bluuebunny/crossref_metadata_2025 huggingface dataset:
How to Overcome Embitterment With Wisdom
Authors: Arnold Christopher P.
Published: July 2022

Expert help on overcoming feelings of embitterment

Understand how these difficult feelings some about
Learn problem-solving skills to reorientate to the future
Also ideal reading for anyone living or working with an embittered person

More about the book
Embitterment is an emotional reaction anyone can have to injustices, humiliation, and breaches of trust. We have probably all encountered embitterment in ourselves or others at some time in our lives. Like other feelings, feelings of embitterment normally subside, but in some cases they can persist and cause a great deal of suffering. When these feelings take control of your life and you can’t let go of the past negative events in your life, then support is needed.

This book helps you understand what embitterment is and how it can come about. It will also help you detach from these negative feelings and find ways to better deal with the hurtful situations, including learning to look to the future. You will learn about problem-solving strategies that focus on the psychology of wisdom and the development of wisdom, which include identifying facts and problem solutions, changing perspectives, self-relativizing, and emotional empathy. It has been scientifically proven that wisdom is a good remedy for embitterment.

This book is ideal support for anyone suffering from embitterment or for family, friends, or colleagues who want to learn how to support someone to not stay stuck in these difficult feelings.
Fluid‐Mediated Mass Transfer Between Mafic and Ultramafic Rocks in Subduction Zones
Authors: Codillo E. A. , Klein F. , Dragovic B. , Marschall H. R. , Baxter E. , Scambelluri M. , Schwarzenbach‬ E.
Published: July 2022

Metasomatic reaction zones between mafic and ultramafic rocks exhumed from subduction zones provide a window into mass‐transfer processes at high pressure. However, accurate interpretation of the rock record requires distinguishing high‐pressure metasomatic processes from inherited oceanic signatures prior to subduction. We integrated constraints from bulk‐rock geochemical compositions and petrophysical properties, mineral chemistry, and thermodynamic modeling to understand the formation of reaction zones between juxtaposed metagabbro and serpentinite as exemplified by the Voltri Massif (Ligurian Alps, Italy). Distinct zones of variably metasomatized metagabbro are dominated by chlorite, amphibole, clinopyroxene, epidote, rutile, ilmenite, and titanite between serpentinite and eclogitic metagabbro. Whereas the precursor serpentinite and oxide gabbro formed and were likely already in contact in an oceanic setting, the reaction zones formed by diffusional Mg‐metasomatism between the two rocks from prograde to peak, to retrograde conditions in a subduction zone. Metasomatism of mafic rocks by Mg‐rich fluids that previously equilibrated with serpentinite could be widespread along the subduction interface, within the subducted slab, and the mantle wedge. Furthermore, the models predict that talc formation by Si‐metasomatism of serpentinite in subduction zones is limited by pressure‐dependent increase in the silica activity buffered by the serpentine‐talc equilibrium. Elevated activities of aqueous Ca and Al species would also favor the formation of chlorite and garnet. Accordingly, unusual conditions or processes would be required to stabilize abundant talc at high P‐T conditions. Alternatively, a different set of mineral assemblages, such as serpentine‐ or chlorite‐rich rocks, may be controlling the coupling‐decoupling transition of the plate interface.
Contrasting Sea‐Ice Algae Blooms in a Changing Arctic Documented by Autonomous Drifting Buoys
Authors: Hill Victoria , Light Bonnie , Steele Michael , Sybrandy Andrew Lowy
Published: July 2022

Novel observations of the seasonal evolution of an ice algal bloom on the Chukchi shelf were collected by two autonomous buoys deployed 180 km apart in first‐year drifting sea ice. High attenuation of blue light in the bottom of the ice indicated considerable accumulation of ice algae biomass with derived Chlorophyll‐a concentrations (Chl a) up to 184 mg m−2. Differences in the magnitude and persistence of ice algae biomass under each buoy appear to have been driven by differences in snow thickness, as ice thickness was similar between the sites. Minimal snow cover (0.02 m) around one buoy was associated with algae growth beginning in mid‐May and lasting 70 days. The second buoy had notably more snow (0.4 m), causing ice algae production to lag behind the first site by approximately 4 weeks. The delay in growth diminished the peak of ice algae Chl a and duration compared to the first site. Light attenuation through the ice was intense enough at both buoys to have a potentially inhibiting impact on water column phytoplankton Chl a. Modeling ice algae growth with observed light intensities determined that nutrients were the limiting resource at the low snow site. In contrast, the algae at the high snow site were light‐limited and never nutrient‐limited. These data point toward changes in ice algae phenology with an earlier and longer window for growth; and nutrients rather than light determining the longevity and magnitude of production.
Effects of Snow and Remineralization Processes on Nutrient Distributions in Multi‐Year Antarctic Landfast Sea Ice
Authors: Sahashi Reishi , Nomura Daiki , Toyota Takenobu , Tozawa Manami , Ito Masato , Wongpan Pat , Ono Kazuya , Simizu Daisuke , Naoki Kazuhiro , Nosaka Yuichi , Tamura Takeshi , Aoki Shigeru , Ushio Shuki
Published: July 2022

