bluuebunny/crossref_metadata_2025 huggingface dataset:
A review on low salinity waterflooding in carbonates: challenges and future perspective
Authors: Nande Soumitra B. , Patwardhan Samarth D.
Published: November 2021

Low salinity waterflooding has gained significant attention and importance in the last decade, as it is seen as an impactful method for recovery of additional oil from carbonate reservoirs. Existing literature does not do justice to the underlying mechanisms that aid in the recovery of additional oil from such rock types. In this paper, we present a comprehensive review of the research conducted on low salinity waterflooding in carbonates and further provide a detailed and critical analysis on the same. The intention of this paper is also to present a condensed research summary on the said topic, and to chart out a detailed roadmap for future work, thereby opening the possibilities of new avenues of research in the field.
Current practices and evaluation of barriers and facilitators to surgical site infection prevention measures in Jimma, Ethiopia
Authors: Berman Leigh R. , Lang Andrew , Gelana Beshea , Starke Samuel , Siraj Dawd , Yilma Daniel , Shirley Daniel
Published: November 2021

Objective:

Surgical site infections (SSIs) greatly burden healthcare systems around the world, particularly in low- and middle-income countries. We sought to employ the Systems Engineering Initiative for Patient Safety (SEIPS) model to better characterize SSI prevention practices and factors affecting adherence to prevention guidelines at Jimma University Medical Center (JUMC).

Design:

Our cross-sectional study consisted of semistructured interviews designed to elicit perceptions of and barriers and facilitators to SSI prevention among surgical staff and observations of current preoperative, perioperative, and postoperative SSI prevention practices in surgical cases. Interviews were recorded, manually transcribed, and thematically coded within the SEIPS framework. Trained observers recorded compliance with the World Health Organization’s SSI prevention recommendations.

Setting:

A tertiary-care hospital in Jimma, Ethiopia.

Participants:

Surgical nurses, surgeons, and anesthetists at JUMC.

Results:

Within 16 individual and group interviews, participants cited multiple barriers to SSI prevention including shortages of water and antiseptic materials, lack of clear SSI guidelines and training, minimal Infection Prevention Control (IPC) interaction with surgical staff, and poor SSI tracking. Observations from nineteen surgical cases revealed high compliance with antibiotic prophylaxis (94.7%), hand scrubbing (100%), sterile gloves and instrument use (100%), incision site sterilization (100%), and use of surgical safety checklist (94.7%) but lower compliance with preoperative bathing (26.3%), MRSA screening (0%), and pre- and postoperative glucose (0%, 10.5%) and temperature (57.9%, 47.3%) monitoring.

Conclusions:

Utilizing the SEIPS model helped identify institution-specific barriers and facilitators that can inform targeted interventions to increase compliance with currently underperformed SSI prevention practices at JUMC.
Bounds for rotating Rayleigh–Bénard convection at large Prandtl number
Authors: Tilgner A.
Published: November 2021

Bounds are derived for rotating Rayleigh–Bénard convection with free slip boundaries as a function of the Rayleigh, Taylor and Prandtl numbers

${\textit {Ra}}$

,

${\textit {Ta}}$

and

${\textit {Pr}}$

. At infinite

${\textit {Pr}}$

and

${\textit {Ta}} > 130$

, the Nusselt number

${\textit {Nu}}$

obeys

${\textit {Nu}} \leqslant \frac {7}{36} \left ({4}/{{\rm \pi} ^2} \right )^{1/3} {\textit {Ra}} {\textit {Ta}}^{-1/3}$

, whereas the kinetic energy density

$E_{kin}$

obeys

$E_{kin} \leqslant ({7}/{72 {\rm \pi}}) \left ({4}/{{\rm \pi} } \right )^{1/3} {\textit {Ra}}^2 {\textit {Ta}}^{-2/3}$

in the frame of reference in which the total momentum is zero, and

$E_{kin} \leqslant ({1}/{2{\rm \pi} ^2})({{\textit {Ra}}^2}/{{\textit {Ta}}})({\textit {Nu}}-1)$

. These three bounds are derived from the momentum equation and the maximum principle for temperature and are extended to general

${\textit {Pr}}$

. The extension to finite

${\textit {Pr}}$

is based on the fact that the maximal velocity in rotating convection at infinite

${\textit {Pr}}$

is bound by

$1.23 {\textit {Ra}} {\textit {Ta}}^{-1/3}$

.
Engaging armed groups at the International Committee of the Red Cross: Challenges, opportunities and COVID-19
Authors: Herbet Irénée , Drevon Jérôme
Published: November 2021

This article examines the presence of 605 armed groups in today's conflict environment by bringing new evidence based on internal research. It looks in particular at the way these non-State entities provide varying degrees of services to the population in the spaces that they control, and how this might impact the way a humanitarian organization like the ICRC engages with them in a dialogue over time. This model of analysis is then used to situate and better explain armed groups’ positions on the COVID crisis.
Forecasting Compound Floods in Complex Coastal Regions
Authors: Moghimi Saeed , Myers Edward , Pe’eri Shachak , Zhang Y. , Yi Fei
Published: November 2021

Coastal communities face more frequent floods in which rain, rivers, and ocean storm surge combine forces. A reliable system that accurately predicts inundation from these events is urgently needed.
Managing Wetlands to Improve Carbon Sequestration
Authors: Krauss Ken , Zhu Zhiliang , Stagg Camille
Published: November 2021

A new book examines research on wetlands from around the world to illustrate how environmental management can improve carbon sequestration while improving the health and function of wetlands.
Light management with quantum nanostructured dots-in-host semiconductors
Authors: Alexandre M. , Águas H. , Fortunato E. , Martins R. , Mendes M. J.
Published: November 2021

