bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance evaluation of the Worms subsurface flow constructed wetland for treating black water using insitu and exsitu analytical methods
Authors: Bedu-Addo Kenneth , Gayh Ulrike , Waltenberg Dennis , De Regil Sánchez Irma Livier
Published: January 2023

This paper evaluates the performance of a subsurface flow constructed wetland at Worms Germany used for the treatment of black and grey water from a non-residential facility. Snap black water samples from four wells made up of a clarifying unit, an activated carbon unit and an aeration unit were analysed insitu using the HACH HQ40d multimeter and exsitu using Sensafe water metals check strips for preliminary metal detection onsite. HACH bar code reagents, a HACH Digital Reactor Block 200 (DRB200) and a HACH DR 3900 Spectrophotometer were subsequently used for the analysis of lead (Pb), chromium (Cr), cadmium (Cd), biochemical oxygen demand (BOD), Chemical Oxygen demand (COD), Ammonium (NH4-N) and Nitrate (NO3-N) in the lab. The removal efficiency for the constructed wetland was in the order BOD > Cr > COD > NH4-N > NO3-N > Pb. The 57.90% removal efficiency of COD for the constructed wetland was due to the higher fractions of inert COD which constitutes a part black water. This makes the use of the BOD/COD ratios of 0.69 and 0.5 for wells 1 and 4 an unreliable index for the determination of amenability of COD in black water with regards to microbial activity at the wetland at Worms. The pH range of 7.2–8.4 of the blackwater is conducive for the growth microbes necessary for the breakdown of organic matter in the black water. Further investigation including plant and sediment analysis over different seasons has to be undertaken if the efficiency of the constructed wetland for nutrients and metals removal is to be optimized.
Whistleblowers as Defenders of Human Rights: The Whistleblower Protection Act in Japan
Authors: Iwasaki Masaki
Published: January 2023

In October 2020, the Government of Japan formulated a National Action Plan (NAP) on Business and Human Rights in response to the United Nations Guiding Principles on Business and Human Rights (UNGPs) and ensuing greater international awareness of violations of human rights by corporations.1 In the NAP, the government of Japan stated that on the basis of the UNGPs, it expects companies to (i) formulate human rights policies, (ii) conduct due diligence with respect to human rights, and (iii) establish grievance mechanisms.2 In order to achieve these goals, businesses need to understand whether and how they are violating human rights and prepare appropriate solutions. Whistleblowers play a crucial role in this process.
Forced rotation enhances cylinder flow-induced vibrations at subcritical Reynolds number
Authors: Bourguet Rémi
Published: January 2023

When a cylinder is mounted on an elastic support within a current, vortex-induced vibrations (VIV) may occur down to a Reynolds number (Re) close to

$20$

, based on the body diameter (

$D$

) and inflow velocity (

$U$

), i.e. below the critical value of

$47$

reported for the onset of flow unsteadiness when the body is fixed. The impact of a forced rotation of the elastically mounted cylinder on the system behaviour is explored numerically for

$Re \leqslant 30$

, over wide ranges of values of the rotation rate (ratio between body surface velocity and

$U$

,

$\alpha \in [0,5]$

) and reduced velocity (inverse of the oscillator natural frequency non-dimensionalized by

$D$

and

$U$

,

$U^\star \in [2,30]$

). The influence of the rotation is not monotonic, but the most prominent effect uncovered in this work is a substantial enhancement of the subcritical-Re, flow-induced vibrations beyond

$\alpha =2$

. This enhancement is twofold. First, the rotation results in a considerable expansion of the vibration/flow unsteadiness region in the

$({Re},U^\star )$

domain, down to

$Re=4$

. Second, the elliptical orbits described by the rotating body are subjected to a major amplification, with a transition from VIV to responses whose magnitude tends to increase unboundedly with

$U^\star$

, even though still synchronized with flow unsteadiness. The emergence of such galloping-like oscillations close to the onset of vibrations disrupts the scenario of gradual vibration growth with Re, as amplitudes larger than

$10$

body diameters may be observed at

$Re=10$

.
Creolization as Method
Authors: Parvulescu Anca , Boatcă Manuela
Published: January 2023

“What took place in the Caribbean,” writes Édouard Glissant, “which could be summed up in the word creolization, approximates the idea of Relation as nearly as possible.”1 For Glissant, the word creolization condenses the history of the Caribbean. This is a history characterized by trans-border connections, culture flows, and the transregional movement of people and capital.2 As the first region to be colonized by Europe in the sixteenth century and the last one to be—incompletely—decolonized in the twentieth, the Caribbean has been shaped by the worldwide demand and supply of colonial labor. It was the destination of nearly half of all the enslaved Africans trafficked into the New World between 1492 and the end of the nineteenth century; of significant numbers of indentured and contracted European laborers during much of the same period; as well as of indentured Indian, Chinese, and Indonesian workers after the formal abolition of slavery at the end of the nineteenth century.3 Subsequently, the first half of the twentieth century saw the emergence of a circuit of intra-regional migration of a labor force to the larger Caribbean islands where US-led corporations operated. After World War II, when labor from the non-independent territories of the Caribbean was recruited to rebuild the postwar economies of western Europe and the United States, the region turned into a source of transcontinental emigration.4 On account of this history, the Caribbean has been theorized in terms of transculturation, creolization, and hybridity; concepts such as “remittance societies,” “circular migration,” or “diaspora,” widely used in transnational studies, have also been coined in relation to the Caribbean.5 More than these other terms, however, the concept of creolization has come to condense both the sedimentation and ramifications of this history.
“It would be a lot easier to hunt whales if they didn’t move.” Addressing marine baseline information challenges in Nunavut’s impact assessment process
Authors: Peletz Nicole , Hanna Kevin , Noble Bram
Published: January 2023

