bluuebunny/crossref_metadata_2025 huggingface dataset:
PING‐Mapper: Open‐Source Software for Automated Benthic Imaging and Mapping Using Recreation‐Grade Sonar
Authors: Bodine C. S. , Buscombe D. , Best R. J. , Redner J. A. , Kaeser A. J.
Published: August 2022

The characterization of benthic habitats is essential for aquatic ecosystem science and management, but is frequently limited by waterbody visibility and depth. Recreation‐grade side‐scan sonar systems are increasingly used to aid scientific inquiries in aquatic environments due to their relative low‐cost, ease of operation, low‐weight, and ease of mounting on a variety of vessels. However, existing procedures and software for post‐processing these data are either limited, closed source, or fail on data from new sonar models, limiting the development of reproducible workflows. Here, we present PING‐Mapper, an open‐source and freely available side‐scan sonar post‐processing toolset for processing and mapping sonar recordings from popular Humminbird instruments. The modular software automatically: (a) decodes sonar recordings from any Humminbird system, (b) exports ping attributes from every sonar channel, (c) uses sonar sensor depth for water column removal, and (d) exports sonogram tiles and georectified mosaics. Sonar channels are processed in parallel for quick decoding and metadata extraction. Major processing wokflows, including georectification and image export, are optimized to scale with computing resources. The software has been extensively tested using data from several rivers of varying character and distribution of depths, but could also be used in estuarine and lacustrine environments. Usage of PING‐Mapper is illustrated in three case studies focused on mapping large woody debris, bathymetric mapping, and visual interpretation and mapping of substrates for selected reaches of the Pearl and Pascagoula river systems in Mississippi.
Electromagnetic Seasons in Schumann Resonance Records
Authors: Koloskov O. V. , Nickolaenko A. P. , Yampolski Yu. M. , Budanov O. V.
Published: August 2022

Results of 6‐year concurrent observations of Schumann resonance at the Ukrainian “Akademik Vernadsky” Antarctic station (65.25°N, 64.25°W) and at SOUSY Arctic facility (Svalbard 78.15°N, 16.05°E) are analyzed and compared. Measurements were performed simultaneously by using similar techniques and the calibrated digital equipment. The long‐term records of two orthogonal horizontal magnetic field components demonstrated seasonal and interannual changes in the peak frequency and intensity of the first Schumann resonance mode. The analysis of the annual variations of these parameters in different hemispheres allowed us to select the “electromagnetic seasons.” We suggest that each “electromagnetic season” corresponds to the characteristic pattern of diurnal peak frequency variation determined by lightning the source‐observer configuration. This configuration is unique for each observation point and varies from one season to another in line with the seasonal latitudinal north‐south drift of world thunderstorms. Our observation has demonstrated the different duration of “electromagnetic seasons” in the Arctic and Antarctic. To study the formal reason of this discrepancy, the final data were processed using the singular value decomposition (SVD) algorithm, which allowed us to identify the principal components (PCs) of the time series. The implementation of this technique to peak frequency variation showed the phase shift between the semiannual PCs at the Southern and Northern Hemispheres that explains the different duration of “electromagnetic seasons.” The SVD of the first Schumann resonance mode intensity demonstrated the phase shift between annual variations in different hemispheres and complicated the behavior of other PCs that deserve a separate study.
Hepatocyte-specific Prominin-1 protects against liver injury-induced fibrosis by stabilizing SMAD7
Authors: Lee Hyun , Yu Dong-Min , Bahn Myeong-Suk , Kwon Young-Jae , Um Min Jee , Yoon Seo Yeon , Kim Ki-Tae , Lee Myoung-Woo , Jo Sung-Je , Lee Sungsoo , Koo Seung-Hoi , Jung Ki Hoon , Lee Jae-Seon , Ko Young-Gyu
Published: August 2022

Prominin-1 (PROM1), also known as CD133, is expressed in hepatic progenitor cells (HPCs) and cholangiocytes of the fibrotic liver. In this study, we show that PROM1 is upregulated in the plasma membrane of fibrotic hepatocytes. Hepatocellular expression of PROM1 was also demonstrated in mice (Prom1CreER; R26TdTom) in which cells expressed TdTom under control of theProm1promoter. To understand the role of hepatocellular PROM1 in liver fibrosis, global and liver-specificProm1-deficient mice were analyzed after bile duct ligation (BDL). BDL-induced liver fibrosis was aggravated with increased phosphorylation of SMAD2/3 and decreased levels of SMAD7 by global or liver-specificProm1deficiency but not by cholangiocyte-specificProm1deficiency. Indeed, PROM1 prevented SMURF2-induced SMAD7 ubiquitination and degradation by interfering with the molecular association of SMAD7 with SMURF2. We also demonstrated that hepatocyte-specific overexpression of SMAD7 ameliorated BDL-induced liver fibrosis in liver-specificProm1-deficient mice. Thus, we conclude that PROM1 is necessary for the negative regulation of TGFβ signaling during liver fibrosis.
A senescence stress secretome is a hallmark of therapy-related myeloid neoplasm stromal tissue occurring soon after cytotoxic exposure
Authors: Kutyna Monika M. , Kok Chung Hoow , Lim Yoon , Tran Elizabeth Ngoc Hoa , Campbell David , Paton Sharon , Thompson-Peach Chloe , Lim Kelly , Cakouros Dimitrios , Arthur Agnes , Hughes Timothy , Kumar Sharad , Thomas Daniel , Gronthos Stan , Hiwase Devendra K.
Published: August 2022