Insightful knowledge on quantum nanostructured materials is paramount to engineer and exploit their vast gamut of applications. Here, a formalism based on the single-band effective mass equation was developed to determine the light absorption of colloidal quantum dots (CQDs) embedded in a wider bandgap semiconductor host, employing only three parameters (dots/host potential barrier, effective mass, and QD size). It was ascertained how to tune such parameters to design the energy level structure and consequent optical response. Our findings show that the CQD size has the biggest effect on the number and energy of the confined levels, while the potential barrier causes a linear shift of their values. While smaller QDs allow wider energetic separation between levels (as desired for most quantum-based technologies), the larger dots with higher number of levels are those that exhibit the strongest absorption. Nevertheless, it was unprecedently shown that such quantum-enabled absorption coefficients can reach the levels (104–105 cm−1) of bulk semiconductors.
GeSnOI mid-infrared laser technology
Authors: Wang Binbin , Sakat Emilie , Herth Etienne , Gromovyi Maksym , Bjelajac Andjelika , Chaste Julien , Patriarche Gilles , Boucaud Philippe , Boeuf Frédéric , Pauc Nicolas , Calvo Vincent , Chrétien Jérémie , Frauenrath Marvin , Chelnokov Alexei , Reboud Vincent , Hartmann Jean-Michel , El Kurdi Moustafa
Published: November 2021

GeSn alloys are promising materials for CMOS-compatible mid-infrared lasers manufacturing. Indeed, Sn alloying and tensile strain can transform them into direct bandgap semiconductors. This growing laser technology however suffers from a number of limitations, such as poor optical confinement, lack of strain, thermal, and defects management, all of which are poorly discussed in the literature. Herein, a specific GeSn-on-insulator (GeSnOI) stack using stressor layers as dielectric optical claddings is demonstrated to be suitable for a monolithically integration of planar Group-IV semiconductor lasers on a versatile photonic platform for the near- and mid-infrared spectral range. Microdisk-shape resonators on mesa structures were fabricated from GeSnOI, after bonding a Ge0.9Sn0.1 alloy layer grown on a Ge strain-relaxed-buffer, itself on a Si(001) substrate. The GeSnOI microdisk mesas exhibited significantly improved optical gain as compared to that of conventional suspended microdisk resonators formed from the as-grown layer. We further show enhanced vertical out-coupling of the disk whispering gallery mode in-plane radiation, with up to 30% vertical out-coupling efficiency. As a result, the GeSnOI approach can be a valuable asset in the development of silicon-based mid-infrared photonics that combine integrated sources in a photonic platform with complex lightwave engineering.
PTEN alleviates maladaptive repair of renal tubular epithelial cells by restoring CHMP2A-mediated phagosome closure
Authors: Wang Huizhen , Wang Yifan , Wang Xin , Huang Huimi , Bao Jingfu , Zhong Wenhui , Li Aiqing
Published: November 2021

Phosphatase and Tensin Homolog on chromosome Ten (PTEN) has emerged as a key protein that governs the response to kidney injury. Notably, renal adaptive repair is important for preventing acute kidney injury (AKI) to chronic kidney disease (CKD) transition. To test the role of PTEN in renal repair after acute injury, we constructed a mouse model that overexpresses PTEN in renal proximal tubular cells (RPTC) by crossing PTENfl-stop-fl mice with Ggt1-Cre mice. Mass spectrometry-based proteomics was performed after subjecting these mice to ischemia/reperfusion (I/R). We found that PTEN was downregulated in renal tubular cells in mice and cultured HK-2 cells subjected to renal maladaptive repair induced by I/R. Renal expression of PTEN negatively correlated with NGAL and fibrotic markers. RPTC-specific PTEN overexpression relieved I/R-induced maladaptive repair, as indicated by alleviative tubular cell damage, apoptosis, and subsequent renal fibrosis. Mass spectrometry analysis revealed that differentially expressed proteins in RPTC-specific PTEN overexpression mice subjected to I/R were significantly enriched in phagosome, PI3K/Akt, and HIF-1 signaling pathway and found significant upregulation of CHMP2A, an autophagy-related protein. PTEN deficiency downregulated CHMP2A and inhibited phagosome closure and autolysosome formation, which aggravated cell injury and apoptosis after I/R. PTEN overexpression had the opposite effect. Notably, the beneficial effect of PTEN overexpression on autophagy flux and cell damage was abolished when CHMP2A was silenced. Collectively, our study suggests that PTEN relieved renal maladaptive repair in terms of cell damage, apoptosis, and renal fibrosis by upregulating CHMP2A-mediated phagosome closure, suggesting that PTEN/CHMP2A may serve as a novel therapeutic target for the AKI to CKD transition.
Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in murine cardiopharyngeal mesoderm
Authors: Nomaru Hiroko , Liu Yang , De Bono Christopher , Righelli Dario , Cirino Andrea , Wang Wei , Song Hansoo , Racedo Silvia E. , Dantas Anelisa G. , Zhang Lu , Cai Chen-Leng , Angelini Claudia , Christiaen Lionel , Kelly Robert G. , Baldini Antonio , Zheng Deyou , Morrow Bernice E.
Published: November 2021