Despite advances in impact assessment (IA) practice in Arctic regions, persistent challenges remain. This article examines how baseline information needs and associated uncertainties are presented and understood in the regulatory context of IA. The focus is on marine-related information needs in the Nunavut IA process. The method used a document review of operational IA reports and focus groups with the Nunavut Impact Review Board – the agency responsible for IA in the territory. The results show that information challenges are largely linked to the availability, suitability and accessibility of data; while challenges to addressing information needs are related to broad capacity constraints, as well as responsibility, and cooperation among parties to the process. Similar to other settings, in Nunavut, there is a need to develop better guidance for parties regarding information uncertainties in IA and how such may be addressed. To help address information needs, there is also a need to clarify the roles, responsibilities and expectations of all parties (e.g. Inuit organisations, proponent, government and communities), as well as improving coordination and advancing collaboration, while also addressing capacity constraints.
The Moral Bindingness of Advance Directives
Authors: Montanari Vergallo Gianluca
Published: January 2023

Professor Latham has written a thought-provoking commentary1 on my paper about advance directives.2 I am grateful for this opportunity to integrate the debate on the moral binding nature of these manifestations of will.
Evidence From Dissolved O2 Isotopes in North Atlantic Deep Water for a Recent Climatic Shift
Authors: Musan Israela , Gildor Hezi , Barkan Eugeni , Smethie William M. , Luz Boaz
Published: January 2023

Anthropogenic‐induced variations of the Atlantic Meridional Overturning Circulation (AMOC) and the associated Deep‐Water Formation (DWF) are a major concern. Using measurements of triple oxygen isotopes in the deep North Atlantic, we present novel evidence for a dramatic decadal to centennial shift in ocean conditions at the source region of DWF. These measurements suggest a recent decrease in the percentage of photosynthetic O2 derived from the source regions of AMOC in the Nordic Seas compared to the Little Ice Age. 1‐D model simulations suggest that a reduction in photosynthetic O2 production can explain the observed decrease. Alternatively, it may indicate a substantial decrease in sea‐ice cover and thus increased air‐sea gas exchange, bringing the isotopic composition of O2 closer to equilibrium with the atmosphere. Our novel data can serve as a benchmark for climate models.
Large‐Eddy Simulation of Sea Spray Impacts on Fluxes in the High‐Wind Boundary Layer
Authors: Richter David H. , Wainwright Charlotte E.
Published: January 2023

The exchange of enthalpy and momentum at the air‐sea interface is an important process in tropical cyclone (TC) development and intensification, and the effects of sea spray have long been uncertain, particularly at high wind speeds. Here we use a coupled large‐eddy simulation and Lagrangian cloud model to run high‐resolution simulations of an idealized, spray‐laden TC boundary layer. Simulations are performed with and without spray generation, using a realistic sea spray generation function over wind speeds relevant to TCs. We show that CD is not affected by spray droplets at 10‐m wind speeds up to 48 m s−1. CE and CH are modified during an initial transient adjustment stage, but quickly relax back to their unladen values due to surface layer saturation. This relaxation occurs faster for higher winds, because the increased spray concentration more rapidly saturates the surface layer.
Impact of Stratospheric Aerosol Injection on the East Asian Winter Monsoon
Authors: Liu Zhaochen , Lang Xianmei , Miao Jiapeng , Jiang Dabang
Published: January 2023

Stratospheric aerosol injection (SAI) has been proposed as a potential measure to alleviate global warming; however, uncertainties exist in its regional climate impacts. This study investigates the influence of the SAI on the East Asian winter monsoon (EAWM) by analyzing the G6sulfur simulation from the Geoengineering Model Intercomparison Project. Our results show that the SAI intensifies the Siberian high and Aleutian low, enhances the low‐level northerly winds along the coast of East Asia and deepens the East Asian trough during 2080–2099, reversing the weakening of EAWM in high‐emission Shared Socioeconomic Pathway scenario (SSP5‐8.5). Comparison between the G6sulfur and SSP5‐8.5 simulations indicates that, the SAI‐induced strong cooling in the central equatorial Pacific excites a poleward‐propagating Rossby wave train and strengthen the EAWM. Meanwhile, the negative vorticity advection in the middle troposphere and the radiative cooling over the Siberian high region caused by SAI also intensify the EAWM.
Mantle Anisotropy in NW Namibia From XKS Splitting: Effects of Asthenospheric Flow, Lithospheric Structures, and Magmatic Underplating
Authors: Komeazi Abolfazl , Kaviani Ayoub , Rümpker Georg
Published: January 2023