Therapy-related myeloid neoplasm (tMN) is considered a direct consequence of DNA damage in hematopoietic stem cells. Despite increasing recognition that altered stroma can also drive leukemogenesis, the functional biology of the tMN microenvironment remains unknown. We performed multiomic (transcriptome, DNA damage response, cytokine secretome and functional profiling) characterization of bone marrow stromal cells from tMN patients. Critically, we also compared (i) patients with myeloid neoplasm and another cancer but without cytotoxic exposure, (ii) typical primary myeloid neoplasm, and (iii) age-matched controls to decipher the microenvironmental changes induced by cytotoxics vs. neoplasia. Strikingly, tMN exhibited a profoundly senescent phenotype with induction of CDKN1A and β-Galactosidase, defective phenotype, and proliferation. Moreover, tMN stroma showed delayed DNA repair and defective adipogenesis. Despite their dormant state, tMN stromal cells were metabolically highly active with a switch toward glycolysis and secreted multiple pro-inflammatory cytokines indicative of a senescent-secretory phenotype that inhibited adipogenesis. Critically, senolytics not only eliminated dormant cells, but also restored adipogenesis. Finally, sequential patient sampling showed senescence phenotypes are induced within months of cytotoxic exposure, well prior to the onset of secondary cancer. Our data underscores a role of senescence in the pathogenesis of tMN and provide a valuable resource for future therapeutics.
Targeting proliferative retinopathy: Arginase 1 limits vitreoretinal neovascularization and promotes angiogenic repair
Authors: Fouda Abdelrahman Y. , Xu Zhimin , Suwanpradid Jutamas , Rojas Modesto , Shosha Esraa , Lemtalsi Tahira , Patel Chintan , Xing Ji , Zaidi Syed A. , Zhi Wenbo , Stansfield Brain K. , Cheng Paul Ning-Man , Narayanan S. Priya , Caldwell R. William , Caldwell Ruth B.
Published: August 2022

Current therapies for treatment of proliferative retinopathy focus on retinal neovascularization (RNV) during advanced disease and can trigger adverse side-effects. Here, we have tested a new strategy for limiting neurovascular injury and promoting repair during early-stage disease. We have recently shown that treatment with a stable, pegylated drug form of the ureohydrolase enzyme arginase 1 (A1) provides neuroprotection in acute models of ischemia/reperfusion injury, optic nerve crush, and ischemic stroke. Now, we have determined the effects of this treatment on RNV, vascular repair, and retinal function in the mouse oxygen-induced retinopathy (OIR) model of retinopathy of prematurity (ROP). Our studies in the OIR model show that treatment with pegylated A1 (PEG-A1), inhibits pathological RNV, promotes angiogenic repair, and improves retinal function by a mechanism involving decreased expression of TNF, iNOS, and VEGF and increased expression of FGF2 and A1. We further show that A1 is expressed in myeloid cells and areas of RNV in retinal sections from mice with OIR and human diabetic retinopathy (DR) patients and in blood samples from ROP patients. Moreover, studies using knockout mice with hemizygous deletion of A1 show worsened RNV and retinal injury, supporting the protective role of A1 in limiting the OIR-induced pathology. Collectively, A1 is critically involved in reparative angiogenesis and neuroprotection in OIR. Pegylated A1 may offer a novel therapy for limiting retinal injury and promoting repair during proliferative retinopathy.
Cell death affecting the progression of gastric cancer
Authors: Wang Haoying , Liu Mengxiao , Zeng Xi , Zheng Ya , Wang Yuping , Zhou Yongning
Published: August 2022

Gastric cancer is a gastrointestinal tumor with high morbidity and mortality rates. Several factors influence its progression, cell death being an important element. In this review, we summarized the effects of necrosis, apoptosis, necroptosis, pyroptosis, ferroptosis, and eight less common cell death modalities on gastric cancer cells and the tumor microenvironment, detailed the molecular mechanisms of various cell death and their major regulatory pathways in gastric cancer, explored the prevalence and complexity of cell death in gastric cancer progression and highlighted the potentials of cell death-related therapies in gastric cancer.
HnRNPK maintains single strand RNA through controlling double-strand RNA in mammalian cells
Authors: Mahale Sagar , Setia Meenakshi , Prajapati Bharat , Subhash Santhilal , Yadav Mukesh Pratap , Thankaswamy Kosalai Subazini , Deshpande Ananya , Kuchlyan Jagannath , Di Marco Mirco , Westerlund Fredrik , Wilhelmsson L. Marcus , Kanduri Chandrasekhar , Kanduri Meena
Published: August 2022

Although antisense transcription is a widespread event in the mammalian genome, double-stranded RNA (dsRNA) formation between sense and antisense transcripts is very rare and mechanisms that control dsRNA remain unknown. By characterizing the FGF-2 regulated transcriptome in normal and cancer cells, we identified sense and antisense transcripts IER3 and IER3-AS1 that play a critical role in FGF-2 controlled oncogenic pathways. We show that IER3 and IER3-AS1 regulate each other’s transcription through HnRNPK-mediated post-transcriptional regulation. HnRNPK controls the mRNA stability and colocalization of IER3 and IER3-AS1. HnRNPK interaction with IER3 and IER3-AS1 determines their oncogenic functions by maintaining them in a single-stranded form. hnRNPK depletion neutralizes their oncogenic functions through promoting dsRNA formation and cytoplasmic accumulation. Intriguingly, hnRNPK loss-of-function and gain-of-function experiments reveal its role in maintaining global single- and double-stranded RNA. Thus, our data unveil the critical role of HnRNPK in maintaining single-stranded RNAs and their physiological functions by blocking RNA-RNA interactions.
Above-room-temperature strong intrinsic ferromagnetism in 2D van der Waals Fe3GaTe2 with large perpendicular magnetic anisotropy
Authors: Zhang Gaojie , Guo Fei , Wu Hao , Wen Xiaokun , Yang Li , Jin Wen , Zhang Wenfeng , Chang Haixin
Published: August 2022

