bluuebunny/crossref_metadata_2025 huggingface dataset:
A lubrication model for bubbly oil lubrication with interfacial effect and thermal effect using the theory of multiphase mixtures
Authors: Li Shaohua , Lin Xiaohui , Jiang Shuyun
Published: November 2023

Bubbly oil lubrication is a type of lubrication method. However, the lubrication model of the bubbly oil has not been thoroughly considered. This paper aims to investigate the modelling for bubbly oil lubrication considering the interfacial effect and thermal effect, and a theoretical model is established based on the theory of multiphase mixtures. The interfacial and thermal effects on the static characteristics of a thrust bearing are analyzed. A test rig for the thrust bearing is developed to measure the static characteristics of the bearing under bubbly oil lubrication. The results show that the bearing static characteristics, i.e. bearing temperature rise, film thickness, friction torque, and volume flow, increase with consideration of three interfacial effects; the bearing temperature rise increases but the film thickness, friction torque, and volume flow rate decrease with consideration of the three thermal effects; the thermal effect on the bearing static characteristics is greater than the interfacial effect.
Saffman–Taylor instability in eccentric cylinders at gaseous cavitation
Authors: Monakhov Anatoliy A. , Bukharin Nikolay
Published: November 2023

A flow of silicon fluid in the gap between eccentric cylinders was studied experimentally. The condition of gaseous cavitation inception during the rotation of internal cylinder was considered. It was shown that at reduction of the gap between cylinders Saffman–Taylor instability appeared on surface of the internal cylinder and then gaseous cavitation was observed. Possibility of one uniform gas formation appearance under this type of instability was demonstrated.
Examining racial and social vulnerability disparities in the outpatient treatment of uncomplicated cystitis at a Southern California Academic Hospital
Authors: McLeod Caleb C. , Al-Fayiz Hadeel , Rodriguez Sasha , Tan Karen K. , Abdul-Mutakabbir Jacinda C.
Published: November 2023

Racially and ethnically minoritized (REM) patients are disproportionately impacted by infectious diseases. In our study, REM patients were more likely to receive care for urinary tract infections in the emergency department or urgent care, were younger, and were more likely to have higher social vulnerability.
Synchronized off-harmonic probe laser with highly variable pulse duration for laser–plasma interaction experiments
Authors: Hornung J. , Zobus Y. , Lorenté H. , Brabetz C. , Zielbauer B. , Bagnoud V.
Published: November 2023

This paper presents the development and experimental utilization of a synchronized off-harmonic laser system designed as a probe for ultra-intense laser–plasma interaction experiments. The system exhibits a novel seed-generation design, allowing for a variable pulse duration spanning over more than three orders of magnitude, from 3.45 picoseconds to 10 nanoseconds. This makes it suitable for various plasma diagnostics and visualization techniques. In a side-view configuration, the laser was employed for interferometry and streaked shadowgraphy of a laser-induced plasma while successfully suppressing the self-emission background of the laser–plasma interaction, resulting in a signal-to-self-emission ratio of 110 for this setup. These properties enable the probe to yield valuable insights into the plasma dynamics and interactions at the PHELIX facility and to be deployed at various laser facilities due to its easy-to-implement design.
The biological standard of living of Korean men under Confucianism, colonialism, capitalism, and communism
Authors: Schwekendiek Daniel J , Jun Seongho , Lewis James B , Park Heejin , Choi Seong-Jin
Published: November 2023

This study focuses on analysing the heights of 10,953 Korean men aged 20 to 40 years who were measured during the Joseon dynasty, the Japanese colonialisation period, and the contemporary period, the latter including both North and South Korea. This study thus provides rare long-term statistical evidence on how biological living standards have developed over several centuries, encompassing Confucianism, colonialism, capitalism, and communism. Using error bar analysis of heights for each historical sample period, this study confirms that heights rose as economic performance improved. For instance, economically poorer North Koreans were expectedly shorter, by about 6 cm, than their peers living in the developed South. Similarly, premodern inhabitants of present-day South Korea, who produced a gross domestic product (GDP) per capita below the world average, were about 4 cm shorter than contemporary South Koreans, who have a mean income above the world average. Along similar lines, North Koreans, who have a GDP per capita akin to that of the premodern Joseon dynasty, have not improved much in height. On the contrary, mean heights of North Koreans were even slightly below (by about 2.4 cm) heights of Joseon dynasty Koreans. All in all, the heights follow a U-shaped pattern across time, wherein heights were lowest during the colonial era. Heights bounced back to Joseon dynasty levels during the interwar period, a time period where South Korea benefitted from international aid, only to rise again and surpass even premodern levels under South Korea’s flourishing market economy.
Anoplocephalid tapeworms in mountain gorillas (Gorilla beringei beringei) inhabiting the Volcanoes National Park, Rwanda
Authors: Červená Barbora , Prokopová Tereza , Cameira Rita Maria , Pafčo Barbora , Samaš Peter , Romportl Dušan , Uwamahoro Carine , Noheri Jean Bosco , Ntwari Adrien Emile , Bahizi Méthode , Nzayisenga Gaspard , Nziza Julius , Gilardi Kirsten , Eckardt Winnie , Ndagijimana Felix , Mudakikwa Antoine , Muvunyi Richard , Uwingeli Prosper , Cranfield Michael , Šlapeta Jan , Petrželková Klára Judita , Modrý David
Published: November 2023