The presence of the Etendeka flood basalts in northwestern Namibia is taken as evidence for the activity of the Tristan da Cunha mantle plume during the continental breakup between Africa and South America. We investigate seismic anisotropy beneath NW Namibia by splitting analysis of core‐refracted teleseismic shear waves (XKS phases) to probe mantle flow and lithospheric deformation related to the tectonic history of the region. We present the results of the joint splitting analysis of XKS data collected from 34 onshore stations and 12 ocean‐bottom seismometers. The fast polarization directions (FPDs) are consistent with a model that combines the effects of lithospheric deformation and large‐scale mantle flow due to the NE motion of the African plate. The dominantly NNW‐SSE‐oriented FPDs in the northern part are likely caused by shallow lithospheric structures. Our observations do not show any strong evidence of a pervasive effect of the Tristan da Cunha mantle plume.
Energy Input of EUV, Solar Wind, and SEPs at Mars: MAVEN Observations During Solar Minimum
Authors: Jolitz R. D. , Rahmati A. , Brain D. A. , Lee C. O. , Lillis R. J. , Thiemann E. , Eparvier F. , Mitchell D. , Halekas J. , Larson D. , Curry S. M. , Jakosky B. M.
Published: January 2023

Solar extreme ultraviolet (EUV) radiation, the solar wind, and solar energetic particles (SEPs) are variable sources of ionization and heating to the Martian atmosphere. Mars Atmosphere Volatile Evolution’s (MAVEN's) elliptical orbit provides a means to characterize these solar drivers immediately upstream of Mars. We have calculated the energy fluxes of EUV, solar wind, and SEPs while MAVEN is outside of the Martian induced magnetosphere. By time‐averaging observations over 2–5 month periods, we reduced short‐term variability to resolve seasonal and solar cycle trends. For the duration spanning the declining phase of solar cycle 24 and three Mars years, the calculated energy fluxes in units of 109 eV/cm2/s were 650–1,400 for EUV, 77–180 for solar wind ions, 2.4–7.4 for solar wind electrons, 0.01–2.7 for SEP ions, and 0–0.4 for SEP electrons. We estimated the fraction of these energy fluxes that would reach the atmosphere and determined that precipitating particle fluxes on the dayside would need to exceed 1012 eV/cm2/s to compare to EUV. We also predicted that SEPs may impart as much or more energy flux than solar wind electrons on the nightside during periods of strong and weak coronal mass ejection activity. We then discussed and decoupled seasonal variation from the solar drivers to reveal trends and outliers as a function of solar cycle. Finally, we compared MAVEN observations during a weak solar cycle to prior estimates of EUV, solar wind, and SEPs from the young sun, and identified times when MAVEN‐observed peak energy fluxes were close to the steady‐state energy fluxes of the ancient solar system.
Basal Stress Fluctuation: Reply to Comment by Cagnoli on “Slope‐Break Collisions: Comment on ‘Insight Into Granular Flow Dynamics Relying on Basal Stress Measurements: From Experimental Flume Tests’ by K. Li et al.”
Authors: Li Kun , Wang Yufeng , Cheng Qiangong , Lin Qiwen , Wu Yue , Long Yanmei
Published: January 2023

In the comment, Cagnoli (2022, https://doi.org/10.1029/2022JB024799) disagrees with our experimental conclusion that the enhanced particle agitation related to the high magnitude basal fluctuating stresses contributes to the granular flow mobility. Instead, he argues that the slope‐break model used in our experiments prevents the granular flows from being as mobile as they could be. In this reply, we restate our viewpoints by further clarifying the experimental variables and evaluating the effects of the additional phenomena raised in our experiments. By considering the granular flow velocities before the slope‐break, a linear correlation between the depth‐average velocity and equivalent friction coefficient is established, indicating that an increasing flow mobility with decreasing fractal dimension D has already been initiated before the slope‐break. Thus, the slope‐break collision has no significant effect on the general trend of the flow mobility versus grain size and the positive correlation between stress fluctuation and granular flow mobility is still valid.
Stable Water Isotopologue Fractionation During Soil‐Water Evaporation: Analysis Using a Coupled Soil‐Atmosphere Model
Authors: Kiemle Stefanie , Heck Katharina , Coltman Edward , Helmig Rainer
Published: January 2023

The atmosphere‐soil system forms a highly coupled system, which makes key processes such as evaporation complex to analyze as the mass, energy, and momentum transfer is influenced by both domains. To enhance the understanding of evaporation processes from soils, stable water isotopologues are suitable tools to trace water movement within these systems as heavier isotopologues enrich in the residual liquid phase. Due to the complex coupled processes involved in simulating soil‐water evaporation accurately, quantifying fractionation during flow and transport processes at the soil‐atmosphere interface remains an open research area. In this work, we present a multi‐phase multi‐component transport model that resolves flow through the near‐surface atmosphere and the soil, and models transport and fractionation of the stable water isotopologues using the numerical simulation environment DuMux. Using this coupled model, we simulate transport and fractionation processes of stable water isotopologues in soils and the atmosphere by solving compositional flow equations and by using suitable coupling conditions at the soil‐atmosphere interface instead of commonly used parameterization. In a series of examples of evaporation from bare soil, the transport and distribution of stable water isotopologues are evaluated numerically with varied conditions and assumptions, including different atmospheric conditions (turbulent/laminar flow, wind speed) and their impact on the spatial and temporal distribution of the isotopic composition. Building on these results, we observed how the enrichment of the isotopologues in soil is linked with the different stages of the evaporation process. A qualitative study is conducted to verify single fractionation processes in our approach.
Estimation of Surface Soil Moisture by a Multi‐Elevation UAV‐Based Ground Penetrating Radar
Authors: Cheng Qinbo , Su Qiuju , Binley Andrew , liu Jintao , Zhang Zhicai , Chen Xi
Published: January 2023