The absence of two-dimensional (2D) van der Waals (vdW) ferromagnetic crystals with both above-room-temperature strong intrinsic ferromagnetism and large perpendicular magnetic anisotropy (PMA) severely hinders practical applications of 2D vdW crystals in next-generation low-power magnetoelectronic and spintronic devices. Here, we report a vdW intrinsic ferromagnetic crystal Fe3GaTe2 that exhibits record-high above-room-temperature Curie temperature (Tc, ~350-380 K) for known 2D vdW intrinsic ferromagnets, high saturation magnetic moment (40.11 emu/g), large PMA energy density (~4.79 × 105 J/m3), and large anomalous Hall angle (3%) at room temperature. Such large room-temperature PMA is better than conventional widely-used ferromagnetic films like CoFeB, and one order of magnitude larger than known 2D vdW intrinsic ferromagnets. Room-temperature thickness and angle-dependent anomalous Hall devices and direct magnetic domains imaging based on Fe3GaTe2 nanosheet have been realized. This work provides an avenue for room-temperature 2D ferromagnetism, electrical control of 2D ferromagnetism and promote the practical applications of 2D-vdW-integrated spintronic devices.
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering
Authors: Hérisson Joan , Duigou Thomas , du Lac Melchior , Bazi-Kabbaj Kenza , Sabeti Azad Mahnaz , Buldum Gizem , Telle Olivier , El Moubayed Yorgo , Carbonell Pablo , Swainston Neil , Zulkower Valentin , Kushwaha Manish , Baldwin Geoff S. , Faulon Jean-Loup
Published: August 2022

Here we introduce the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Standard formats like SBML and SBOL are used throughout to enforce the compatibility of the tools. In a study carried out at four different sites, we illustrate the link between pathway design and engineering with the building of a library of E. coli lycopene-producing strains. We also benchmark our workflows on literature and expert validated pathways. Overall, we find an 83% success rate in retrieving the validated pathways among the top 10 pathways generated by the workflows.
Divergent changes in particulate and mineral-associated organic carbon upon permafrost thaw
Authors: Liu Futing , Qin Shuqi , Fang Kai , Chen Leiyi , Peng Yunfeng , Smith Pete , Yang Yuanhe
Published: August 2022

Permafrost thaw can stimulate microbial decomposition and induce soil carbon (C) loss, potentially triggering a positive C-climate feedback. However, earlier observations have concentrated on bulk soil C dynamics upon permafrost thaw, with limited evidence involving soil C fractions. Here, we explore how the functionally distinct fractions, including particulate and mineral-associated organic C (POC and MAOC) as well as iron-bound organic C (OC-Fe), respond to permafrost thaw using systematic measurements derived from one permafrost thaw sequence and five additional thermokarst-impacted sites on the Tibetan Plateau. We find that topsoil POC content substantially decreases, while MAOC content remains stable and OC-Fe accumulates due to the enriched Fe oxides after permafrost thaw. Moreover, the proportion of MAOC and OC-Fe increases along the thaw sequence and at most of the thermokarst-impacted sites. The relatively enriched stable soil C fractions would alleviate microbial decomposition and weaken its feedback to climate warming over long-term thermokarst development.
Emergent second law for non-equilibrium steady states
Authors: Freitas José Nahuel , Esposito Massimiliano
Published: August 2022

The Gibbs distribution universally characterizes states of thermal equilibrium. In order to extend the Gibbs distribution to non-equilibrium steady states, one must relate the self-information $${{{{{{{\mathcal{I}}}}}}}}(x)=-\!\log ({P}_{{{{{{{{\rm{ss}}}}}}}}}(x))$$
I

(

x

)

=
−

log

(

P

ss

(

x

)

)

of microstate x to measurable physical quantities. This is a central problem in non-equilibrium statistical physics. By considering open systems described by stochastic dynamics which become deterministic in the macroscopic limit, we show that changes $${{\Delta }}{{{{{{{\mathcal{I}}}}}}}}={{{{{{{\mathcal{I}}}}}}}}({x}_{t})-{{{{{{{\mathcal{I}}}}}}}}({x}_{0})$$
Δ
I
=
I

(

x

t

)

−
I

(

x

0

)

in steady state self-information along deterministic trajectories can be bounded by the macroscopic entropy production Σ. This bound takes the form of an emergent second law $${{\Sigma }}+{k}_{b}{{\Delta }}{{{{{{{\mathcal{I}}}}}}}}\,\ge \,0$$
Σ
+

k

b

Δ
I

≥

0
, which contains the usual second law Σ ≥ 0 as a corollary, and is saturated in the linear regime close to equilibrium. We thus obtain a tighter version of the second law of thermodynamics that provides a link between the deterministic relaxation of a system and the non-equilibrium fluctuations at steady state. In addition to its fundamental value, our result leads to novel methods for computing non-equilibrium distributions, providing a deterministic alternative to Gillespie simulations or spectral methods.
Investigation of the evolution of Pd-Pt supported on ceria for dry and wet methane oxidation
Authors: Divins Núria. J. , Braga Andrea , Vendrell Xavier , Serrano Isabel , Garcia Xènia , Soler Lluís , Lucentini Ilaria , Danielis Maila , Mussio Andrea , Colussi Sara , Villar-Garcia Ignacio J. , Escudero Carlos , Trovarelli Alessandro , Llorca Jordi
Published: August 2022

