bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation Methods for Breast Cancer Prediction in Machine Learning Field
Authors: Zhang Zirui , Li Zixuan
Published: August 2022

Breast cancer is the most common malignant tumor found in women, and there is no cure for advanced breast cancer. Early detection and treatment can effectively improve patient survival. This paper uses five machine learning classification models, namely Support Vector Machine (SVM), Logistic Regression (LR), Decision Tree (DT), Random Forest (RF), and K-Nearest Neighbors Algorithm (KNN). The training data for the five models are provided by the Wisconsin Breast Cancer Dataset (WBCD). By evaluating and comparing the performance of the five models in accuracy, F1Score, ROC curve, and PR curve, the study finds that LR has the best performance.
“Soothe the spirits with a loving heart” psychological assistance project for orphans and disabled children in orphanages
Authors: Jiang Qiuwei , Yan Qiangwe
Published: August 2022

In this paper, the research results of characteristic project of practical education in colleges and universities in Hubei Province, “Soothe the spirits with a loving heart ” psychological assistance project (Project No. 2017SJJPD2002), has been reported. The project is a public benefit activity in which the undergraduate psychological service team of Wuhan Textile University goes to the orphanages to offer psychological assistance. Many psychological assistances were offered by students for the orphans and disabled children in orphanages through various forms such as companionship, lectures, group counseling and quality development, which not only promoted the formation of a good mentality for orphans and disabled children in orphanages, but also strengthened the mental quality and improved interpersonal communication skills of college students. What’s more, it created a practical platform for college students relying on social benefit services to develop a sense of responsibility and promote their personal self-realization.
Research on the development of global digital tax and countermeasures of Chinese digital tax
Authors: Fu Shiwen , Yuan Jianguo , Chen Zhiqiang
Published: August 2022

International taxation faces challenges brought by the development of the digital economy. Countries around the world and relevant international organizations, based on different positions, advocate or oppose the establishment of digital tax collection policies. This paper aims to summarize the development status of digital tax collection supervision policies of major countries and international organizations, to analyze the impact of the digital tax in combination with the development of China’s digital economy, and try to put forward policy suggestions for the development of China’s digital tax.
Overview of research on the application of virtual reality to spatial cognitive ability
Authors: Bao An , Wei Qiang , Sun Yan
Published: August 2022

The experimental environment created by the virtual reality technology for the Spatial Cognitive Ability Research Institute cannot be replaced by the traditional experimental environment. Given this, this study reviews the research on spatial cognitive ability using virtual reality technology from the aspects of concept development and application category of virtual reality spatial cognitive ability. On this basis, this study summarizes the shortcomings of current research and proposes the direction of future research to provide ideas and references for researchers of spatial cognitive ability of virtual reality.
Endovascular Treatment Strategy for Acute Basilar Artery Occlusion with Unexpected Right-Sided Aortic Arch
Authors: Mizowaki Takashi , Fujita Atsushi , Miura Shinichi , Nakahara Masahiro , Tanaka Hirotomo , Matsumoto Shinichi , Takaishi Yoshiyuki , Kondoh Takeshi
Published: August 2022

A right-sided aortic arch (RAA) is a rare variant of the aortic arch found. We present a case of endovascular treatment (EVT) for acute basilar artery (BA) occlusion with an RAA. A 70-year-old man developed acute ischemic stroke due to BA occlusion. During urgent EVT for BA occlusion with an RAA, which was observed unexpectedly, navigation of the catheter to the target vessel was achieved as a result of an early change in the access route. Flexible treatment strategies are warranted for cases of unexpected anatomical variant in the fight against time for emergent cases, such as acute ischemic stroke.
Medical Research Conduct and Publication during Higher Education in Syria: Attitudes, Barriers, Practices, and Possible Solutions
Authors: Hanafi Ibrahem , Haj Kassem Luma , Hanafi Mouaz , Ahmad Sulafa , Abbas Ola , Hajeer Mohammad Younis , Alsalkini Marah , Alahdab Fares
Published: August 2022

Background: The huge workload on doctors especially residents, who are the main health care providers in public hospitals, in addition to the vanishing incomes and lack of personal safety during the decade-long Syrian crisis, led to further hurdles in the focus on research. Postgraduate students in the medical and paramedical fields must conduct original research projects as part of their graduation requirements. However, this does not reflect on research publications coming from Syria.

Methods: This is a nation-wide cross-sectional study targeting medical, dental, and pharmacy postgraduate students who are at the phase of planning for their required projects. The questionnaire aimed to capture their attitudes toward research, perceived barriers, and previous research experiences in order to suggest evidence-based recommendations.

Results: The sample consisted of 429 residents representing about 22% of the target population. Nearly all the participants had positive opinion toward the important role of medical research and the significance of their participation. Agreement was also clear regarding perceived barriers, including the lack of adequate training and research facility. Seventy-one percent of the participants were not involved in any research before the time of their master theses, less than 13% of them had submitted an article for publication, and less than 5% had submitted more than one paper. Despite that, high-quality internet connectivity and rich English writing skills were associated with further research experiences. Additionally, mentors' support and self-paced learning of research skills had significant positive impact on students' research contributions with odds ratios of 2.04 [[95% Confidence Interval]: 1.02–4.06] and 2.68 [1.48–4.84], respectively.