Cestodes of the family Anoplocephalidae parasitize a wide range of usually herbivorous hosts including e.g. rodents, ungulates, primates, elephants and hyraxes. While in some hosts, the epidemiology of the infection is well studied, information is lacking in others. In this study of mountain gorillas in the Virunga Massif, an extensive sample set comprising adult cestodes collected via necropsies, proglottids shed in feces, and finally, fecal samples from both night nests and identified individuals were analysed. Anoplocephala gorillae was the dominant cestode species detected in night nest samples and individually known gorillas, of which only 1 individual hosted a Bertiella sp. It was shown that the 2 species can be distinguished through microscopy based on egg morphology and polymerase chain reaction (PCR) assays for diagnostics of both species were provided. Sequences of mitochondrial (cox 1) and nuclear (ITS1, 18S rDNA, 28S rDNA) markers were used to evaluate the phylogenetic position of the 2 cestodes detected in mountain gorillas. Both types of fecal samples, from night nests and from identified individuals, provided comparable information about the prevalence of anoplocephalid cestodes, although the analysis of samples collected from identified gorilla individuals showed significant intra-individual fluctuation of A. gorillae egg shedding within a short period. Therefore, multiple samples should be examined to obtain reliable data for wildlife health management programmes, especially when application of anthelmintic treatment is considered. However, while A. gorillae is apparently a common symbiont of mountain gorillas, it does not seem to impair the health of its host.
Dual-systems models of the genetic architecture of impulsive personality traits: neurogenetic evidence of distinct but related factors
Authors: Miller Alex P. , Gizer Ian R.
Published: November 2023

Background

Dual-systems models, positing an interaction between two distinct and competing systems (i.e. top-down self-control, and bottom-up reward- or emotion-based drive), provide a parsimonious framework for investigating the interplay between cortical and subcortical brain regions relevant to impulsive personality traits (IPTs) and their associations with psychopathology. Despite recent developments in multivariate analysis of genome-wide association studies (GWAS), molecular genetic investigations of these models have not been conducted.

Methods

Using IPT GWAS, we conducted confirmatory genomic structural equation models (GenomicSEM) to empirically evaluate dual-systems models of the genetic architecture of IPTs. Genetic correlations between dual-systems factors and relevant cortical and subcortical neuroimaging phenotypes (regional/structural volume, cortical surface area, cortical thickness) were estimated and compared.

Results

GenomicSEM dual-systems models underscored important sources of shared and unique genetic variance between top-down and bottom-up constructs. Specifically, a dual-systems genomic model consisting of sensation seeking and lack of self-control factors demonstrated distinct but related sources of genetic influences (rg = 0.60). Genetic correlation analyses provided evidence of differential associations between dual-systems factors and cortical neuroimaging phenotypes (e.g. lack of self-control negatively associated with cortical thickness, sensation seeking positively associated with cortical surface area). No significant associations were observed with subcortical phenotypes.

Conclusions

Dual-systems models of the genetic architecture of IPTs tested were consistent with study hypotheses, but associations with relevant neuroimaging phenotypes were mixed (e.g. no associations with subcortical volumes). Findings demonstrate the utility of dual-systems models for studying IPT genetic influences, but also highlight potential limitations as a framework for interpreting IPTs as endophenotypes for psychopathology.
Long-run management of Greenland's fishery on Greenland halibut (Reinhardtius hippoglossoides)
Authors: Jensen Frank , Hoff Ayoe , Jacobsen Jette Bredahl , Meilby Henrik
Published: November 2023

In this paper, we consider four scenarios for economic optimal management of a fisheries resource by a high sea and coastal fleet segment. These scenarios differ with respect to whether a common or two separate fish stocks are considered and whether the profit from land-based processing is included. The model is parametrized using the Greenland halibut fishery on the west coast of Greenland as an empirical case. For this fishery, we show that the relative ranking of the optimal high sea industry harvest and profit compared to the coastal industry harvest and profit depends on the chosen scenario. When comparing the scenarios for optimal management and the actual situation, we find that the fish stock tends to be overexploited.
The reaction of CIMMYT durum wheat genotypes to Fusarium pseudograminearum at seedling and adult plant stages
Authors: Yılmaz Olgaç Doğu , Karakaya Aziz , Erginbas-Orakci Gul , Aydoğan Sinan , Ammar Karim , Dababat Abdelfattah A.
Published: November 2023

