bluuebunny/crossref_metadata_2025 huggingface dataset:
Intergenerational nutrition benefits of India’s national school feeding program
Authors: Chakrabarti Suman , Scott Samuel P. , Alderman Harold , Menon Purnima , Gilligan Daniel O.
Published: July 2021

India has the world’s highest number of undernourished children and the largest school feeding program, the Mid-Day Meal (MDM) scheme. As school feeding programs target children outside the highest-return “first 1000-days” window, they have not been included in the global agenda to address stunting. School meals benefit education and nutrition in participants, but no studies have examined whether benefits carry over to their children. Using nationally representative data on mothers and their children spanning 1993 to 2016, we assess whether MDM supports intergenerational improvements in child linear growth. Here we report that height-for-age z-score (HAZ) among children born to mothers with full MDM exposure was greater (+0.40 SD) than that in children born to non-exposed mothers. Associations were stronger in low socioeconomic strata and likely work through women’s education, fertility, and health service utilization. MDM was associated with 13–32% of the HAZ improvement in India from 2006 to 2016.
TSC2 regulates lysosome biogenesis via a non-canonical RAGC and TFEB-dependent mechanism
Authors: Alesi Nicola , Akl Elie W. , Khabibullin Damir , Liu Heng-Jia , Nidhiry Anna S. , Garner Emma R. , Filippakis Harilaos , Lam Hilaire C. , Shi Wei , Viswanathan Srinivas R. , Morroni Manrico , Ferguson Shawn M. , Henske Elizabeth P.
Published: July 2021

Tuberous Sclerosis Complex (TSC) is caused by TSC1 or TSC2 mutations, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1). Transcription factor EB (TFEB), a master regulator of lysosome biogenesis, is negatively regulated by mTORC1 through a RAG GTPase-dependent phosphorylation. Here we show that lysosomal biogenesis is increased in TSC-associated renal tumors, pulmonary lymphangioleiomyomatosis, kidneys from Tsc2+/− mice, and TSC1/2-deficient cells via a TFEB-dependent mechanism. Interestingly, in TSC1/2-deficient cells, TFEB is hypo-phosphorylated at mTORC1-dependent sites, indicating that mTORC1 is unable to phosphorylate TFEB in the absence of the TSC1/2 complex. Importantly, overexpression of folliculin (FLCN), a GTPase activating protein for RAGC, increases TFEB phosphorylation at the mTORC1 sites in TSC2-deficient cells. Overexpression of constitutively active RAGC is sufficient to relocalize TFEB to the cytoplasm. These findings establish the TSC proteins as critical regulators of lysosomal biogenesis via TFEB and RAGC and identify TFEB as a driver of the proliferation of TSC2-deficient cells.
Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy
Authors: Richter M. L. , Deligiannis I. K. , Yin K. , Danese A. , Lleshi E. , Coupland P. , Vallejos C. A. , Matchett K. P. , Henderson N. C. , Colome-Tatche M. , Martinez-Jimenez C. P.
Published: July 2021

Single-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity, we have developed a single-nucleus RNA-seq2 method tailored for the comprehensive analysis of the nuclear transcriptome from frozen tissues, allowing the dissection of all cell types present in the liver, regardless of cell size or cellular fragility. We use this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that ploidy states are associated with different metabolic potential, and gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobule. Our work reveals a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes.
VCP maintains nuclear size by regulating the DNA damage-associated MDC1–p53–autophagy axis in Drosophila
Authors: Chang Ya-Chu , Peng Yu-Xiang , Yu Bo-Hua , Chang Henry C. , Liang Pei-Shin , Huang Ting-Yi , Shih Chao-Jie , Chu Li-An , Sang Tzu-Kang
Published: July 2021

The maintenance of constant karyoplasmic ratios suggests that nuclear size has physiological significance. Nuclear size anomalies have been linked to malignant transformation, although the mechanism remains unclear. By expressing dominant-negative TER94 mutants in Drosophila photoreceptors, here we show disruption of VCP (valosin-containing protein, human TER94 ortholog), a ubiquitin-dependent segregase, causes progressive nuclear size increase. Loss of VCP function leads to accumulations of MDC1 (mediator of DNA damage checkpoint protein 1), connecting DNA damage or associated responses to enlarged nuclei. TER94 can interact with MDC1 and decreases MDC1 levels, suggesting that MDC1 is a VCP substrate. Our evidence indicates that MDC1 accumulation stabilizes p53A, leading to TER94K2A-associated nuclear size increase. Together with a previous report that p53A disrupts autophagic flux, we propose that the stabilization of p53A in TER94K2A-expressing cells likely hinders the removal of nuclear content, resulting in aberrant nuclear size increase.
Transparent origami glass
Authors: Xu Yang , Li Ye , Zheng Ning , Zhao Qian , Xie Tao
Published: July 2021

The art of origami has emerged as an engineering tool with ever increasing potential, but the technique is typically limited to soft and deformable materials. Glass is indispensable in many applications, but its processing options are limited by its brittle nature and the requirement to achieve optical transparency. We report a strategy that allows making three dimensional transparent glass with origami techniques. Our process starts from a dynamic covalent polymer matrix with homogeneously dispersed silica nanoparticles. Particle cavitation and dynamic bond exchange offer two complementary plasticity mechanisms that allow the nanocomposite to be permanently folded into designable geometries. Further pyrolysis and sintering convert it into transparent three dimensional glass. Our method expands the scope of glass shaping and potentially opens up its utilities in unexplored territories.
The role of genetic polymorphisms in endolysosomal ion channels TPC2 and P2RX4 in cancer pathogenesis, prognosis, and diagnosis: a genetic association in the UK Biobank
Authors: Alharbi Abeer F. , Parrington John
Published: July 2021