Conclusion: Lack of training and mentorship, in addition to several common barriers to medical research, hampered residents' capacity of conducting and publishing research despite their positive attitudes toward it. Nevertheless, the variance within our sample exposed a promising window for implementing low-cost institutional and individual solutions such as peer-run self-paced training opportunities and long-distance mentoring.
Multifractional Brownian motion characterization based on Hurst exponent estimation and statistical learning
Authors: Szarek Dawid , Jabłoński Ireneusz , Krapf Diego , Wyłomańska Agnieszka
Published: August 2022

This paper proposes an approach for the estimation of a time-varying Hurst exponent to allow accurate identification of multifractional Brownian motion (MFBM). The contribution provides a prescription for how to deal with the MFBM measurement data to solve regression and classification problems. Theoretical studies are supplemented with computer simulations and real-world examples. Those prove that the procedure proposed in this paper outperforms the best-in-class algorithm.
Long-term stability of GaAs/AlAs terahertz quantum-cascade lasers
Authors: Schrottke L. , Lü X. , Biermann K. , Gellie P. , Grahn H. T.
Published: August 2022

We have investigated high-performance GaAs/AlAs terahertz (THz) quantum-cascade lasers (QCLs) with respect to the long-term stability of their operating parameters. The output power of lasers that contain an additional, thick AlAs refractive-index contrast layer underneath the cascade structure decreases after three months by about 35%. The deterioration of these lasers is attributed to the oxidation processes in this contrast layer starting from the facets. However, GaAs/AlAs THz QCLs with an Al0.9Ga0.1As refractive-index contrast layer exhibit long-term stability of the operating parameters over many years even when they are exposed to atmospheric conditions. Therefore, these lasers are promising high-power radiation sources in the terahertz spectral region for commercial applications.
Influence pathway of iron ions with different valences for methane fermentation of vegetable waste
Authors: Li Jiang , Lei Yunhui , Pu Xiaodong , Liu Yi , Tang Ya
Published: August 2022

Anaerobic digestion (AD) is a promising approach for vegetable waste (VW) recycling and energy recovery but methanogenesis is always inhibited by acid accumulation. The addition of a mixture of iron and other elements has proved effective on reducing acid inhibition during AD of VW, but the effect of use of iron alone has rarely been assessed. In the present study, we compared the effects of Fe0 and Fe2+ on methane fermentation from VW at an organic loading rate of 1.5 gVS/L/d. The results indicated that Fe0 maintained a pH > 7.7, oxidation reduction potential <−520, and methane production rate (MPR) at 250–300 mL/gVS/d. Partial least squares path modeling and correlation analysis revealed Fe0 maintained pH for high MPR mainly through enhancing the conversion of propionic and butyric acids to acetic acid, causing the total acid decreasing to 1500 mg/L. In contrast, Fe2+ caused an accumulation of all volatile fatty acids up to 4000 mg/L and aggravated acid inhibition, resulting in a significant reduction in MPR to 148 mL/gVS/d. In all treatments, the influence of ammonia nitrogen was not significant. This study provided a direction for the determination of engineering monitoring indicators and regulation measures in AD of VW.
Simulation research on near-neutral electrochemical corrosion of ferrite–pearlite pipeline steel
Authors: Yan Hao , Chen Gang , Huang Shipeng , Dai Yao , Liao Kun
Published: August 2022

The problem of electrochemical corrosion of buried pipelines in near-neutral electrolytes leads to defects in or even fracture of oil and gas pipelines and the leakage of natural gas. Based on the principle of material diffusion and migration, the research object established an electrochemical corrosion model under the metallographic structure of pipes with ferritic–pearlitic pipeline steel. The results show that the most severe corrosion occurs at the center of the corrosion on the surface of the pipeline steel in a near-neutral corrosive environment. In addition, due to corrosion product accumulation, the material corrosion rate increased by about 38%. The electrolyte potential near the corrosion electrode is smaller, the ion concentration near the electrode is the highest, and the mass transfer phenomenon around the corrosion electrode is obvious. When the material undergoes metallographic corrosion, the corrosion is more severe. This research method can be used to predict the electrochemical corrosion occurring in the metal structure of buried pipelines and has some guidance for the assessment of the integrity of the external surface of buried pipes.
Solid-phase epitaxy of a CuAlO2 template on c-Al2O3 for delafossite growth
Authors: Huon Amanda , Ok Jong Mok , Yoon Sangmoon , Lupini Andrew R. , Lee Ho Nyung
Published: August 2022