Efficiently treating methane emissions in transportation remains a challenge. Here, we investigate palladium and platinum mono- and bimetallic ceria-supported catalysts synthesized by mechanical milling and by traditional impregnation for methane total oxidation under dry and wet conditions, reproducing those present in the exhaust of natural gas vehicles. By applying a toolkit of in situ synchrotron techniques (X-ray diffraction, X-ray absorption and ambient pressure photoelectron spectroscopies), together with transmission electron microscopy, we show that the synthesis method greatly influences the interaction and structure at the nanoscale. Our results reveal that the components of milled catalysts have a higher ability to transform metallic Pd into Pd oxide species strongly interacting with the support, and achieve a modulated PdO/Pd ratio than traditionally-synthesized catalysts. We demonstrate that the unique structures attained by milling are key for the catalytic activity and correlate with higher methane conversion and longer stability in the wet feed.
Achieving efficient power generation by designing bioinspired and multi-layered interfacial evaporator
Authors: Sun Zhuangzhi , Han Chuanlong , Gao Shouwei , Li Zhaoxin , Jing Mingxing , Yu Haipeng , Wang Zuankai
Published: August 2022

Water evaporation is a natural phase change phenomenon occurring any time and everywhere. Enormous efforts have been made to harvest energy from this ubiquitous process by leveraging on the interaction between water and materials with tailored structural, chemical and thermal properties. Here, we develop a multi-layered interfacial evaporation-driven nanogenerator (IENG) that further amplifies the interaction by introducing additional bionic light-trapping structure for efficient light to heat and electric generation on the top and middle of the device. Notable, we also rationally design the bottom layer for sufficient water transport and storage. We demonstrate the IENG performs a spectacular continuous power output as high as 11.8 μW cm−2 under optimal conditions, more than 6.8 times higher than the currently reported average value. We hope this work can provide a new bionic strategy using multiple natural energy sources for effective power generation.
Self-shrinking soft demoulding for complex high-aspect-ratio microchannels
Authors: Fan Dongliang , Yuan Xi , Wu Wenyu , Zhu Renjie , Yang Xin , Liao Yuxuan , Ma Yunteng , Xiao Chufan , Chen Cheng , Liu Changyue , Wang Hongqiang , Qin Peiwu
Published: August 2022

Microchannels are the essential elements in animals, plants, and various artificial devices such as soft robotics, wearable sensors, and organs-on-a-chip. However, three-dimensional (3D) microchannels with complex geometry and a high aspect ratio remain challenging to generate by conventional methods such as soft lithography, template dissolution, and matrix swollen processes, although they are widespread in nature. Here, we propose a simple and solvent-free fabrication method capable of producing monolithic microchannels with complex 3D structures, long length, and small diameter. A soft template and a peeling-dominant template removal process are introduced to the demoulding process, which is referred to as soft demoulding here. In combination with thermal drawing technology, microchannels with a small diameter (10 µm), a high aspect ratio (6000, length-to-diameter), and intricate 3D geometries are generated. We demonstrate the vast applicability and significant impact of this technology in multiple scenarios, including soft robotics, wearable sensors, soft antennas, and artificial vessels.
Translational challenges and opportunities in biofilm science: a BRIEF for the future
Authors: Highmore C. J. , Melaugh G. , Morris R. J. , Parker J. , Direito S. O. L. , Romero M. , Soukarieh F. , Robertson S. N. , Bamford N. C.
Published: August 2022

Biofilms are increasingly recognised as a critical global issue in a multitude of industries impacting health, food and water security, marine sector, and industrial processes resulting in estimated economic cost of $5 trillion USD annually. A major barrier to the translation of biofilm science is the gap between industrial practices and academic research across the biofilms field. Therefore, there is an urgent need for biofilm research to notice and react to industrially relevant issues to achieve transferable outputs. Regulatory frameworks necessarily bridge gaps between different players, but require a clear, science-driven non-biased underpinning to successfully translate research. Here we introduce a 2-dimensional framework, termed the Biofilm Research-Industrial Engagement Framework (BRIEF) for classifying existing biofilm technologies according to their level of scientific insight, including the understanding of the underlying biofilm system, and their industrial utility accounting for current industrial practices. We evidence the BRIEF with three case studies of biofilm science across healthcare, food & agriculture, and wastewater sectors highlighting the multifaceted issues around the effective translation of biofilm research. Based on these studies, we introduce some advisory guidelines to enhance the translational impact of future research.
Longitudinal corpus callosum microstructural decline in early-stage Parkinson’s disease in association with akinetic-rigid symptom severity
Authors: Amandola Matthew , Sinha Agniva , Amandola Mark J. , Leung Hoi-Chung
Published: August 2022