Fusarium pseudograminearum is one of the important crown rot agents that reduces the quality and quantity of wheat plants. The pathogen is common in the world and 10–35% yield losses due to disease have been reported. Identifying resistant durum wheat genotypes is the best approach to control the disease due to the limited control options available. Currently, there are only a few genotypes available with partial resistance to Fusarium crown rot globally. In this study, a total of 199 durum wheat genotypes provided by the International Wheat and Maize Improvement Center (CIMMYT), Mexico, and five control genotypes were tested for their resistance reactions to F. pseudograminearum under both growth room and greenhouse conditions. Out of the 199 genotypes tested under growth room conditions; 15, 20, 134 and 30 genotypes exhibited resistant, moderately resistant, moderately susceptible and susceptible reactions, respectively. Under greenhouse conditions; 19, 16, 121 and 43 genotypes were found resistant, moderately resistant, moderately susceptible and susceptible, respectively. Two durum wheat genotypes (# 84 and # 197, CIMMYT genotype numbers 7409071 and 7410562) showed seedling and adult plant resistance to F. pseudograminearum. The newly identified resistant genotypes for crown rot caused by F. pseudograminearum seem promising for breeding programmes, especially these two lines which showed resistance at both seedling and adult plant stages.
Identification of Oryza glaberrima as a potential resistance source to rice root-knot nematode, Meloidogyne graminicola
Authors: Kaur Gurwinder , Dhillon Narpinderjeet Kaur , Singh Gurpreet , Vikal Yogesh , Kaur Navneet , Gill Adeshpal Singh , Neelam Kumari , Singh Jagveer , Bhatia Dharminder , Mangat Gurjit Singh
Published: November 2023

The root-knot nematodes (RKN) (Meloidogyne graminicola) are a devastating threat to rice worldwide. The cultivated germplasm is either susceptible or moderately resistant to rice RKN. Therefore, there is a need to identify resistance sources against M. graminicola as an eco-friendly management strategy. The present study evaluated the host response of Oryza sativa genotypes comprising basmati, non-basmati improved varieties, their advanced breeding lines (83) and Oryza glaberrima accessions (42) against M. graminicola in the nematode-infested plot for two consecutive years. All O. sativa genotypes exhibited susceptible responses, while O. glaberrima accessions showed variable levels of resistance. Three of the O. glaberrima accessions (IRGC102196, IRGC102538 and IRGC102557) were highly resistant. M. graminicola significantly affected plant growth parameters in susceptible genotypes compared to resistant O. glaberrima accessions. The results were supported by histopathological studies that showed apparent giant cell formation in PR121 while penetration and development of M. graminicola juveniles were low in the O. glaberrima acc. IRGC102196. In silico analysis indicated that none of the reported nematode resistance genes from different crops had homology with the rice genome. The two anti-nematode genes (Oryzacystatin-I and Oryzacystatin-II) from O. sativa japonica revealed homology with O. sativa cv. PR121 and O. glaberrima acc. IRGC102206. Comparative analysis of these genes between PR121 and O. glaberrima acc. IRGC102206 resulted in the identification of SNPs/InDels that could be associated with nematode resistance. The identified SNPs/InDels could be validated, and further molecular studies are needed to provide insights into the resistance mechanism against rice RKN.
Finding Common Ground in the Field to Inform Science Policy
Authors: Siomades Sunday , Schneider Blair , Connolly Andy
Published: November 2023

The Kansas Geological Survey’s annual Field Conference takes scientists, producers, legislators, and public officials around the state to spark conversation about natural resources.
The Indian Easterly Jet During the Pre‐Monsoon Season in India
Authors: Croad Hannah L. , Shonk Jonathan K. P. , Chevuturi Amulya , Turner Andrew G. , Hodges Kevin I.
Published: November 2023

We identify for the first time an Indian Easterly Jet (IEJ) in the mid‐troposphere during the pre‐monsoon using reanalysis data. The IEJ is weaker and smaller than the African Easterly Jet over West Africa, with a climatological location of 10°N, 60–90°E, 700 hPa, and strength 6–7 m s−1 during March–May. The IEJ is a thermal wind associated with low‐level meridional gradients in temperature (positive) and moisture (negative), resulting from equatorward moist convection and poleward dry convection. The IEJ is associated with a negative meridional potential vorticity gradient, therefore satisfying the Charney‐Stern necessary condition for instability. However, no wave activity is detected, suggesting that the potential for combined barotropic‐baroclinic instability is not often realized. IEJ strong (weak) years feature increased (reduced) near‐surface temperatures and drier (wetter) conditions over India. This study provides an introduction to the IEJ's role in pre‐monsoon dynamics, and a platform for further research.
Statistical Properties of the Distribution and Generation of Kinetic‐Scale Flux Ropes in the Terrestrial Dayside Magnetosheath
Authors: Xiao Y. C. , Yao S. T. , Guo R. L. , Shi Q. Q. , Zong Q. G. , Zhang H. , Bai S. C. , Hamrin M. , Pitkänen T. , Tian A. M. , Degeling A. W. , Liu J.
Published: November 2023

The generation of kinetic‐scale flux ropes (KSFRs) is closely related to magnetic reconnection. Both flux ropes and reconnection sites are detected in the magnetosheath and can impact the dynamics upstream of the magnetopause. In this study, using the Magnetospheric Multiscale satellite, 12,623 KSFRs with a scale <20 RCi are statistically studied in the Earth's dayside magnetosheath. It is found that they are mostly generated near the bow shock (BS), and propagate downstream in the magnetosheath. Their quantity significantly increases as the scale decreases, consistent with a flux rope coalescence model. Moreover, the solar wind parameters can control the occurrence rate of KSFRs. They are more easily generated at high Mach number, large proton density, and weak magnetic field strength of the solar wind, similar to the conditions that favor BS reconnection. Our study shows a close connection between KSFR generation and BS reconnection.
Airborne Doppler Radar Observations of Tropical Cyclone Boundary Layer Kinematic Structure and Evolution During Landfall
Authors: Rogers Robert F. , Zhang Jun A.
Published: November 2023