Thin-film growth of ABO2 delafossites has recently attracted significant attention due to its attractive transport properties and potential applications. A fundamental requirement for achieving high-quality thin films is the availability of lattice matching substrates and chemical compatibility. However, there are still many obstacles to achieving high-quality thin films. Here, we report a process to further engineer a template ABO2 delafossite structure by solid-phase epitaxy of CuAlO2 on the surface of a commercial sapphire substrate, which offers a promising route to growing high-quality epitaxial thin films. The starting reagents involve a layer of polycrystalline Cu2O deposited on a c-Al2O3 substrate by pulsed laser deposition (PLD). Subsequent thermal treatment activates a solid-state interface reaction between the film and substrate, producing a CuAlO2 thin film. The reaction temperature and dwell time parameters were optimized in this study to prepare a phase diagram for CuAlO2 samples without phase impurities. This method provides an essential stepping-stone toward the approachability of a lattice matching template (i.e., substrate-buffer layer) for ABO2 heterostructures. An example of successful epitaxial growth of highly conducting PdCrO2 is also demonstrated by using a CuAlO2 buffer layer.
Combined physiological responses and differential expression of drought-responsive genes preliminarily explain the drought resistance mechanism of
Authors: Wang Leiting , Jian Zhongling , Wang Puchang , Zhao Lili , Chen Keke
Published: August 2022

Lotus corniculatus L. is a perennial high-quality legume forage species but is vulnerable to drought, and water deficit reduces productivity. To understand the drought response mechanism of L. corniculatus, we investigated physiological responses under drought stress and constructed suppression subtractive hybridisation (SSH) cDNA libraries to isolate drought-inducible genes and quantitatively study the expression levels of candidate drought- responsive genes. Genes encoding calmodulin-like protein, mitogen-activated protein kinase, indole-3-acetic acid-induced protein, ser/thr-protein phosphatase homolog-related proteins, and β-galactosidase-related protein with hydrolysis activity were isolated and considered the main factors that explained the resistance of L. corniculatus to drought. Approximately 632 expressed sequence tags (ESTs) were identified and confirmed in the constructed SSH library. The Gene Ontology (GO) analysis revealed that these genes were involved mainly in transcription processes, protein synthesis, material metabolism, catalytic reactions, sugar metabolism, and photosynthesis. The interaction between the functions of these drought-related genes and the physiological responses preliminarily explains the drought resistance mechanisms of L. corniculatus.
Inter- and trans-generational effects of gestational ghrelin imbalance on development and reproduction in the mouse
Authors: Torres Pedro Javier , Luque Eugenia Mercedes , Ramírez Nicolás David , Carlini Valeria Paola , Martini Ana Carolina
Published: August 2022

Context and aims We have demonstrated that ghrelin (Ghrl) participates in fetal programming, since intragestational hyperghrelinaemia increased pup’s growth and a Ghrl-receptor antagonist accelerated offspring’s sexual maturation and impaired their adult reproductive function. Now, we aim to analyse if these phenotypic changes (found in F1) also occurred in F2 and/or F3 generations. Methods We treated mice dams (F0), with 4 nmol/animal/day of Ghrl or 6 nmol/animal/day of an antagonist [Ant:(d-Lys3)GHRP6] from day 1 of pregnancy until delivery. When F1 female pups reached adulthood, they were paired to obtain F2, and subsequently, F2 females were paired to obtain F3. Parameters evaluated in F2 and F3 pups were: growth, physical development, neurobiological maturation, puberty onset and in adulthood, reproductive function. Key results The F2 and F3 Ant groups showed a significant increase in litter size. Although no differences were detected in the weight of these pups at birth, in adulthood, they were heavier. At F3, pups from the Ant group showed advanced incisors eruption and eye opening compared to controls. Furthermore, F3 male pups from the Ant group showed earlier testis descent, although in adulthood, these males exhibited reduced sperm concentration in comparison to Ghrl. No differences were detected in F2 or F3 females regarding puberty onset or reproduction. Conclusions and implications Some fetal programming effects of Ghrl seen in F1, also appeared transgenerationally. Since many women at reproductive age suffer from conditions with reduced Ghrl levels (i.e. obesity or polycystic ovarian syndrome), these results could be relevant to the health of their descendants.
Hot, wet and rare: modelling the occupancy dynamics of the narrowly distributed Dixie Valley toad
Authors: Rose Jonathan P. , Kleeman Patrick M. , Halstead Brian J.
Published: August 2022

Context Small population sizes and no possibility of metapopulation rescue put narrowly distributed endemic species under elevated risk of extinction from anthropogenic change. Desert spring wetlands host many endemic species that require aquatic habitat and are isolated by the surrounding xeric terrestrial habitat. Aims We sought to model the occupancy dynamics of the Dixie Valley toad (Anaxyrus williamsi), a recently described species endemic to a small desert spring wetland complex in Nevada, USA. Methods We divided the species’ range into 20 m × 20 m cells and surveyed for Dixie Valley toads at 60 cells during six primary periods from 2018 to 2021, following an occupancy study design. We analysed our survey data by using a multi-state dynamic occupancy model to estimate the probability of adult occurrence, colonisation, site survival, and larval occurrence and the relationship of each to environmental covariates. Key results The detection probabilities of adult and larval toads were affected by survey length and time of day. Adult Dixie Valley toads were widely distributed, with detections in 75% of surveyed cells at some point during the 3-year study, whereas larvae were observed only in 20% of cells during the study. Dixie Valley toad larvae were more likely to occur in cells far from spring heads with a high coverage of surface water, low emergent vegetation cover, and water temperatures between 20°C and 28°C. Adult toads were more likely to occur in cells with a greater coverage of surface water and water depth >10 cm. Cells with more emergent vegetation cover and surface water were more likely to be colonised by adult toads. Conclusions Our results showed that Dixie Valley toads are highly dependent on surface water in both spring and autumn. Adults and larvae require different environmental conditions, with larvae occurring farther from spring heads and in fewer cells. Implications Disturbances to the hydrology of the desert spring wetlands in Dixie Valley could threaten the persistence of this narrowly distributed toad.
Environmental context dependency in species interactions
Authors: Liu Owen R. , Gaines Steven D.
Published: August 2022

