bluuebunny/crossref_metadata_2025 huggingface dataset:
CircLIFR suppresses hepatocellular carcinoma progression by sponging miR-624-5p and inactivating the GSK-3β/β-catenin signaling pathway
Authors: Yang Lei , Tan Wenliang , Wei Yingcheng , Xie Zhiqin , Li Wenxin , Ma Xiaowu , Wang Qingbin , Li Huilong , Zhang Ziyu , Shang Changzhen , Chen Yajin
Published: May 2022

Circular RNAs have been reported to play essential roles in the tumorigenesis and progression of various cancers. However, the biological processes and mechanisms involved in hepatocellular carcinoma (HCC) remain unclear. Initial RNA-sequencing data and qRT-PCR results in our cohort showed that hsa_circ_0072309 (also called circLIFR) was markedly downregulated in HCC tissues. Kaplan–Meier analysis indicated that higher levels of circLIFR in HCC patients correlated with favorable overall survival and recurrence-free survival rates. Both in vitro and in vivo experiments indicated that circLIFR inhibited the proliferation and invasion abilities of HCC cells. We therefore conducted related experiments to explore the mechanism of circLIFR in HCC. Fluorescence in situ hybridization results revealed that circLIFR was mainly located in the cytoplasm, and RNA immunoprecipitation assays indicated that circLIFR was significantly enriched by Ago2 protein. These results suggested that circLIFR may function as a sponge of miRNAs to regulate HCC progression. We further conducted bioinformatics prediction as well as dual-luciferase reporter assays, and the results of which showed that circLIFR could sponge miR-624-5p to stabilize glycogen synthase kinase 3β (GSK-3β) expression. Loss and gain of function experiments demonstrated that regulation of the expression of miR-624-5p or GSK-3β markedly affected HCC progression induced by circLIFR. Importantly, we also proved that circLIFR could facilitate the degradation of β-catenin and prevent its translocation to the nucleus in HCC cells. Overall, our study demonstrated that circLIFR acts as a tumor suppressor in HCC by regulating miR-624-5p and inactivating the GSK-3β/β-catenin signaling pathway.
piR-823 inhibits cell apoptosis via modulating mitophagy by binding to PINK1 in colorectal cancer
Authors: Wang Shuling , Jiang Xiaoyu , Xie Xiaoli , Yin Jie , Zhang Jiuna , Liu Ting , Chen Shujia , Wang Yijun , Zhou Xue , Wang Yongjuan , Cui Ruolin , Jiang Huiqing
Published: May 2022

Mitophagy plays a vital role in the maintenance of mitochondrial homeostasis and tumorigenesis. Noncoding RNA piR-823 contributes to colorectal tumorigenesis. In this study, we aim to evaluate piR-823-mediated mitophagy and its mechanistic association with colorectal cancer (CRC). Digital gene expression analysis was performed to explore the potential functions of piR-823. A piR-823 antagomir (Ant-823) was used to inhibit piR-823 expression, and piR-823 mimics (mimics-823) were used to increase piR-823 expression. Mitophagy was measured in vivo and in vitro by immunofluorescence and western blot analysis. JC-1 staining, ATP production, real-time PCR, and western blot analysis were used to measure changes in mitochondrial quality and number. siRNA transfection was used to inhibit mitophagy, and CCCP was used to induce mitophagy. RNA pull-down assays and RNA-binding protein immunoprecipitation assays were conducted to investigate the molecular mechanisms. Here, we found that CRC cells transfected with Ant-823 presented an altered expression of autophagic and mitophagy genes by Digital gene expression analysis. Ant-823 could promote Parkin activation and mitophagy in vitro and in vivo, followed by mitochondrial loss and dysfunction of some mitochondria, whereas mimics-823 exerted the opposite effects in CRC cells. The inhibition of mitophagy by siParkin alleviated Ant-823-induced mitochondrial loss and dysfunction, as well as apoptosis to a certain extent. Furthermore, piR-823 was found to interact with PINK1 and promote its ubiquitination and proteasome-dependent degradation, thus alleviating mitophagy. Finally, these findings were verifed in samples obtained by patients affected by colorectal cancer. In conclusion, we identify a novel mechanism by which piR-823 regulates mitophagy during CRC tumorigenesis by increasing PINK1 degradation.
Intelligent wireless theranostic contact lens for electrical sensing and regulation of intraocular pressure
Authors: Yang Cheng , Wu Qianni , Liu Junqing , Mo Jingshan , Li Xiangling , Yang Chengduan , Liu Ziqi , Yang Jingbo , Jiang Lelun , Chen Weirong , Chen Hui-jiuan , Wang Ji , Xie Xi
Published: May 2022

Engineering wearable devices that can wirelessly track intraocular pressure and offer feedback-medicine administrations are highly desirable for glaucoma treatments, yet remain challenging due to issues of limited sizes, wireless operations, and wireless cross-coupling. Here, we present an integrated wireless theranostic contact lens for in situ electrical sensing of intraocular pressure and on-demand anti-glaucoma drug delivery. The wireless theranostic contact lens utilizes a highly compact structural design, which enables high-degreed integration and frequency separation on the curved and limited surface of contact lens. The wireless intraocular pressure sensing modulus could ultra-sensitively detect intraocular pressure fluctuations, due to the unique cantilever configuration design of capacitive sensing circuit. The drug delivery modulus employs an efficient wireless power transfer circuit, to trigger delivery of anti-glaucoma drug into aqueous chamber via iontophoresis. The minimally invasive, smart, wireless and theranostic features endow the wireless theranostic contact lens as a highly promising system for glaucoma treatments.
Human-ignited fires result in more extreme fire behavior and ecosystem impacts
Authors: Hantson Stijn , Andela Niels , Goulden Michael L. , Randerson James T.
Published: May 2022