Airborne Doppler radar observations of the wind field in the tropical cyclone boundary layer (TCBL) during the landfall of Hurricane Ida (2021) are examined here. Asymmetries in tangential and radial flow are governed by tropical cyclone (TC) motion and vertical wind shear prior to landfall, while frictional effects dominate the asymmetry location during landfall. Strong TCBL inflow on the offshore‐flow side of Ida occurs during landfall, while the location of the peak tangential wind at the top of the TCBL during this period is located on the onshore‐flow side. A comparison of these observations with a numerical simulation of TC landfall shows many consistencies with the modeling study, though there are some notable differences that may be related to differences in the characteristics of the land surface between the simulation and the observations here.
A Novel Temperature Anomaly Source Diagnostic: Method and Application to the 2021 Heatwave in the Pacific Northwest
Authors: Papritz Lukas , Röthlisberger Matthias
Published: November 2023

Quantitative methods to pinpoint the origin of atmospheric temperature anomalies (T′) associated with heatwaves are pivotal for the construction of physically plausible synoptic storylines of heatwave formation and their evaluation in models. Here, we combine a Lagrangian T′ decomposition with concepts from moisture tracking techniques to identify where and when the principal physical processes generate T′ and to attribute these sources to synoptic weather systems. Applying this framework to near‐surface and free‐tropospheric T′ associated with the record‐shattering 2021 heatwave in the Pacific Northwest shows that ascending, diabatic air streams in North Pacific cyclones contribute more than 50% of free‐tropospheric T′, whereas near‐surface T′ is mainly produced by local subsidence and diabatic heating with only marginal upstream contributions. Since free‐tropospheric T′ facilitates near‐surface accumulation of locally produced T′ by rendering the atmosphere stable to moist convection, our findings corroborate the notion of top‐down induced heatwave formation fueled by upstream diabatic processes.
Northern Hemisphere Summer Insolation and Ice Volume Driven Variations in Hydrological Environment in Southwest China
Authors: Wu Yao , Warken Sophie , Frank Norbert , Mielke Aaron , Chen Chao‐Jun , Li Jun‐Yun , Li Ting‐Yong
Published: November 2023

The interpretation of stalagmite δ18O in terms of reflecting Asian summer monsoon (ASM) precipitation is still elusive. Here, we present high‐resolution stalagmite trace element ratios (X/Ca, X = Mg, Sr, Ba) records from southwest China covering 116.09 to 4.07 ka BP. δ18O, δ13C, and X/Ca values exhibit clear precessional cycles, with δ18O values reflecting ASM circulation/intensity, while X/Ca ratios capture local precipitation or evapotranspiration variations. Our results show that Northern Hemisphere summer insolation (NHSI) is the main driver of ASM intensity and precipitation phase variation, but global ice volume modulates the response magnitude of summer precipitation to insolation. During the Last Glacial Maximum, high ice volumes caused significant monsoon precipitation to decrease. In contrast to modern observations of the tripolar distribution of precipitation in China, our record is consistent with paleo‐precipitation records in southern and northern China.
PRAME induces genomic instability in uveal melanoma
Authors: Kurtenbach Stefan , Sanchez Margaret I. , Kuznetsoff Jeffim , Rodriguez Daniel A. , Weich Natalia , Dollar James J. , Cruz Anthony , Kurtenbach Sarah , Field Matthew G. , Durante Michael A. , Decatur Christina , Sorouri Mahsa , Lai Fan , Yenisehirli Gulum , Fang Bin , Shiekhattar Ramin , Pelaez Daniel , Correa Zelia M. , Verdun Ramiro E. , Harbour J. William
Published: November 2023

PRAME is a CUL2 ubiquitin ligase subunit that is normally expressed in the testis but becomes aberrantly overexpressed in many cancer types in association with aneuploidy and metastasis. Here, we show that PRAME is expressed predominantly in spermatogonia around the time of meiotic crossing-over in coordination with genes mediating DNA double strand break repair. Expression of PRAME in somatic cells upregulates pathways involved in meiosis, chromosome segregation and DNA repair, and it leads to increased DNA double strand breaks, telomere dysfunction and aneuploidy in neoplastic and non-neoplastic cells. This effect is mediated at least in part by ubiquitination of SMC1A and altered cohesin function. PRAME expression renders cells susceptible to inhibition of PARP1/2, suggesting increased dependence on alternative base excision repair pathways. These findings reveal a distinct oncogenic function of PRAME that can be targeted therapeutically in cancer.
Glucocorticoid treatment influences prostate cancer cell growth and the tumor microenvironment via altered glucocorticoid receptor signaling in prostate fibroblasts
Authors: Eigentler Andrea , Handle Florian , Schanung Silvia , Degen Antonia , Hackl Hubert , Erb Holger H. H. , Fotakis Georgios , Hoefer Julia , Ploner Christian , Jöhrer Karin , Heidegger Isabel , Pircher Andreas , Klotz Werner , Herold Manfred , Schäfer Georg , Culig Zoran , Puhr Martin
Published: November 2023