Recent studies have implicated important roles for endolysosomal ion channels in cancer biology. We used UK Biobank data to characterise the relationships between genetic variants in two genes coding for endolysosomal ion channels—i.e. TPCN2 and P2RX4—and cancer in terms of the definition of tumour types, susceptibility, and prognosis. We investigated these relationships at both global and local levels with regard to specific types of cancer, including malignant neoplasms of the brain, breast, bronchus, lung, colon, lymphoid and haematopoietic systems, skin, ovary, prostate, rectum, thyroid gland, lip, oral cavity, pharynx, and urinary tract. Apart from rs3829241 (p value < 0.05), all the genetic variants were in Hardy–Weinberg equilibrium. We included 468,436 subjects in the analysis and stratified them into two major cohorts: cancer-free controls (385,253) and cancer cases (83,183). For the first time, we report novel associations between genetic variants of TPCN2 and P2RX4 and cancer/cancer subtypes in the UK Biobank’s population. Genotype GG in TPCN2 rs3750965 was significantly associated with a decreased risk of cancer and an increased risk of lip, oral cavity, and pharynx cancer and cancer recurrence in patients with prostate cancer, and genotypes GA/GG were associated with a significantly lower risk of developing various malignant neoplasms (involving melanoma, prostate, mesothelial, and soft tissues). rs35264875:TA was associated with a high risk of cancer at the global level, with subtypes of cancer at the local level (including breast, colon, prostate, and stated or presumed primary cancer of lymphoid, haematopoietic, and related tissue), and with a significantly low risk of cancer metastasis. rs72932540:GA was associated with a higher incidence of cancer/cancer subtypes (including breast, melanoma, and rectal cancer), and genotypes GA/GG were associated with an increased risk of prostate cancer. The P2RX4 rs25644 allele GG was associated with a high risk of prostate cancer, whereas it was associated with a low risk of cancer recurrence in patients with prostate cancer. Genotypes GA/GG in rs28360472 were associated with an increased risk of breast, mesothelial, and soft tissue cancers but with a decreased risk of colon cancer. We also provide insights into the pathophysiological contributions made by these significant polymorphisms to cancer/cancer subtypes and their effects on expression or channel activity. Further investigations of these genetic variants could help identify novel cancer biomarkers and facilitate the development of new diagnostic and therapeutic strategies. This would constitute a further step towards personalised cancer care.
The 2021 update of the EPA’s adverse outcome pathway database
Authors: Mortensen Holly M. , Senn Jonathan , Levey Trevor , Langley Phillip , Williams Antony J.
Published: July 2021

The EPA developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Here we present the most recent version of the EPA Adverse Outcome Pathway Database (AOP-DB), version 2. AOP-DB v.2 introduces several substantial updates, which include automated data pulls from the AOP-Wiki 2.0, the integration of tissue-gene network data, and human AOP-gene data by population, semantic mapping and SPARQL endpoint creation, in addition to the presentation of the first publicly available AOP-DB web user interface. Potential users of the data may investigate specific molecular targets of an AOP, the relation of those gene/protein targets to other AOPs, cross-species, pathway, or disease-AOP relationships, or frequencies of AOP-related functional variants in particular populations, for example. Version updates described herein help inform new testable hypotheses about the etiology and mechanisms underlying adverse outcomes of environmental and toxicological concern.
Global soil moisture data derived through machine learning trained with in-situ measurements
Authors: O. Sungmin , Orth Rene
Published: July 2021

While soil moisture information is essential for a wide range of hydrologic and climate applications, spatially-continuous soil moisture data is only available from satellite observations or model simulations. Here we present a global, long-term dataset of soil moisture derived through machine learning trained with in-situ measurements, SoMo.ml. We train a Long Short-Term Memory (LSTM) model to extrapolate daily soil moisture dynamics in space and in time, based on in-situ data collected from more than 1,000 stations across the globe. SoMo.ml provides multi-layer soil moisture data (0–10 cm, 10–30 cm, and 30–50 cm) at 0.25° spatial and daily temporal resolution over the period 2000–2019. The performance of the resulting dataset is evaluated through cross validation and inter-comparison with existing soil moisture datasets. SoMo.ml performs especially well in terms of temporal dynamics, making it particularly useful for applications requiring time-varying soil moisture, such as anomaly detection and memory analyses. SoMo.ml complements the existing suite of modelled and satellite-based datasets given its distinct derivation, to support large-scale hydrological, meteorological, and ecological analyses.
Methylene Blue has a potent antiviral activity against SARS-CoV-2 and H1N1 influenza virus in the absence of UV-activation in vitro
Authors: Cagno Valeria , Medaglia Chiara , Cerny Andreas , Cerny Thomas , Zwygart Arnaud Charles-Antoine , Cerny Erich , Tapparel Caroline
Published: July 2021