California has experienced a rapid increase in burned area over the past several decades. Although fire behavior is known to be closely tied to ecosystem impacts, most analysis of changing fire regimes has focused solely on area burned. Here we present a standardized database of wildfire behavior, including daily fire rate-of-spread and fire radiative power for large, multiday wildfires in California during 2012–2018 using remotely-sensed active fire observations. We observe that human-ignited fires start at locations with lower tree cover and during periods with more extreme fire weather. These characteristics contribute to more explosive growth in the first few days following ignition for human-caused fires as compared to lightning-caused fires. The faster fire spread, in turn, yields a larger ecosystem impact, with tree mortality more than three times higher for fast-moving fires (>1 km day−1) than for slow moving fires (<0.5 km day−1). Our analysis shows how human-caused fires can amplify ecosystem impacts and highlights the importance of limiting human-caused fires during period of extreme fire weather for meeting forest conservation targets under scenarios of future change.
Cortical Cyclin A controls spindle orientation during asymmetric cell divisions in Drosophila
Authors: Darnat Pénélope , Burg Angélique , Sallé Jérémy , Lacoste Jérôme , Louvet-Vallée Sophie , Gho Michel , Audibert Agnès
Published: May 2022

The coordination between cell proliferation and cell polarity is crucial to orient the asymmetric cell divisions to generate cell diversity in epithelia. In many instances, the Frizzled/Dishevelled planar cell polarity pathway is involved in mitotic spindle orientation, but how this is spatially and temporally coordinated with cell cycle progression has remained elusive. Using Drosophila sensory organ precursor cells as a model system, we show that Cyclin A, the main Cyclin driving the transition to M-phase of the cell cycle, is recruited to the apical-posterior cortex in prophase by the Frizzled/Dishevelled complex. This cortically localized Cyclin A then regulates the orientation of the division by recruiting Mud, a homologue of NuMA, the well-known spindle-associated protein. The observed non-canonical subcellular localization of Cyclin A reveals this mitotic factor as a direct link between cell proliferation, cell polarity and spindle orientation.
Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences
Authors: Luo Zhiyuan , Zhang Jiacheng , Fei Jingyi , Ke Shengdong
Published: May 2022

The N6-methyladenosine (m6A) modification is deposited to nascent transcripts on chromatin, but its site-specificity mechanism is mostly unknown. Here we model the m6A deposition to pre-mRNA by iM6A (intelligent m6A), a deep learning method, demonstrating that the site-specific m6A methylation is primarily determined by the flanking nucleotide sequences. iM6A accurately models the m6A deposition (AUROC = 0.99) and uncovers surprisingly that the cis-elements regulating the m6A deposition preferentially reside within the 50 nt downstream of the m6A sites. The m6A enhancers mostly include part of the RRACH motif and the m6A silencers generally contain CG/GT/CT motifs. Our finding is supported by both independent experimental validations and evolutionary conservation. Moreover, our work provides evidences that mutations resulting in synonymous codons can affect the m6A deposition and the TGA stop codon favors m6A deposition nearby. Our iM6A deep learning modeling enables fast paced biological discovery which would be cost-prohibitive and unpractical with traditional experimental approaches, and uncovers a key cis-regulatory mechanism for m6A site-specific deposition.
Targeted detection of cancer at the cellular level during biopsy by near-infrared confocal laser endomicroscopy
Authors: Kennedy Gregory T. , Azari Feredun S. , Bernstein Elizabeth , Nadeem Bilal , Chang Ashley , Segil Alix , Carlin Sean , Sullivan Neil T. , Encarnado Emmanuel , Desphande Charuhas , Kularatne Sumith , Gagare Pravin , Thomas Mini , Kucharczuk John C. , Christien Gaetan , Lacombe Francois , Leonard Kaela , Low Philip S. , Criton Aline , Singhal Sunil
Published: May 2022

Suspicious nodules detected by radiography are often investigated by biopsy, but the diagnostic yield of biopsies of small nodules is poor. Here we report a method—NIR-nCLE—to detect cancer at the cellular level in real-time during biopsy. This technology integrates a cancer-targeted near-infrared (NIR) tracer with a needle-based confocal laser endomicroscopy (nCLE) system modified to detect NIR signal. We develop and test NIR-nCLE in preclinical models of pulmonary nodule biopsy including human specimens. We find that the technology has the resolution to identify a single cancer cell among normal fibroblast cells when co-cultured at a ratio of 1:1000, and can detect cancer cells in human tumors less than 2 cm in diameter. The NIR-nCLE technology rapidly delivers images that permit accurate discrimination between tumor and normal tissue by non-experts. This proof-of-concept study analyzes pulmonary nodules as a test case, but the results may be generalizable to other malignancies.
Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction
Authors: Wang Jingyao , Zhang Shihe , Lu Hongfang , Xu Heng
Published: May 2022