The poles of the heart and branchiomeric muscles of the face and neck are formed from the cardiopharyngeal mesoderm within the pharyngeal apparatus. They are disrupted in patients with 22q11.2 deletion syndrome, due to haploinsufficiency of TBX1, encoding a T-box transcription factor. Here, using single cell RNA-sequencing, we now identify a multilineage primed population within the cardiopharyngeal mesoderm, marked by Tbx1, which has bipotent properties to form cardiac and branchiomeric muscle cells. The multilineage primed cells are localized within the nascent mesoderm of the caudal lateral pharyngeal apparatus and provide a continuous source of cardiopharyngeal mesoderm progenitors. Tbx1 regulates the maturation of multilineage primed progenitor cells to cardiopharyngeal mesoderm derivatives while restricting ectopic non-mesodermal gene expression. We further show that TBX1 confers this balance of gene expression by direct and indirect regulation of enriched genes in multilineage primed progenitors and downstream pathways, partly through altering chromatin accessibility, the perturbation of which can lead to congenital defects in individuals with 22q11.2 deletion syndrome.
Measuring the photoelectron emission delay in the molecular frame
Authors: Rist Jonas , Klyssek Kim , Novikovskiy Nikolay M. , Kircher Max , Vela-Pérez Isabel , Trabert Daniel , Grundmann Sven , Tsitsonis Dimitrios , Siebert Juliane , Geyer Angelina , Melzer Niklas , Schwarz Christian , Anders Nils , Kaiser Leon , Fehre Kilian , Hartung Alexander , Eckart Sebastian , Schmidt Lothar Ph. H. , Schöffler Markus S. , Davis Vernon T. , Williams Joshua B. , Trinter Florian , Dörner Reinhard , Demekhin Philipp V. , Jahnke Till
Published: November 2021

How long does it take to emit an electron from an atom? This question has intrigued scientists for decades. As such emission times are in the attosecond regime, the advent of attosecond metrology using ultrashort and intense lasers has re-triggered strong interest on the topic from an experimental standpoint. Here, we present an approach to measure such emission delays, which does not require attosecond light pulses, and works without the presence of superimposed infrared laser fields. We instead extract the emission delay from the interference pattern generated as the emitted photoelectron is diffracted by the parent ion’s potential. Targeting core electrons in CO, we measured a 2d map of photoelectron emission delays in the molecular frame over a wide range of electron energies. The emission times depend drastically on the photoelectrons’ emission directions in the molecular frame and exhibit characteristic changes along the shape resonance of the molecule.
Independent infections of porcine deltacoronavirus among Haitian children
Authors: Lednicky John A. , Tagliamonte Massimiliano S. , White Sarah K. , Elbadry Maha A. , Alam Md. Mahbubul , Stephenson Caroline J. , Bonny Tania S. , Loeb Julia C. , Telisma Taina , Chavannes Sonese , Ostrov David A. , Mavian Carla , Beau De Rochars Valery Madsen , Salemi Marco , Morris J. Glenn
Published: November 2021

Coronaviruses have caused three major epidemics since 2003, including the ongoing SARS-CoV-2 pandemic. In each case, the emergence of coronavirus in our species has been associated with zoonotic transmissions from animal reservoirs1,2, underscoring how prone such pathogens are to spill over and adapt to new species. Among the four recognized genera of the family Coronaviridae, human infections reported so far have been limited to alphacoronaviruses and betacoronaviruses3–5. Here we identify porcine deltacoronavirus strains in plasma samples of three Haitian children with acute undifferentiated febrile illness. Genomic and evolutionary analyses reveal that human infections were the result of at least two independent zoonoses of distinct viral lineages that acquired the same mutational signature in the genes encoding Nsp15 and the spike glycoprotein. In particular, structural analysis predicts that one of the changes in the spike S1 subunit, which contains the receptor-binding domain, may affect the flexibility of the protein and its binding to the host cell receptor. Our findings highlight the potential for evolutionary change and adaptation leading to human infections by coronaviruses outside of the previously recognized human-associated coronavirus groups, particularly in settings where there may be close human–animal contact.
SPME-LC/MS-based serum metabolomic phenotyping for distinguishing ovarian cancer histologic subtypes: a pilot study
Authors: Olkowicz Mariola , Rosales-Solano Hernando , Kulasingam Vathany , Pawliszyn Janusz
Published: November 2021

Epithelial ovarian cancer (EOC) is the most common cause of death from gynecological cancer. The outcomes of EOC are complicated, as it is often diagnosed late and comprises several heterogenous subtypes. As such, upfront treatment can be highly challenging. Although many significant advances in EOC management have been made over the past several decades, further work must be done to develop early detection tools capable of distinguishing between the various EOC subtypes. In this paper, we present a sophisticated analytical pipeline based on solid-phase microextraction (SPME) and three orthogonal LC/MS acquisition modes that facilitates the comprehensive mapping of a wide range of analytes in serum samples from patients with EOC. PLS-DA multivariate analysis of the metabolomic data was able to provide clear discrimination between all four main EOC subtypes: serous, endometrioid, clear cell, and mucinous carcinomas. The prognostic performance of discriminative metabolites and lipids was confirmed via multivariate receiver operating characteristic (ROC) analysis (AUC value > 88% with 20 features). Further pathway analysis using the top 57 dysregulated metabolic features showed distinct differences in amino acid, lipid, and steroids metabolism among the four EOC subtypes. Thus, metabolomic profiling can serve as a powerful tool for complementing histology in classifying EOC subtypes.
SuperSelective primer pairs for sensitive detection of rare somatic mutations
Authors: Kramer Fred Russell , Vargas Diana Yaneth
Published: November 2021