Methylene blue is an FDA (Food and Drug Administration) and EMA (European Medicines Agency) approved drug with an excellent safety profile. It displays broad-spectrum virucidal activity in the presence of UV light and has been shown to be effective in inactivating various viruses in blood products prior to transfusions. In addition, its use has been validated for methemoglobinemia and malaria treatment. In this study, we first evaluated the virucidal activity of methylene blue against influenza virus H1N1 upon different incubation times and in the presence or absence of light activation, and then against SARS-CoV-2. We further assessed the therapeutic activity of methylene blue by administering it to cells previously infected with SARS-CoV-2. Finally, we examined the effect of co-administration of the drug together with immune serum. Our findings reveal that methylene blue displays virucidal preventive or therapeutic activity against influenza virus H1N1 and SARS-CoV-2 at low micromolar concentrations and in the absence of UV-activation. We also confirm that MB antiviral activity is based on several mechanisms of action as the extent of genomic RNA degradation is higher in presence of light and after long exposure. Our work supports the interest of testing methylene blue in clinical studies to confirm a preventive and/or therapeutic efficacy against both influenza virus H1N1 and SARS-CoV-2 infections.
Transcriptome profiling by combined machine learning and statistical R analysis identifies TMEM236 as a potential novel diagnostic biomarker for colorectal cancer
Authors: Maurya Neha Shree , Kushwaha Sandeep , Chawade Aakash , Mani Ashutosh
Published: July 2021

Colorectal cancer (CRC) is a common cause of cancer-related deaths worldwide. The CRC mRNA gene expression dataset containing 644 CRC tumor and 51 normal samples from the cancer genome atlas (TCGA) was pre-processed to identify the significant differentially expressed genes (DEGs). Feature selection techniques Least absolute shrinkage and selection operator (LASSO) and Relief were used along with class balancing for obtaining features (genes) of high importance. The classification of the CRC dataset was done by ML algorithms namely, random forest (RF), K-nearest neighbour (KNN), and artificial neural networks (ANN). The significant DEGs were 2933, having 1832 upregulated and 1101 downregulated genes. The CRC gene expression dataset had 23,186 features. LASSO had performed better than Relief for classifying tumor and normal samples through ML algorithms namely RF, KNN, and ANN with an accuracy of 100%, while Relief had given 79.5%, 85.05%, and 100% respectively. Common features between LASSO and DEGs were 38, from them only 5 common genes namely, VSTM2A, NR5A2, TMEM236, GDLN, and ETFDH had shown statistically significant survival analysis. Functional review and analysis of the selected genes helped in downsizing the 5 genes to 2, which are VSTM2A and TMEM236. Differential expression of TMEM236 was statistically significant and was markedly reduced in the dataset which solicits appreciation for assessment as a novel biomarker for CRC diagnosis.
Movement patterns and activity levels are shaped by the neonatal environment in Antarctic fur seal pups
Authors: Nagel Rebecca , Mews Sina , Adam Timo , Stainfield Claire , Fox-Clarke Cameron , Toscani Camille , Langrock Roland , Forcada Jaume , Hoffman Joseph I.
Published: July 2021

Tracking studies of juveniles are rare compared to those of adults, and consequently little is known about the influence of intrinsic and extrinsic factors on activity during this critical life stage. We used hourly GPS data, collected from 66 Antarctic fur seal pups from birth until moulting, to investigate the explanatory power of multiple individual-based and environmental variables on activity levels. Pups were sampled from two nearby breeding colonies of contrasting density during two subsequent years, and a two-state hidden Markov model was used to identify modalities in their movement behaviour, specifically ‘active’ and ‘inactive’ states. We found that movement was typified by central place exploration, with active movement away from and subsequent return to a location of inactivity. The probability of such directed exploration was unaffected by several factors known to influence marine mammal movement including sex, body condition, and temperature. Compared to pups born at the high-density colony, pups at low-density were more active, increased their activity with age, and transitioned earlier into the tussock grass, which offers protection from predators and extreme weather. Our study illustrates the importance of extrinsic factors, such as colony of birth, to early-life activity patterns and highlights the adaptive potential of movement.
Effects of long-term norepinephrine treatment on normal immortalized ovarian and fallopian tube cells
Authors: Dash Sweta , Yoder Sean , Mesa Tania , Smith Andrew , Cen Ling , Eschrich Steven , Armaiz-Pena Guillermo N. , Monteiro Alvaro N. A.
Published: July 2021

Sustained adrenergic stimulation by norepinephrine (NE) contributes to ovarian carcinoma metastasis and impairment of chemotherapy response. Although the effect of sustained NE stimulation in cancer progression is well established, less is known about its role in cancer initiation. To determine the extent to which stress hormones influence ovarian cancer initiation, we conducted a long-term (> 3 months; > 40 population doublings) experiment in which normal immortalized fallopian tube secretory (iFTSEC283) and ovarian surface epithelial (iOSE11) cell lines and their isogenic pairs containing a p53 mutation (iFTSEC283p53R175H; iOSE11p53R175H), were continuously exposed to NE (100 nM, 1 μM, 10 μM). Fallopian tube cells displayed a p53-independent increase in proliferation and colony-forming ability in response to NE, while ovarian surface epithelial cells displayed a p53-independent decrease in both assays. Fallopian tube cells with mutant p53 showed a mild loss of chromosomes and TP53 status was also a defining factor in transcriptional response of fallopian tube cells to long-term NE treatment.
COUnty aggRegation mixup AuGmEntation (COURAGE) COVID-19 prediction
Authors: Er Siawpeng , Yang Shihao , Zhao Tuo
Published: July 2021