The measurement of soil moisture is important for a wide range of applications, including ecosystem conservation and agricultural management. However, most traditional measurement methods, for example, time‐domain reflectometry (TDR), are unsuitable for mapping field scale variability. In this study, we propose a method that uses an unmanned aerial vehicle (UAV) to support a ground penetrating radar (GPR) system for spatial scanning investigation at different elevations above ground level. This method measures the surface reflectivity to estimate the soil moisture, exploiting the linear relationship between the ratio of the reflected and the direct wave amplitudes along with the reciprocal of GPR antenna height. This relationship is deduced in this study based on the point source assumptions of a transmitter antenna and ground reflections, which is confirmed by numerical simulation results using the gprMax software. Unlike previous air‐launched GPR methods, the UAV‐GPR method presented here removes the limitations of a steady transmitter power and a fixed GPR survey height and the need for calibration of antenna transfer functions and geophysical inversion calculations, and thus is simpler and more convenient for field applications. We test the method at field sites within the riparian zone and a river‐island grassland adjacent to the Yangtze River. The results from the field study illustrate comparable measured soil moisture to those obtained invasively using TDR. The root mean square error of surface reflectivity and soil moisture values between UAV‐GPR with eight antenna height investigations and TDR in the grassland are 0.03 and 0.05 cm3/cm3, respectively.
Classification of Stream, Hyperconcentrated, and Debris Flow Using Dimensional Analysis and Machine Learning
Authors: Du Junhan , Zhou Gordon G. D. , Tang Hui , Turowski Jens M. , Cui Kahlil F. E.
Published: January 2023

Extreme rainfall events in mountainous environments usually induce significant sediment runoff or mass movements—debris flows, hyperconcentrated flows and stream flows—that pose substantial threats to human life and infrastructure. However, understanding of the sediment transport mechanisms that control these torrent processes remains incomplete due to the lack of comprehensive field data. This study uses a unique field data set to investigate the characteristics of the transport mechanisms of different channelized sediment‐laden flows. Results confirm that sediments in hyperconcentrated flows and stream flows are mainly supported by viscous shear and turbulent stresses, while grain collisional stresses dominate debris‐flow dynamics. Lahars, a unique sediment transport process in volcanic environments, exhibit a wide range of transport mechanisms similar to those in the three different flow types. Furthermore, the Einstein number (dimensionless sediment flux) exhibits a power‐law relationship with the dimensionless flow discharge. Machine learning is then used to draw boundaries in the Einstein number‐dimensionless discharge scheme to classify one flow from the other and thereby aid in developing appropriate hazard assessments for torrential processes in mountainous and volcanic environments based on measurable hydrologic and geomorphic parameters. The proposed scheme provides a universal criterion that improves existing classification methods that depend solely on the sediment concentration for quantifying the runoff‐to‐debris flow transition relevant to landscape evolution studies and hazard assessments.
Galectin-7 reprograms skin carcinogenesis by fostering innate immune evasive programs
Authors: Pinto Nicolás A. , Abba Martín C. , Laporte Lorena , Pérez Sáez Juan M. , Blidner Ada G. , Torres Nicolás I. , Morales Rosa M. , Gatto Sabrina G. , Bach Camila A. , Veigas Florencia , García Rivello Hernán J. , Song Peng , Frederiksen Jane H. , Rasmussen Lene Juel , Poirier Francoise , Croci Diego O. , Sundblad Victoria , Rabinovich Gabriel A. , Cerliani Juan P.
Published: January 2023

Non-melanoma skin cancer (NMSC) has risen dramatically as a result of chronic exposure to sunlight ultraviolet (UV) radiation, climatic changes and clinical conditions associated with immunosuppression. In spite of considerable progress, our understanding of the mechanisms that control NMSC development and their associated molecular and immunological landscapes is still limited. Here we demonstrated a critical role for galectin-7 (Gal-7), a β-galactoside-binding protein preferentially expressed in skin tissue, during NMSC development. Transgenic mice (Tg46) overexpressing Gal-7 in keratinocytes showed higher number of papillomas compared to WT mice or mice lacking Gal-7 (Lgals7−/−) when subjected to a skin carcinogenesis protocol, in which tumor initiator 7,12-dimethylbenz[a]anthracene (DMBA) and tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate (TPA) were sequentially administered. RNAseq analysis of Tg46 tumor lesions revealed a unique profile compatible with cells of the myelomonocytic lineage infiltrating these tumors, an effect that was substantiated by a higher number of CD11b+Gr1+ cells in tumor-draining lymph nodes. Heightened c-Met activation and Cxcl-1 expression in Tg46 lesions suggested a contribution of this pathway to the recruitment of these cells. Remarkably, Gal-7 bound to the surface of CD11b+Ly6ChiLy6Glo monocytic myeloid cells and enhanced their immunosuppressive activity, as evidenced by increased IL-10 and TGF-β1 secretion, and higher T-cell inhibitory activity. In vivo, carcinogen-treated Lgals7−/− animals adoptively transferred with Gal-7-conditioned monocytic myeloid cells developed higher number of papillomas, whereas depletion of these cells in Tg46-treated mice led to reduction in the number of tumors. Finally, human NMSC biopsies showed increased LGALS7 mRNA and Gal-7 protein expression and displayed transcriptional profiles associated with myeloid programs, accompanied by elevated CXCL1 expression and c-Met activation. Thus, Gal-7 emerges as a critical mediator of skin carcinogenesis and a potential therapeutic target in human NMSC.
Caspase-9 driven murine model of selective cell apoptosis and efferocytosis
Authors: Batoon Lena , Koh Amy J. , Kannan Rahasudha , McCauley Laurie K. , Roca Hernan
Published: January 2023