We elucidated the effects of snow and remineralization processes on nutrient distributions in multi‐year landfast sea ice (fast ice) in Lützow‐Holm Bay, East Antarctica. Based on sea‐ice salinity, oxygen isotopic ratios, and thin section analyses, we found that the multi‐year fast ice grew upward due to the year‐by‐year accumulation of snow. Compared to ice of seawater origin, nutrient concentrations in shallow fast ice were low due to replacement by clean and fresh snow. In deeper ice of seawater origin (the lower half of the multi‐year fast ice column), remineralization was dominated by the degradation of organic matter. By comparison between first‐ and muti‐year ice, the biological uptake and the remineralization were dominated in relatively young ice and older ice, respectively, under the physical process of brine drainage.
Stability of the Jupiter Southern Polar Vortices Inspected Through Vorticity Using Juno/JIRAM Data
Authors: Scarica P. , Grassi D. , Mura A. , Adriani A. , Ingersoll A. , Li C. , Piccioni G. , Sindoni G. , Moriconi M. L. , Plainaki C. , Altieri F. , Cicchetti A. , Dinelli B. M. , Filacchione G. , Migliorini A. , Noschese R. , Sordini R. , Stefani S. , Tosi F. , Turrini D.
Published: July 2022

The Jovian InfraRed Auroral Mapper (JIRAM) onboard the NASA Juno mission monitored the evolution of Jupiter’s polar cyclones since their first observation ever in February 2017. Data acquired by JIRAM have revealed cloudy cyclones organized in a complex, yet stable geometrical pattern at both poles. Several studies have investigated the dynamics and the structure of these cyclones, to understand the physical mechanisms behind their formation and evolution. In this work, we present vorticity maps deduced from the wind fields for the region poleward of ∼−80°, which has been extensively covered over the last four years of observations. The cyclonic features related to the stable polar cyclones are embedded in a slightly, but diffused anticyclonic circulation, in which short‐living anticyclones emerge with respect to the surroundings. Although the general stability of both the cyclones and the whole system is strongly confirmed by this work, variations in the shape of the vortices, as well as changes in the local structures, have been observed.
Ensemble Representation of Satellite Precipitation Uncertainty Using a Nonstationary, Anisotropic Autocorrelation Model
Authors: Hartke Samantha H. , Wright Daniel B. , Li Zhe , Maggioni Viviana , Kirschbaum Dalia B. , Khan Sana
Published: July 2022

The usefulness of satellite multi‐sensor precipitation (SMP) and other satellite‐informed precipitation products in water resources modeling can be hindered by substantial errors which vary considerably with spatiotemporal scale. One approach to cope with these errors is to combine SMPs with ensemble generation methods, such that each ensemble member reflects one plausible realization of the true—but unknown—precipitation. This requires replicating the spatiotemporal autocorrelation structure of SMP errors. The climatology of this structure is unknown for most locations due to a lack of ground‐reference observations, while the unique anisotropy and nonstationarity within any particular precipitation system limit the relevance of this climatology to the depiction of individual storm systems. Characterizing and simulating autocorrelation across spatiotemporal scales has thus been called a grand challenge within the precipitation community. We introduce the Space‐Time Rainfall Error and Autocorrelation Model (STREAM), which combines uncalibrated, anisotropic and nonstationary SMP spatiotemporal correlation modeling with a pixel‐scale precipitation error model to stochastically generate ensemble precipitation fields that resemble “ground truth” precipitation. We generate STREAM precipitation ensembles at high resolution (1‐hr, 0.1°) and evaluate these ensembles at multiple scales. STREAM ensembles consistently bracket ground‐truth observations and replicate the autocorrelation structure of ground‐truth precipitation fields. STREAM is compatible with pixel‐scale error/uncertainty formulations beyond those presented here, and could be applied to other precipitation sources such as numerical weather predictions or blended products. Although ground truth is used here to parameterize pixel‐scale uncertainty, if combined with other recent work in SMP uncertainty characterization, STREAM could be used without any ground data.
Rock Abundance and Erosion Rate at the Zhurong Landing Site in Southern Utopia Planitia on Mars
Authors: Chen Zeyu , Wu Bo , Wang Yiran , Liu Shuo , Li Zhaojin , Yang Chenyu , Dong Jie , Rao Wei
Published: July 2022

Rocks on the Martian surface exhibit signatures of geological activities. Rock distribution is also an important factor for landing site selection for exploration missions. This study investigated the rock abundance and erosion rate at the landing site of the Chinese Mars rover, Zhurong, in southern Utopia Planitia. A convolutional neural network based method was developed for rock detection from the images (0.7 m/pixel) obtained by using the high‐resolution imaging camera (HiRIC) onboard the Tianwen‐1 orbiter. Approximately 10,000 rocks with a minimum diameter of 1.4 m (2 pixels on the image) were extracted from the HiRIC images covering the Zhurong landing site and its neighboring region. According to the results, the rock abundance at the Zhurong landing site was approximately 5%. Measurements from the ground images acquired by the Zhurong rover after landing confirmed a rock abundance of approximately 5% at the landing site, consistent with the orbital measurement before landing. Furthermore, we investigated the rock erosion rate at the Zhurong landing region. Rock abundance was negatively correlated with the crater retention age and positively correlated with crater diameter. The obtained rock breakdown rate (0.054 nm/y to 0.074 nm/y) and surface denudation rate by filled volume of craters (0.104 nm/y to 0.209 nm/y) were in agreement with the values previously reported for the Amazonian period on Mars. The low erosion rate implies a dry climate and the absence of fluvial erosion processes in the Amazonian period.
Mechanically Coupled Areas on the Plate Interface in the Nankai Trough, Japan and a Possible Seismic and Aseismic Rupture Scenario for Megathrust Earthquakes
Authors: Saito Tatsuhiko , Noda Akemi
Published: July 2022