The global spread of COVID-19, the disease caused by the novel coronavirus SARS-CoV-2, has casted a significant threat to mankind. As the COVID-19 situation continues to evolve, predicting localized disease severity is crucial for advanced resource allocation. This paper proposes a method named COURAGE (COUnty aggRegation mixup AuGmEntation) to generate a short-term prediction of 2-week-ahead COVID-19 related deaths for each county in the United States, leveraging modern deep learning techniques. Specifically, our method adopts a self-attention model from Natural Language Processing, known as the transformer model, to capture both short-term and long-term dependencies within the time series while enjoying computational efficiency. Our model solely utilizes publicly available information for COVID-19 related confirmed cases, deaths, community mobility trends and demographic information, and can produce state-level predictions as an aggregation of the corresponding county-level predictions. Our numerical experiments demonstrate that our model achieves the state-of-the-art performance among the publicly available benchmark models.
Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress
Authors: Entrambasaguas Laura , Ruocco Miriam , Verhoeven Koen J. F. , Procaccini Gabriele , Marín-Guirao Lazaro
Published: July 2021

The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpGO/E ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants’ latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants.
Motion blur invariant for estimating motion parameters of medical ultrasound images
Authors: Honarvar Shakibaei Asli Barmak , Zhao Yifan , Erkoyuncu John Ahmet
Published: July 2021

High-quality medical ultrasound imaging is definitely concerning motion blur, while medical image analysis requires motionless and accurate data acquired by sonographers. The main idea of this paper is to establish some motion blur invariant in both frequency and moment domain to estimate the motion parameters of ultrasound images. We propose a discrete model of point spread function of motion blur convolution based on the Dirac delta function to simplify the analysis of motion invariant in frequency and moment domain. This model paves the way for estimating the motion angle and length in terms of the proposed invariant features. In this research, the performance of the proposed schemes is compared with other state-of-the-art existing methods of image deblurring. The experimental study performs using fetal phantom images and clinical fetal ultrasound images as well as breast scans. Moreover, to validate the accuracy of the proposed experimental framework, we apply two image quality assessment methods as no-reference and full-reference to show the robustness of the proposed algorithms compared to the well-known approaches.
Incidence and outcomes of refractory immune thrombocytopenic purpura in children: a retrospective study in a single institution
Authors: Ito Masataka , Yagasaki Hiroshi , Kanezawa Koji , Shimozawa Katsuyoshi , Hirai Maiko , Morioka Ichiro
Published: July 2021

Treatment of children with refractory immune thrombocytopenic purpura (ITP) is challenging and poorly established. We retrospectively reviewed the clinical data of 87 patients under the age of 16 years who were diagnosed with ITP from April 1998 to March 2017 in our institution. Refractory ITP was defined as a platelet count of < 50 × 109/L at 14 days after receiving intravenous immunoglobulin (IVIG) and prednisolone. We presumed that there was a pathophysiological overlap between refractory ITP and refractory thrombocytopenia (RT): a subtype of refractory cytopenia of childhood (RCC). Immunosuppressive therapies including anti-thymocyte globulin and cyclosporine (CsA) have been adopted for children with RCC in Japan. Thus, from 2009 onwards, we changed the diagnosis from refractory ITP to RT and introduced CsA for refractory ITP/RT. Nine of 42 patients developed refractory ITP in the 1998–2008 group, who received conventional treatments such as IVIG and steroid therapy. Eight of 45 patients developed refractory ITP in the 2009–2017 group, who received CsA with or without IVIG therapy. The response rate at three years after diagnosis was significantly higher in the 2009–2017 group (98%) than in the 1998–2008 group (83%) (p = 0.019). In conclusion, our strategy of introducing CsA for refractory ITP/RT contributed to better outcomes.
Dual effects of 9-cis retinoic acid on ACTH-dependent hyperplastic adrenal tissues
Authors: Pecori Giraldi Francesca , Sesta Antonella , Tapella Laura , Cassarino Maria Francesca , Castelli Luigi
Published: July 2021

Retinoids play a pivotal role in adrenal development and differentiation. Recent clinical trials revealed therapeutic potential of both all-trans and 9-cis retinoic acid in patients with cortisol excess due to a pituitary ACTH-secreting adenoma and indicated that retinoids might act also on the adrenal. Aim of the present study was to evaluate the effect of 9-cis retinoic acid on adrenals from patients with ACTH-dependent Cushing’s syndrome. Adrenal specimens from six patients with Cushing’s disease were incubated with 10 nM–1 µM 9-cis retinoic acid with and without 10 nM ACTH. Cortisol secretion was measured by immunoassay and expression of genes involved in steroidogenesis as well as retinoic acid action were evaluated by real-time RT-PCR. Incubation with 10–100 nM 9-cis retinoic acid increased spontaneous cortisol secretion and expression of STAR and CYP17A. On the other hand, in wells treated with ACTH, 9-cis retinoic acid markedly diminished ACTH receptor upregulation and no stimulatory effect on cortisol secretion or steroidogenic enzyme synthesis was observed. ACTH itself increased ligand-induced retinoic acid receptor expression, possibly enhancing sensitivity to retinoic acid. Our findings indicate that the effect of 9-cis retinoic acid in presence of ACTH is distinct from unchallenged wells and support the hypothesis of a direct adrenal action in patients with Cushing’s disease.
Toward applications of near-field radiative heat transfer with micro-hotplates
Authors: Marconot Olivier , Juneau-Fecteau Alexandre , Fréchette Luc G.
Published: July 2021