Previous diffusion tensor imaging (DTI) studies of Parkinson’s disease (PD) show reduced microstructural integrity of the corpus callosum (CC) relative to controls, although the characteristics of such callosal degradation remain poorly understood. Here, we utilized a longitudinal approach to identify microstructural decline in the entire volume of the CC and its functional subdivisions over 2 years and related the callosal changes to motor symptoms in early-stage PD. The study sample included 61 PD subjects (N = 61, aged 45–82, 38 M & 23 F, H&Y ≤ 2) from the Parkinson’s Progressive Markers Initiative database (PPMI). Whole-brain voxel-wise results revealed significant fractional anisotropy (FA) and mean diffusivity (MD) changes in the CC, especially in the genu and splenium. Using individually drawn CC regions of interest (ROI), our analysis further revealed that almost all subdivisions of the CC show significant decline in FA to certain extents over the two-year timeframe. Additionally, FA seemed lower in the right hemisphere of the CC at both time-points, and callosal FA decline was associated with FA and MD decline in widespread cortical and subcortical areas. Notably, multiple regression analysis revealed that across-subject akinetic-rigid severity was negatively associated with callosal FA at baseline and 24 months follow-up, and the effect was strongest in the anterior portion of the CC. These results suggest that callosal microstructure alterations in the anterior CC may serve as a viable biomarker for akinetic-rigid symptomology and disease progression, even in early PD.
A scheme to create and verify scalable entanglement in optical lattice
Authors: Zhou You , Xiao Bo , Li Meng-Da , Zhao Qi , Yuan Zhen-Sheng , Ma Xiongfeng , Pan Jian-Wei
Published: August 2022

To achieve scalable quantum information processing, great efforts have been devoted to the creation of large-scale entangled states in various physical systems. Ultracold atom in optical lattice is considered as one of the promising platforms due to its feasible initialization and parallel manipulation. In this work, we propose an efficient scheme to generate and characterize global entanglement in the optical lattice. With only two-layer quantum circuits, the generation utilizes two-qubit entangling gates based on the superexchange interaction in double wells. The parallelism of these operations enables the generation to be fast and scalable. To verify the entanglement of this non-stabilizer state, we mainly design three complementary detection protocols which are less resource-consuming compared to the full tomography. In particular, one just needs two homogenous local measurement settings to identify the entanglement property. Our entanglement generation and verification protocols provide the foundation for the further quantum information processing in optical lattice.
Socioeconomic roots of academic faculty
Authors: Morgan Allison C. , LaBerge Nicholas , Larremore Daniel B. , Galesic Mirta , Brand Jennie E. , Clauset Aaron
Published: August 2022

Despite the special role of tenure-track faculty in society, training future researchers and producing scholarship that drives scientific and technological innovation, the sociodemographic characteristics of the professoriate have never been representative of the general population. Here we systematically investigate the indicators of faculty childhood socioeconomic status and consider how they may limit efforts to diversify the professoriate. Combining national-level data on education, income and university rankings with a 2017–2020 survey of 7,204 US-based tenure-track faculty across eight disciplines in STEM, social science and the humanities, we show that faculty are up to 25 times more likely to have a parent with a Ph.D. Moreover, this rate nearly doubles at prestigious universities and is stable across the past 50 years. Our results suggest that the professoriate is, and has remained, accessible disproportionately to the socioeconomically privileged, which is likely to deeply shape their scholarship and their reproduction.
Assessment of blood perfusion quality in laparoscopic colorectal surgery by means of Machine Learning
Authors: Arpaia Pasquale , Bracale Umberto , Corcione Francesco , De Benedetto Egidio , Di Bernardo Alessandro , Di Capua Vincenzo , Duraccio Luigi , Peltrini Roberto , Prevete Roberto
Published: August 2022

An innovative algorithm to automatically assess blood perfusion quality of the intestinal sector in laparoscopic colorectal surgery is proposed. Traditionally, the uniformity of the brightness in indocyanine green-based fluorescence consists only in a qualitative, empirical evaluation, which heavily relies on the surgeon’s subjective assessment. As such, this leads to assessments that are strongly experience-dependent. To overcome this limitation, the proposed algorithm assesses the level and uniformity of indocyanine green used during laparoscopic surgery. The algorithm adopts a Feed Forward Neural Network receiving as input a feature vector based on the histogram of the green band of the input image. It is used to (i) acquire information related to perfusion during laparoscopic colorectal surgery, and (ii) support the surgeon in assessing objectively the outcome of the procedure. In particular, the algorithm provides an output that classifies the perfusion as adequate or inadequate. The algorithm was validated on videos captured during surgical procedures carried out at the University Hospital Federico II in Naples, Italy. The obtained results show a classification accuracy equal to $$99.9\%$$

99.9
%

, with a repeatability of $$1.9\%$$

1.9
%

. Finally, the real-time operation of the proposed algorithm was tested by analyzing the video streaming captured directly from an endoscope available in the OR.
Genomic epidemiology and emergence of SARS-CoV-2 variants of concern in the United Arab Emirates
Authors: Alsafar Habiba , Albreiki Mohammed , Mousa Mira , Azman Syafiq Kamarul , Vurivi Hema , Waasia Fathimathuz , Ruta Dymitr , Alhosani Farida , Almazrouei Shereena , Abuyadek Rowan , Selvaraj Francis , Chaves-Coira Irene , Zvereff Val , Abdel-Malek Mohamed A. Y. , Alkaabi Nawal , Uddin Maimunah , Al Awadhi Tayba , Al Marzouqi Nada , Al Attar Fatma , Al Shamsi Safeiya , Al Shehhi Fatima , Alteneiji Hala , Mohamed Kalthoom , Al Muhairi Noor , AlRand Hussain , Fikri Asma , Henschel Andreas
Published: August 2022