Apoptosis and efficient efferocytosis are integral to growth, development, and homeostasis. The heterogeneity of these mechanisms in different cells across distinct tissues renders it difficult to develop broadly applicable in vivo technologies. Here, we introduced a novel inducible caspase-9 (iCasp9) mouse model which allowed targeted cell apoptosis and further facilitated investigation of concomitant efferocytosis. We generated iCasp9+/+ mice with conditional expression of chemically inducible caspase-9 protein that is triggered in the presence of Cre recombinase. In vitro, bone marrow cells from iCasp9+/+ mice showed expression of the iCasp9 protein when transduced with Cre-expressing adenovirus. Treatment of these cells with the chemical dimerizer (AP20187/AP) resulted in iCasp9 processing and cleaved caspase-3 upregulation, indicating successful apoptosis induction. The in vivo functionality and versatility of this model was demonstrated by crossing iCasp9+/+ mice with CD19-Cre and Osteocalcin (OCN)-Cre mice to target CD19+ B cells or OCN+ bone-lining osteoblasts. Immunofluorescence and/or immunohistochemical staining in combination with histomorphometric analysis of EGFP, CD19/OCN, and cleaved caspase-3 expression demonstrated that a single dose of AP effectively induced apoptosis in CD19+ B cells or OCN+ osteoblasts. Examination of the known efferocytes in the target tissues showed that CD19+ cell apoptosis was associated with infiltration of dendritic cells into splenic B cell follicles. In the bone, where efferocytosis remains under-explored, the use of iCasp9 provided direct in vivo evidence that macrophages are important mediators of apoptotic osteoblast clearance. Collectively, this study presented the first mouse model of iCasp9 which achieved selective apoptosis, allowing examination of subsequent efferocytosis. Given its unique feature of being controlled by any Cre-expressing mouse lines, the potential applications of this model are extensive and will bring forth more insights into the diversity of mechanisms and cellular effects induced by apoptosis including the physiologically important efferocytic process that follows.
To be or not to be a fat burner, that is the question for cpt1c in cancer cells
Authors: Fadó Rut , Zagmutt Sebastian , Herrero Laura , Muley Helena , Rodríguez-Rodríguez Rosalía , Bi Huichang , Serra Dolors , Casals Núria
Published: January 2023

There is an urgent need to identify reliable genetic biomarkers for accurate diagnosis, prognosis, and treatment of different tumor types. Described as a prognostic marker for many tumors is the neuronal protein carnitine palmitoyltransferase 1 C (CPT1C). Several studies report that CPT1C is involved in cancer cell adaptation to nutrient depletion and hypoxia. However, the molecular role played by CPT1C in cancer cells is controversial. Most published studies assume that, like canonical CPT1 isoforms, CPT1C is a mediator of fatty acid transport to mitochondria for beta-oxidation, despite the fact that CPT1C has inefficient catalytic activity and is located in the endoplasmic reticulum. In this review, we collate existing evidence on CPT1C in neurons, showing that CPT1C is a sensor of nutrients that interacts with and regulates other proteins involved in lipid metabolism and transport, lysosome motility, and the secretory pathway. We argue, therefore, that CPT1C expression in cancer cells is not a direct regulator of fat burn, but rather is a regulator of lipid metabolic reprograming and cell adaptation to environmental stressors. We also review the clinical relevance of CPT1C as a prognostic indicator and its contribution to tumor growth, cancer invasiveness, and cell senescence. This new and integrated vision of CPT1C function can help better understand the metabolic plasticity of cancer cells and improve the design of therapeutic strategies.
The mechanisms of gastric mucosal injury: focus on initial chief cell loss as a key target
Authors: Deng Zilin , Zhu Jiaxing , Ma Zhiyuan , Yi Zhiqiang , Tuo Biguang , Li Taolang , Liu Xuemei
Published: January 2023

Diffuse gastric mucosal injury is a chronic injury with altered cell differentiation, including spasmolytic polypeptide expression metaplasia (SPEM) and intestinal metaplasia (IM), which are considered precancerous lesions of gastric cancer (GC). Previously, most studies have focused on how parietal cell loss causes SPEM through transdifferentiation of chief cells. In theory, alteration or loss of chief cells seems to be a secondary phenomenon due to initial partial cell loss. However, whether initial chief cell loss causes SPEM needs to be further investigated. Currently, increasing evidence shows that initial chief cell loss is sufficient to induce gastric mucosal injury, including SPEM and IM, and ultimately lead to GC. Therefore, we summarized the two main types of models that explain the development of gastric mucosal injury due to initial chief cell loss. We hope to provide a novel perspective for the prevention and treatment of diffuse gastric mucosal injury.
Neural mechanisms underlying the hierarchical construction of perceived aesthetic value
Authors: Iigaya Kiyohito , Yi Sanghyun , Wahle Iman A. , Tanwisuth Sandy , Cross Logan , O’Doherty John P.
Published: January 2023