SuperSelective primers, by virtue of their unique design, enable the selective exponential amplification of rare DNA fragments containing somatic mutations in the presence of abundant closely related wild-type DNA fragments. However, when a SuperSelective primer is used in conjunction with a conventional reverse primer, linear amplification of the abundant wild-type fragments occurs, and this may lead to a late arising signal that can be confused with the late arising signal from the rare mutant fragments. We have discovered that the use of a pair of SuperSelective primers, one specific for the target mutation in a plus strand, and the other specific for the same mutation in the complementary minus strand, but both possessing 3′-terminal nucleotides that are complementary to the mutation, significantly suppresses the linear amplification of the related wild-type sequence, and prevents the generation of false mutant sequences due to mis-incorporation by the DNA polymerase. As a consequence, the absence of mutant fragments in a sample does not give rise to a false-positive signal, and the presence of mutant fragments in a sample is clearly distinguishable as a true-positive signal. The use of SuperSelective primer pairs should enhance the sensitivity of multiplex PCR assays that identify and quantitate somatic mutations in liquid biopsies obtained from patients with cancer, thereby enabling the choice of a targeted therapy, the determination of its effectiveness over time, and the substitution of a more appropriate therapy as new mutations arise.
Detection of cancer stem cells by EMT-specific biomarker-based peptide ligands
Authors: Chen Yi-An , Ho Cheau-Ling , Ku Min-Tzu , Hwu Luen , Lu Cheng-Hsiu , Chiu Sain-Jhih , Chang Wen-Yi , Liu Ren-Shyan
Published: November 2021

The occurrence of epithelial-mesenchymal transition (EMT) within tumors, which enables invasion and metastasis, is linked to cancer stem cells (CSCs) with drug and radiation resistance. We used two specific peptides, F7 and SP peptides, to detect EMT derived cells or CSCs. Human tongue squamous carcinoma cell line-SAS transfected with reporter genes was generated and followed by spheroid culture. A small molecule inhibitor-Unc0642 and low-dose ionizing radiation (IR) were used for induction of EMT. Confocal microscopic imaging and fluorescence-activated cell sorting analysis were performed to evaluate the binding ability and specificity of peptides. A SAS xenograft mouse model with EMT induction was established for assessing the binding affinity of peptides. The results showed that F7 and SP peptides not only specifically penetrated into cytoplasm of SAS cells but also bound to EMT derived cells and CSCs with high nucleolin and vimentin expression. In addition, the expression of CSC marker and the binding of peptides were increased in tumors isolated from Unc0642/IR-treated groups. Our study demonstrates the potential of these peptides for detecting EMT derived cells or CSCs and might provide an alternative isolation method for these subpopulations within the tumor in the future.
Principles governing control of aggregation and dispersion of aqueous graphene oxide
Authors: Suter James L. , Coveney Peter V.
Published: November 2021

Controlling the structure of graphene oxide (GO) phases and their smaller analogues, graphene (oxide) quantum dots (GOQDs), is vitally important for any of their widespread intended applications: highly ordered arrangements of nanoparticles for thin-film or membrane applications of GO, dispersed nanoparticles for composite materials and three-dimensional porous arrangements for hydrogels. In aqueous environments, it is not only the chemical composition of the GO flakes that determines their morphologies; external factors such as pH and the coexisting cations also influence the structures formed. By using accurate models of GO that capture the heterogeneity of surface oxidation and very large-scale coarse-grained molecular dynamics that can simulate the behaviour of GO at realistic sizes of GOQDs, the driving forces that lead to the various morphologies in aqueous solution are resolved. We find the morphologies are determined by a complex interplay between electrostatic, $${\pi }$$
π
–$${\pi }$$
π
and hydrogen bonding interactions. Assembled morphologies can be controlled by changing the degree of oxidation and the pH. In acidic aqueous solution, the GO flakes vary from fully aggregated over graphitic domains to partial aggregation via hydrogen bonding between hydroxylated domains, leading to the formation of planar extended flakes at high oxidation ratios and stacks at low oxidation ratios. At high pH, where the edge carboxylic acid groups are deprotonated, electrostatic repulsion leads to more dispersion, but a variety of aggregation behaviour is surprisingly still observed: over graphitic regions, via hydrogen bonding and “face-edge” interactions. Calcium ions cause additional aggregation, with a greater number of “face-face” and “edge-edge” aggregation mechanisms, leading to irregular aggregated structures. “Face-face” aggregation mechanisms are enhanced by the GO flakes possessing distinct domains of hydroxylated and graphitic regions, with $${\pi }$$
π
–$${\pi }$$
π
and hydrogen bonding interactions prevalent between these regions on aggregated flakes respectively. These findings furnish explanations for the aggregation characteristics of GO and GOQDs, and provide computational methods to design directed synthesis routes for self-assembled and associated applications.
3D hotspot matrix of Au nanoparticles on Au island film with a spacer layer of dithiol molecules for highly sensitive surface-enhanced Raman spectroscopy
Authors: Lee Dong-Jin , Kim Dae Yu
Published: November 2021

Engineering of efficient plasmonic hotspots has been receiving great attention to enhance the sensitivity of surface-enhanced Raman scattering (SERS). In the present study, we propose a highly sensitive SERS platform based on Au nanoparticles (AuNPs) on Au island film (AuIF) with a spacer layer of 1,4-benzenedimethanethiol (BDMT). The three-dimensional (3D) hotspot matrix has been rationally designed based on the idea of employing 3D hotspots with a vertical nanogap between AuIF and AuNPs after generating large area two-dimensional hotspots of AuIF. AuNPs@BDMT@AuIF are fabricated by functionalizing BDMT on AuIF and then immobilizing AuNPs. The SERS performance is investigated with Rhodamine 6G as a probe molecule and the determined enhancement factor is 1.3 × 105. The AuNPs@BDMT@AuIF are then employed to detect thiram, which is used as a fungicide, with a detection limit of 13 nM. Our proposed platform thus shows significant potential for use in highly sensitive SERS sensors.
Functional roles of multiple Ton complex genes in a Sphingobium degrader of lignin-derived aromatic compounds
Authors: Fujita Masaya , Yano Shodai , Shibata Koki , Kondo Mizuki , Hishiyama Shojiro , Kamimura Naofumi , Masai Eiji
Published: November 2021

