bluuebunny/crossref_metadata_2025 huggingface dataset:
Plasma biomarkers in chronic single moderate–severe traumatic brain injury
Authors: Spitz Gershon , Hicks Amelia J , McDonald Stuart J , Dore Vincent , Krishnadas Natasha , O’Brien Terence J , O’Brien William T , Vivash Lucy , Law Meng , Ponsford Jennie L , Rowe Christopher , Shultz Sandy R
Published: September 2024

Blood biomarkers are an emerging diagnostic and prognostic tool that reflect a range of neuropathological processes following traumatic brain injury (TBI). Their effectiveness in identifying long-term neuropathological processes after TBI is unclear. Studying biomarkers in the chronic phase is vital because elevated levels in TBI might result from distinct neuropathological mechanisms during acute and chronic phases. Here, we examine plasma biomarkers in the chronic period following TBI and their association with amyloid and tau PET, white matter microarchitecture, brain age and cognition.

We recruited participants ≥40 years of age who had suffered a single moderate–severe TBI ≥10 years previously between January 2018 and March 2021. We measured plasma biomarkers using single molecule array technology [ubiquitin C-terminal hydrolase L1 (UCH-L1), neurofilament light (NfL), tau, glial fibrillary acidic protein (GFAP) and phosphorylated tau (P-tau181)]; PET tracers to measure amyloid-β (18F-NAV4694) and tau neurofibrillary tangles (18F-MK6240); MRI to assess white matter microstructure and brain age; and the Rey Auditory Verbal Learning Test to measure verbal-episodic memory.

A total of 90 post-TBI participants (73% male; mean = 58.2 years) were recruited on average 22 years (range = 10–33 years) post-injury, and 32 non-TBI control participants (66% male; mean = 57.9 years) were recruited. Plasma UCH-L1 levels were 67% higher {exp(b) = 1.67, P = 0.018, adjusted P = 0.044, 95% confidence interval (CI) [10% to 155%], area under the curve = 0.616} and P-tau181 were 27% higher {exp(b) = 1.24, P = 0.011, adjusted P = 0.044, 95% CI [5% to 46%], area under the curve = 0.632} in TBI participants compared with controls. Amyloid and tau PET were not elevated in TBI participants. Higher concentrations of plasma P-tau181, UCH-L1, GFAP and NfL were significantly associated with worse white matter microstructure but not brain age in TBI participants. For TBI participants, poorer verbal-episodic memory was associated with higher concentration of P-tau181 {short delay: b = −2.17, SE = 1.06, P = 0.043, 95% CI [−4.28, −0.07]; long delay: bP-tau = −2.56, SE = 1.08, P = 0.020, 95% CI [−4.71, −0.41]}, tau {immediate memory: bTau = −6.22, SE = 2.47, P = 0.014, 95% CI [−11.14, −1.30]} and UCH-L1 {immediate memory: bUCH-L1 = −2.14, SE = 1.07, P = 0.048, 95% CI [−4.26, −0.01]}, but was not associated with functional outcome.

Elevated plasma markers related to neuronal damage and accumulation of phosphorylated tau suggest the presence of ongoing neuropathology in the chronic phase following a single moderate–severe TBI. Plasma biomarkers were associated with measures of microstructural brain disruption on MRI and disordered cognition, further highlighting their utility as potential objective tools to monitor evolving neuropathology post-TBI.
Torpor expression and patterns in 3 sympatric rodents from Inner Mongolia
Authors: Chi Qing-Sheng , Sukhchuluun Gansukh , Wen Jing , Wang De-Hua , Geiser Fritz
Published: September 2024