Bringing bodies close together at sub-micron distances can drastically enhance radiative heat transfer, leading to heat fluxes greater than the blackbody limit set by Stefan–Boltzmann law. This effect, known as near-field radiative heat transfer (NFRHT), has wide implications for thermal management in microsystems, as well as technological applications such as direct heat to electricity conversion in thermophotovoltaic cells. Here, we demonstrate NFRHT from microfabricated hotplates made by surface micromachining of $$\hbox {SiO}_2$$

SiO
2

/$$\hbox {SiN}$$
SiN
thin films deposited on a sacrificial amorphous Si layer. The sacrificial layer is dry etched to form wide membranes ($${100}\,\upmu \hbox {m} \times {100}\,\upmu \hbox {m}$$

100

μ
m
×
100

μ
m

) separated from the substrate by nanometric distances. Nickel traces allow both resistive heating and temperature measurement on the micro-hotplates. We report on two samples with measured gaps of $${610}\,\hbox {nm}$$

610

nm

and $${280}\,\hbox {nm}$$

280

nm

. The membranes can be heated up to $${250}\,^{\circ }\hbox {C}$$

250

∘

C

under vacuum with no mechanical damage. At $${120}\,^{\circ }\hbox {C}$$

120

∘

C

we observed a 6.4-fold enhancement of radiative heat transfer compared to far-field emission for the smallest gap and a 3.5-fold enhancement for the larger gap. Furthermore, the measured transmitted power exhibits an exponential dependence with respect to gap size, a clear signature of NFRHT. Calculations of photon transmission probabilities indicate that the observed increase in heat transfer can be attributed to near-field coupling by surface phonon-polaritons supported by the $$\hbox {SiO}_2$$

SiO
2

films. The fabrication process presented here, relying solely on well-established surface micromachining technology, is a key step toward integration of NFRHT in industrial applications.
Inferring the ecological niche of bat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species
Authors: Hassanin Alexandre , Tu Vuong Tan , Curaudeau Manon , Csorba Gabor
Published: July 2021

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus, Rhinolophus affinis, Rhinolophus malayanus, and Rhinolophus shameli. Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene (CO1) from georeferenced bats of the four Rhinolophus species identified as reservoirs of viruses closely related to SARS-CoV-2. Haplotype networks were constructed in order to investigate patterns of genetic diversity among bat populations of Southeast Asia and China. No strong geographic structure was found for the four Rhinolophus species, suggesting high dispersal capacity. The ecological niche of bat viruses closely related to SARS-CoV-2 was predicted using the four localities in which bat viruses were recently discovered and the localities where bats showed the same CO1 haplotypes than virus-positive bats. The ecological niche of bat viruses related to SARS-CoV was deduced from the localities where bat viruses were previously detected. The results show that the ecological niche of bat viruses related to SARS-CoV2 includes several regions of mainland Southeast Asia whereas the ecological niche of bat viruses related to SARS-CoV is mainly restricted to China. In agreement with these results, human populations in Laos, Vietnam, Cambodia, and Thailand appear to be much less affected by the COVID-19 pandemic than other countries of Southeast Asia. In the climatic transitional zone between the two ecological niches (southern Yunnan, northern Laos, northern Vietnam), genomic recombination between highly divergent viruses is more likely to occur. Considering the limited data and the risk of recombinant bat-CoVs emergence as the source of new pandemics in humans, the bat populations in these regions should be under surveillance.
From head micro-motions towards CSF dynamics and non-invasive intracranial pressure monitoring
Authors: Mládek Arnošt , Gerla Václav , Šeba Petr , Kolář Vladimír , Skalický Petr , Whitley Helen , Lhotská Lenka , Beneš Vladimír , Bradáč Ondřej
Published: July 2021

Continuous monitoring of the intracranial pressure (ICP) is essential in neurocritical care. There are a variety of ICP monitoring systems currently available, with the intraventricular fluid filled catheter transducer currently representing the “gold standard”. As the placement of catheters is associated with the attendant risk of infection, hematoma formation, and seizures, there is a need for a reliable, non-invasive alternative. In the present study we suggest a unique theoretical framework based on differential geometry invariants of cranial micro-motions with the potential for continuous non-invasive ICP monitoring in conservative traumatic brain injury (TBI) treatment. As a proof of this concept, we have developed a pillow with embedded mechanical sensors and collected an extensive dataset (> 550 h on 24 TBI coma patients) of cranial micro-motions and the reference intraparenchymal ICP. From the multidimensional pulsatile curve we calculated the first Cartan curvature and constructed a ”fingerprint” image (Cartan map) associated with the cerebrospinal fluid (CSF) dynamics. The Cartan map features maxima bands corresponding to a pressure wave reflection corresponding to a detectable skull tremble. We give evidence for a statistically significant and patient-independent correlation between skull micro-motions and ICP time derivative. Our unique differential geometry-based method yields a broader and global perspective on intracranial CSF dynamics compared to rather local catheter-based measurement and has the potential for wider applications.
Cell type-specific roles of PAR1 in Coxsackievirus B3 infection
Authors: Bode Michael F. , Schmedes Clare M. , Egnatz Grant J. , Bharathi Vanthana , Hisada Yohei M. , Martinez David , Kawano Tomohiro , Weithauser Alice , Rosenfeldt Leah , Rauch Ursula , Palumbo Joseph S. , Antoniak Silvio , Mackman Nigel
Published: July 2021