Little is known about how the brain computes the perceived aesthetic value of complex stimuli such as visual art. Here, we used computational methods in combination with functional neuroimaging to provide evidence that the aesthetic value of a visual stimulus is computed in a hierarchical manner via a weighted integration over both low and high level stimulus features contained in early and late visual cortex, extending into parietal and lateral prefrontal cortices. Feature representations in parietal and lateral prefrontal cortex may in turn be utilized to produce an overall aesthetic value in the medial prefrontal cortex. Such brain-wide computations are not only consistent with a feature-based mechanism for value construction, but also resemble computations performed by a deep convolutional neural network. Our findings thus shed light on the existence of a general neurocomputational mechanism for rapidly and flexibly producing value judgements across an array of complex novel stimuli and situations.
A natural biological adhesive from snail mucus for wound repair
Authors: Deng Tuo , Gao Dongxiu , Song Xuemei , Zhou Zhipeng , Zhou Lixiao , Tao Maixian , Jiang Zexiu , Yang Lian , Luo Lan , Zhou Ankun , Hu Lin , Qin Hongbo , Wu Mingyi
Published: January 2023

The discovery of natural adhesion phenomena and mechanisms has advanced the development of a new generation of tissue adhesives in recent decades. In this study, we develop a natural biological adhesive from snail mucus gel, which consists a network of positively charged protein and polyanionic glycosaminoglycan. The malleable bulk adhesive matrix can adhere to wet tissue through multiple interactions. The biomaterial exhibits excellent haemostatic activity, biocompatibility and biodegradability, and it is effective in accelerating the healing of full-thickness skin wounds in both normal and diabetic male rats. Further mechanistic study shows it effectively promotes the polarization of macrophages towards the anti-inflammatory phenotype, alleviates inflammation in chronic wounds, and significantly improves epithelial regeneration and angiogenesis. Its abundant heparin-like glycosaminoglycan component is the main active ingredient. These findings provide theoretical and material insights into bio-inspired tissue adhesives and bioengineered scaffold designs.
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota
Authors: Zhao Jinzhi , Yang Yi , Xu Hua , Zheng Jianxujie , Shen Chengpin , Chen Tian , Wang Tao , Wang Bing , Yi Jia , Zhao Dan , Wu Enhui , Qin Qin , Xia Li , Qiao Liang
Published: January 2023

Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.
Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease
Authors: Meng Guofeng , Xu Hong , Lu Dong , Li Shensuo , Zhao Zhenzhen , Li Haohao , Zhang Weidong
Published: January 2023

Recently, increasing studies are indicating a close association between dysregulated enhancers and neurodegenerative diseases, such as Alzheimer’s disease (AD). However, their contributions were poorly defined for lacking direct links to disease genes. To bridge this gap, we presented the Hi-C datasets of 4 AD patients, 4 dementia-free aged and 3 young subjects, including 30 billion reads. As applications, we utilized them to link the AD risk SNPs and dysregulated epigenetic marks to the target genes. Combining with epigenetic data, we observed more detailed interactions among regulatory regions and found that many known AD risk genes were under long-distance promoter-enhancer interactions. For future AD and aging studies, our datasets provide a reference landscape to better interpret findings of association and epigenetic studies for AD and aging process.
An open database on global coal and metal mine production
Authors: Jasansky Simon , Lieber Mirko , Giljum Stefan , Maus Victor
Published: January 2023

While the extraction of natural resources has been well documented and analysed at the national level, production trends at the level of individual mines are more difficult to uncover, mainly due to poor availability of mining data with sub-national detail. In this paper, we contribute to filling this gap by presenting an open database on global coal and metal mine production on the level of individual mines. It is based on manually gathered information from more than 1900 freely available reports of mining companies, where every data point is linked to its source document, ensuring full transparency. The database covers 1171 individual mines and reports mine-level production for 80 different materials in the period 2000–2021. Furthermore, also data on mining coordinates, ownership, mineral reserves, mining waste, transportation of mining products, as well as mineral processing capacities (smelters and mineral refineries) and production is included.
Electrotaxis behavior of droplets composed of aqueous Belousov-Zhabotinsky solutions suspended in oil phase
Authors: Back Oliver , Asally Munehiro , Wang Zuowei , Hayashi Yoshikatsu
Published: January 2023

Taxis is ubiquitous in biological and physical chemistry systems as a response to various external stimulations. We prepared aqueous droplets containing Belousov-Zhabotinsky (BZ) solutions suspended on an oleic acid oil phase subject to DC electric field and found that these BZ droplets undergo chemically driven translational motion towards the negative electrode under DC electric field. This electrotaxis phenomenon originates from the field-induced inhomogeneous distribution of reactants, in particular Br$$^{-}$$-ions, and consequently the biased location of the leading centers towards the positive electrode. We define the ’leading center’ (LC) as a specific location within the droplet where the BZ chemical wave (target pattern) is initiated. The chemical wave generated from the LC propagates passing the droplet center of mass and creates a gradient of interfacial tension when reaching the droplet-oil interface on the other side, resulting in a momentum exchange between the droplet and oil phases which drives the droplet motion in the direction of the electric field. A greater electric field strength renders a more substantial electrotaxis effect.
Connectivity-based parcellation of the amygdala and identification of its main white matter connections
Authors: Avecillas-Chasin Josue M. , Levinson Simon , Kuhn Taylor , Omidbeigi Mahmoud , Langevin Jean-Philippe , Pouratian Nader , Bari Ausaf
Published: January 2023