TonB-dependent transporters (TBDTs) mediate outer membrane transport of nutrients using the energy derived from proton motive force transmitted from the TonB–ExbB–ExbD complex localized in the inner membrane. Recently, we discovered ddvT encoding a TBDT responsible for the uptake of a 5,5-type lignin-derived dimer in Sphingobium sp. strain SYK-6. Furthermore, overexpression of ddvT in an SYK-6-derivative strain enhanced its uptake capacity, improving the rate of platform chemical production. Thus, understanding the uptake system of lignin-derived aromatics is fundamental for microbial conversion-based lignin valorization. Here we examined whether multiple tonB-, exbB-, and exbD-like genes in SYK-6 contribute to the outer membrane transport of lignin-derived aromatics. The disruption of tonB2–6 and exbB3 did not reduce the capacity of SYK-6 to convert or grow on lignin-derived aromatics. In contrast, the introduction of the tonB1–exbB1–exbD1–exbD2 operon genes into SYK-6, which could not be disrupted, promoted the conversion of β-O-4-, β-5-, β-1-, β-β-, and 5,5-type dimers and monomers, such as ferulate, vanillate, syringate, and protocatechuate. These results suggest that TonB-dependent uptake involving the tonB1 operon genes is responsible for the outer membrane transport of the above aromatics. Additionally, exbB2/tolQ and exbD3/tolR were suggested to constitute the Tol-Pal system that maintains the outer membrane integrity.
Biphasic (5–2%) oxygen concentration strategy significantly improves the usable blastocyst and cumulative live birth rates in in vitro fertilization
Authors: Brouillet Sophie , Baron Chloé , Barry Fatima , Andreeva Aneta , Haouzi Delphine , Gala Anna , Ferrières-Hoa Alice , Loup Vanessa , Anahory Tal , Ranisavljevic Noémie , Gaspari Laura , Hamamah Samir
Published: November 2021

Oxygen (O2) concentration is approximately 5% in the fallopian tube and 2% in the uterus in humans. A “back to nature” approach could increase in vitro fertilization (IVF) outcomes. This hypothesis was tested in this monocentric observational retrospective study that included 120 couples who underwent two IVF cycles between 2014 and 2019. Embryos were cultured at 5% from day 0 (D0) to D5/6 (monophasic O2 concentration strategy) in the first IVF cycle, and at 5% O2 from D0 to D3 and 2% O2 from D3 to D5/6 (biphasic O2 concentration strategy) in the second IVF cycle. The total and usable blastocyst rates (44.4% vs. 54.8%, p = 0.049 and 21.8% vs. 32.8%, p = 0.002, respectively) and the cumulative live birth rate (17.9% vs. 44.1%, p = 0.027) were significantly higher with the biphasic (5%-2%) O2 concentration strategy. Whole transcriptome analysis of blastocysts donated for research identified 707 RNAs that were differentially expressed in function of the O2 strategy (fold-change > 2, p value < 0.05). These genes are mainly involved in embryo development, DNA repair, embryonic stem cell pluripotency, and implantation potential. The biphasic (5–2%) O2 concentration strategy for preimplantation embryo culture could increase the “take home baby rate”, thus improving IVF cost-effectiveness and infertility management.
Single-cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis
Authors: Bais Abha S. , Cerqueira Débora M. , Clugston Andrew , Bodnar Andrew J. , Ho Jacqueline , Kostka Dennis
Published: November 2021

The kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. Defects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single-cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle-related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. In addition, augmented expression of cell cycle related genes Birc5, Cks2, Ccnb1, Ccnd1 and Tuba1a/b was detected in immature distal tubules, suggesting cell cycle regulation may be required for early events of nephron patterning and tubular fusion between the distal nephron and collecting duct epithelia.
TGF-β-mediated epithelial–mesenchymal transition and tumor-promoting effects in CMT64 cells are reflected in the transcriptomic signature of human lung adenocarcinoma
Authors: Miyashita Naoya , Enokido Takayoshi , Horie Masafumi , Fukuda Kensuke , Urushiyama Hirokazu , Strell Carina , Brunnström Hans , Micke Patrick , Saito Akira , Nagase Takahide
Published: November 2021

Epithelial–mesenchymal transition (EMT) is a cellular process during which epithelial cells acquire mesenchymal phenotypes. Cancer cells undergo EMT to acquire malignant features and TGF-β is a key regulator of EMT. Here, we demonstrate for the first time that TGF-β could elicit EMT in a mouse lung adenocarcinoma cell line. TGF-β signaling activation led to cell morphological changes corresponding to EMT and enhanced the expression of mesenchymal markers and EMT-associated transcription factors in CMT64 lung cancer cells. RNA-sequencing analyses revealed that TGF-β increases expression of Tead transcription factors and an array of Tead2 target genes. TGF-β stimulation also resulted in alternative splicing of several genes including Cd44, tight junction protein 1 (Tjp1), and Cortactin (Cttn). In parallel with EMT, TGF-β enhanced cell growth of CMT64 cells and promoted tumor formation in a syngeneic transplantation model. Of clinical importance, the expression of TGF-β-induced genes identified in CMT64 cells correlated with EMT gene signatures in human lung adenocarcinoma tissue samples. Furthermore, TGF-β-induced gene enrichment was related to poor prognosis, underscoring the tumor-promoting role of TGF-β signaling in lung adenocarcinoma. Our cellular and syngeneic transplantation model would provide a simple and useful experimental tool to study the significance of TGF-β signaling and EMT.
Effects of species and geo-information on the 137Cs concentrations in edible wild mushrooms and plants collected by residents after the Fukushima nuclear accident
Authors: Komatsu Masabumi , Hashimoto Shoji , Matsuura Toshiya
Published: November 2021