Quantifying the stress distribution or finding mechanically coupled areas on the plate interface is fundamentally important for conjecturing megathrust earthquakes that may occur in the future. Kinematically coupled areas, or slip deficit distributions, on plate interfaces were commonly estimated by geodetic‐data analyses. However, mechanically coupled areas are not identical to the kinematically coupled areas. The present study develops an inversion method to estimate the stress rate distribution as mechanically coupled areas. We apply this method to the Nankai trough subduction zone, southwestern Japan to detect mechanically coupled areas. Some of the estimated coupled areas correspond to the rupture areas of historical earthquakes. Others are in a deeper part, which may release the stress as aseismic slip. We then construct a rupture scenario that can occur in the Nankai trough in the future based on the estimated mechanical coupling, assuming that an effective stress accumulation period is 100 years. The scenario consists of a foreshock of MW 8.0 followed by an afterslip of MW 7.7 and a mainshock of MW 8.2. Although the moment magnitude of the afterslip is slightly smaller than the foreshock, the strain energy released by the foreshock is significantly larger than the afterslip. In order to compare events when the stress drops are significantly different, it is useful to use the minimum released strain energy, or available energy, to characterize the magnitude of the events.
Variability of Hydration Across the Southern Hemisphere of the Moon as Observed by Deep Impact
Authors: Laferriere K. L. , Sunshine J. M. , Feaga L. M.
Published: July 2022

Measurements of the 3 μm absorption feature, associated with the presence of hydroxyl and potentially molecular water, were first observed in 2009 by three separate spacecraft’ observations. Subsequent observations have revealed widespread but variable hydration over the sunlit regions of the Moon. The variability can help to disentangle the individual contributions of OH and H2O to the 3 μm absorption feature and provide insight into the mechanism of production and loss of OH/H2O on the lunar surface. We investigate the spatial and diurnal variations of hydration on the southern hemisphere of the Moon as observed by the Deep Impact spacecraft during the lunar flybys in 2009 at spatial scales of 30–70 km/pixel. For a subset of observations of across the lunar south polar region (∼2% of the lunar surface), repeat coverage includes three different times spanning half a lunar day, allowing for exploration of diurnal variability. We determine that OH/H2O is widespread but variable across the lunar south pole. At all but the lowest temperatures observed, highland regions have stronger hydration absorption features than the maria. Changes in band strength demonstrate variable loss rates controlled by surface temperatures with H2O lost quicker at higher temperatures. Observed variability in the band shape strongly suggests higher H2O abundance at low temperatures. These observations are strong evidence that the unique shape of the 3 μm band is due to both OH and H2O. The rapid diurnal evolution of the absorption feature implies that migration of these constituents occurs locally over short distances driven by temperature changes.
Reconstructing Sediment Transport by Migrating Bedforms in the Physical and Spectral Domains
Authors: Lee Jiyong , Singh Arvind , Guala Michele
Published: July 2022

Characteristics of migrating bedforms are often used to indirectly quantify the volumetric sediment flux in fluvial environments. Yet, the range of bedform scales that actually contribute to the sediment transport remains elusive. We performed a series of experiments under four different transport stages in a large‐scale sediment recirculating flume. Three independent variables were simultaneously measured: 2D spatio‐temporal bathymetry z(x, y, t), high frequency temporal bed elevations at fixed locations z(t), and temporal change of the sediment weight carried by migrating bedforms near the channel outlet qm(t). Both the measured spatio‐temporal bed evolution and the sediment discharge were analyzed using bedform tracking and Fourier decomposition. We found that small, rapidly migrating secondary bedforms emerge as a main contributor to the sediment transport and to the propagation of larger primary bedforms that slowly migrate underneath. This critical information allows us to define the range of transport‐contributing scales that must be accounted for in a scale‐dependent sediment mass flux model to enable the estimation of the total bedform transport from bed elevation time series.
Classifying Mixing Regimes in Ponds and Shallow Lakes
Authors: Holgerson Meredith A. , Richardson David C. , Roith Joseph , Bortolotti Lauren E. , Finlay Kerri , Hornbach Daniel J. , Gurung Kshitij , Ness Andrew , Andersen Mikkel R. , Bansal Sheel , Finlay Jacques C. , Cianci‐Gaskill Jacob A. , Hahn Shannon , Janke Benjamin D. , McDonald Cory , Mesman Jorrit P. , North Rebecca L. , Roberts Cassandra O. , Sweetman Jon N. , Webb Jackie R.
Published: July 2022

Lakes are classified by thermal mixing regimes, with shallow waterbodies historically categorized as continuously mixing systems. Yet, recent studies demonstrate extended summertime stratification in ponds, underscoring the need to reassess thermal classifications for shallow waterbodies. In this study, we examined the summertime thermal dynamics of 34 ponds and shallow lakes across temperate North America and Europe to categorize and identify the drivers of different mixing regimes. We identified three mixing regimes: rarely (n = 18), intermittently (n = 10), and often (n = 6) mixed, where waterbodies mixed an average of 2%, 26%, and 75% of the study period, respectively. Waterbodies in the often mixed category were larger (≥4.17 ha) and stratification weakened with increased wind shear stress, characteristic of “shallow lakes.” In contrast, smaller waterbodies, or “ponds,” mixed less frequently, and stratification strengthened with increased shortwave radiation. Shallow ponds (<0.74 m) mixed intermittently, with daytime stratification often breaking down overnight due to convective cooling. Ponds ≥0.74 m deep were rarely or never mixed, likely due to limited wind energy relative to the larger density gradients associated with slightly deeper water columns. Precipitation events weakened stratification, even causing short‐term mixing (hours to days) in some sites. By examining a broad set of shallow waterbodies, we show that mixing regimes are highly sensitive to very small differences in size and depth, with potential implications for ecological and biogeochemical processes. Ultimately, we propose a new framework to characterize the variable mixing regimes of ponds and shallow lakes.
Cardiac-specific overexpression of Ndufs1 ameliorates cardiac dysfunction after myocardial infarction by alleviating mitochondrial dysfunction and apoptosis
Authors: Qi Bingchao , Song Liqiang , Hu Lang , Guo Dong , Ren Gaotong , Peng Tingwei , Liu Mingchuan , Fang Yexian , Li Chunyu , Zhang Mingming , Li Yan
Published: July 2022