Many eukaryotic genes contain alternative promoters with distinct expression patterns. How these promoters are differentially regulated remains elusive. Here, we apply single-molecule imaging to quantify the transcriptional regulation of two alternative promoters (P1 and P2) of the Bicoid (Bcd) target gene hunchback in syncytial blastoderm Drosophila embryos. Contrary to the previous notion that Bcd only activates P2, we find that Bcd activates both promoters via the same two enhancers. P1 activation is less frequent and requires binding of more Bcd molecules than P2 activation. Using a theoretical model to relate promoter activity to enhancer states, we show that the two promoters follow common transcription kinetics driven by sequential Bcd binding at the two enhancers. Bcd binding at either enhancer primarily activates P2, while P1 activation relies more on Bcd binding at both enhancers. These results provide a quantitative framework for understanding the kinetic mechanisms of complex eukaryotic gene regulation.
Zeolite-confined subnanometric PtSn mimicking mortise-and-tenon joinery for catalytic propane dehydrogenation
Authors: Ma Sicong , Liu Zhi-Pan
Published: May 2022

Heterogeneous catalysts are often composite materials synthesized via several steps of chemical transformation, and thus the atomic structure in composite is a black-box. Herein with machine-learning-based atomic simulation we explore millions of structures for MFI zeolite encapsulated PtSn catalyst, demonstrating that the machine-learning enhanced large-scale potential energy surface scan offers a unique route to connect the thermodynamics and kinetics within catalysts’ preparation procedure. The functionalities of the two stages in catalyst preparation are now clarified, namely, the oxidative clustering and the reductive transformation, which form separated Sn4O4 and PtSn alloy clusters in MFI. These confined clusters have high thermal stability at the intersection voids of MFI because of the formation of “Mortise-and-tenon Joinery”. Among, the PtSn clusters with high Pt:Sn ratios (>1:1) are active for propane dehydrogenation to propene, ∼103 in turnover-of-frequency greater than conventional Pt3Sn metal. Key recipes to optimize zeolite-confined metal catalysts are predicted.
Robust and tunable Weyl phases by coherent infrared phonons in ZrTe5
Authors: Aryal Niraj , Jin Xilian , Li Qiang , Liu Mengkun , Tsvelik A. M. , Yin Weiguo
Published: May 2022

Ultrafast control of structural and electronic properties of various quantum materials has recently sparked great interest. In particular, photoinduced switching between distinct topological phases has been considered a promising route to realize quantum computers. Here we use first-principles and effective Hamiltonian methods to show that in ZrTe5, lattice distortions corresponding to all three types of zone-center infrared optical phonon modes can drive the system from a topological insulator to a Weyl semimetal. Thus achieved Weyl phases are robust, highly tunable, and one of the cleanest due to the proximity of the Weyl points to the Fermi level and a lack of other carriers. We also find that Berry curvature dipole moment, induced by the dynamical inversion symmetry breaking, gives rise to various nonlinear effects that oscillate with the amplitude of the phonon modes. These nonlinear effects present an ultrafast switch for controlling the Weyltronics-enabled quantum system.
Chromatin structure predicts survival in glioma patients
Authors: Garrett Matthew C. , Albano Rebecca , Carnwath Troy , Shah Sanjit , Woo Daniel , Lamba Michael , Plas David R. , Paranjpe Aditi , Roskin Krishna , Zhao Chuntao , Lu Richard
Published: May 2022

The pathological changes in epigenetics and gene regulation that accompany the progression of low-grade to high-grade gliomas are under-studied. The authors use a large set of paired atac-seq and RNA-seq data from surgically resected glioma specimens to infer gene regulatory relationships in glioma. Thirty-eight glioma patient samples underwent atac-seq sequencing and 16 samples underwent additional RNA-seq analysis. Using an atac-seq/RNA-seq correlation matrix, atac-seq peaks were paired with genes based on high correlation values (|r2| > 0.6). Samples clustered by IDH1 status but not by grade. Surprisingly there was a trend for IDH1 mutant samples to have more peaks. The majority of peaks are positively correlated with survival and positively correlated with gene expression. Constructing a model of the top six atac-seq peaks created a highly accurate survival prediction model (r2 = 0.68). Four of these peaks were still significant after controlling for age, grade, pathology, IDH1 status and gender. Grade II, III, and IV (primary) samples have similar transcription factors and gene modules. However, grade IV (recurrent) samples have strikingly few peaks. Patient-derived glioma cultures showed decreased peak counts following radiation indicating that this may be radiation-induced. This study supports the notion that IDH1 mutant and IDH1 wildtype gliomas have different epigenetic landscapes and that accessible chromatin sites mapped by atac-seq peaks tend to be positively correlated with expression. The data in this study leads to a new model of treatment response wherein glioma cells respond to radiation therapy by closing open regions of DNA.
A neuromuscular model of human locomotion combines spinal reflex circuits with voluntary movements
Authors: Ramadan Rachid , Geyer Hartmut , Jeka John , Schöner Gregor , Reimann Hendrik
Published: May 2022