Ecological interactions are not uniform across time and can vary with environmental conditions. Yet, interactions among species are often measured with short-term controlled experiments whose outcomes can depend greatly on the particular environmental conditions under which they are performed. As an alternative, we use empirical dynamic modeling to estimate species interactions across a wide range of environmental conditions directly from existing long-term monitoring data. In our case study from a southern California kelp forest, we test whether interactions between multiple kelp and sea urchin species can be reliably reconstructed from time-series data and whether those interactions vary predictably in strength and direction across observed fluctuations in temperature, disturbance, and low-frequency oceanographic regimes. We show that environmental context greatly alters the strength and direction of species interactions. In particular, the state of the North Pacific Gyre Oscillation seems to drive the competitive balance between kelp species, asserting bottom-up control on kelp ecosystem dynamics. We show the importance of specifically studying variation in interaction strength, rather than mean interaction outcomes, when trying to understand the dynamics of complex ecosystems. The significant context dependency in species interactions found in this study argues for a greater utilization of long-term data and empirical dynamic modeling in studies of the dynamics of other ecosystems.
Atmospheric forcing dominates winter Barents-Kara sea ice variability on interannual to decadal time scales
Authors: Liu Zhongfang , Risi Camille , Codron Francis , Jian Zhimin , Wei Zhongwang , He Xiaogang , Poulsen Christopher J. , Wang Yue , Chen Dong , Ma Wentao , Cheng Yanyan , Bowen Gabriel J.
Published: August 2022

The last two decades have seen a dramatic decline and strong year-to-year variability in Arctic winter sea ice, especially in the Barents-Kara Sea (BKS), changes that have been linked to extreme midlatitude weather and climate. It has been suggested that these changes in winter sea ice arise largely from a combined effect of oceanic and atmospheric processes, but the relative importance of these processes is not well established. Here, we explore the role of atmospheric circulation patterns on BKS winter sea ice variability and trends using observations and climate model simulations. We find that BKS winter sea ice variability is primarily driven by a strong anticyclonic anomaly over the region, which explains more than 50% of the interannual variability in BKS sea-ice concentration (SIC). Recent intensification of the anticyclonic anomaly has warmed and moistened the lower atmosphere in the BKS by poleward transport of moist-static energy and local processes, resulting in an increase in downwelling longwave radiation. Our results demonstrate that the observed BKS winter sea-ice variability is primarily driven by atmospheric, rather than oceanic, processes and suggest a persistent role of atmospheric forcing in future Arctic winter sea ice loss.
Strategic intergroup alliances increase access to a contested resource in male bottlenose dolphins
Authors: Connor Richard C. , Krützen Michael , Allen Simon J. , Sherwin William B. , King Stephanie L.
Published: August 2022

Efforts to understand human social evolution rely largely on comparisons with nonhuman primates. However, a population of bottlenose dolphins in Shark Bay, Western Australia, combines a chimpanzee-like fission-fusion grouping pattern, mating system, and life history with the only nonhuman example of strategic multilevel male alliances. Unrelated male dolphins form three alliance levels, or “orders”, in competition over females: both within-group alliances (i.e., first- and second-order) and between-group alliances (third-order), based on cooperation between two or more second-order alliances against other groups. Both sexes navigate an open society with a continuous mosaic of overlapping home ranges. Here, we use comprehensive association and consortship data to examine fine-scale alliance relationships among 121 adult males. This analysis reveals the largest nonhuman alliance network known, with highly differentiated relationships among individuals. Each male is connected, directly or indirectly, to every other male, including direct connections with adult males outside of their three-level alliance network. We further show that the duration with which males consort females is dependent upon being well connected with third-order allies, independently of the effect of their second-order alliance connections, i.e., alliances between groups increase access to a contested resource, thereby increasing reproductive success. Models of human social evolution traditionally link intergroup alliances to other divergent human traits, such as pair bonds, but our study reveals that intergroup male alliances can arise directly from a chimpanzee-like, promiscuous mating system without one-male units, pair bonds, or male parental care.
False-positive IRESes from
Hoxa9
and other genes resulting from errors in mammalian 5′ UTR annotations
Authors: Akirtava Christina , May Gemma E. , McManus C. Joel
Published: August 2022