Myocardial infarction (MI) is the leading cause of premature death among adults. Cardiomyocyte death and dysfunction of the remaining viable cardiomyocytes are the main pathological factors of heart failure after MI. Mitochondrial complexes are emerging as critical mediators for the regulation of cardiomyocyte function. However, the precise roles of mitochondrial complex subunits in heart failure after MI remain unclear. Here, we show that NADH:ubiquinone oxidoreductase core subunit S1 (Ndufs1) expression is decreased in the hearts of heart failure patients and mice with myocardial infarction. Furthermore, we found that cardiac-specific Ndufs1 overexpression alleviates cardiac dysfunction and myocardial fibrosis in the healing phase of MI. Our results demonstrated that Ndufs1 overexpression alleviates MI/hypoxia-induced ROS production and ROS-related apoptosis. Moreover, upregulation of Ndufs1 expression improved the reduced activity of complex I and impaired mitochondrial respiratory function caused by MI/hypoxia. Given that mitochondrial function and cardiomyocyte apoptosis are closely related to heart failure after MI, the results of this study suggest that targeting Ndufs1 may be a potential therapeutic strategy to improve cardiac function in patients with heart failure.
Hollow nanoparticles synthesized via Ostwald ripening and their upconversion luminescence-mediated Boltzmann thermometry over a wide temperature range
Authors: An Ran , Liang Yuan , Deng Ruiping , Lei Pengpeng , Zhang Hongjie
Published: July 2022

Upconversion nanoparticles (UCNPs) with hollow structures exhibit many fascinating optical properties due to their special morphology. However, there are few reports on the exploration of hollow UCNPs and their optical applications, mainly because of the difficulty in constructing hollow structures by conventional methods. Here, we report a one-step template-free method to synthesize NaBiF4:Yb,Er (NBFYE) hollow UCNPs via Ostwald ripening under solvothermal conditions. Moreover, we also elucidate the possible formation mechanism of hollow nanoparticles (HNPs) by studying the growth process of nanoparticles in detail. By changing the contents of polyacrylic acid and H2O in the reaction system, the central cavity size of NBFYE nanoparticles can be adjusted. Benefiting from the structural characteristics of large internal surface area and high surface permeability, NBFYE HNPs exhibit excellent luminescence properties under 980 nm near-infrared irradiation. Importantly, NBFYE hollow UCNPs can act as self-referenced ratiometric luminescent thermometers under 980 nm laser irradiation, which are effective over a wide temperature range from 223 K to 548 K and have a maximum sensitivity value of 0.0065 K−1 at 514 K. Our work clearly demonstrates a novel method for synthesizing HNPs and develops their applications, which provides a new idea for constructing hollow structure UCNPs and will also encourage researchers to further explore the optical applications of hollow UCNPs.
Blocking glycine utilization inhibits multiple myeloma progression by disrupting glutathione balance
Authors: Xia Jiliang , Zhang Jingyu , Wu Xuan , Du Wanqing , Zhu Yinghong , Liu Xing , Liu Zhenhao , Meng Bin , Guo Jiaojiao , Yang Qin , Wang Yihui , Wang Qinglin , Feng Xiangling , Xie Guoxiang , Shen Yi , He Yanjuan , Xiang Juanjuan , Wu Minghua , An Gang , Qiu Lugui , Jia Wei , Zhou Wen
Published: July 2022

Metabolites in the tumor microenvironment are a critical factor for tumor progression. However, the lack of knowledge about the metabolic profile in the bone marrow (BM) microenvironment of multiple myeloma (MM) limits our understanding of MM progression. Here, we show that the glycine concentration in the BM microenvironment is elevated due to bone collagen degradation mediated by MM cell-secreted matrix metallopeptidase 13 (MMP13), while the elevated glycine level is linked to MM progression. MM cells utilize the channel protein solute carrier family 6 member 9 (SLC6A9) to absorb extrinsic glycine subsequently involved in the synthesis of glutathione (GSH) and purines. Inhibiting glycine utilization via SLC6A9 knockdown or the treatment with betaine suppresses MM cell proliferation and enhances the effects of bortezomib on MM cells. Together, we identify glycine as a key metabolic regulator of MM, unveil molecular mechanisms governing MM progression, and provide a promising therapeutic strategy for MM treatment.
Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features
Authors: Nguyen Luan , Van Hoeck Arne , Cuppen Edwin
Published: July 2022