Protease-activated receptor 1 (PAR1) is widely expressed in humans and mice, and is activated by a variety of proteases, including thrombin. Recently, we showed that PAR1 contributes to the innate immune response to viral infection. Mice with a global deficiency of PAR1 expressed lower levels of CXCL10 and had increased Coxsackievirus B3 (CVB3)-induced myocarditis compared with control mice. In this study, we determined the effect of cell type-specific deletion of PAR1 in cardiac myocytes (CMs) and cardiac fibroblasts (CFs) on CVB3-induced myocarditis. Mice lacking PAR1 in either CMs or CFs exhibited increased CVB3 genomes, inflammatory infiltrates, macrophages and inflammatory mediators in the heart and increased CVB3-induced myocarditis compared with wild-type controls. Interestingly, PAR1 enhanced poly I:C induction of CXCL10 in rat CFs but not in rat neonatal CMs. Importantly, activation of PAR1 reduced CVB3 replication in murine embryonic fibroblasts and murine embryonic cardiac myocytes. In addition, we showed that PAR1 reduced autophagy in murine embryonic fibroblasts and rat H9c2 cells, which may explain how PAR1 reduces CVB3 replication. These data suggest that PAR1 on CFs protects against CVB3-induced myocarditis by enhancing the anti-viral response whereas PAR1 on both CMs and fibroblasts inhibits viral replication.
Characterize traction–separation relation and interfacial imperfections by data-driven machine learning models
Authors: Ferdousi Sanjida , Chen Qiyi , Soltani Mehrzad , Zhu Jiadeng , Cao Pengfei , Choi Wonbong , Advincula Rigoberto , Jiang Yijie
Published: July 2021

Interfacial mechanical properties are important in composite materials and their applications, including vehicle structures, soft robotics, and aerospace. Determination of traction–separation (T–S) relations at interfaces in composites can lead to evaluations of structural reliability, mechanical robustness, and failures criteria. Accurate measurements on T–S relations remain challenging, since the interface interaction generally happens at microscale. With the emergence of machine learning (ML), data-driven model becomes an efficient method to predict the interfacial behaviors of composite materials and establish their mechanical models. Here, we combine ML, finite element analysis (FEA), and empirical experiments to develop data-driven models that characterize interfacial mechanical properties precisely. Specifically, eXtreme Gradient Boosting (XGBoost) multi-output regressions and classifier models are harnessed to investigate T–S relations and identify the imperfection locations at interface, respectively. The ML models are trained by macroscale force–displacement curves, which can be obtained from FEA and standard mechanical tests. The results show accurate predictions of T–S relations (R2 = 0.988) and identification of imperfection locations with 81% accuracy. Our models are experimentally validated by 3D printed double cantilever beam specimens from different materials. Furthermore, we provide a code package containing trained ML models, allowing other researchers to establish T–S relations for different material interfaces.
Efficient water desalination with graphene nanopores obtained using artificial intelligence
Authors: Wang Yuyang , Cao Zhonglin , Barati Farimani Amir
Published: July 2021

Two-dimensional nanomaterials, such as graphene, have been extensively studied because of their outstanding physical properties. Structure and topology of nanopores on such materials can be important for their performances in real-world engineering applications, like water desalination. However, discovering the most efficient nanopores often involves a very large number of experiments or simulations that are expensive and time-consuming. In this work, we propose a data-driven artificial intelligence (AI) framework for discovering the most efficient graphene nanopore for water desalination. Via a combination of deep reinforcement learning (DRL) and convolutional neural network (CNN), we are able to rapidly create and screen thousands of graphene nanopores and select the most energy-efficient ones. Molecular dynamics (MD) simulations on promising AI-created graphene nanopores show that they have higher water flux while maintaining rival ion rejection rate compared to the normal circular nanopores. Irregular shape with rough edges geometry of AI-created pores is found to be the key factor for their high water desalination performance. Ultimately, this study shows that AI can be a powerful tool for nanomaterial design and screening.
Selective therapeutic strategy for p53-deficient cancer by targeting dysregulation in DNA repair
Authors: Zonneville Justin , Wang Moyi , Alruwaili Mohammed M. , Smith Brandon , Melnick Megan , Eng Kevin H. , Melendy Thomas , Park Ben Ho , Iyer Renuka , Fountzilas Christos , Bakin Andrei V.
Published: July 2021

Breast carcinomas commonly carry mutations in the tumor suppressor p53, although therapeutic efforts to target mutant p53 have previously been unfruitful. Here we report a selective combination therapy strategy for treatment of p53 mutant cancers. Genomic data revealed that p53 mutant cancers exhibit high replication activity and express high levels of the Base-Excision Repair (BER) pathway, whereas experimental testing showed substantial dysregulation in BER. This defect rendered accumulation of DNA damage in p53 mutant cells upon treatment with deoxyuridine analogues. Notably, inhibition of poly (ADP-ribose) polymerase (PARP) greatly enhanced this response, whereas normal cells responded with activation of the p53-p21 axis and cell cycle arrest. Inactivation of either p53 or p21/CDKN1A conferred the p53 mutant phenotype. Preclinical animal studies demonstrated a greater anti-neoplastic efficacy of the drug combination (deoxyuridine analogue and PARP inhibitor) than either drug alone. This work illustrates a selective combination therapy strategy for p53 mutant cancers that will improve survival rates and outcomes for thousands of breast cancer patients.
Predicting an optimal oxide/metal catalytic interface for hydrodeoxygenation chemistry of biomass derivatives
Authors: Deo Shyam , Janik Michael J.
Published: July 2021