Despite significant therapeutic advances in recent years, treatment of metastatic prostate cancer (PCa) remains palliative, owing to the inevitable occurrence of drug resistance. There is increasing evidence that epithelial glucocorticoid receptor (GR) signaling and changes in the tumor-microenvironment (TME) play important roles in this process. Since glucocorticoids (GCs) are used as concomitant medications in the course of PCa treatment, it is essential to investigate the impact of GCs on stromal GR signaling in the TME. Therefore, general GR mRNA and protein expression was assessed in radical prostatectomy specimens and metastatic lesions. Elevated stromal GR signaling after GC treatment resulted in altered GR-target gene, soluble protein expression, and in a morphology change of immortalized and primary isolated cancer-associated fibroblasts (CAFs). Subsequently, these changes affected proliferation, colony formation, and 3D-spheroid growth of multiple epithelial PCa cell models. Altered expression of extra-cellular matrix (ECM) and adhesion-related proteins led to an ECM remodeling. Notably, androgen receptor pathway inhibitor treatments did not affect CAF viability. Our findings demonstrate that GC-mediated elevated GR signaling has a major impact on the CAF secretome and the ECM architecture. GC-treated fibroblasts significantly influence epithelial tumor cell growth and must be considered in future therapeutic strategies.
PSMD14 stabilizes estrogen signaling and facilitates breast cancer progression via deubiquitinating ERα
Authors: Yang Penghe , Yang Xiao , Wang Dehai , Yang Huijie , Li Zhongbo , Zhang Chenmiao , Zhang Shuqing , Zhu Jian , Li Xin , Su Peng , Zhuang Ting
Published: November 2023

The over-activation of ERα signaling is regarded as the major driver for luminal breast cancers, which could be effective controlled via selective estrogen receptor modulators (SERM), such as tamoxifen. The endocrine resistance is still a challenge for breast cancer treatment, while recently studies implicate the post-translational modification on ERα play important roles in endocrine resistance. The stability of ERα protein and ERα transcriptome are subject to a balance between E3 ubiquitin ligases and deubiquitinases. Through deubiquitinases siRNA library screening, we discover PSMD14 as a critical deubiquitinase for ERα signaling and breast cancer progression. PSMD14 could facilitate breast cancer progression through ERα signaling in vitro and in vivo, while pharmaceutical inhibition of PSMD14 via Thiolutin could block the tumorigenesis in breast cancer. In endocrine resistant models, PSMD14 inhibition could de-stabilize the resistant form of ERα (Y537S) and restore tamoxifen sensitivity. Molecular studies reveal that PSMD14 could inhibition K48-linked poly-ubiquitination on ERα, facilitate ERα transcriptome. Interestingly, ChIP assay shows that ERα could bind to the promoter region of PSMD14 and facilitate its gene transcription, which indicates PSMD14 is both the upstream modulator and downstream target for ERα signaling in breast cancer. In general, we identified a novel positive feedback loop between PSMD14 and ERα signaling in breast cancer progression, while blockade of PSMD14 could be a plausible strategy for luminal breast cancer.
An autonomous laboratory for the accelerated synthesis of novel materials
Authors: Szymanski Nathan J. , Rendy Bernardus , Fei Yuxing , Kumar Rishi E. , He Tanjin , Milsted David , McDermott Matthew J. , Gallant Max , Cubuk Ekin Dogus , Merchant Amil , Kim Haegyeom , Jain Anubhav , Bartel Christopher J. , Persson Kristin , Zeng Yan , Ceder Gerbrand
Published: November 2023

To close the gap between the rates of computational screening and experimental realization of novel materials1,2, we introduce the A-Lab, an autonomous laboratory for the solid-state synthesis of inorganic powders. This platform uses computations, historical data from the literature, machine learning (ML) and active learning to plan and interpret the outcomes of experiments performed using robotics. Over 17 days of continuous operation, the A-Lab realized 41 novel compounds from a set of 58 targets including a variety of oxides and phosphates that were identified using large-scale ab initio phase-stability data from the Materials Project and Google DeepMind. Synthesis recipes were proposed by natural-language models trained on the literature and optimized using an active-learning approach grounded in thermodynamics. Analysis of the failed syntheses provides direct and actionable suggestions to improve current techniques for materials screening and synthesis design. The high success rate demonstrates the effectiveness of artificial-intelligence-driven platforms for autonomous materials discovery and motivates further integration of computations, historical knowledge and robotics.
The genetic legacy of the expansion of Bantu-speaking peoples in Africa
Authors: Fortes-Lima Cesar A. , Burgarella Concetta , Hammarén Rickard , Eriksson Anders , Vicente Mário , Jolly Cecile , Semo Armando , Gunnink Hilde , Pacchiarotti Sara , Mundeke Leon , Matonda Igor , Muluwa Joseph Koni , Coutros Peter , Nyambe Terry S. , Cikomola Justin Cirhuza , Coetzee Vinet , de Castro Minique , Ebbesen Peter , Delanghe Joris , Stoneking Mark , Barham Lawrence , Lombard Marlize , Meyer Anja , Steyn Maryna , Malmström Helena , Rocha Jorge , Soodyall Himla , Pakendorf Brigitte , Bostoen Koen , Schlebusch Carina M.
Published: November 2023