Hyperconserved genomic sequences have great promise for understanding core biological processes. It has been recently proposed that scores of hyperconserved 5′ untranslated regions (UTRs), also known as transcript leaders (hTLs), encode internal ribosome entry sites (IRESes) that drive cap-independent translation, in part, via interactions with ribosome expansion segments. However, the direct functional significance of such interactions has not yet been definitively demonstrated. We provide evidence that the putative IRESes previously reported in Hox gene hTLs are rarely included in transcript leaders. Instead, these regions function independently as transcriptional promoters. In addition, we find the proposed RNA structure of the putative
Hoxa9
IRES is not conserved. Instead, sequences previously shown to be essential for putative IRES activity encode a hyperconserved transcription factor binding site (E-box) that contributes to its promoter activity and is bound by several transcription factors, including
USF1
and
USF2
. Similar E-box sequences enhance the promoter activities of other putative
Hoxa
gene IRESes. Moreover, we provide evidence that the vast majority of hTLs with putative IRES activity overlap transcriptional promoters, enhancers, and 3′ splice sites that are most likely responsible for their reported IRES activities. These results argue strongly against recently reported widespread IRES-like activities from hTLs and contradict proposed interactions between ribosomal expansion segment ES9S and putative IRESes. Furthermore, our work underscores the importance of accurate transcript annotations, controls in bicistronic reporter assays, and the power of synthesizing publicly available data from multiple sources.
Accumulation and maintenance of information in evolution
Authors: Hledík Michal , Barton Nick , Tkačik Gašper
Published: August 2022

Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.
Concentrated incarceration and the public-housing-to-prison pipeline in New York City neighborhoods
Authors: Holder Jay , Calaff Ivan , Maricque Brett , Tran Van C.
Published: August 2022

Using public housing developments as a strategic site, our research documents a distinct pathway linking disadvantaged context to incarceration—the public-housing-to-prison pipeline. Focusing on New York City Housing Authority (NYCHA) housing developments as a case study, we find that incarceration rates in NYCHA tracts are 4.6 times higher than those in non-NYCHA tracts. More strikingly, 94% of NYCHA tracts report rates above the median value for non-NYCHA tracts. Moreover, 17% of New York State’s incarcerated population originated from just 372 NYCHA tracts. Compared with non-NYCHA tracts, NYCHA tracts had higher shares of Black residents and were significantly more disadvantaged. This NYCHA disadvantage in concentrated incarceration is also robust at different spatial scales. Our findings have implications for policies and programs to disrupt community-based pipelines to prison.
A Gauss’s law analysis of redox active adsorbates on semiconductor electrodes: The charging and faradaic currents are not independent
Authors: Vasquez Robert , Waelder Jacob , Liu Yifan , Bartels Hannah , Maldonado Stephen
Published: August 2022

A detailed framework for modeling and interpreting the data in totality from a cyclic voltammetric measurement of adsorbed redox monolayers on semiconductor electrodes has been developed. A three-layer model consisting of the semiconductor space-charge layer, a surface layer, and an electrolyte layer is presented that articulates the interplay between electrostatic, thermodynamic, and kinetic factors in the electrochemistry of a redox adsorbate on a semiconductor. Expressions are derived that describe the charging and faradaic current densities individually, and an algorithm is demonstrated that allows for the calculation of the total current density in a cyclic voltammetry measurement as a function of changes in the physical properties of the system (e.g., surface recombination, dielectric property of the surface layer, and electrolyte concentration). The most profound point from this analysis is that the faradaic and charging current densities can be coupled. That is, the common assumption that these contributions to the total current are always independent is not accurate. Their interrelation can influence the interpretation of the charge-transfer kinetics under certain experimental conditions. More generally, this work not only fills a long-standing knowledge gap in electrochemistry but also aids practitioners advancing energy conversion/storage strategies based on redox adsorbates on semiconductor electrodes.
Nile waterscapes facilitated the construction of the Giza pyramids during the 3rd millennium BCE
Authors: Sheisha Hader , Kaniewski David , Marriner Nick , Djamali Morteza , Younes Gamal , Chen Zhongyuan , El-Qady Gad , Saleem Amr , Véron Alain , Morhange Christophe
Published: August 2022

The pyramids of Giza originally overlooked a now defunct arm of the Nile. This fluvial channel, the Khufu branch, enabled navigation to the Pyramid Harbor complex but its precise environmental history is unclear. To fill this knowledge gap, we use pollen-derived vegetation patterns to reconstruct 8,000 y of fluvial variations on the Giza floodplain. After a high-stand level concomitant with the African Humid Period, our results show that Giza’s waterscapes responded to a gradual insolation-driven aridification of East Africa, with the lowest Nile levels recorded at the end of the Dynastic Period. The Khufu branch remained at a high-water level (∼40% of its Holocene maximum) during the reigns of Khufu, Khafre, and Menkaure, facilitating the transportation of construction materials to the Giza Pyramid Complex.
Ligand diversity contributes to the full activation of the jasmonate pathway inMarchantia polymorpha
Authors: Kneeshaw Sophie , Soriano Gonzalo , Monte Isabel , Hamberg Mats , Zamarreño Ángel M. , García-Mina Jose M. , Franco-Zorrilla José Manuel , Kato Nobuki , Ueda Minoru , Rey-Stolle Ma Fernanda , Barbas Coral , Michavila Santiago , Gimenez-Ibanez Selena , Jimenez-Aleman Guillermo H. , Solano Roberto
Published: August 2022