Existing models of human walking use low-level reflexes or neural oscillators to generate movement. While appropriate to generate the stable, rhythmic movement patterns of steady-state walking, these models lack the ability to change their movement patterns or spontaneously generate new movements in the specific, goal-directed way characteristic of voluntary movements. Here we present a neuromuscular model of human locomotion that bridges this gap and combines the ability to execute goal directed movements with the generation of stable, rhythmic movement patterns that are required for robust locomotion. The model represents goals for voluntary movements of the swing leg on the task level of swing leg joint kinematics. Smooth movements plans towards the goal configuration are generated on the task level and transformed into descending motor commands that execute the planned movements, using internal models. The movement goals and plans are updated in real time based on sensory feedback and task constraints. On the spinal level, the descending commands during the swing phase are integrated with a generic stretch reflex for each muscle. Stance leg control solely relies on dedicated spinal reflex pathways. Spinal reflexes stimulate Hill-type muscles that actuate a biomechanical model with eight internal joints and six free-body degrees of freedom. The model is able to generate voluntary, goal-directed reaching movements with the swing leg and combine multiple movements in a rhythmic sequence. During walking, the swing leg is moved in a goal-directed manner to a target that is updated in real-time based on sensory feedback to maintain upright balance, while the stance leg is stabilized by low-level reflexes and a behavioral organization switching between swing and stance control for each leg. With this combination of reflex-based stance leg and voluntary, goal-directed control of the swing leg, the model controller generates rhythmic, stable walking patterns in which the swing leg movement can be flexibly updated in real-time to step over or around obstacles.
Age-related cognitive effects of the COVID-19 pandemic restrictions and associated mental health changes in Germans
Authors: Menze Inga , Mueller Patrick , Mueller Notger G. , Schmicker Marlen
Published: May 2022

Restrictive means to reduce the spread of the COVID-19 pandemic have not only imposed broad challenges on mental health but might also affect cognitive health. Here we asked how restriction-related changes influence cognitive performance and how age, perceived loneliness, depressiveness and affectedness by restrictions contribute to these effects. 51 Germans completed three assessments of an online based study during the first lockdown in Germany (April 2020), a month later, and during the beginning of the second lockdown (November 2020). Participants completed nine online cognitive tasks of the MyBrainTraining and online questionnaires about their perceived strain and impact on lifestyle factors by the situation (affectedness), perceived loneliness, depressiveness as well as subjective cognitive performance. The results suggested a possible negative impact of depressiveness and affectedness on objective cognitive performance within the course of the lockdown. The younger the participants, the more pronounced these effects were. Loneliness and depressiveness moreover contributed to a worse evaluation of subjective cognition. In addition, especially younger individuals reported increased distress. As important educational and social input has partly been scarce during this pandemic and mental health problems have increased, future research should also assess cognitive long-term consequences.
Helical Indexing in Real Space
Authors: Sun Chen , Gonzalez Brenda , Jiang Wen
Published: May 2022

Biological structures with helical symmetries of distinct twist, rise, and axial symmetry are abundant and span a wide range of organisms and functions. Performing de novo helical indexing remains challenging because of the steep learning curve involved in Fourier space layer lines. The unknown amount of out-of-plane tilt and the existence of multiple conformations of the helices further complicate indexing. In this work, we introduce a real-space indexing method that leverages the prior knowledge of the tilt and in-plane angles of the helical filaments/tubes, robust ab initio 3D reconstruction capabilities in single particle cryo-EM to obtain asymmetric reconstructions, and automatic indexing of helical parameters directly from the asymmetric density maps. We validated this approach using data from multiple helical structures of distinct helical symmetries, diameters, flexibility, data qualities, and heterogeneous states. The fully automated tool we introduce for real space indexing, HI3D, uses the 2D lattice in the autocorrelation of the cylindrical projection of a 3D density map to identify the helical symmetry. HI3D can often successfully determine the helical parameters of a suboptimal 3D density map, including ab initio single particle asymmetric reconstructions and sub-tomogram averages, with intermediate evidence that can also help assess the map quality. Furthermore, this open-source HI3D is usable independently as a Web application that can be accessed free of installation. With these methods, de novo helical indexing will be significantly more accessible to researchers investigating structures of helical filaments/tubes using cryo-EM.
Conventional and digital Ki67 evaluation and their correlation with molecular prognosis and morphological parameters in luminal breast cancer
Authors: Pons Laura , Hernández-León Laura , Altaleb Ahmad , Ussene Esperança , Iglesias Roman , Castillo Ana , Rodríguez-Martínez Paula , Castella Eva , Quiroga Vanesa , Felip Eudald , Cirauqui Beatriz , Margelí Mireia , Fernández Pedro Luis
Published: May 2022

Digital counting methods were developed to decrease the high intra- and inter-observer variability of immunohistochemical markers such as Ki67, with most presenting a good correlation coefficient (CC). Since Ki67 is one of the major contributors to Oncotype DX, it is conceivable that Ki67 expression and the recurrence score (RS) obtained by the multigene panel are positively correlated. We decided first to test to what extent conventional and digital Ki67 quantification methods correlate in daily practice and, second, to determine which of these methods correlates better with the prognostic capacity of the Oncotype DX test. Both Ki67 evaluations were performed in 89 core biopsies with a diagnosis of estrogen receptor (ER) positive HER2-negative breast cancer (BC). Cases were, thus, classified twice for surrogate subtype: first by conventional analysis and then by digital evaluation. The Oncotype RS was obtained in 55 cases that were subsequently correlated to Ki67 evaluation by both methods. Conventional and digital Ki67 evaluation showed good concordance and correlation (CC = 0.81 (95% CI 0.73–0.89)). The correlation of Oncotype DX risk groups and surrogate derived subtypes was slightly higher for the digital technique (rs = 0.46, p < 0.01) compared to the conventional method (rs = 0.39, p < 0.01), even though both were statistically significant. In conclusion, we show that digital evaluation could be an alternative to conventional counting, and also has advantages for predicting the risk established by the Oncotype DX test in ER-positive BC. This study also supports the importance of an accurate Ki67 analysis which can influence the decision to submit ER-positive HER2-negative BC to prognostic molecular platforms.
Characterising the unity and diversity of executive functions in a within-subject fMRI study
Authors: Saylik Rahmi , Williams Adrian L. , Murphy Robin A. , Szameitat Andre J.
Published: May 2022