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1–7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we contribute insights into this expansion that started 6,000–4,000 years ago in western Africa. We genotyped 1,763 participants, including 1,526 Bantu speakers from 147 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals8. We show that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the Democratic Republic of Congo as possible crossroads of interaction. Using spatially explicit methods9 and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial-founder migration model. We further show that Bantu speakers received significant gene flow from local groups in regions they expanded into. Our genetic dataset provides an exhaustive modern-day African comparative dataset for ancient DNA studies10 and will be important to a wide range of disciplines from science and humanities, as well as to the medical sector studying human genetic variation and health in African and African-descendant populations.
MSL2 ensures biallelic gene expression in mammals
Authors: Sun Yidan , Wiese Meike , Hmadi Raed , Karayol Remzi , Seyfferth Janine , Martinez Greene Juan Alfonso , Erdogdu Niyazi Umut , Deboutte Ward , Arrigoni Laura , Holz Herbert , Renschler Gina , Hirsch Naama , Foertsch Arion , Basilicata Maria Felicia , Stehle Thomas , Shvedunova Maria , Bella Chiara , Pessoa Rodrigues Cecilia , Schwalb Bjoern , Cramer Patrick , Manke Thomas , Akhtar Asifa
Published: November 2023

In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter–enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
Disease-specific tau filaments assemble via polymorphic intermediates
Authors: Lövestam Sofia , Li David , Wagstaff Jane L. , Kotecha Abhay , Kimanius Dari , McLaughlin Stephen H. , Murzin Alexey G. , Freund Stefan M. V. , Goedert Michel , Scheres Sjors H. W.
Published: November 2023

Intermediate species in the assembly of amyloid filaments are believed to play a central role in neurodegenerative diseases and may constitute important targets for therapeutic intervention1,2. However, structural information about intermediate species has been scarce and the molecular mechanisms by which amyloids assemble remain largely unknown. Here we use time-resolved cryogenic electron microscopy to study the in vitro assembly of recombinant truncated tau (amino acid residues 297–391) into paired helical filaments of Alzheimer’s disease or into filaments of chronic traumatic encephalopathy3. We report the formation of a shared first intermediate amyloid filament, with an ordered core comprising residues 302–316. Nuclear magnetic resonance indicates that the same residues adopt rigid, β-strand-like conformations in monomeric tau. At later time points, the first intermediate amyloid disappears and we observe many different intermediate amyloid filaments, with structures that depend on the reaction conditions. At the end of both assembly reactions, most intermediate amyloids disappear and filaments with the same ordered cores as those from human brains remain. Our results provide structural insights into the processes of primary and secondary nucleation of amyloid assembly, with implications for the design of new therapies.
A probable Keplerian disk feeding an optically revealed massive young star
Authors: McLeod Anna F. , Klaassen Pamela D. , Reiter Megan , Henshaw Jonathan , Kuiper Rolf , Ginsburg Adam
Published: November 2023

The canonical picture of star formation involves disk-mediated accretion, with Keplerian accretion disks and associated bipolar jets primarily observed in nearby, low-mass young stellar objects (YSOs). Recently, rotating gaseous structures and Keplerian disks have been detected around several massive (M > 8 M⊙) YSOs (MYSOs)1–4, including several disk-jet systems5–7. All the known MYSO systems are in the Milky Way, and all are embedded in their natal material. Here we report the detection of a rotating gaseous structure around an extragalactic MYSO in the Large Magellanic Cloud. The gas motion indicates that there is a radial flow of material falling from larger scales onto a central disk-like structure. The latter exhibits signs of Keplerian rotation, so that there is a rotating toroid feeding an accretion disk and thus the growth of the central star. The system is in almost all aspects comparable to Milky Way high-mass YSOs accreting gas from a Keplerian disk. The key difference between this source and its Galactic counterparts is that it is optically revealed rather than being deeply embedded in its natal material as is expected of such a massive young star. We suggest that this is the consequence of the star having formed in a low-metallicity and low-dust content environment. Thus, these results provide important constraints for models of the formation and evolution of massive stars and their circumstellar disks.
FOXP3 recognizes microsatellites and bridges DNA through multimerization
Authors: Zhang Wenxiang , Leng Fangwei , Wang Xi , Ramirez Ricardo N. , Park Jinseok , Benoist Christophe , Hur Sun
Published: November 2023