Cancers of unknown primary (CUP) origin account for ∼3% of all cancer diagnoses, whereby the tumor tissue of origin (TOO) cannot be determined. Using a uniformly processed dataset encompassing 6756 whole-genome sequenced primary and metastatic tumors, we develop Cancer of Unknown Primary Location Resolver (CUPLR), a random forest TOO classifier that employs 511 features based on simple and complex somatic driver and passenger mutations. CUPLR distinguishes 35 cancer (sub)types with ∼90% recall and ∼90% precision based on cross-validation and test set predictions. We find that structural variant derived features increase the performance and utility for classifying specific cancer types. With CUPLR, we could determine the TOO for 82/141 (58%) of CUP patients. Although CUPLR is based on machine learning, it provides a human interpretable graphical report with detailed feature explanations. The comprehensive output of CUPLR complements existing histopathological procedures and can enable improved diagnostics for CUP patients.
Mitigating sarcoplasmic reticulum stress limits disuse-induced muscle loss in hindlimb unloaded mice
Authors: Khan Amir Ali , Gul Muhammad Tehsil , Karim Asima , Ranade Anu , Azeem Muhammad , Ibrahim Zeinab , Ramachandran Gopika , Nair Vidhya A. , Ahmad Firdos , Elmoselhi Adel , Qaisar Rizwan
Published: July 2022

Muscle disuse in the hindlimb unloaded (HU) mice causes significant atrophy and weakness. However, the cellular and molecular mechanisms driving disuse-muscle atrophy remain elusive. We investigated the potential contribution of proteins dysregulation by sarcoplasmic reticulum (SR), a condition called SR stress, to muscle loss during HU. Male, c57BL/6j mice were assigned to ground-based controls or HU groups treated with vehicle or 4-phenylbutyrate (4-PBA), a potent inhibitor of SR stress, once a day for three weeks. We report that the 4-PBA reduced the SR stress and partly reversed the muscle atrophy and weakness in the HU mice. Transcriptome analysis revealed that several genes were switched on (n = 3688) or differentially expressed (n = 1184) due to HU. GO, and KEGG term analysis revealed alterations in pathways associated with the assembly of cilia and microtubules, extracellular matrix proteins regulation, calcium homeostasis, and immune modulation during HU. The muscle restoration with 4-PBA partly reversed these changes along with differential and unique expression of several genes. The analysis of genes among the two comparisons (HU-v vs. control and HU-t vs. HU-v.) shows 841 genes were overlapped between the two comparisons and they may be regulated by 4-PBA. Altogether, our findings suggest that the pharmacological suppression of SR stress may be an effective strategy to prevent disuse-induced muscle weakness and atrophy.
Full-color-tunable phosphorescence of antimony-doped lead halide single crystal
Authors: Liao Jin-Feng , Zhang Zhipeng , Wang Bingzhe , Tang Zikang , Xing Guichuan
Published: July 2022

Although multiple emissive phosphors are of great fundamental interest and practical importance, it is still challenging to achieve full-color tunable luminescence in a single-component material. Herein, we present an antimony-doped lead halide single crystal (C10NH22)2PbBr4: Sb3+ with widely tunable red/green/blue/white luminescence. Extrinsic Sb3+ dopants provide host another active sites to capture photo-generated excitons, thus triggering blue/red dual emission. Moreover, a reversible thermal-induced phase transition transforms blue/red emission into green/red dual emission. Both two phases exhibit intriguing excitation-wavelength dependent emission, affording a whole color gamut covering the red-green-blue (RGB) color triangle on the CIE 1931 diagram. Experimental and theoretical calculation studies reveal two emitters work independently, which paves the way for the multimode optical control and promotes the development of multifunctional luminescent materials.
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
Authors: Boninsegna Lorenzo , Yildirim Asli , Polles Guido , Zhan Yuxiang , Quinodoz Sofia A. , Finn Elizabeth H. , Guttman Mitchell , Zhou Xianghong Jasmine , Alber Frank
Published: July 2022

A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin. We demonstrate that multimodal data integration can compensate for systematic errors in some of the data and can greatly increase accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency (‘rare’) interchromosomal contacts to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multimodal data integration for genome structure analysis, available through the Integrative Genome Modeling software package.
Reference database of teeth images from the Family Bovidae
Authors: Brophy Juliet K. , Matthews Gregory J.
Published: July 2022

Researchers typically rely on fossils from the Family Bovidae to generate African paleoenvironmental reconstructions due to their strict ecological tendencies. Bovids have dominated the southern African fauna for the past four million years and, therefore, dominate the fossil faunal assemblages, especially isolated teeth. Traditionally, researchers reference modern and fossil comparative collections to identify teeth. However, researchers are limited by the specific type and number of bovids at each institution. B.O.V.I.D. (Bovidae Occlusal Visual IDentification) is a repository of images of the occlusal surface of bovid teeth. The dataset currently includes extant bovids from 7 tribes and 20 species (~3900). B.O.V.I.D. contains two scaled images per specimen: a color and a black and white (binarized) image. The database is a useful reference for identifying bovid teeth. The large sample size also allows one to observe the natural variation that exists in each taxa. The binarized images can be used in statistical shape analyses, such as taxonomic classification. B.O.V.I.D. is a valuable supplement to other methods for taxonomically identifying bovid teeth.
Cell mediated remodeling of stiffness matched collagen and fibrin scaffolds
Authors: Jagiełło Alicja , Castillo Ulysses , Botvinick Elliot
Published: July 2022