After the accident at the Fukushima Daiichi Nuclear Power Plant (FDNPP), much of the wild and edible mushrooms and plants in the surrounding areas were contaminated with radiocesium (137Cs). To elucidate their concentration characteristics, we analyzed 137Cs radioactivity data in edible forest products brought in for food inspection by the residents of Kawauchi Village, 12–30 km away from the FDNPP, from 2012 to 2019. A Bayesian model to estimate 137Cs concentration was constructed. Parameters of the normalized concentration of species (NCsp) for mushrooms were similar to those of the same species obtained in a previous study. Although NCsp values were highly varied among species, mycorrhizal mushrooms tended to have high NCsp values, followed by saprotrophic mushrooms, and wild edible plants values were low. Also, half of mycorrhizal mushroom species (8 of 16) showed an increasing trend in concentration with time; however, saprotrophic mushrooms and wild plants generally demonstrated a decreasing trend (22 of 24). The model considering the sub-village location information decreased the error of individual samples by 40% compared to the model not considering any location information, indicating that the detailed geo-information improved estimation accuracy. Our results indicate that the radioactivity data from samples collected by local residents can be used to accurately assess internal exposure to radiation due to self-consumption of contaminated wild mushrooms and plants.
Novel role of zonulin in the pathophysiology of gastro-duodenal transit: a clinical and translational study
Authors: Martinez Enid E. , Lan Jinggang , Konno Takumi , Miranda-Ribera Alba , Fiorentino Maria , Mehta Nilesh M. , Fasano Alessio
Published: November 2021

We examined the relationship between zonulin and gastric motility in critical care patients and a translational mouse model of systemic inflammation. Gastric motility and haptoglobin (HP) 2 isoform quantification, proxy for zonulin, were examined in patients. Inflammation was triggered by lipopolysaccharide (LPS) injection inC57Bl/6zonulin transgenic mouse (Ztm) and wildtype (WT) mice as controls, and gastro-duodenal transit was examined by fluorescein-isothiocyanate, 6 and 12 h after LPS-injection. Serum cytokines and zonulin protein levels, and zonulin gastric-duodenal mRNA expression were examined. Eight of 20 patients [14 years, IQR (12.25, 18)] developed gastric dysmotility and were HP2 isoform-producing. HP2 correlated with gastric dysmotility (r = − 0.51, CI − 0.81 to 0.003, p = 0.048). LPS injection induced a time-dependent increase in IL-6 and KC-Gro levels in all mice (p < 0.0001). Gastric dysmotility was reduced similarly in Ztm and WT mice in a time-dependent manner. Ztm had 16% faster duodenal motility than WT mice 6H post-LPS, p = 0.01. Zonulin mRNA expression by delta cycle threshold (dCT) was higher in the stomach (9.7, SD 1.4) than the duodenum (13.9, SD 1.4) 6H post-LPS, p = 0.04. Serum zonulin protein levels were higher in LPS-injected mice compared to vehicle-injected animals in a time-dependent manner. Zonulin correlated with gastric dysmotility in patients. A mouse model had time-dependent gastro-duodenal dysmotility after LPS-injection that paralleled zonulin mRNA expression and protein levels.
The brain’s structural differences between postherpetic neuralgia and lower back pain
Authors: Qiu Jianxing , Du Mengjiao , Yang Junzhe , Lin Zengmao , Qin Naishan , Sun Xiaowei , Li Linling , Zou Rushi , Wei Juan , Wu Bing , Liu Jing , Zhang Zhiguo
Published: November 2021

The purpose is to explore the brain’s structural difference in local morphology and between-region networks between two types of peripheral neuropathic pain (PNP): postherpetic neuralgia (PHN) and lower back pain (LBP). A total of 54 participants including 38 LBP and 16 PHN patients were enrolled. The average pain scores were 7.6 and 7.5 for LBP and PHN. High-resolution structural T1 weighted images were obtained. Both grey matter volume (GMV) and morphological connectivity (MC) were extracted. An independent two-sample t-test with false discovery rate (FDR) correction was used to identify the brain regions where LBP and PHN patients showed significant GMV difference. Next, we explored the differences of MC network between LBP and PHN patients and detected the group differences in network properties by using the two-sample t-test and FDR correction. Compared with PHN, LBP patients had significantly larger GMV in temporal gyrus, insula and fusiform gyrus (p < 0.05). The LBP cohort had significantly stronger MC in the connection between right precuneus and left opercular part of inferior frontal gyrus (p < 0.05). LBP patients had significantly stronger degree in left anterior cingulate gyrus and left rectus gyrus (p < 0.05) while had significantly weaker degree than PHN patients in left orbital part of middle frontal gyrus, left supplementary motor area and left superior parietal lobule (p < 0.05). LBP and PHN patients had significant differences in the brain’s GMV, MC, and network properties, which implies that different PNPs have different neural mechanisms concerning pain modulation.
Identifying subtypes of depression in clinician-annotated text: a retrospective cohort study
Authors: Kung Benson , Chiang Maurice , Perera Gayan , Pritchard Megan , Stewart Robert
Published: November 2021