FOXP3 is a transcription factor that is essential for the development of regulatory T cells, a branch of T cells that suppress excessive inflammation and autoimmunity1–5. However, the molecular mechanisms of FOXP3 remain unclear. Here we here show that FOXP3 uses the forkhead domain—a DNA-binding domain that is commonly thought to function as a monomer or dimer—to form a higher-order multimer after binding to TnG repeat microsatellites. The cryo-electron microscopy structure of FOXP3 in a complex with T3G repeats reveals a ladder-like architecture, whereby two double-stranded DNA molecules form the two ‘side rails’ bridged by five pairs of FOXP3 molecules, with each pair forming a ‘rung’. Each FOXP3 subunit occupies TGTTTGT within the repeats in a manner that is indistinguishable from that of FOXP3 bound to the forkhead consensus motif (TGTTTAC). Mutations in the intra-rung interface impair TnG repeat recognition, DNA bridging and the cellular functions of FOXP3, all without affecting binding to the forkhead consensus motif. FOXP3 can tolerate variable inter-rung spacings, explaining its broad specificity for TnG-repeat-like sequences in vivo and in vitro. Both FOXP3 orthologues and paralogues show similar TnG repeat recognition and DNA bridging. These findings therefore reveal a mode of DNA recognition that involves transcription factor homomultimerization and DNA bridging, and further implicates microsatellites in transcriptional regulation and diseases.
Identification of constrained sequence elements across 239 primate genomes
Authors: Kuderna Lukas F. K. , Ulirsch Jacob C. , Rashid Sabrina , Ameen Mohamed , Sundaram Laksshman , Hickey Glenn , Cox Anthony J. , Gao Hong , Kumar Arvind , Aguet Francois , Christmas Matthew J. , Clawson Hiram , Haeussler Maximilian , Janiak Mareike C. , Kuhlwilm Martin , Orkin Joseph D. , Bataillon Thomas , Manu Shivakumara , Valenzuela Alejandro , Bergman Juraj , Rouselle Marjolaine , Silva Felipe Ennes , Agueda Lidia , Blanc Julie , Gut Marta , de Vries Dorien , Goodhead Ian , Harris R. Alan , Raveendran Muthuswamy , Jensen Axel , Chuma Idriss S. , Horvath Julie E. , Hvilsom Christina , Juan David , Frandsen Peter , Schraiber Joshua G. , de Melo Fabiano R. , Bertuol Fabrício , Byrne Hazel , Sampaio Iracilda , Farias Izeni , Valsecchi João , Messias Malu , da Silva Maria N. F. , Trivedi Mihir , Rossi Rogerio , Hrbek Tomas , Andriaholinirina Nicole , Rabarivola Clément J. , Zaramody Alphonse , Jolly Clifford J. , Phillips-Conroy Jane , Wilkerson Gregory , Abee Christian , Simmons Joe H. , Fernandez-Duque Eduardo , Kanthaswamy Sree , Shiferaw Fekadu , Wu Dongdong , Zhou Long , Shao Yong , Zhang Guojie , Keyyu Julius D. , Knauf Sascha , Le Minh D. , Lizano Esther , Merker Stefan , Navarro Arcadi , Nadler Tilo , Khor Chiea Chuen , Lee Jessica , Tan Patrick , Lim Weng Khong , Kitchener Andrew C. , Zinner Dietmar , Gut Ivo , Melin Amanda D. , Guschanski Katerina , Schierup Mikkel Heide , Beck Robin M. D. , Karakikes Ioannis , Wang Kevin C. , Umapathy Govindhaswamy , Roos Christian , Boubli Jean P. , Siepel Adam , Kundaje Anshul , Paten Benedict , Lindblad-Toh Kerstin , Rogers Jeffrey , Marques Bonet Tomas , Farh Kyle Kai-How
Published: November 2023

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.
Overview of Protein Flavours
Authors: Zhao Jing , Liu Changqi , Raza Ali
Published: November 2023

As the world population increases, there are rising demands for high-quality proteins. Besides their nutritional values, proteins also contribute important physiochemical functionalities to the foods they are used in. Another key aspect of protein ingredients is flavour, which has not been as extensively studied and well understood as their nutritional and functional properties. This chapter provides an overview of the global protein market, sensory and flavour properties and problems associated with food protein ingredients, and using proteins and peptides as precursors to generate flavours through the Maillard reaction. The contents covered in this chapter introduce the opportunities and challenges of food proteins and the background of the technical studies to be discussed in the following chapters of the book.
Consumer Perceptions of Food Proteins and Protein-enriched Foods
Authors: Zhao Jing , Xu Minwei , Baker Jesse , Kinsey Sarah
Published: November 2023

Protein ingredients are of great interest to consumers due to their nutritional value. Due to religious reasons and a rising concern about environmental impact, proteins from plants, algae, cultured meat, and edible insects are gaining interest. However, consumer acceptance of protein ingredients is hindered by off-flavors, undesirable textures and colors, and other cultural reasons. This chapter discusses the current knowledge on consumer acceptance of food protein ingredients, e.g., protein concentrate, isolate, and hydrolysate, and food protein-based and enhanced food products. Consumer acceptance from both survey studies and consumer sensory studies is included.
Chemical and Instrumental Characterization of Protein–Flavor Interactions
Authors: Anantharamkrishnan Vaidhyanathan , Reineccius Gary A.
Published: November 2023

In all fields of science, the ability to advance understanding and knowledge is tied to the ability to measure outcomes. As early as 1920, it was observed that the composition of a food influences the sensory perception of aroma compounds added to it. However, it was not until the early 1960s that gas chromatographic instrumentation became available to measure how and what was responsible for influencing flavor perception as the food composition was altered. The early methods were fairly simple, depending on headspace analysis to gain an understanding. Headspace methodologies lacked sensitivity to work in the range of human perception on many aroma compounds, and thus, more sensitive methods were developed, such as equilibrium dialysis and headspace concentration techniques. The most recent developments in this area employ sophisticated mass spectrometry to measure how flavor compounds react with food proteins and where they react within the protein. This chapter tracks the development of methodology and learning focusing on both weak (ionic, hydrophilic, and hydrophobic) and strong (covalent) bonding of flavor compounds to various protein sources.
The Flavour of Dairy Proteins
Authors: McGorrin Robert J.
Published: November 2023

This chapter discusses the current research findings regarding the flavour of bovine milk protein concentrates and isolates, including processing and storage effects on the flavour and flavour stability of protein ingredients. Covered topics include the characteristics of major odour and taste compounds, the source and influencing factors of flavour compound formation, and the potential methods for eliminating undesirable off-flavours in dairy protein products.
Nuclear spin relaxation
Authors: Kowalewski Jozef
Published: November 2023