Behavioural studies investigating the relationship between Executive Functions (EFs) demonstrated evidence that different EFs are correlated with each other, but also that they are partially independent from each other. Neuroimaging studies investigating such an interrelationship with respect to the functional neuroanatomical correlates are sparse and have revealed inconsistent findings. To address this question, we created four tasks derived from the same basic paradigm, one each for updating, inhibition, switching, and dual-tasking. We assessed brain activity through functional magnetic resonance imaging (fMRI) in twenty-nine participants while they performed the four EF tasks plus control tasks. For the analysis, we first determined the neural correlates of each EF by subtracting the respective control tasks from the EF tasks. We tested for unity in EF tasks by calculating the conjunction across these four “EF-minus-control” contrasts. This identified common areas including left lateral frontal cortices [middle and superior frontal gyrus (BA 6)], medial frontal cortices (BA 8) as well as parietal cortices [inferior and superior parietal lobules (BA 39/7)]. We also observed areas activated by two or three EF tasks only, such as frontoparietal areas [e.g., SFG (BA8) right inferior parietal lobule (BA 40), left precuneus (BA 7)], and subcortical regions [bilateral thalamus (BA 50)]. Finally, we found areas uniquely activated for updating [bilateral MFG (BA 8) and left supramarginal gyrus (BA 39)], inhibition (left IFG BA 46), and dual-tasking [left postcentral gyrus (BA 40)]. These results demonstrate that the functional neuroanatomical correlates of the four investigated EFs show unity as well as diversity.
Developmental differences in the impact of perceptual salience on short-term memory performance and meta-memory skills
Authors: Pedale Tiziana , Mastroberardino Serena , Capurso Michele , Macrì Simone , Santangelo Valerio
Published: May 2022

In everyday life, individuals are surrounded by many stimuli that compete to access attention and memory. Evidence shows that perceptually salient stimuli have more chances to capture attention resources, thus to be encoded into short-term memory (STM). However, the impact of perceptual salience on STM at different developmental stages is entirely unexplored. Here we assessed STM performance and meta-memory skills of 6, 10, and 18 years-old participants (total N = 169) using a delayed match-to-sample task. On each trial, participants freely explored a complex (cartoon-like) scene for 4 s. After a retention interval of 4 s, they discriminated the same/different position of a target-object extracted from the area of maximal or minimal salience of the initially-explored scene. Then, they provided a confidence judgment of their STM performance, as an index of meta-memory skills. When taking into account ‘confident’ responses, we found increased STM performance following targets at maximal versus minimal salience only in adult participants. Similarly, only adults showed enhanced meta-memory capabilities following maximal versus minimal salience targets. These findings documented a late development in the impact of perceptual salience on STM performance and in the improvement of metacognitive capabilities to properly judge the content of one’s own memory representation.
Pseudorapidity dependence of the bulk properties of hadronic medium in pp collisions at 7 TeV
Authors: Ajaz Muhammad , Haj Ismail Abd Al Karim , Waqas Muhammad , Suleymanov Mais , AbdelKader Atef , Suleymanov Rustam
Published: May 2022

The measured charged particle $$p_T$$

p
T

spectra in proton-proton collisions obtained by the CMS experiment at CERN is compared with the simulation results of EPOS–LHC and Pythia8.24 models at 7 TeV center-of-mass energy. The Pythia8.24 model describes the experimental data very well, particularly in the high $$p_T$$

p
T

region. The model also predicts the $$p_T$$

p
T

spectra for $$|$$
|
$$\eta $$
η
$$|$$
|
< 2.4 at 0 $$\le $$
≤
$$p_T$$

p
T

$$\le $$
≤
6 $$\text {GeV/}c$$

GeV/
c

. The EPOS–LHC model underpredicts the $$p_T$$

p
T

spectra from 0.1 to 2 $$\text {GeV/}c$$

GeV/
c

in all $$\eta $$
η
bins for about 20% and the $$p_T$$

p
T

spectrum from 0.1 to 4.2 $$\text {GeV/}c$$

GeV/
c

for $$|$$
|
$$\eta $$
η
$$|$$
|
< 2.4 by about 15% while reasonably predicts well for $$p_T$$

p
T

> 4.2 $$\text {GeV/}c$$

GeV/
c

within the experimental errors. Furthermore, to get information about collective properties of the hadronic matter, modified Hagedorn function with embedded transverse flow velocity and thermodynamically consistent Tsallis distribution functions are used to fit the experimental data and simulated results. The values of $$\chi ^2/ndf$$

χ
2

/
n
d
f

show that the functions fit the data and simulation results well. The parameter extracted by the functions: $$\beta _T$$

β
T

, $$T_0$$

T
0

, and $$T_{eff}$$

T

eff

decreases with increasing $$\eta $$
η
. The decrease in $$\beta _T$$

β
T

with increasing $$\eta $$
η
is due to the large energy deposition in lower rapidity bins producing rapid expansion due to large pressure gradient resulting quick expansion of the fireball. Similarly, large energy transfer in the lower pseudo-rapidity bin results in higher degree of excitation of the system which results larger values of $$T_0$$