Since the declaration of SARS-CoV-2 outbreak as a pandemic, the United Arab Emirates (UAE) public health authorities have adopted strict measures to reduce transmission as early as March 2020. As a result of these measures, flight suspension, nationwide RT-PCR and surveillance of viral sequences were extensively implemented. This study aims to characterize the epidemiology, transmission pattern, and emergence of variants of concerns (VOCs) and variants of interests (VOIs) of SARS-CoV-2 in the UAE, followed by the investigation of mutations associated with hospitalized cases. A total of 1274 samples were collected and sequenced from all seven emirates between the period of 25 April 2020 to 15 February 2021. Phylogenetic analysis demonstrated multiple introductions of SARS-CoV-2 into the UAE in the early pandemic, followed by a local spread of root clades (A, B, B.1 and B.1.1). As the international flight resumed, the frequencies of VOCs surged indicating the January peak of positive cases. We observed that the hospitalized cases were significantly associated with the presence of B.1.1.7 (p < 0.001), B.1.351 (p < 0.001) and A.23.1 (p = 0.009). Deceased cases are more likely to occur in the presence of B.1.351 (p < 0.001) and A.23.1 (p = 0.022). Logistic and ridge regression showed that 51 mutations are significantly associated with hospitalized cases with the highest proportion originated from S and ORF1a genes (31% and 29% respectively). Our study provides an epidemiological insight of the emergence of VOCs and VOIs following the borders reopening and worldwide travels. It provides reassurance that hospitalization is markedly more associated with the presence of VOCs. This study can contribute to understand the global transmission of SARS-CoV-2 variants.
Efficient enumeration-selection computational strategy for adaptive chemistry
Authors: Guo Yachong , Werner Marco , Baulin Vladimir A.
Published: August 2022

Design problems of finding efficient patterns, adaptation of complex molecules to external environments, affinity of molecules to specific targets, dynamic adaptive behavior of chemical systems, reconstruction of 3D structures from diffraction data are examples of difficult to solve optimal design or inverse search problems. Nature inspires evolution strategies to solve design problems that are based on selection of successful adaptations and heritable traits over generations. To exploit this strategy in the creation of new materials, a concept of adaptive chemistry was proposed to provide a route for synthesis of self-adapting molecules that can fit to their environment. We propose a computational method of an efficient exhaustive search exploiting massive parallelization on modern GPUs, which finds a solution for an inverse problem by solving repetitively a direct problem in the mean field approximation. One example is the search for a composition of a copolymer that allows the polymer to translocate through a lipid membrane at a minimal time. Another example is a search of a copolymer sequence that maximizes the polymer load in the micelle defined by the radial core-shell potentials. The length and the composition of the sequence are adjusted to fit into the restricted environment. Hydrogen bonding is another pathway of adaptation to the environment through reversible links. A linear polymer that interacts with water through hydrogen bonds adjusts the position of hydrogen bonds along the chain as a function of the concentration field around monomers. In the last example, branching of the molecules is adjusted to external fields, providing molecules with annealed topology, that can be flexibly changed by changing external conditions. The method can be generalized and applied to a broad spectrum of design problems in chemistry and physics, where adaptive behavior in multi-parameter space in response to environmental conditions lead to non-trivial patterns or molecule architectures and compositions. It can further be combined with machine learning or other optimization techniques to explore more efficiently the parameter space.
The increased analgesic efficacy of cold therapy after an unsuccessful analgesic experience is associated with inferior parietal lobule activation
Authors: Choi Jae Chan , Park Hae-Jeong , Park Jeong A. , Kang Dae Ryong , Choi Young-Seok , Choi SoHyun , Lee Hong Gyu , Choi Jun-Ho , Choi In-Ho , Yoon Min Woo , Lee Jong-Min , Kim Jinhee
Published: August 2022

Prior experiences of successful and failed treatments are known to influence the efficacy of a newly applied treatment. However, whether that carry-over effect applies to non-pharmacological treatments is unknown. This study investigated how a failed treatment history with placebo analgesic cream affected the therapeutic outcomes of cold-pack treatment. The neural correlates underlying those effects were also explored using functional magnetic resonance imaging. The effect of the placebo analgesic cream was induced using placebo conditioning with small (44.5 °C to 43.7 °C, negative experience) and large (44.5 °C to 40.0 °C, positive experience) thermal stimuli changes. After the placebo conditioning, brain responses and self-reported evaluations of the effect of subsequent treatment with a cold-pack were contrasted between the two groups. The negative experience group reported less pain and lower anxiety scores in the cold-pack condition than the positive experience group and exhibited significantly greater activation in the right inferior parietal lobule (IPL), which is known to be involved in pain relief. These findings suggest that an unsatisfying experience with an initial pain-relief treatment could increase the expectations for the complementary treatment outcome and improve the analgesic effect of the subsequent treatment. The IPL could be associated with this expectation-induced pain relief process.
Comprehensive characterization of flavonoid derivatives in young leaves of core-collected soybean (Glycine max L.) cultivars based on high-resolution mass spectrometry
Authors: Lee Suji , Kim Heon-Woong , Lee So-Jeong , Kwon Ryeong Ha , Na Hyemin , Kim Ju Hyung , Choi Yu-Mi , Yoon Hyemyeong , Kim Yong-Suk , Wee Chi-Do , Yoo Seon Mi , Lee Sang Hoon
Published: August 2022