The amygdala plays a role in emotion, learning, and memory and has been implicated in behavioral disorders. Better understanding of the amygdala circuitry is crucial to develop new therapies for these disorders. We used data from 200 healthy-subjects from the human connectome project. Using probabilistic tractography, we created population statistical maps of amygdala connectivity to brain regions involved in limbic, associative, memory, and reward circuits. Based on the amygdala connectivity with these regions, we applied k-means clustering to parcellate the amygdala into three clusters. The resultant clusters were averaged across all subjects and the main white-matter pathways of the amygdala from each averaged cluster were generated. Amygdala parcellation into three clusters showed a medial-to-lateral pattern. The medial cluster corresponded with the centromedial and cortical nuclei, the basal cluster with the basal nuclei and the lateral cluster with the lateral nuclei. The connectivity analysis revealed different white-matter pathways consistent with the anatomy of the amygdala circuit. This in vivo connectivity-based parcellation of the amygdala delineates three clusters of the amygdala in a mediolateral pattern based on its connectivity with brain areas involved in cognition, memory, emotion, and reward. The human amygdala circuit presented in this work provides the first step for personalized amygdala circuit mapping for patients with behavioral disorders.
Novel loci for hyperglycemia identified by QTL mapping of longitudinal phenotypes and congenic analysis
Authors: Babaya Naru , Itoi-Babaya Michiko , Ueda Hironori , Kobayashi Misato , Noso Shinsuke , Hiromine Yoshihisa , Ishikawa Akira , Fujisawa Tomomi , Ikegami Hiroshi
Published: January 2023

We previously reported that four hyperglycemia loci are located on three chromosomes in the Nagoya-Shibata-Yasuda (NSY) mouse model, commonly used to study type 2 diabetes. However, we did not search for hyperglycemia loci across all chromosomes. In this study, we performed quantitative trait loci (QTLs) mapping of longitudinal phenotypes from crosses between NSY (hyperglycemic) and C3H (normoglycemic) mice. We identified four new QTLs for hyperglycemia, namely Nidd5nsy, Nidd6nsy, Nidd1c3h, and Nidd2c3h, on Chromosome 1, 4, 10, and 13, respectively. These QTLs were associated with hyperglycemia in young mice and had attenuated effects in older mice. Nidd5nsy and Nidd6nsy were hyperglycemic with NSY alleles, and Nidd1c3h and Nidd2c3h were hyperglycemic with C3H alleles. We further bred Nidd5nsy congenic mice and demonstrated that Nidd5nsy has a strong effect on hyperglycemia when young, accompanied by insulin resistance and visceral fat accumulation. These results showed that the effects of individual QTLs strengthened or weakened with age, and that the sum of the effects of QTLs captured the age-related deterioration of glucose tolerance in individuals. Our results support the importance of longitudinal phenotypes in the genetic analysis of polygenic traits and have implications for the genetic basis and pathogenesis of type 2 diabetes in humans.
Dual color pH probes made from silica and polystyrene nanoparticles and their performance in cell studies
Authors: Srivastava Priyanka , Tavernaro Isabella , Scholtz Lena , Genger Claudia , Welker Pia , Schreiber Frank , Meyer Klas , Resch-Genger Ute
Published: January 2023

Ratiometric green–red fluorescent nanosensors for fluorometrically monitoring pH in the acidic range were designed from 80 nm-sized polystyrene (PS) and silica (SiO2) nanoparticles (NPs), red emissive reference dyes, and a green emissive naphthalimide pH probe, analytically and spectroscopically characterized, and compared regarding their sensing performance in aqueous dispersion and in cellular uptake studies. Preparation of these optical probes, which are excitable by 405 nm laser or LED light sources, involved the encapsulation of the pH-inert red-fluorescent dye Nile Red (NR) in the core of self-made carboxylated PSNPs by a simple swelling procedure and the fabrication of rhodamine B (RhB)-stained SiO2-NPs from a silane derivative of pH-insensitive RhB. Subsequently, the custom-made naphthalimide pH probe, that utilizes a protonation-controlled photoinduced electron transfer process, was covalently attached to the carboxylic acid groups at the surface of both types of NPs. Fluorescence microscopy studies with the molecular and nanoscale optical probes and A549 lung cancer cells confirmed the cellular uptake of all probes and their penetration into acidic cell compartments, i.e., the lysosomes, indicated by the switching ON of the green naphthalimide fluorescence. This underlines their suitability for intracellular pH sensing, with the SiO2-based nanosensor revealing the best performance regarding uptake speed and stability.
Pre-analytical sample handling effects on tear fluid protein levels
Authors: Gijs Marlies , Arumugam Sinthuja , van de Sande Nienke , Webers Carroll A. B. , Sethu Swaminathan , Ghosh Arkasubhra , Shetty Rohit , Vehof Jelle , Nuijts Rudy M. M. A.
Published: January 2023