This review covers the progress in the field of NMR relaxation in fluids during 2022. The emphasis is on comparatively simple liquids and solutions of physico-chemical and chemical interest, in analogy with the previous periods, but selected biophysics-related topics (here, I also include some work on relaxation in solid biomaterials) and relaxation-related studies on more complex systems (macromolecular solutions, liquid crystalline systems, glassy and porous materials) are also covered. Section 2 of the chapter is concerned with general, physical and experimental aspects of nuclear spin relaxation, while Section 3 is concentrated on applications.
NMR of soft matter systems
Authors: Wallace Matthew
Published: November 2023

This chapter summarises recent advances and applications of solid-state, solution-state and gel-state NMR techniques to study soft matter systems. Original research articles published between March 2022 and March 2023 are discussed that cover liquid crystals, surfactants, gels, polymer solutions and other soft matter systems. Each section of the review focuses on a different NMR technique, including 1D and 2D solution-state experiments, 2H NMR, nuclear Overhauser effect (NOE) measurements, pulsed-field gradient (diffusion) NMR, relaxation measurements, experiments on quadrupolar counterions and solid-state NMR.
Core–shell oxygen-deficient Fe2O3 polyhedron serves as an efficient host for sulfur cathode
Authors: Pu Jun , Huang Ziyang , Wang Jie , Tan Yun , Fan Shanshan , Wang Zhenghua
Published: November 2023

Iron oxide@C polyhedron rich in oxygen defects is beneficial to the adsorption and kinetic conversion of polysulfide.
Engineered fluorogenic HaloTag ligands for turn-on labelling in live cells
Authors: Lampkin Bryan J. , Kritzer Joshua A.
Published: November 2023

Fluorogenic dyes enable wash-free turn-on fluorescent readouts. Here, we report novel fluorogenic HaloTag benzothiadiazole dyes for cellular imaging by optimizing for both dye brightness and low background in cells.
Perpendicular magnetic anisotropy and magneto-optical properties of Bi,Mn:YIG epitaxial films
Authors: Jiang Jiewen , Dai Yun , Shang Jiamin , Zhang Zhen , Su Liangbi , Cheng Maojie , Sun Dunlu , Stupakiewicz A. , Wu Anhua
Published: November 2023

Bi,Mn co-doped Y3Fe5O12 films with good crystallinity, great magneto-optical properties and high perpendicular magnetic anisotropy field (>3000 Oe) were prepared via liquid phase epitaxy.
Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins
Authors: Keith Alasdair D. , Sawyer Elizabeth B. , Choy Desmond C. Y. , Xie Yuhang , Biggs George S. , Klein Oskar James , Brear Paul D. , Wales David J. , Barker Paul D.
Published: November 2023

Energy landscape theory can supplement standard biophysical techniques to investigate anaerobic heme breakdown across a family of hemoproteins.
Experimental phase diagram and its temporal evolution for submicron 2-methylglutaric acid and ammonium sulfate aerosol particles
Authors: Huang Qishen , Pitta Kiran R. , Constantini Kayla , Ott Emily-Jean E. , Zuend Andreas , Freedman Miriam Arak
Published: November 2023

The experimental phase diagram for liquid–liquid phase separation in submicrometer aerosol particles converges with theory as equilibration time is increased.
Fabrication of mesopore-rich HZSM-5 to boost the degradation of plastic wastes
Authors: Song Chenggong , Hou Xu , Zhou Hao , Qiao Huimin , Yin Li , Huang Jing , Yuan Enxian , Cui Tingting
Published: November 2023

An increase of mesopore volume in HZSM-5 zeolites reduced the degradation temperature of plastic wastes.
Excited-state dynamics and fluorescence lifetime of cryogenically cooled green fluorescent protein chromophore anions
Authors: Rasmusssen Anne P. , Pedersen Henrik B. , Andersen Lars H.
Published: November 2023

The intrinsic fluorescence lifetime and excited state barrier of the green fluorescent protein (GFP) model chromophore HBDI anion are found in the gas-phase by fs-pump pulse measurements.
Fe-induced crystalline–amorphous interface engineering of a NiMo-based heterostructure for enhanced water oxidation
Authors: Zhang Junming , Fang Yingjian , Chen Yao , Gao Yang , Zhang Xiaojie , Tang Tao , Tian Baoqiang , Xiao He , Zhao Man , Luo Ergui , Hu Tianjun , Jia Jianfeng , Wu Haishun
Published: November 2023

Engineering heterostructure with unique surface/interface structure is one of the effective strategies to develop highly active noble-metal-free catalysts for oxygen evolution reaction.
Coplanar binuclear group 4 post-metallocene complexes supported by chelating μ-(σ2-aryl) ligands: characterisation and olefin polymerisation catalysis
Authors: Li Yufang , Liu Qian , Bao Junhui , Yiu Shek-Man , Chan Michael C. W.
Published: November 2023

Rigid binuclear assemblies with M⋯M distances and syn binding sites that are amenable for cooperative reactivity have been structurally characterised; the Ti2 catalysts are more active than anti and mono-Ti controls and produced higher-Mw polymers.