Most previous studies have been focused on isoflavone profile with biological activities from soybean seed and its related products. However, in the present study, eighty-three flavonoid derivatives (55 flavonols, 9 flavones and 19 isoflavones) were comprehensively identified and quantified from young leaves of 21 core-collected soybean cultivars based on ultra-performance liquid chromatography-diode array detector with quadrupole time of flight/mass spectrometry (UPLC-DAD-QToF/MS). Among total flavonoids from soybean leaves (SLs), the abundant flavonols (83.6%) were primarily composed of di- and tri- glycosides combined to the aglycones (K, kaempferol; Q, quercetin; I, isorhamnetin). Particularly, K-rich SLs (yellow coated seed), Nongrim 51 (breeding line) and YJ208-1 (landrace) contained mainly kaempferol 3-O-(2″-O-glucosyl-6″-O-rhamnosyl)galactoside and 3-O-(2″,6″-di-O-rhamnosyl)galactoside, and were expected to be superior cultivars by their higher flavonoids. Besides, the new tri-I-glycosides (soyanins I–V) were presented as predominant components in Junyeorikong (landrace, black). Thus, this study suggest that the SLs can be considered as valuable edible resources due to their rich flavonoids. Also, these detailed profiles will support breeding of superior varieties with excellent biological activities as well as relationship with seed anthocyanins production, and contribute to perform metabolomics approach to investigate the changes of SLs flavonols during the leaf growth and fermentation in further research.
Distribution of SOCD along different offshore distances in China's fresh-water lake-Chaohu under different habitats
Authors: Yao Xiaojie , Wang Jingjing , Xie Xinyun , Jiang Dan , Xu Xiaoniu
Published: August 2022

Carbon storage in wetland ecosystems is an important part of the carbon cycle of terrestrial ecosystems and provides important ecosystem services. Chaohu Wetland is a typical freshwater lake wetland in China. In this study, soil and plant samples were collected every 500 m through three sample lines of different vegetation habitats (estuarine banks, woodlands and shrub beaches) and different offshore distances, revealing the spatial distribution characteristics of soil organic carbon density (SOCD) in Chaohu wetland. The overall SOCD of Chaohu wetland was low, with different habitats ranking as Woodland > Estuary and riverside > Shrub and beach. SOCD of different offshore distances had no obvious law, and the SOCD decreased significantly with soil depth. The plant biomass was significantly higher at the woodland habitat than at other habitats. Most of soil nutrient indicators were the highest at the woodland habitat, while the estuary-riverside habitat had the highest N and P contents. Soil and plant nutrients at different offshore distances had no obvious change patterns. The contents of soil K, Ca, Mg, and N were significantly positively correlated with SOCD, but soil bulk density and pH were significantly negatively correlated with SOCD, and vegetation P content was significantly negatively correlated with SOCD. The spatial pattern of SOCD changes in this lake coastal wetland was determined by the combined effects of plant nutrients, biomass, and soil physical and chemical properties. Our results indicate Chaohu wetlands may have been experiencing serious degradation. The SOCD of Chaohu wetland is lower than that of other wetlands in China, which is mainly affected by human activities. Different offshore distances and habitat heterogeneity are the main factors affecting the soil carbon cycle of the wetland.
Elemental analysis of single ambient aerosol particles using laser-induced breakdown spectroscopy
Authors: Heikkilä Paavo , Rostedt Antti , Toivonen Juha , Keskinen Jorma
Published: August 2022

Analysing the composition of aerosol particles is essential when studying their health effects, sources and atmospheric impacts. In many environments the relevant particles occur in very low concentrations, meaning that their analysis requires efficient single particle techniques. Here we introduce a novel method to analyse the elemental composition of single aerosol particles sampled directly from the aerosol phase using size amplification aided aerosol charging (SAAC), linear electrodynamic quadrupole (LEQ) and laser-induced breakdown spectroscopy. We present results of the charging and focusing efficiencies of the SAAC and of the LEQ, and a proof-of-concept of the analysis method. The proof-of-concept test series was conducted with particle diameters down to 300 nm, sampled directly from the aerosol phase. The method shows unprecedented performance for spectroscopic submicron particle analysis from arbitrarily low concentrations and has exceptional potential for a portable analysis platform for various applications in the field of aerosol research.
High-efficiency decomposition of eggshell membrane by a keratinase from Meiothermus taiwanensis
Authors: Lien Ya-Chu , Lai Shu-Jung , Lin Chai-Yi , Wong Ken-Pei , Chang Matt S. , Wu Shih-Hsiung
Published: August 2022

Eggshell membrane (ESM), a plentiful biological waste, consists of collagen-like proteins and glycosaminoglycans (GAGs) such as hyaluronic acid (HA). Here we used a keratinase (oeMtaker)-mediated system to decompose ESM. The best reaction condition was established by incubating the solution containing oeMtaker, sodium sulfite, and ESM with a weight ratio of 1:120:600. ESM enzymatic hydrolysate (ESM-EH) showed a high proportion of essential amino acids and type X collagen peptides with 963–2259 Da molecular weights. The amounts of GAGs and sulfated GAGs in ESM-EH were quantified as 6.4% and 0.7%, respectively. The precipitated polysaccharides with an average molecular weight of 1300–1700 kDa showed an immunomodulatory activity by stimulating pro-inflammatory cytokines (IL-6 and TNF-α) production. In addition, a microorganism-based system was established to hydrolyze ESM by Meiothermus taiwanensis WR-220. The amounts of GAGs and sulfated GAGs in the system were quantified as 0.9% and 0.1%, respectively. Based on our pre-pilot tests, the system shows great promise in developing into a low-cost and high-performance process. These results indicate that the keratinase-mediated system could hydrolyze ESM more efficiently and produce more bioactive substances than ever for therapeutical applications and dietary supplements.
Ultrafast laser inscribed waveguides in tailored fluoride glasses: an enabling technology for mid-infrared integrated photonics devices
Authors: Fernandez Toney T. , Johnston B. , Gross S. , Cozic S. , Poulain M. , Mahmodi H. , Kabakova I. , Withford M. , Fuerbach A.
Published: August 2022