In plants, jasmonate signaling regulates a wide range of processes from growth and development to defense responses and thermotolerance. Jasmonates, such as jasmonic acid (JA), (+)-7-iso-jasmonoyl-l-isoleucine (JA-Ile), 12-oxo-10,15(Z)-phytodienoic acid (OPDA), and dinor-12-oxo-10,15(Z)-phytodienoic acid (dn-OPDA), are derived from C18 (18 Carbon atoms) and C16 polyunsaturated fatty acids (PUFAs), which are found ubiquitously in the plant kingdom. Bryophytes are also rich in C20 and C22 long-chain polyunsaturated fatty acids (LCPUFAs), which are found only at low levels in some vascular plants but are abundant in organisms of other kingdoms, including animals. The existence of bioactive jasmonates derived from LCPUFAs is currently unknown. Here, we describe the identification of an OPDA-like molecule derived from a C20 fatty acid (FA) in the liverwortMarchantia polymorpha(Mp), which we term (5Z,8Z)-10-(4-oxo-5-((Z)-pent-2-en-1-yl)cyclopent-2-en-1-yl)deca-5,8-dienoic acid (C20-OPDA). This molecule accumulates upon wounding and, when applied exogenously, can activate known Coronatine Insensitive 1 (COI1) –dependent and –independent jasmonate responses. Furthermore, we identify a dn-OPDA–like molecule (Δ4-dn-OPDA) deriving from C20-OPDA and demonstrate it to be a ligand of the jasmonate coreceptor (MpCOI1–Mp Jasmonate-Zinc finger inflorescence meristem domain [MpJAZ]) inMarchantia. By analyzing mutants impaired in the production of LCPUFAs, we elucidate the major biosynthetic pathway of C20-OPDA and Δ4-dn-OPDA. Moreover, using a double mutant compromised in the production of both Δ4-dn-OPDA and dn-OPDA, we demonstrate the additive nature of these molecules in the activation of jasmonate responses. Taken together, our data identify a ligand of MpCOI1 and demonstrate LCPUFAs as a source of bioactive jasmonates that are essential to the immune response ofM. polymorpha.
Trade-offs of lipid remodeling in a marine predator–prey interaction in response to phosphorus limitation
Authors: Guillonneau Richard , Murphy Andrew R. J. , Teng Zhao-Jie , Wang Peng , Zhang Yu-Zhong , Scanlan David J. , Chen Yin
Published: August 2022

Phosphorus (P) is a key nutrient limiting bacterial growth and primary production in the oceans. Unsurprisingly, marine microbes have evolved sophisticated strategies to adapt to P limitation, one of which involves the remodeling of membrane lipids by replacing phospholipids with non-P-containing surrogate lipids. This strategy is adopted by both cosmopolitan marine phytoplankton and heterotrophic bacteria and serves to reduce the cellular P quota. However, little, if anything, is known of the biological consequences of lipid remodeling. Here, using the marine bacterium
Phaeobacter
sp. MED193 and the ciliate
Uronema marinum
as a model, we sought to assess the effect of remodeling on bacteria–protist interactions. We discovered an important trade-off between either escape from ingestion or resistance to digestion. Thus,
Phaeobacter
grown under P-replete conditions was readily ingested by
Uronema
, but not easily digested, supporting only limited predator growth. In contrast, following membrane lipid remodeling in response to P depletion,
Phaeobacter
was less likely to be captured by
Uronema
, thanks to the reduced expression of mannosylated glycoconjugates. However, once ingested, membrane-remodeled cells were unable to prevent phagosome acidification, became more susceptible to digestion, and, as such, allowed rapid growth of the ciliate predator. This trade-off between adapting to a P-limited environment and susceptibility to protist grazing suggests the more efficient removal of low-P prey that potentially has important implications for the functioning of the marine microbial food web in terms of trophic energy transfer and nutrient export efficiency.
Cross-modal and cross-language activation in bilinguals reveals lexical competition even when words or signs are unheard or unseen
Authors: Villameriel Saúl , Costello Brendan , Giezen Marcel , Carreiras Manuel
Published: August 2022

We exploit the phenomenon of cross-modal, cross-language activation to examine the dynamics of language processing. Previous within-language work showed that seeing a sign coactivates phonologically related signs, just as hearing a spoken word coactivates phonologically related words. In this study, we conducted a series of eye-tracking experiments using the visual world paradigm to investigate the time course of cross-language coactivation in hearing bimodal bilinguals (Spanish–Spanish Sign Language) and unimodal bilinguals (Spanish/Basque). The aim was to gauge whether (and how) seeing a sign could coactivate words and, conversely, how hearing a word could coactivate signs and how such cross-language coactivation patterns differ from within-language coactivation. The results revealed cross-language, cross-modal activation in both directions. Furthermore, comparison with previous findings of within-language lexical coactivation for spoken and signed language showed how the impact of temporal structure changes in different modalities. Spoken word activation follows the temporal structure of that word only when the word itself is heard; for signs, the temporal structure of the sign does not govern the time course of lexical access (location coactivation precedes handshape coactivation)—even when the sign is seen. We provide evidence that, instead, this pattern of activation is motivated by how common in the lexicon the sublexical units of the signs are. These results reveal the interaction between the perceptual properties of the explicit signal and structural linguistic properties. Examining languages across modalities illustrates how this interaction impacts language processing.
Adaptive exchange sustains cullin–RING ubiquitin ligase networks and proper licensing of DNA replication
Authors: Zhang Yaru , Jost Marco , Pak Ryan A. , Lu Daniel , Li Jing , Lomenick Brett , Garbis Spiros D. , Li Chi-Ming , Weissman Jonathan S. , Lipford James Russell , Deshaies Raymond J.
Published: August 2022