Cells are known to continuously remodel their local extracellular matrix (ECM) and in a reciprocal way, they can also respond to mechanical and biochemical properties of their fibrous environment. In this study, we measured how stiffness around dermal fibroblasts (DFs) and human fibrosarcoma HT1080 cells differs with concentration of rat tail type 1 collagen (T1C) and type of ECM. Peri-cellular stiffness was probed in four directions using multi-axes optical tweezers active microrheology (AMR). First, we found that neither cell type significantly altered local stiffness landscape at different concentrations of T1C. Next, rat tail T1C, bovine skin T1C and fibrin cell-free hydrogels were polymerized at concentrations formulated to match median stiffness value. Each of these hydrogels exhibited distinct fiber architecture. Stiffness landscape and fibronectin secretion, but not nuclear/cytoplasmic YAP ratio differed with ECM type. Further, cell response to Y27632 or BB94 treatments, inhibiting cell contractility and activity of matrix metalloproteinases, respectively, was also dependent on ECM type. Given differential effect of tested ECMs on peri-cellular stiffness landscape, treatment effect and cell properties, this study underscores the need for peri-cellular and not bulk stiffness measurements in studies on cellular mechanotransduction.
Periodically taken photographs reveal the effect of pollinator insects on seed set in lotus flowers
Authors: Nagai Mihoko , Higuchi Yohei , Ishikawa Yusei , Guo Wei , Fukatsu Tokihiro , Baba Yuki G. , Takada Mayura B.
Published: July 2022

Understanding of pollination systems is an important topic for evolutionary ecology, food production, and biodiversity conservation. However, it is difficult to grasp the whole picture of an individual system, because the activity of pollinators fluctuates depending on the flowering period and time of day. In order to reveal effective pollinator taxa and timing of visitation to the reproductive success of plants under the complex biological interactions and fluctuating abiotic factors, we developed an automatic system to take photographs at 5-s intervals to get near-complete flower visitation by pollinators during the entire flowering period of selected flowers ofNelumbo nuciferaand track the reproductive success of the same flowers until fruiting. Bee visits during the early morning hours of 05:00–07:59 on the second day of flowering under optimal temperatures with no rainfall or strong winds contributed strongly to seed set, with possible indirect negative effects by predators of the pollinators. Our results indicate the availability of periodic and consecutive photography system in clarifying the plant-pollinator interaction and its consequence to reproductive success of the plant. Further development is required to build a monitoring system to collect higher-resolution time-lapse images and automatically identify visiting insect species in the natural environment.
65,000-years of continuous grinding stone use at Madjedbebe, Northern Australia
Authors: Hayes Elspeth H. , Fullagar Richard , Field Judith H. , Coster Adelle C.F. , Matheson Carney , Nango May , Djandjomerr Djaykuk , Marwick Ben , Wallis Lynley A. , Smith Mike A. , Clarkson Chris
Published: July 2022

Grinding stones and ground stone implements are important technological innovations in later human evolution, allowing the exploitation and use of new plant foods, novel tools (e.g., bone points and edge ground axes) and ground pigments. Excavations at the site of Madjedbebe recovered Australia’s (if not one of the world’s) largest and longest records of Pleistocene grinding stones, which span the past 65 thousand years (ka). Microscopic and chemical analyses show that the Madjedbebe grinding stone assemblage displays the earliest known evidence for seed grinding and intensive plant use, the earliest known production and use of edge-ground stone hatchets (aka axes), and the earliest intensive use of ground ochre pigments in Sahul (the Pleistocene landmass of Australia and New Guinea). The Madjedbebe grinding stone assemblage reveals economic, technological and symbolic innovations exemplary of the phenotypic plasticity of Homo sapiens dispersing out of Africa and into Sahul.
Retinal drusen counts are increased in inflammatory bowel disease, and with longer disease duration, more complications and associated IgA glomerulonephritis
Authors: Nicklason E. , Ham Y. , Ng D. , Glance S. , Abel K. , Harraka P. , Mack H. , Colville D. , Savige J.
Published: July 2022

Retinal drusen are deposits of inflammatory proteins that are found in macular degeneration and glomerulonephritis and result, in part, from complement activation. This was a cross-sectional observational study of individuals with inflammatory bowel disease (IBD) recruited from a Gastroenterology clinic who underwent non-mydriatic retinal photography. Deidentified images were examined for drusen, and drusen counts and size were compared with matched controls, and examined for clinical associations. The cohort with IBD comprised 19 individuals with ulcerative colitis, 41 with Crohn’s disease and three with indeterminate colitis, including 34 males (54%) and an overall median age of 48 (IQR 23) years. Their median IBD duration was 7 (IQR 10) years, median CRP level was 7 (IQR 14) mg/L, and 28 (44%) had complications (fistula, stricture, bowel resection etc.), while 28 with Crohn’s disease (68%) had colonic involvement. Drusen counts were higher in IBD than controls (12 ± 34, 3 ± 8 respectively, p = 0.04). Counts ≥ 10 were also more common (14, 22%, and 4, 6%, p = 0.02, OR 4.21, 95%CI 1.30 to 13.63), and associated with longer disease duration (p = 0.01, OR 1.06, 95%CI 1.00 to 1.13), an increased likelihood of complications (p = 0.003, OR 6.90, 95%CI 1.69 to 28.15) and higher CRP levels at recruitment (p = 0.008, OR1.02, 95%CI 1.00 to 1.05). Increased retinal drusen were found in all four individuals with Crohn’s disease and IgA glomerulonephritis. IBD and drusen may share pathogenetic mechanisms and underlying risk factors such as complement activation.
Geriatric nutritional risk index is associated with retinopathy in patients with type 2 diabetes
Authors: Cho AJin , Hong Yun Soo , Park Hayne Cho , Kim Do Hyoung , Shin Young Joo , Lee Young-Ki
Published: July 2022