Current criteria for depression are imprecise and do not accurately characterize its distinct clinical presentations. As a result, its diagnosis lacks clinical utility in both treatment and research settings. Data-driven efforts to refine criteria have typically focused on a limited set of symptoms that do not reflect the disorder’s heterogeneity. By contrast, clinicians often write about patients in depth, creating descriptions that may better characterize depression. However, clinical text is not commonly used to this end. Here we show that clinically relevant depressive subtypes can be derived from unstructured electronic health records. Five subtypes were identified amongst 18,314 patients with depression treated at a large mental healthcare provider by using unsupervised machine learning: severe-typical, psychotic, mild-typical, agitated, and anergic-apathetic. Subtypes were used to place patients in groups for validation; groups were found to be associated with future outcomes and characteristics that were consistent with the subtypes. These associations suggest that these categorizations are actionable due to their validity with respect to disease prognosis. Moreover, they were derived with automated techniques that might theoretically be widely implemented, allowing for future analyses in more varied populations and settings. Additional research, especially with respect to treatment response, may prove useful in further evaluation.
Microplastics increase susceptibility of amphibian larvae to the chytrid fungus Batrachochytrium dendrobatidis
Authors: Bosch Jaime , Thumsová Barbora , López-Rojo Naiara , Pérez Javier , Alonso Alberto , Fisher Matthew C. , Boyero Luz
Published: November 2021

Microplastics (MPs), a new class of pollutants that pose a threat to aquatic biodiversity, are of increasing global concern. In tandem, the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) causing the disease chytridiomycosis is emerging worldwide as a major stressor to amphibians. We here assess whether synergies exist between this infectious disease and MP pollution by mimicking natural contact of a highly susceptible species (midwife toads, Alytes obstetricans) with a Bd-infected reservoir species (fire salamanders, Salamandra salamandra) in the presence and absence of MPs. We found that MP ingestion increases the burden of infection by Bd in a dose-dependent manner. However, MPs accumulated to a greater extent in amphibians that were not exposed to Bd, likely due to Bd-damaged tadpole mouthparts interfering with MP ingestion. Our experimental approach showed compelling interactions between two emergent processes, chytridiomycosis and MP pollution, necessitating further research into potential synergies between these biotic and abiotic threats to amphibians.
Magnetic composite of γ-Fe2O3 hollow sphere and palladium doped nitrogen-rich mesoporous carbon as a recoverable catalyst for C–C coupling reactions
Authors: Malmir Masoume , Heravi Majid M. , Amiri Zahra , Kafshdarzadeh Kosar
Published: November 2021

In this article, palladated-magnetic nitrogen doped porous carbon was prepared from nano magneticγ-Fe2O3hollow sphere (h-Fe2O3) with high specific surface area and pore volume. To the purpose, initially h-Fe2O3was prepared and covered with glucose via hydrothermal treatment with subsequent polymerization of organic shell. The polymerization of melamine-resorcinol–formaldehyde (MRF) was achieved in the presence of Cl-functionalized glucose coated h-Fe2O3(h-Fe2O3@glu-MRF). Next, the prepared magnetic core–shell hollow sphere was palladated followed by carbonization to yield Pd@h-Fe2O3@C introducing more pores in its structure. The resulted compound, Pd@h-Fe2O3@C, was fully characterized, showing that carbonization process expressively increased the specific surface area. The resulted Pd@h-Fe2O3@C was successfully used for promoting C–C coupling reactions under mild reaction conditions as a heterogeneous catalyst and its activity was compared with some prepared control catalysts. This novel catalyst was magnetically separated simply by a magnet bar and recycled and reused at least in five consecutive runs, without considerable loss of its activity. It is note mentioning that, high recyclability with low Pd leaching are another gains of this protocol.
Nanomaterial-based bioorthogonal nanozymes for biological applications
Authors: Fedeli Stefano , Im Jungkyun , Gopalakrishnan Sanjana , Elia James L. , Gupta Aarohi , Kim Dongkap , Rotello Vincent M.
Published: November 2021

Nanomaterials encapsulate bioorthogonal catalysts enabling their application in biological environment for sustained production of functional molecules.
Portable point-of-care diagnostic devices: an updated review
Authors: Shu Tong , Hunter Haley , Zhou Ziping , Sun Yanping , Cheng Xiaojun , Ma Jianxin , Su Lei , Zhang Xueji , Serpe Michael J.
Published: November 2021

This review highlights recent examples of point-of-care (POC) diagnostics for detecting nucleic acids, proteins, bacteria, and other biomarkers, all focused on highlighting the positive impact of POC on society and human health.
Swim bladder as an alternative biomaterial for bioprosthetic valves
Authors: Li Ning , Li Xin , Ma Ye , Qiao Fan , Bai Yifan , Liu Xiaohong , Xu Zhiyun
Published: November 2021

Valvular structural deterioration and calcification are the main indications for secondary intervention after bioprosthetic valve replacement, promoting an urgent requirement for more durable cardiovascular biomaterials for clinical applications.
Glutathione-degradable polydopamine nanoparticles as a versatile platform for fabrication of advanced photosensitisers for anticancer therapy
Authors: Dai Gaole , Choi Chun Kit K. , Choi Chung Hang Jonathan , Fong Wing-Ping , Ng Dennis K. P.
Published: November 2021

A glutathione-responsive polydopamine-based nanoplatform has been developed which can be used to fabricate biodegradable, tumour-targeting and activatable nanophotosensitisers for targeted photodynamic therapy.
Characterisation of bone regeneration in 3D printed ductile PCL/PEG/hydroxyapatite scaffolds with high ceramic microparticle concentrations
Authors: Cao Chuanliang , Huang Pengren , Prasopthum Aruna , Parsons Andrew J. , Ai Fanrong , Yang Jing
Published: November 2021

3D printed flexible and ductile composite scaffolds with high ceramic particle concentrations and their in vivo bone regeneration performance.
Shock wave induced phase transition from crystalline to the amorphous state of lead nitrate crystals
Authors: Sivakumar A. , Eniya P. , Dhas S. Sahaya Jude , Kumar Raju Suresh , Almansour Abdulrahman I. , Sivashanmugan Kundan , Sundar J. Kalyana , Dhas S. A. Martin Britto
Published: November 2021