Tear fluid is emerging as a source of non-invasive biomarkers, both for ocular and systemic conditions. Accurate quantification of tear proteins can be improved by standardizing methods to collect and process tear fluid. The aim of this study was to determine sample handling factors that may influence the tear protein biomarker profile. Tear fluid was collected using Schirmer’s strips. Tear proteins were extracted by elution through centrifugation. Total protein content was determined using the bicinchoninic acid assay. Key concepts that apply to the entire sample processing cycle are tear sampling, tear storage, protein extraction and data normalization. Differences in wetting or migration length were observed between Schirmer’s strips from different manufacturers, and between protein-free and protein-rich solutions. One unit of migration length (mm) did not correspond to one unit of volume (µL). A positive correlation (r = 0.6671, p < 0.0001) was observed between migration length and total tear protein content. The most beneficial storage conditions were strips that were not stored (+ 21.8%), or underwent ‘wet’ storage (+ 11.1%). Protein recovery was the highest in 400 µL extraction buffer and independent of protein molecular weight. This study helps to explain inter- and intra-variability that is often seen with tear biomarker research. This information is critical to ensure accuracy of test results, as tear biomarkers will be used for patient management and in clinical trials in the near future. This study also highlights the need for standardization of Schirmer’s strip manufacturing, tear fluid processing and analyte concentration normalization.
Complete chloroplast genome molecular structure, comparative and phylogenetic analyses of Sphaeropteris lepifera of Cyatheaceae family: a tree fern from China
Authors: Hu Qingdi , Qian Renjuan , Zhang Yanjun , Ma Xiaohua , Ye Youju , Zhang Xule , Lin Lin , Liu Hongjian , Zheng Jian
Published: January 2023

Sphaeropteris lepifera is a tree fern in the Cyatheaceae, a family that has played an important role in the evolution of plant systems. This study aimed to analyze the complete chloroplast genome of S. lepifera and compared it with previously published chloroplast genomes Cyatheaceae family. The chloroplast genome of S. lepifera comprised 162,114 bp, consisting of a large single copy (LSC) region of 86,327 bp, a small single copy (SSC) region of 27,731 bp and a pair of inverted repeats (IRa and IRb) of 24,028 bp each. The chloroplast genome encoded 129 genes, comprising 32 transfer RNAs, 8 ribosomal RNAs, and 89 protein-coding genes. Comparison of the genomes of 7 Cyatheaceae plants showed that the chloroplast genome of S. lepifera was missing the gene trnV-UAC. Expansion of the SSC region led to the difference in the chloroplast genome size of S. lepifera. Eight genes, atpI, ccsA, petA, psaB, rpl16, rpoA, rpoC1, and ycf2 have high nucleic acid diversity and can be regarded as potential molecular markers. The genes trnG-trnR and atpB were suitable for DNA barcodes between different communities of S. lepifera. The S. lepifera groups in Zhejiang Province probably diffused from Pingtan and Ningde, Fujian. The results will provide a basis for species identification, biological studies, and endangerment mechanism of S. lepifera.
Additive pre-diagnostic and diagnostic value of routine blood-based biomarkers in the detection of colorectal cancer in the UK Biobank cohort
Authors: Tanriver Gizem , Kocagoncu Ece
Published: January 2023

Survival rates from colorectal cancer (CRC) are drastically higher if the disease is detected and treated earlier. Current screening guidelines involve stool-based tests and colonoscopies, whose acceptability and uptake remains low. Routinely collected blood-based biomarkers may offer a low-cost alternative or aid for detecting CRC. Here we aimed to evaluate the pre-diagnostic and diagnostic value of a wide-range of multimodal biomarkers in the UK Biobank dataset, including sociodemographic, lifestyle, medical, physical, and blood and urine-based measures in detecting CRC. We performed a Cox proportional hazard and a tree-boosting model alongside feature selection methods to determine optimal combination of biomarkers. In addition to the modifiable lifestyle factors of obesity, alcohol consumption and cardiovascular health, we showed that blood-based biomarkers that capture the immune response, lipid profile, liver and kidney function are associated with CRC risk. Following feature selection, the final Cox and tree-boosting models achieved a C-index of 0.67 and an AUC of 0.76 respectively. We show that blood-based biomarkers collected in routine examinations are sensitive to preclinical and clinical CRC. They may provide an additive value and improve diagnostic accuracy of current screening tools at no additional cost and help reduce burden on the healthcare system.
Ingestion of rubber tips of artificial turf fields by goldfish
Authors: Chiba Rihito , Fujinuma Ryosuke , Yoshitomi Tomoyasu , Shimizu Yasuo , Kobayashi Makito
Published: January 2023

Marine microplastics are one of the global environmental issues. The present study examined whether rubber tips of artificial sports fields could be marine microplastics. We observed the migration of rubber tips from the artificial turf field to the surrounding ditch connected to sewer pipes and then examined the ingestion of rubber tips using the goldfish Carassius auratus. The rubber tips found in sediments in the ditch suggest that the rubber tips could be sent to the river and released into the ocean. The goldfish ingested rubber tips with or without fish feed, and rubber tips were found in the intestine. However, the fish discharged the rubber tips within 48 h after ingestion. These results indicate that ingestion of the rubber tips was not accidental but an active behavior. Therefore, artificial turf sports fields could be a source of marine microplastics and may cause hazardous effects on wild fishes through ingestion.