vivo is dependent on de novo core protein translation
Authors: Berke Jan Martin , Tan Ying , Sauviller Sarah , Wu Dai-tze , Zhang Ke , Conceição-Neto Nádia , Moreno Alfonso Blázquez , Kong Desheng , Kukolj George , Li Chris , Zhu Ren , Nájera Isabel , Pauwels Frederik 
Published: September 2023

ABSTRACTBackground and aimsCapsid assembly (CA) is a critical step in the hepatitis B virus (HBV) life cycle, mediated by the viral core protein. CA is the target for various new anti-viral candidate therapeutics known as capsid assembly modulators (CAMs) of which the CAM-aberrant (CAM-A) class induces aberrant shaped core protein structures and lead to hepatocyte cell death. The aim of the studies was to identify the mechanism of action of the CAM-A modulators leading to HBV infected hepatocyte elimination.MethodsThe CAM-A mediated mechanism of HBsAg reduction was evaluated in vitro in a stable HBV replicating cell line and in vivo in AAV-HBV transduced C57BL/6, C57BL/6 SCID and HBV-infected chimeric mice with humanized livers.ResultsIn vivo treatment with CAM-A modulators induced pronounced reductions in HBe- and HBsAg which were associated with a transient increase in ALT. Both HBs- and HBeAg reduction and ALT increase were delayed in C57BL/6 SCID and chimeric mice, suggesting that adaptive immune responses may indirectly contribute to this phenotype. However, depletion of CD8+ T-cells in transduced wild-type mice did not have a negative impact on antigen reduction, indicating that CD8+ T-cell responses are not essential.Coinciding with the transient ALT elevation in AAV-HBV transduced mice, we observed a transient increase in markers related to endoplasmic reticulum stress and apoptosis as well as cytokines related to apoptosis pathways, followed by the detection of a proliferation marker. Pathway enrichment analysis of microarray data revealed that antigen presentation pathway (MHC-I) was upregulated, overlapping with observed apoptosis. Combination treatment with HBV-specific siRNA demonstrated that CAM-A mediated HBsAg reduction is dependent on de novo core protein translation and that the effect is dependent on high levels of core protein expression, which will likely focus the CHB sub-population that could respond.ConclusionCAM-A treatment eradicates HBV infected hepatocytes with high core protein levels through the induction of apoptosis a promising approach as part of a regimen to achieve functional cure.Lay summaryTreatment with hepatitis B virus (HBV) capsid assembly modulators that induce the formation of aberrant HBV core protein structures (CAM-A) leads to programmed cell death, apoptosis, of HBV-infected hepatocytes and subsequent reduction of HBV antigens, which differentiates CAM-A from other CAMs. The effect is dependent on thede novosynthesis and high levels of core protein.
ATE1 activates ER-stress and UPR pathways in glioblastoma
Authors: Macedo-da-Silva Janaina , Oba-Shinjo Sueli Mieko , Rosa-Fernandes Lívia , Soares Roseli da Silva , Lerario Antonio Marcondes , Moretti Isabele Fattoti , Laurentino Talita de Sousa , Cintra Ricardo Cesar , Marie Suely Kazue Nagahashi , Palmisano Giuseppe 
Published: September 2023

ABSTRACTPost-translational modifications (PTM) have been recognized as a relevant regulation of key processes in cancer pathophysiology, such as cell migration, adhesion, and proliferation. N-terminal protein arginylation is an emerging PTM involved in tumor progression; however, the mechanisms by which this modification influences these events are poorly understood and vary according to cancer type. Glioblastoma (GBM) is an aggressive intra-axial brain tumor associated with poor prognosis, low survival, and high recurrence rate. We performed a study combiningin silico,in vitro, and patients samples analysis to understand the impact of N-terminal protein arginylation in GBM, including overexpression and silencing ofATE1in GBM-U87MG cell line with RNASeq analysis, immunofluorescence, and validation of the identified targets at the protein level by immunoblotting. The arginylation pattern differed in GBM compared with non-neoplastic brain tissues, and upregulation of ATE1 was associated with increased tumor cell proliferation. We identified a strong activation of the unfolded protein response (UPR) pathway associated with increased ATE1 level, inducing autophagy and not apoptosis. Protein arginylation in GBM proved to be an important mechanism for tumor growth, with the recycling of cell substrates by autophagy, providing fitness for tumor cells. The expressions of the main markers of UPR and autophagy pathways were validated in human GBM samples, reinforcing the role of ATE1 in the most aggressive brain tumor.
Predicting Chinese stock prices using convertible bond: an evidence-based neural network approach
Authors: Maneejuk Paravee , Zou Binxiong , Yamaka Woraphon 
Published: September 2023

PurposeThe primary objective of this study is to investigate whether the inclusion of convertible bond prices as important inputs into artificial neural networks can lead to improved accuracy in predicting Chinese stock prices. This novel approach aims to uncover the latent potential inherent in convertible bond dynamics, ultimately resulting in enhanced precision when forecasting stock prices.Design/methodology/approachThe authors employed two machine learning models, namely the backpropagation neural network (BPNN) model and the extreme learning machine neural networks (ELMNN) model, on empirical Chinese financial time series data.FindingsThe results showed that the convertible bond price had a strong predictive power for low-market-value stocks but not for high-market-value stocks. The BPNN algorithm performed better than the ELMNN algorithm in predicting stock prices using the convertible bond price as an input indicator for low-market-value stocks. In contrast, ELMNN showed a significant decrease in prediction accuracy when the convertible bond price was added.Originality/valueThis study represents the initial endeavor to integrate convertible bond data into both the BPNN model and the ELMNN model for the purpose of predicting Chinese stock prices.
Activity-based working and their impact on organisational culture – employees’ perspectives
Authors: Nanayakkara Kusal , Wilkinson Sara Jane , Halvitigala Dulani 
Published: September 2023

Purpose
This paper aims to examine how the existing organisational culture of organisations changed with the introduction of activity-based working (ABW) office layouts from the employees’ perspectives.

Design/methodology/approach
A questionnaire was used to measure the influence of introducing ABW. The study focused on three different industry sectors in Australia – financial, IT and government – and one organisation from each sector who had introduced ABW during the period of 2012–2019 was selected. The Competing Value Framework was used to measure the dimensions of organisational culture. A paired sample test was used to measure the changes in employees’ perceptions after the layout changes.

Findings
Findings identify that the nature of workplace designs has a considerable impact on an organisation’s corporate culture which can be used to leverage and change its culture. However, some noticeable discrepancy between the perceptions of public and private sector employees was identified, where public sector employees felt that standardised procedures still governed their actions even in ABW layouts.

Originality/value
This research highlights that workplace designs directly influence culture by supporting the engagement, motivation and behaviours of the employees. It emphasises the importance of in-depth examination of the behavioural and attitudinal characteristics of employees to obtain a better understanding of how they interact in ABW layouts. Such an analysis provides the context for a more inclusive understanding of the operation of modern office layouts.