Cop9 signalosome (CSN) regulates the function of cullin–RING E3 ubiquitin ligases (CRLs) by deconjugating the ubiquitin-like protein NEDD8 from the cullin subunit. To understand the physiological impact of CSN function on the CRL network and cell proliferation, we combined quantitative mass spectrometry and genome-wide CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) screens to identify factors that modulate cell viability upon inhibition of CSN by the small molecule CSN5i-3. CRL components and regulators strongly modulated the antiproliferative effects of CSN5i-3, and in addition we found two pathways involved in genome integrity, SCF
FBXO5
–APC/C–GMNN and CUL4
DTL
–SETD8, that contribute substantially to the toxicity of CSN inhibition. Our data highlight the importance of CSN-mediated NEDD8 deconjugation and adaptive exchange of CRL substrate receptors in sustaining CRL function and suggest approaches for leveraging CSN inhibition for the treatment of cancer.
Alum-anchored intratumoral retention improves the tolerability and antitumor efficacy of type I interferon therapies
Authors: Lutz Emi A. , Agarwal Yash , Momin Noor , Cowles Sarah C. , Palmeri Joseph R. , Duong Ellen , Hornet Vladlena , Sheen Allison , Lax Brianna M. , Rothschilds Adrienne M. , Irvine Darrell J. , Spranger Stefani , Wittrup K. Dane
Published: August 2022

Effective antitumor immunity in mice requires activation of the type I interferon (IFN) response pathway. IFNα and IFNβ therapies have proven promising in humans, but suffer from limited efficacy and high toxicity. Intratumoral IFN retention ameliorates systemic toxicity, but given the complexity of IFN signaling, it was unclear whether long-term intratumoral retention of type I IFNs would promote or inhibit antitumor responses. To this end, we compared the efficacy of IFNα and IFNβ that exhibit either brief or sustained retention after intratumoral injection in syngeneic mouse tumor models. Significant enhancement in tumor retention, mediated by anchoring these IFNs to coinjected aluminum-hydroxide (alum) particles, greatly improved both their tolerability and efficacy. The improved efficacy of alum-anchored IFNs could be attributed to sustained pleiotropic effects on tumor cells, immune cells, and nonhematopoietic cells. Alum-anchored IFNs achieved high cure rates of B16F10 tumors upon combination with either anti-PD-1 antibody or interleukin-2. Interestingly however, these alternative combination immunotherapies yielded disparate T cell phenotypes and differential resistance to tumor rechallenge, highlighting important distinctions in adaptive memory formation for combinations of type I IFNs with other immunotherapies.
Brain endothelial STING1 activation by
Plasmodium
-sequestered heme promotes cerebral malaria via type I IFN response
Authors: Pais Teresa F. , Ali Hajrabibi , Moreira da Silva Joana , Duarte Nádia , Neres Rita , Chhatbar Chintan , Acúrcio Rita C. , Guedes Rita C. , Strano Moraes Maria Carolina , Costa-Silva Bruno , Kalinke Ulrich , Penha-Gonçalves Carlos
Published: August 2022

Cerebral malaria (CM) is a life-threatening form of
Plasmodium falciparum
infection caused by brain inflammation. Brain endothelium dysfunction is a hallmark of CM pathology, which is also associated with the activation of the type I interferon (IFN) inflammatory pathway. The molecular triggers and sensors eliciting brain type I IFN cellular responses during CM remain largely unknown. We herein identified the stimulator of interferon response cGAMP interactor 1 (STING1) as the key innate immune sensor that induces
Ifnβ1
transcription in the brain of mice infected with
Plasmodium berghei
ANKA (
Pba
). This STING1/IFNβ-mediated response increases brain CXCL10 governing the extent of brain leukocyte infiltration and blood–brain barrier (BBB) breakdown, and determining CM lethality. The critical role of brain endothelial cells (BECs) in fueling type I IFN–driven brain inflammation was demonstrated in brain endothelial–specific IFNβ-reporter and STING1-deficient
Pba
-infected mice, which were significantly protected from CM lethality. Moreover, extracellular particles (EPs) released from
Pba
-infected erythrocytes activated the STING1-dependent type I IFN response in BECs, a response requiring intracellular acidification. Fractionation of the EPs enabled us to identify a defined fraction carrying hemoglobin degradation remnants that activates STING1/IFNβ in the brain endothelium, a process correlated with heme content. Notably, stimulation of STING1-deficient BECs with heme, docking experiments, and in vitro binding assays unveiled that heme is a putative STING1 ligand. This work shows that heme resultant from the parasite heterotrophic activity operates as an alarmin, triggering brain endothelial inflammatory responses via the STING1/IFNβ/CXCL10 axis crucial to CM pathogenesis and lethality.
Controlled growth of a high selectivity interface for seawater electrolysis
Authors: Gao Yang , Xue Yurui , He Feng , Li Yuliang
Published: August 2022