T
0

and $$T_{eff}$$

T

eff

. The values of the fit constant $$N_0$$

N
0

increase with $$\eta $$
η
where the values of $$N_0$$

N
0

extracted from Pythia8.24 are closer to the data than the EPOS–LHC model. The Pythia8.24 model has better prediction than the EPOS–LHC model which might be connected to its flow-like features and color re-connections resulting from different Parton interactions in the initial and final state.
Oyster reef restoration facilitates the recovery of macroinvertebrate abundance, diversity, and composition in estuarine communities
Authors: Searles Adam R. , Gipson Emily E. , Walters Linda J. , Cook Geoffrey S.
Published: May 2022

Historic declines in oyster populations have resulted in diminished production of ecosystem services and habitat function in many estuaries. Due to the important role of oysters in ecosystem function, scientists and resource managers have employed oyster reef restoration to mitigate declines, recover essential ecosystem services, and better habitat function. Yet, there are knowledge gaps regarding the impact of restoration efforts on ecologically valuable mid-trophic level organisms inhabiting these systems. To address this knowledge gap, here we quantify macroinvertebrate species abundance, community diversity, and composition on experimental restored oyster reefs before and after restoration, and from live (positive control) and dead (negative control) reefs in the Indian River Lagoon, Florida. Species diversity and composition on restored reefs shifted towards states similar to live (positive control) reefs within 12 months of restoration. Recovery of species abundance occurred within 18 months of restoration. The results presented herein quantify the effect of restoration on resident macroinvertebrates and provide timelines of recovery for each attribute of these communities. Further, this study presents an actionable and transferable framework for identifying effective single-species metrics of restoration success across ecosystems. The application of this framework will provide managers and researchers with tools to improve the efficiency and efficacy of post-restoration monitoring. By doing so, this study contributes significantly to the improvement of broader restoration practices in an era of unprecedented habitat loss.
Vagus nerve stimulation using a miniaturized wirelessly powered stimulator in pigs
Authors: Habibagahi Iman , Omidbeigi Mahmoud , Hadaya Joseph , Lyu Hongming , Jang Jaeeun , Ardell Jeffrey L. , Bari Ausaf A. , Babakhani Aydin
Published: May 2022

Neuromodulation of peripheral nerves has been clinically used for a wide range of indications. Wireless and batteryless stimulators offer important capabilities such as no need for reoperation, and extended life compared to their wired counterparts. However, there are challenging trade-offs between the device size and its operating range, which can limit their use. This study aimed to examine the functionality of newly designed wirelessly powered and controlled implants in vagus nerve stimulation for pigs. The implant used near field inductive coupling at 13.56 MHz industrial, scientific, and medical band to harvest power from an external coil. The circular implant had a diameter of 13 mm and weighed 483 mg with cuff electrodes. The efficiency of the inductive link and robustness to distance and misalignment were optimized. As a result, the specific absorption rate was orders of magnitude lower than the safety limit, and the stimulation can be performed using only 0.1 W of external power. For the first time, wireless and batteryless VNS with more than 5 cm operation range was demonstrated in pigs. A total of 84 vagus nerve stimulations (10 s each) have been performed in three adult pigs. In a quantitative comparison of the effectiveness of VNS devices, the efficiency of systems on reducing heart rate was similar in both conventional (75%) and wireless (78.5%) systems. The pulse width and frequency of the stimulation were swept on both systems, and the response for physiological markers was drawn. The results were easily reproducible, and methods used in this study can serve as a basis for future wirelessly powered implants.
The effect of melatonin on the mouse ameloblast-lineage cell line ALCs
Authors: Pan Jing , Ren Qianhui , Yang Zhao , Guo Ying , Kwon Kubin , Shen Checheng , Wang Yueying , Ji Fang
Published: May 2022

Melatonin plays a critical role in promoting the proliferation of osteoblasts and the growth and development of dental papilla cells. However, the effect and mechanism of melatonin on the growth and development of ALCs still need to be explored. CCK8 assay was used for the evaluation of cell numbers. qRT-PCR was used to identify the differentially expressed genes in ALCs after melatonin treatment. The number and morphology of ALCs were investigated by confocal microscopy. Alkaline phosphatase assay and Alizarin red S staining were used for measuring mineralization. Then, we focused on observing the crucial factors of the signaling pathway by RNA-seq and qRT-PCR. Melatonin limited the cell number of ALCs in a dose-dependent manner and promoted the production of actin fibers. A high concentration of melatonin significantly promoted the mRNA levels of enamel matrix proteins and the formation of mineralized nodules. RNA-seq data showed that Wnt signaling pathway may be involved in the differentiation of ALCs under the influence of melatonin. This study suggests that melatonin plays a regulatory role in the cell number, differentiation, and mineralization of the ALCs, and then shows the relationship between the Wnt signaling pathway with the ALCs under melatonin.
Inflammatory indices obtained from routine blood tests show an inflammatory state associated with disease progression in engineered stone silicosis patients
Authors: García-Núñez Alejandro , Jiménez-Gómez Gema , Hidalgo-Molina Antonio , Córdoba-Doña Juan Antonio , León-Jiménez Antonio , Campos-Caro Antonio
Published: May 2022