The geriatric nutritional risk index (GNRI) is a nutrition-related risk assessment tool and has been used in various clinical settings. The relationship between body mass index (BMI) and the associated risk of diabetic retinopathy (DR) remains inconclusive. We aimed to evaluate the association between GNRI and DR in patients with type 2 diabetes. We included a total of 1359 patients with type 2 diabetes who followed up in our diabetes clinic and underwent fundus photographic examinations from August 2006 to February 2014. DR was assessed by retinal ophthalmologists using comprehensive ophthalmologic examinations. Patients were divided into tertiles according to their GNRI category. Patients in a lower GNRI tertile tended to have a higher proportion of nonproliferative DR (NPDR) and proliferative DR (PDR) compared with those in the other tertiles. The risk of PDR was higher in patients included in GNRI tertile 1 (Odds ratio (OR) 2.252, 95% Confidence Interval (CI) 1.080–4.823, P = 0.033) and GNRI tertile 2 (OR 2.602, 95% CI 1.323–5.336, P = 0.007) compared with those in GNRI tertile 3. In patients with lower GNRIs, the prevalence of DR was higher than in those with higher GNRIs. When GNRI was compared with BMI using the area under the curve, overall accuracy was high in GNRI. The risk of PDR was high in patients with low GNRI and there is an inverse association between GNRI scores and prevalence of DR. GNRI might be a useful tool to predict DR in patients with type 2 diabetes.
Machine learning techniques for identification of carcinogenic mutations, which cause breast adenocarcinoma
Authors: Shah Asghar Ali , Malik Hafiz Abid Mahmood , Mohammad AbdulHafeez , Khan Yaser Daanial , Alourani Abdullah
Published: July 2022

Breast adenocarcinoma is the most common of all cancers that occur in women. According to the United States of America survey, more than 282,000 breast cancer patients are registered each year; most of them are women. Detection of cancer at its early stage saves many lives. Each cell contains the genetic code in the form of gene sequences. Changes in the gene sequences may lead to cancer. Replication and/or recombination in the gene base sometimes lead to a permanent change in the nucleotide sequence of the genome, called a mutation. Cancer driver mutations can lead to cancer. The proposed study develops a framework for the early detection of breast adenocarcinoma using machine learning techniques. Every gene has a specific sequence of nucleotides. A total of 99 genes are identified in various studies whose mutations can lead to breast adenocarcinoma. This study uses the dataset taken from 4127 human samples, including men and women from more than 12 cohorts. A total of 6170 mutations in gene sequences are used in this study. Decision Tree, Random Forest, and Gaussian Naïve Bayes are applied to these gene sequences using three evaluation methods: independent set testing, self-consistency testing, and tenfold cross-validation testing. Evaluation metrics such as accuracy, specificity, sensitivity, and Mathew’s correlation coefficient are calculated. The decision tree algorithm obtains the best accuracy of 99% for each evaluation method.
Cationic protein 8 plays multiple roles in Galleria mellonella immunity
Authors: Kordaczuk Jakub , Sułek Michał , Mak Paweł , Zdybicka-Barabas Agnieszka , Śmiałek Justyna , Wojda Iwona
Published: July 2022

Galleria mellonellacationic protein 8 (GmCP8) is a hemolymph protein previously identified as an opsonin and an inhibitor of fungal proteases. In this work, we showed its bactericidal activity towardPseudomonas entomophila,Pseudomonas aeruginosa,Bacillus thuringiensis,Staphylococcus aureus, andEscherichia coliand against yeast-like fungiCandida albicans. The activity againstE. coliwas correlated with bacterial membrane permeabilization. In turn, in the case ofP. entomophila,B. thuringiensis,andC. albicans, the atomic force microscopy analysis of the microbial surface showed changes in the topography of cells and changes in their nanomechanical properties. GmCP8 also showed the inhibitory activity toward the serine protease trypsin and the metalloproteinase thermolysin. The expression of the gene encoding the GmCP8 protein did not increase either in the gut or in the fat body ofG. mellonellaafter oral infection withP. entomophila. Similarly, the amount of GmCP8 in the hemolymph ofG. mellonelladid not change in immune-challenged insects. However, when GmCP8 was injected into theG. mellonellahemocel, a change in the survival curve was observed in the infected larvae. Our results shed new light on the function of GmCP8 protein in insect immunity, indicating its role in humoral defence mechanisms.
Missing eddy feedback may explain weak signal-to-noise ratios in climate predictions
Authors: Hardiman Steven C. , Dunstone Nick J. , Scaife Adam A. , Smith Doug M. , Comer Ruth , Nie Yu , Ren Hong-Li
Published: July 2022

The signal-to-noise paradox that climate models are better at predicting the real world than their own ensemble forecast members highlights a serious and currently unresolved model error, adversely affecting climate predictions and introducing uncertainty into climate projections. By computing the magnitude of feedback between transient eddies and large-scale flow anomalies in multiple seasonal forecast systems, this study shows that current systems underestimate this positive eddy feedback, and that this deficiency is strongly linked to weak signal-to-noise ratios in ensemble mean predictions. Improved eddy feedback is further shown to be linked to greater teleconnection strength between the El Niño Southern Oscillation and the Arctic Oscillation and to stronger predictable signals. We also present a technique to estimate the potential gain in skill that may come from eliminating eddy feedback deficiency, showing that skill could double in some extratropical regions, significantly improving predictions of the Arctic Oscillation.
Nanomaterials in electro-organic synthesis
Authors: Iqbal A. , Zai J. , Zhang Y.
Published: July 2022