Shock wave induced phase transition of Pa3̄–Pa3̄ – high-pressure phase – amorphous for the 0, 1, 2 and 3rd shocked conditions is reported for the technologically important lead nitrate crystal.
Fragmentation and rearrangement of Breslow intermediates: branches to both radical and ionic pathways
Authors: Hsieh Ming-Hsiu , Yu Jen-Shiang K.
Published: November 2021

Radical and ionic pathways of fragmentation and the rearrangement of Breslow intermediates coexist, depending on the protonation state of the hydroxyl group.
One-dimensional transition metal dichalcogenide lateral heterostructures
Authors: Jiang Jin-Wu
Published: November 2021

The lateral stitching of two different transition metal dichalcogenide nanotubes yields a new tubular structure, a one-dimensional lateral heterostructure, which has an abnormal misfit strain distribution.
Covalent organic frameworks as multifunctional materials for chemical detection
Authors: Meng Zheng , Mirica Katherine A.
Published: November 2021

This review highlights how the unique properties of COFs are harnessed to develop different types of chemical detection systems based on the principles of chromism, luminescence, electrical transduction, chromatography, spectrometry, and others.
Mechanistic effects of solvent systems on the Ni–Sn-catalyzed hydrodeoxygenation of lignin derivatives to none-oxygenates
Authors: He Han , Luo Ding , Ma Hao , Xia Shuqian
Published: November 2021

The influence of water on the organic reaction system and bimetallic Ni–Sn catalyst and the solvent property analysis of the cresol hydrodeoxygenation process to produce completely deoxidised product selective promoters.
High-dose ferric citrate supplementation attenuates omega-3 polyunsaturated fatty acid biosynthesisviadownregulating delta 5 and 6 desaturases in rats with high-fat diet-induced obesity
Authors: Faradina Amelia , Tseng Sung-Hui , Tung Te-Hsuan , Huang Shih-Yi , Lee Yu-Chieh , Skalny Anatoly V. , Tinkov Alexey A. , Chen Seu-Hwa , Chuang Yung-Kun , Chang Jung-Su
Published: November 2021

High dose ferric citrate supplementation attenuated n-3 PUFAs biosynthesis in rats with HFD-induced obesityviadownregulating Δ-6 and Δ-5 desaturases. Decreased n-3 PUFAs and the converting enzymes were correlated with levels of liver iron and MDA.
Curcumin supplementation improves biomarkers of oxidative stress and inflammation in conditions of obesity, type 2 diabetes and NAFLD: updating the status of clinical evidence
Authors: Mokgalaboni Kabelo , Ntamo Yonela , Ziqubu Khanyisani , Nyambuya Tawanda M. , Nkambule Bongani B. , Mazibuko-Mbeje Sithandiwe E. , Gabuza Kwazikwakhe B. , Chellan Nireshni , Tiano Luca , Dludla Phiwayinkosi V.
Published: November 2021

The mechanism of action of curcumin targets diverse markers of both oxidative stress and inflammation to mitigate metabolic syndromes such as obesity, T2D, NAFLD, or even dyslipidemia. Arrow pointing up: Increase; Arrow pointing down: decrease.
New ferrocene-integrated multifunctional guanidine surfactants: synthesis, spectroscopic elucidation, DNA interaction studies, and DFT calculations
Authors: Nawaz Sameen , Asghar Faiza , Patujo Jahangeer , Fatima Saira , Murtaza Babar , Munir Shamsa , Naz Mehwish , Badshah Amin , Butler Ian S.
Published: November 2021

Investigation of three new ferrocene appended guanidines as potential surfactants, antioxidants and DNA binders with DFT measurements.
The formation and release of aurothioglucose from thioglucose-loaded gold nanoparticles by NIR irradiation: a combined anti-cancer effect of thermotherapy and chemotherapy without the risk of uncontrollable drug burst release and leakage
Authors: Lai Lantao , Bi Guangming , Sun Yiwei , Shen Mingyi , Su Yubo , Che Xin , Meng Dali
Published: November 2021

Gold nanoparticles (GNPs) have thermotherapy effect on several kinds of solid tumors under the irradiation of near infrared light (NIR).
S-Scheme heterojunction based on the in situ coated core–shell NiCo2S4@WS2 photocatalyst was constructed for efficient photocatalytic hydrogen evolution
Authors: Xu Shengming , Xu Jing , Hu Linying , Liu Ye , Ma Lijun
Published: November 2021

A core–shell structure was formed on the surface of NCS in situ loaded with WS, and efficient photocatalytic hydrogen evolution was achieved by constructing a reasonable S-scheme heterojunction.
The facile fabrication and high-performance sensing of glucose of sea-urchin-like CoFeLDH/PBA/NF heterojunction
Authors: Liu Tian , Chen Chen , Xiong Dengke , Wang Jiang , Lu Chunxiao , Ying Shuanglu , Kong Yuxuan , Yi Fei-Yan
Published: November 2021

The sea-urchin-like CoFeLDH/PBA/NF heterojunction was successfully synthesized, exhibiting excellent glucose sensing performance with ultra-high sensitivity, outstanding reproducibility, stability and selectivity.
Size-induced amorphous structure in tungsten oxide nanoparticles
Authors: Juelsholt Mikkel , Anker Andy S. , Christiansen Troels Lindahl , Jørgensen Mads Ry Vogel , Kantor Innokenty , Sørensen Daniel Risskov , Jensen Kirsten M. Ø.
Published: November 2021

The properties of functional materials are intrinsically linked to their atomic structure. Here, the nano-size effects on the atomic structure of tungsten oxides are deduced, showing that the smallest particles observed are amorphous.