Complex reaction paths, such as hydrodeoxygenation of multi-oxygenated reactants like furfuryl alcohol, can benefit from a close connection between multi-component (oxide–metal) catalytic sites.
Exploring different photocatalytic behaviors of CdxZn1−xSeyS1−y gradient-alloyed quantum dots via composition regulation
Authors: Ying Xiangjing , Liu Yuxin , Liu Zheng , Zhang Menglong , Wang Chuanglei , Wang Weizhe , Gu Huaimin , Huang Runda , Luo Dongxiang , Liu Xiao
Published: July 2021

Different photocatalytic behaviors of CdxZn1−xSeyS1−y gradient alloyed quantum dots via composition regulation.
Thin ZIF-8 nanosheets synthesized in hydrophilic TRAPs
Authors: Sasaki Koki , Okue Tsuyoshi , Shu Yasuhiro , Miyake Koji , Uchida Yoshiaki , Nishiyama Norikazu
Published: July 2021

Several nm thick ZIF-8 nanosheets can be synthesized from multiple hydrophilic precursors in the hydrophilic space inside bilayers in a decane solution of the amphiphile Brij L4.
Introducing a nested multimedia fate and transport model for organic contaminants (NEM)
Authors: Breivik Knut , Eckhardt Sabine , McLachlan Michael S. , Wania Frank
Published: July 2021

Nesting allows a new global modelling tool to combine computational efficiency with the fine spatial resolution required for many applications.
Lactiplantibacillus plantarum 22A-3-induced TGF-β1 secretion from intestinal epithelial cells stimulated CD103+ DC and Foxp3+ Treg differentiation and amelioration of colitis in mice
Authors: Lamubol Jarukan , Ohto Nobuaki , Kuwahara Hiroshige , Mizuno Masashi
Published: July 2021

LP22A3 induced TGF-β1 secretion from IECs of the small intestine through TLR2, and resulted in the promotion of Foxp3+ Treg and CD103+ DC population, which secreted anti-inflammatory cytokines providing a protective condition in the intestine.
In vitro fecal fermentation profiles and microbiota responses of pulse cell wall polysaccharides: enterotype effect
Authors: Yu Miaomiao , Arıoğlu-Tuncil Seda , Xie Zhuqing , Fu Xiong , Huang Qiang , Chen Tingting , Zhang Bin
Published: July 2021

The gut microbiota community of individuals is predominated by diverse fiber-utilizing bacteria, and might have distinct fermentation outcomes for a given dietary substrate.
Standardisation needs for organ on chip devices
Authors: Piergiovanni Monica , Leite Sofia B. , Corvi Raffaella , Whelan Maurice
Published: July 2021

Standards can demonstrate technological and biological relevance, increase industry implementation and support regulatory acceptance. This article will give you an overview on the state of play and future needs in standardisation for OoC.
(Hydroxy)apatite on cement: insights into a new surface treatment
Authors: Turner Ronald J. , Bots Pieter , Richardson Alan , Bingham Paul A. , Scrimshire Alex , Brown Andrew , S’Ari Mark , Harrington John , Cumberland Susan A. , Renshaw Joanna C. , Baker Matthew J. , Edwards Paul R. , Jenkins Cerys , Hamilton Andrea
Published: July 2021

We have developed a conceptual model describing the formation and mineralisation processes of hydroxyapatite during biogenic and abiotic treatment on cement surfaces.
Atomic vibration as an indicator of the propensity for configurational rearrangements in metallic glasses
Authors: Fan Huiyang , Fan Zhao , Liu Xiongjun , Lu Zhaoping , Ma En
Published: July 2021

Vibrational parameters fare better in correlating with local properties than purely static structural parameters.
Engineering hollow carbon spheres: directly from solid resin spheres to porous hollow carbon spheres via air induced linker cleaving
Authors: Li Neng , Qin Bihui , Kang Hongfei , Cai Nana , Huang Suping , Xiao Qi
Published: July 2021

A facile novel one-step air induced linker cleaving (AILC) method was developed to synthesize hollow carbon spheres (HCSs).
Highly stretchable, high efficiency room temperature self-healing polyurethane adhesive based on hydrogen bonds – applicable to solid rocket propellants
Authors: Jing Tu , Heng Xu , Guifeng Xiang , Ling Chen , Pingyun Li , Xiaode Guo
Published: July 2021

The introduction of weak hydrogen bonds based on the isophorone structure enables the polymer to have high stretchability and self-healing ability at room temperature to heal propellant damage.
Light-mediated controlled and classical polymerizations of less-activated monomers under high-pressure conditions
Authors: Maksym Paulina , Tarnacka Magdalena , Bernat Roksana , Dzienia Andrzej , Szelwicka Anna , Hachuła Barbara , Chrobok Anna , Paluch Marian , Kamiński Kamil
Published: July 2021

An entirely new robust setup combining light and high pressure was applied to polymerize less-activated monomersviathree different “green” polymerization protocols.
Syntheses of five new layered quaternary chalcogenides SrScCuSe3, SrScCuTe3, BaScCuSe3, BaScCuTe3, and BaScAgTe3: crystal structures, thermoelectric properties, and electronic structures
Authors: Ishtiyak Mohd , Jana Subhendu , Karthikeyan R. , Ramesh M. , Tripathy Bikash , Malladi Sairam K. , Niranjan Manish K. , Prakash Jai
Published: July 2021