Patients with silicosis caused by occupational exposure to engineered stone (ES) present a rapid progression from simple silicosis (SS) to progressive massive fibrosis (PMF). Patient classification follows international rules based on radiology and high-resolution computed tomography (HRCT), but limited studies, if any, have explored biomarkers from routine clinical tests that can be used as predictors of disease status. Our objective was thus to investigate circulating biomarker levels and systemic inflammatory indices in ES silicosis patients whose exposure to ES dust ended several years ago. Ninety-one adult men, ex-workers in the manufacturing of ES, 53 diagnosed with SS and 38 with PMF, and 22 healthy male volunteers (HC) as controls not exposed to ES dust, were recruited. The following circulating levels of biomarkers like lactate dehydrogenase (LDH), angiotensin-converting-enzyme (ACE), protein C reactive (PCR), rheumatoid factor, alkaline phosphatase and fibrinogen were obtained from clinical reports after being measured from blood samples. As biochemical markers, only LDH (HC = 262 ± 48.1; SS = 315.4 ± 65.4; PMF = 337.6 ± 79.3 U/L), ACE (HC = 43.1 ± 18.4; SS = 78.2 ± 27.2; PMF = 86.1 ± 23.7 U/L) and fibrinogen (HC = 182.3 ± 49.1; SS = 212.2 ± 43.5; PMF = 256 ± 77.3 U/L) levels showed a significant sequential increase, not been observed for the rest of biomarkers, in the HC → SS → PMF direction. Moreover, several systemic inflammation indices neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte ratio (LMR), platelet-to-lymphocyte ratio (PLR), systemic inflammation response index (SIRI), systemic immune-inflammation index (SII), aggregate index of systemic inflammation (AISI) derived from whole blood cell counts showed significant differences between the HC, SS and PMF groups. All these biomarkers were analyzed using receiver operating characteristic (ROC) curves, and the results provided moderately high sensitivity and specificity for discriminating between ES silicosis patient groups and healthy controls. Our study reveals that some inflammatory biomarkers, easily available from routine blood analysis, are present in ES silicosis patients even several years after cessation of exposure to ES silica dust and they could help to know the progression of the disease.
Chronotype at the beginning of secondary school and school timing are both associated with chronotype development during adolescence
Authors: Rodríguez Ferrante Guadalupe , Goldin Andrea Paula , Sigman Mariano , Leone María Juliana
Published: May 2022

The misalignment between late chronotypes and early school start times affect health, performance and psychological well-being of adolescents. Here we test whether, and how, the baseline chronotype (i.e. chronotype at the beginning of secondary school) and the school timing affect the magnitude and the direction of the developmental change in chronotype during adolescence. We evaluated a sample of Argentinian students (n = 259) who were randomly assigned to attend school in the morning (07:45 a.m.–12:05 p.m.), afternoon (12:40 p.m.–05:00 p.m.) or evening (05:20 p.m.–09:40 p.m.) school timings. Importantly, chronotype and sleep habits were assessed longitudinally in the same group of students along secondary school (at 13–14 y.o. and 17–18 y.o.). Our results show that: (1) although chronotypes partially align with class time, this effect is insufficient to fully account for the differences observed in sleep-related variables between school timings; (2) both school timing and baseline chronotype are independently associated with the direction and the magnitude of change in chronotype, with greater delays related to earlier baseline chronotypes and later school timings. The practical implications of these results are challenging and should be considered in the design of future educational timing policies to improve adolescents’ well-being.
Temporal phytoremediation potential for heavy metals and bacterial abundance in drainage water
Authors: El-Liethy Mohamed Azab , Dakhil Mohammed A. , El-Keblawy Ali , Abdelaal Mohamed , Halmy Marwa Waseem A. , Elgarhy Abdelbaky Hossam , Kamika Ilunga , El-Sherbeny Ghada A. , Mwaheb Mai Ali
Published: May 2022

Drainage water in developing countries has a high abundance of pathogenic bacteria and high levels of toxic and mutagenic pollutants. Remediation of drainage water is important in water-poor counties, especially with the growing need to secure sustainability of safe water resources to fulfill increasing demands for agriculture. Here, we assess the efficiency of macrophyte Pistiastratiotes to remediate a polluted drain in Egypt, rich in macronutrients, heavy metals, and different types of pathogenic and non-pathogenic bacteria. Drainage water was sampled monthly, for a year, to assess seasonal changes in bacterial abundance, water physicochemical properties (transparency, temperature, dissolved oxygen, EC, pH, N, P, and K), and heavy metals contents (Pb, Zn, and Co) in a polluted drain dominated with P.stratiotes. The ability of P.stratiotes to rhizofiltrate the three heavy metals was calculated. The results showed seasonal variations in the plant rhizofiltration potential of Co and Salmonella abundance. The highest values of dissolved oxygen (12.36 mg/L) and macronutrient elements (N and P) were attained in the winter. The counts of total coliform, fecal coliform, fecal streptococci, and in Salmonella spp. were the highest in the summer. P.stratiotes accumulated Pb more than Zn and Co. The highest levels of rhizofiltration were in summer for Pb and Co and in the autumn for Zn. Canonical correspondence analysis (CCA) showed that the variation in the bacterial abundance and plant rhizofiltration potential was strongly and significantly affected by water-dissolved oxygen. Moreover, the rhizofiltration potential of Pb and Co showed a positive correlation with water N. Overall, P.stratiotes could be proposed as a potential biomonitor for heavy metals in polluted water.
Infected food web and ecological stability
Authors: Mougi Akihiko
Published: May 2022