Overall seawater electrolysis is an important direction for the development of hydrogen energy conversion. The key issues include how to achieve high selectivity, activity, and stability in seawater electrolysis reactions. In this report, the heterostructures of graphdiyne-RhOx-graphdiyne (GDY/RhOx/GDY) were constructed by in situ-controlled growth of GDY on RhOxnanocrystals. A double layer interface ofsp-hybridized carbon-oxide-Rhodium (sp-C∼O-Rh) was formed in this system. The microstructures at the interface are composed of active sites ofsp-C∼O-Rh. The obvious electron-withdrawing surface enhances the catalytic activity with orders of magnitude, while the GDY outer of the metal oxides guarantees the stability. The electron-donating and withdrawingsp-C∼O-Rh structures enhance the catalytic activity, achieving high-performance overall seawater electrolysis with very small cell voltages of 1.42 and 1.52 V at large current densities of 10 and 500 mA cm−2at room temperatures and ambient pressures, respectively. The compositional and structural superiority of the GDY-derivedsp-C-metal-oxide active center offers great opportunities to engineer tunable redox properties and catalytic performance for seawater electrolysis and beyond. This is a typical successful example of the rational design of catalytic systems.
A proteolytic pathway coordinates cell division and heterocyst differentiation in the cyanobacterium
Anabaena
sp. PCC 7120
Authors: Xing Wei-Yue , Liu Jing , Zhang Ju-Yuan , Zeng Xiaoli , Zhang Cheng-Cai
Published: August 2022

The filamentous, multicellular cyanobacterium
Anabaena
sp. PCC 7120 (
Anabaena
) is a prokaryotic model for the study of cell differentiation and cell-cell interactions. Upon combined-nitrogen deprivation,
Anabaena
forms a particular cell type, heterocyst, for aerobic nitrogen fixation. Heterocysts are semiregularly spaced among vegetative cells. Heterocyst differentiation is coupled to cell division, but the underlying mechanism remains unclear. This mechanism could be mediated by the putative protease HetF, which is a divisome component and is necessary for heterocyst differentiation. In this study, by suppressor screening, we identified PatU3, as a negative regulator acting downstream of HetF for cell division and heterocyst development. The inactivation of
patU3
restored the capacity of cell division and heterocyst differentiation in the Δ
hetF
mutant, and overexpression of
patU3
inhibited both processes in the wild-type background. We demonstrated that PatU3 was a specific substrate of the protease activity of HetF. Consequently, PatU3 accumulated in the
hetF
-deficient mutant, which was responsible for the resultant mutant phenotype. The cleavage site of PatU3 by HetF was mapped after the Arg117 residue, whose mutation made PatU3 resistant to HetF processing, and mimicked the effect of
hetF
deletion. Our results provided evidence that HetF regulated cell division and heterocyst differentiation by controlling the inhibitory effects of PatU3. This proteolytic pathway constituted a mechanism for the coordination between cell division and differentiation in a prokaryotic model used for studies on developmental biology and multicellularity.
Breaking down antibiotic resistance in methicillin-resistant
Staphylococcus aureus
: Combining antimicrobial photodynamic and antibiotic treatments
Authors: Willis Jace A. , Cheburkanov Vsevolod , Chen Shaorong , Soares Jennifer M. , Kassab Giulia , Blanco Kate C. , Bagnato Vanderlei S. , de Figueiredo Paul , Yakovlev Vladislav V.
Published: August 2022

The widespread use of antibiotics drives the evolution of antimicrobial-resistant bacteria (ARB), threatening patients and healthcare professionals. Therefore, the development of novel strategies to combat resistance is recognized as a global healthcare priority. The two methods to combat ARB are development of new antibiotics or reduction in existing resistances. Development of novel antibiotics is a laborious and slow-progressing task that is no longer a safe reserve against looming risks. In this research, we suggest a method for reducing resistance to extend the efficacious lifetime of current antibiotics. Antimicrobial photodynamic therapy (aPDT) is used to generate reactive oxygen species (ROS) via the photoactivation of a photosensitizer. ROS then nonspecifically damage cellular components, leading to general impairment and cell death. Here, we test the hypothesis that concurrent treatment of bacteria with antibiotics and aPDT achieves an additive effect in the elimination of ARB. Performing aPDT with the photosensitizer methylene blue in combination with antibiotics chloramphenicol and tetracycline results in significant reductions in resistance for two methicillin-resistant
Staphylococcus aureus
(MRSA) strains, USA300 and RN4220. Additional resistant
S. aureus
strain and antibiotic combinations reveal similar results. Taken together, these results suggest that concurrent aPDT consistently decreases
S. aureus
resistance by improving susceptibility to antibiotic treatment. In turn, this development exhibits an alternative to overcome some of the growing MRSA challenge.