Five new layered transition metal-based chalcogenides (SrScCuSe3, SrScCuTe3, BaScCuSe3, BaScCuTe3, and BaScAgTe3) were discovered by the exploratory solid-state method.
Insights into the device structure, processing and material design for an organic thin-film transistor towards functional circuit integration
Authors: Guo Xiaojun , Han Lei , Hou Xiao
Published: July 2021

Tremendous efforts in material chemistry and processing techniques have enabled organic thin-film transistors (OTFTs) for various functional circuits and systems.
In situ formed lithium ionic conductor thin film on the surface of high-crystal-layered LiCoO2 as a high-voltage cathode material
Authors: Li Liewu , Yuan Qi , Ye Shenghua , Fu Yonghuan , Ren Xiangzhong , Zhang Qianling , Liu Jianhong
Published: July 2021

The LiCoO2@Li4SiO4 cathode was prepared by a facile interface engineering technique and was found to deliver enhanced structural and electrochemical cycling stability at a high cut-off voltage of 4.5 V.
Multi-shaped strain soliton networks and moiré-potential-modulated band edge states in twisted bilayer SiC
Authors: Kang Dawei , Zuo Zheng-Wei , Wang Zhaowu , Ju Weiwei
Published: July 2021

Tuning the interlayer twist angle provides a new degree of freedom to exploit the potentially excellent properties of two dimensional layered materials.
Development of biodegradable zein-based bilayer coatings for drug-eluting stents
Authors: Lenzuni Martina , Suarato Giulia , Miele Dalila , Carzino Riccardo , Ruggeri Marco , Bertorelli Rosalia , Sandri Giuseppina , Athanassiou Athanassia
Published: July 2021

Zein-based biodegradable bilayer coatings were successfully prepared and characterized. Release profiles, antioxidant potential, and biocompatibility were investigated, aiming for more sustainable coatings for drug-eluting stents.
History, versatility and future prospects of oscillatory carbonylation reactions of alkynes
Authors: Novakovic Katarina , Bruk Lev , Temkin Oleg
Published: July 2021

The BT-GN reactions are versatile chemical oscillators, oscillating in pH, redox potential and turbidity, and releasing heat in a pulsatile manner. The reaction system has a potential to be coupled with intelligent materials and yield applications.
Combined first-principles calculations and experimental study on the photocatalytic mechanism of natural dolomite
Authors: Hou Xiaomin , Cheng Qi , Wang Jianrong , Wu Qingfeng , Zhang Weibin
Published: July 2021

Natural dolomite exhibits notable photocatalytic activity due to the isomorphous substitution of Fe2+ for Mg2+ in the lattice, implying that it can be used as a low-cost photocatalyst.
A plasmon-enhanced theranostic nanoplatform for synergistic chemo-phototherapy of hypoxic tumors in the NIR-II window
Authors: Chen Ming-Ming , Hao Hai-Li , Zhao Wei , Zhao Xueli , Chen Hong-Yuan , Xu Jing-Juan
Published: July 2021

A plasmon-enhanced theranostic nanoplatform for synergistic chemo-phototherapy (PTT/PDT) of hypoxic tumors in the NIR-II window.
An expanded halogen bonding scale using astatine
Authors: Liu Lu , Rahali Seyfeddine , Maurice Rémi , Gomez Pech Cecilia , Montavon Gilles , Le Questel Jean-Yves , Graton Jérôme , Champion Julie , Galland Nicolas
Published: July 2021

Based on the halogen bonding between astatine monoiodide (AtI) and 16 Lewis bases, the newly established pKBAtI scale indicates that the halogen bond basicity of AtI follows the order C ≤ O ≤ S ≈ Se for the acceptor atomic site.
Harnessing electrochemical pH gradient for direct air capture with hydrogen and oxygen by-products in a calcium-based loop
Authors: Zhou Congquan , Ni Jihong , Chen Huiqi , Guan Xiaofei
Published: July 2021

A large pH gradient generated electrochemically in a neutral water electrolysis cell is harnessed for direct air capture (DAC) in addition to simultaneous production of CO2, O2 and H2 in separate chambers.
Properties of twisted topological defects in 2D nematic liquid crystals
Authors: Pearce D. J. G. , Kruse K.
Published: July 2021

We introduce the concept of twisted topological defects to describe out of phase defects in non-equilibrium systems. We investigate how these twists affect the relaxation dynamics of the nematic texture and demonstrate non-trivial, controllable defect trajectories.
Fluoroarene derivative based passivation of perovskite solar cells exhibiting excellent ambient and thermo-stability achieving efficiency >20%
Authors: Hossain Maimur , Garai Rabindranath , Gupta Ritesh Kant , Arunagirinathan Rahul Narasimhan , Iyer Parameswar Krishnan
Published: July 2021

Trap states in perovskite thin films were passivated effectively by pentafluoroaniline (PFA) additive, thereby significantly enhancing the photovoltaic performances as well as the overall device stability.
Stabilizing TiO2/CH3NH3PbI3 heterostructure and enhancing interface trap passivation for efficient and stable perovskite solar cells
Authors: Xu Shendong , Liang Zheng , Zheng Haiying , Zhang Liying , Xu Xiaoxiao , Xu Huifen , Zhu Liangzheng , Ye Jiajiu , Liu Guozhen , Pan Xu
Published: July 2021

A new strategy using organic super-halide salt tetrabutylammonium borohydride (TABH) was proposed to improve the stability of soft TiO2/CH3NH3PbI3 heterostructure and the photovoltaic performance of perovskite solar cells.