Zirconium fluoride (ZBLAN) glass, the standard material used in fiber-based mid-infrared photonics, has been re-designed to enable the fabrication of high index-contrast low-loss waveguides via femtosecond laser direct writing. We demonstrate that in contrast to pure ZBLAN, a positive index change of close to 10−2 can be induced in hybrid zirconium/hafnium (Z/HBLAN) glasses during ultrafast laser inscription and show that this can be explained by an electron cloud distortion effect that is driven by the existence of two glass formers with contrasting polarizability. High numerical aperture (NA) type-I waveguides that support a well confined 3.1 μm wavelength mode with a mode-field diameter (MFD) as small as 12 μm have successfully been fabricated. These findings open the door for the fabrication of mid-infrared integrated photonic devices that can readily be pigtailed to existing ZBLAN fibers.
The implications of crustal architecture and transcrustal upflow zones on the metal endowment of a world-class mineral district
Authors: Jørgensen Taus R. C. , Gibson Harold L. , Roots Eric A. , Vayavur Rajesh , Hill Graham J. , Snyder David B. , Naghizadeh Mostafa
Published: August 2022

Earth’s mineral deposits show a non-uniform spatial distribution from the craton-scale, to the scale of individual mineral districts. Although this pattern of differential metal endowment is underpinned by lithospheric-scale processes the geological features that cause clustering of deposits remains enigmatic. The integration of geological and geophysical (seismic, gravity, and magnetotelluric) features has produced the first whole-of-crust image through an iconic Neoarchean volcanic complex and mineral district in the Abitibi Greenstone Belt, Superior Province, Canada. Observations indicate an asymmetry in surface geology, structure, and crustal architecture that defines deep transcrustal magmatic-hydrothermal upflow zones and the limits of the Noranda District ore system. Here, extreme volcanogenic massive sulfide (VMS) endowment is confined to a smaller area adjacent to an ancestral transcrustal structure interpreted to have localized and optimized magmatic and ore forming processes. Although lithospheric-scale evolutionary processes might act as the fundamental control on metal endowment, the new crustal reconstruction explains the clustering of deposits on both belt and district scales. The results highlight a strong magmatic control on metal and in particular Au endowment in VMS systems. Overprinting by clusters of ca. 30 Ma younger orogenic Au deposits suggest the ore systems accessed an upper lithospheric mantle enriched in Au and metals.
Improved cognitive performance in trace amine-associated receptor 5 (TAAR5) knock-out mice
Authors: Maggi Silvia , Bon Carlotta , Gustincich Stefano , Tucci Valter , Gainetdinov Raul R. , Espinoza Stefano
Published: August 2022

Trace amine-associated receptors (TAARs) are a family of G protein-coupled receptors present in mammals in the brain and several peripheral organs. Apart from its olfactory role, TAAR5 is expressed in the major limbic brain areas and regulates brain serotonin functions and emotional behaviours. However, most of its functions remain undiscovered. Given the role of serotonin and limbic regions in some aspects of cognition, we used a temporal decision-making task to unveil a possible role of TAAR5 in cognitive processes. We found that TAAR5 knock-out mice showed a generally better performance due to a reduced number of errors and displayed a greater rate of improvement at the task than WT littermates. However, task-related parameters, such as time accuracy and uncertainty have not changed significantly. Overall, we show that TAAR5 modulates specific domains of cognition, highlighting a new role in brain physiology.
Aberrant gene expression of superoxide dismutases in Chlamydia trachomatis-infected recurrent spontaneous aborters
Authors: Ray Ankita , Bhati Tanu , Pradhan Dibyabhaba , Arora Renu , Parvez Suhel , Rastogi Sangita
Published: August 2022

Study aimed to characterize the expression of antioxidant genes SOD1 and SOD2 in Chlamydia trachomatis-induced recurrent spontaneous aborters and further determine their role by in silico analysis. First void urine was collected from 130 non-pregnant women with history of recurrent spontaneous abortion (RSA) (Group I) and 130 non-pregnant women (Group II; control) attending Obstetrics and Gynecology Department, SJH, New Delhi, India. C. trachomatis detection was performed by conventional PCR in urine. Gene expression of SOD1 and SOD2 was performed by quantitative real-time PCR. Further, its interacting partners were studied by in silico analysis. 22 patients were positive for C. trachomatis in Group I. Significant upregulation was observed for SOD2 gene in C. trachomatis-infected RSA patients while SOD1 was found to be downregulated. Increased concentration of oxidative stress biomarkers 8-hydroxyguanosine and 8-isoprostane was found in C. trachomatis-infected RSA patients. Protein–protein interaction (PPI) of SOD proteins and its interacting partners viz.; CCS, GPX1, GPX2, GPX3, GPX4, GPX5, GPX7, GPX8, CAT, PRDX1, TXN, SIRT3, FOXO3, and AKT1 were found to be involved in MAPK, p53 and foxo signaling pathways. Molecular pathways involved in association with SODs indicate reactive oxygen species (ROS) detoxification, apoptotic pathways and cell cycle regulation. Overall data revealed alleviated levels of SOD2 gene and decreased expression of SOD1 gene in response to C. trachomatis-infection leading to production of oxidative stress and RSA.