Parasites are widespread in nature. Nevertheless, they have only recently been incorporated into food web studies and community ecology. Earlier studies revealed the large effects of parasites on food web network structures, suggesting that parasites affect food web dynamics and their stability. However, our understanding of the role of parasites in food web dynamics is limited to a few theoretical studies, which only assume parasite-induced mortality or virulence as a typical characteristic of parasites, without any large difference in terms of predation effects. Here, I present a food web model with parasites in which parasites change the mortality and interaction strengths of hosts by affecting host activity. The infected food web shows that virulence and infection rate have virtually no effect on food web stability without any difference in interaction strengths between susceptible and infected individuals. However, if predation rates are weakened through a restriction of the activity of infected individuals, virulence and infection rate can greatly influence stability: diseases with lower virulence and higher transmission rate tend to increase stability. The stabilization is stronger in cascade than random food webs. The present results suggest that parasites can greatly influence food web stability if parasite-induced diseases prevent host foraging activity. Parasite-induced infectious disease, by weaking species interactions, may play a key role in maintaining food webs.
Deep learning model for the automatic classification of COVID-19 pneumonia, non-COVID-19 pneumonia, and the healthy: a multi-center retrospective study
Authors: Nishio Mizuho , Kobayashi Daigo , Nishioka Eiko , Matsuo Hidetoshi , Urase Yasuyo , Onoue Koji , Ishikura Reiichi , Kitamura Yuri , Sakai Eiro , Tomita Masaru , Hamanaka Akihiro , Murakami Takamichi
Published: May 2022

This retrospective study aimed to develop and validate a deep learning model for the classification of coronavirus disease-2019 (COVID-19) pneumonia, non-COVID-19 pneumonia, and the healthy using chest X-ray (CXR) images. One private and two public datasets of CXR images were included. The private dataset included CXR from six hospitals. A total of 14,258 and 11,253 CXR images were included in the 2 public datasets and 455 in the private dataset. A deep learning model based on EfficientNet with noisy student was constructed using the three datasets. The test set of 150 CXR images in the private dataset were evaluated by the deep learning model and six radiologists. Three-category classification accuracy and class-wise area under the curve (AUC) for each of the COVID-19 pneumonia, non-COVID-19 pneumonia, and healthy were calculated. Consensus of the six radiologists was used for calculating class-wise AUC. The three-category classification accuracy of our model was 0.8667, and those of the six radiologists ranged from 0.5667 to 0.7733. For our model and the consensus of the six radiologists, the class-wise AUC of the healthy, non-COVID-19 pneumonia, and COVID-19 pneumonia were 0.9912, 0.9492, and 0.9752 and 0.9656, 0.8654, and 0.8740, respectively. Difference of the class-wise AUC between our model and the consensus of the six radiologists was statistically significant for COVID-19 pneumonia (p value = 0.001334). Thus, an accurate model of deep learning for the three-category classification could be constructed; the diagnostic performance of our model was significantly better than that of the consensus interpretation by the six radiologists for COVID-19 pneumonia.
Analysis of rhodopsin G protein-coupled receptor orthologs reveals semiochemical peptides for parasite (Schistosoma mansoni) and host (Biomphalaria glabrata) interplay
Authors: Phan Phong , Liang Di , Zhao Min , Wyeth Russell C. , Fogarty Conor , Duke Mary G. , McManus Donald P. , Wang Tianfang , Cummins Scott F.
Published: May 2022

Schistosomiasis is a medically significant disease caused by helminth parasites of the genus Schistosoma. The schistosome life cycle requires chemically mediated interactions with an intermediate (aquatic snail) and definitive (human) host. Blocking parasite development within the snail stage requires improved understanding of the interactions between the snail host and the Schistosoma water-borne free-living form (miracidium). Innovations in snail genomics and aquatic chemical communication provide an ideal opportunity to explore snail-parasite coevolution at the molecular level. Rhodopsin G protein-coupled receptors (GPCRs) are of particular interest in studying how trematode parasites navigate towards their snail hosts. The potential role of GPCRs in parasites makes them candidate targets for new antihelminthics that disrupt the intermediate host life-cycle stages, thus preventing subsequent human infections. A genomic-bioinformatic approach was used to identify GPCR orthologs between the snail Biomphalaria glabrata and miracidia of its obligate parasite Schistosoma mansoni. We show that 8 S. mansoni rhodopsin GPCRs expressed within the miracidial stage share overall amino acid similarity with 8 different B. glabrata rhodopsin GPCRs, particularly within transmembrane domains, suggesting conserved structural features. These GPCRs include an orphan peptide receptor as well as several with strong sequence homologies with rhabdomeric opsin receptors, a serotonin receptor, a sulfakinin (SK) receptor, an allatostatin-A (buccalin) receptor and an FMRFamide receptor. Buccalin and FMRFa peptides were identified in water conditioned by B. glabrata, and we show synthetic buccalin and FMRFa can stimulate significant rates of change of direction and turn-back responses in S. mansoni miracidia. Ortholog GPCRs were identified in S. mansoni miracidia and B. glabrata. These GPCRs may detect similar ligands, including snail-derived odorants that could facilitate miracidial host finding. These results lay the foundation for future research elucidating the mechanisms by which GPCRs mediate host finding which can lead to the potential development of novel anti-schistosome interventions.