The rapidly increasing energy demand by the growing human population is causing severe depletion of fossil fuels with rising environmental concerns. Incidentally, electrochemical organic synthesis is accepted as an eco-friendly method for producing diverse molecules driven by electricity and offers potential scope towards establishing sustainable energy solutions. In view of this, the present chapter highlights illustrative examples of such electrochemical reactions in the context of the nanocatalysts used for the synthesis of organic molecules. The ever-growing field of nanocatalysts and their use in the electrosynthesis of organic substances is still in its infancy. There are just a few research findings describing the role of nanomaterials as substituting toxic redox reagents. We have presented the electro-organic synthesis in terms of electro-oxidation and electro-reduction reactions. We expect that the use of nanomaterials for the electrosynthesis of organic materials will attract the serious attention of synthetic chemists, as it could be a significant way to develop interesting organic substances.
Exploration of the photocatalytic cycle for sacrificial hydrogen evolution by conjugated polymers containing heteroatoms
Authors: Prentice Andrew W. , Zwijnenburg Martijn A.
Published: July 2022

We analyze the photocatalytic activity of heteroatom containing linear conjugated polymers for sacrificial hydrogen evolution using a recently proposed photocatalytic cycle.
Unraveling gelation kinetics, arrested dynamics and relaxation phenomena in filamentous colloids by photon correlation imaging
Authors: Usuelli Mattia , Ruzzi Vincenzo , Buzzaccaro Stefano , Nyström Gustav , Piazza Roberto , Mezzenga Raffaele
Published: July 2022

Photon correlation imaging unveiled gelation kinetics and stress relaxation in colloidal filamentous gels, set by perfusion of ions. We observed a linear-in-time evolution of the gelation front, and ionic-strength dependant rearrangement dynamics.
Development of non-viral vectors for neuronal-targeted delivery of CRISPR-Cas9 RNA-proteins as a therapeutic strategy for neurological disorders
Authors: Shalaby Karim E. , Aouida Mustapha , Gupta Vijay , Abdesselem Houari , El-Agnaf Omar M. A.
Published: July 2022

Peptide-based non-viral vectors for CRISPR therapeutic delivery.
Mesenchymal stem cell-derived exosome mitigates colitis via the modulation of the gut metagenomics–metabolomics–farnesoid X receptor axis
Authors: Ocansey Dickson Kofi Wiredu , Zhang Zhiyu , Xu Xinwei , Liu Lianqin , Amoah Samuel , Chen Xiang , Wang Bo , Zhang Xu , Mao Fei
Published: July 2022

IBD is associated with chronic gut immune dysregulation and altered microbiome and metabolite composition. MSC-Ex mitigates DSS-induced IBD in mice by modulating the gut metagenomics–metabolomics–FXR axis.
Antimicrobial activity of piezoelectric polymer: piezoelectricity as the reason for damaging bacterial membrane
Authors: Gazvoda Lea , Perišić Nanut Milica , Spreitzer Matjaž , Vukomanović Marija
Published: July 2022

Piezoelectric poly-l-lactide nanotubes mechanically deformed with ultrasound selectively destroy bacterial membranes, exhibiting a contact-based antimicrobial effect.
A novel docetaxel derivative exhibiting potent anti-tumor activity and high safety in preclinical animal models
Authors: Wang Yao , Wang Penghui , zhou Linzhu , Su Yue , Zhou Yongfeng , Zhu Xinyuan , Huang Wei , Yan Deyue
Published: July 2022

DTX-AI effectively suppresses the growth of HeLa-tumor and A549-tumor xenografts in vivo and increases the survival rate of mice. It is expected to be a promising ‘me-better’ anti-tumor drug with higher efficiency and lower toxicity in clinic.
Selective detection of sulfasalazine antibiotic and its controllable photodegradation into 5-aminosalicylic acid by visible-light-responsive metal–organic framework
Authors: Li Han-Shu , Gong Yuxuan , Ji Chen , Wu Pengyan , Gao Bingzhuo , Du Yufan , Wang Jian
Published: July 2022

An Eosin Y-based MOF exhibits high selectivity for the detection of sulfasalazine antibiotic and its controllable degradation into 5-aminosalicylic acid with excellent catalytic activity and recyclability.
Co-digestive ripening assisted phase-controlled synthesis of Ag–Sn intermetallic nanoparticles and their dye degradation activity
Authors: Bhatia Geetanjali , Jagirdar Balaji R.
Published: July 2022

ε-Ag3Sn intermetallic nanoparticles were prepared by the solvated metal atom dispersion method in conjunction with co-digestive ripening of Ag and Sn colloids. The Ag3Sn nanoparticles showed excellent photocatalytic dye degradation activity.
Enhanced visible light photocatalytic hydrogen production over poly(dibenzothiophene-S,S-dioxide)-based heterostructures decorated by Earth-abundant layered double hydroxides
Authors: Luo Jingsong , Wu Jun , Liu Yuxiang , Yuan Jiahuan , Wang Feng
Published: July 2022

PSO@NiFeLDH-15 exhibited the highest photocatalytic activity with a rate of 52.8 mmol h−1 g−1 at an optimal content without a Pt cocatalyst under visible light irradiation.
Trinuclear zinc calix[4]arenes: synthesis, structure, and ring opening polymerization studies
Authors: Xing Tian , Frese Josef W. A. , Derbyshire Max , Glenister Mollie A. , Elsegood Mark R. J. , Redshaw Carl
Published: July 2022

Zinc complexes containing near-linear Zn3 motifs and bearing 1,3-dialkoxycalix[4]arene ligands have been structurally characterized, and are capable of the ROP of ε-caprolactone affording cyclic and linear products of low to medium molecular weight.