The diversity of rodents in Asian deserts is high. Nevertheless, little is known about their use of daily torpor and hibernation, which are employed by many small mammals worldwide for energy and water conservation to permit survival under adverse environmental conditions. We quantified for the first time, using temperature transponders and data loggers, long-term torpor expression and patterns in sympatric desert hamsters Phodopus roborovskii, striped hamsters Cricetulus barabensis and 3-toed jerboas Dipus sagitta under controlled conditions. Animals were live-trapped in Inner Mongolia in August and held in captivity under short photoperiods and low ambient temperatures (Tas) for about 6 months. Both hamster species (~half of individuals) expressed spontaneous (food available) daily torpor. Daily torpor in desert hamsters was less frequent and shallower than that in striped hamsters, which also had longer torpor bouts during torpor at Ta 15.8 ± 0.4 °C. Only one individual jerboa entered hibernation spontaneously at Ta 6.2 ± 0.5°C, but all hibernated after food deprivation. The 2 hamster species only slightly changed their body mass during the acclimation, whereas jerboas greatly increased their body mass by 27.9% during the first 2 months of acclimation probably as a preparation for the hibernating season. Our data show that short photoperiod and moderately low Ta induces spontaneous daily torpor in the 2 hamster species, suggesting that it is used regularly in the wild. Hibernation in Jerboas occurred at Ta 6.2 ± 0.5 °C especially when food was withheld suggesting limited food availability is the proximate trigger of their hibernation.
Anticoagulant-related bleeding as a sign of underlying tumoural lesions in patients with atrial fibrillation: a nationwide cohort study
Authors: Proesmans Kristiaan , Grymonprez Maxim , Rottey Sylvie , Lahousse Lies
Published: September 2024

Aims

Bleeding events are a well-known complication of oral anticoagulant (OAC) use in patients with atrial fibrillation (AF). While these are undesirable, bleedings could have a warning potential for underlying tumoural lesions. Therefore, we aimed to investigate the association between anticoagulant-related bleeding and newly diagnosed tumoural lesions in a nationwide cohort study.

Methods and results

Using Belgian nationwide data, AF patients without any tumoural lesions were included when initiating OACs between 2013 and 2019. The absolute and relative risks of newly diagnosed tumoural lesions were investigated in OAC users with vs. without an OAC-related bleeding event. Analyses were additionally stratified by tumoural lesion, location-specific bleeding, and OAC type. A total of 230 386 OAC users were included, among whom 35 192 persons were diagnosed with a tumoural lesion during follow-up. Persons with a clinically relevant bleeding during OAC use had a tumoural lesion incidence of 15.33 per 100 person-years compared to an incidence of 5.22 per 100 person-years in persons without bleeding. Site-specific gastrointestinal, urogenital, respiratory, and intracranial bleeding events were respectively associated with a significantly increased risk of incident gastrointestinal [adjusted hazard ratio (aHR) 8.13 (95% confidence interval (CI): 7.08–9.34)], urological [aHR 12.73 (95% CI: 10.56–15.35)], respiratory [aHR 4.91 (95% CI: 3.24–7.44)], and intracranial tumoural lesions [aHR 27.89 (95% CI: 16.53–47.04)].

Conclusion

Bleeding events in AF patients initiated on OAC were associated with an increased risk of tumoural lesions. Therefore, OAC-related bleeding events could unmask an underlying tumoural lesion.
Local exposure to refugees changed attitudes to ethnic minorities in the Netherlands
Authors: Achard Pascal , Albrecht Sabina , Ghidoni Riccardo , Cettolin Elena , Suetens Sigrid
Published: September 2024

We investigate the effect of exposure to refugees on locals’ preferences with regard to ethnic minorities using individual-level panel data from the Netherlands. The data combine self-reported preferences with administrative data on the residential locations of the locals and the refugees. The study period is marked by a sudden inflow of refugees in some neighbourhoods. We find that individuals living close to newly installed refugee facilities developed a more positive attitude towards ethnic minorities and became less supportive of anti-immigration parties compared to individuals living farther away. An investigation of mechanisms suggests that the local effect is due to contact between residents and refugees.
Don DeLillo’s Falling Man as Cultural Trauma Fiction
Authors: Mullis Courtney
Published: September 2024

The sociological concept of cultural trauma provides a useful lens for understanding large-scale traumatic events and their literary legacies because this concept recognizes the historical, social, and cultural aspects of trauma rather than limiting its scope to the experiences of individuals or small collectives. The terrorist attacks on 11 September 2001 initiated widespread trauma through the spectacle of the planes colliding with the World Trade Center and the Pentagon. Literature after 9/11 is both a product of cultural trauma and a means of exploring the profound effects of that trauma. Some 9/11 novels are part of a subgenre I call Cultural Trauma Fiction, which depicts and explores the effect of a large-scale traumatic event on a culture. Texts within this subgenre represent multiple identities and perspectives, engage with cultural concerns about memorializing the trauma, consider the ethics of representing that trauma through different media, and advance counternarratives that challenge dominant government or media narratives about the trauma. Don DeLillo’s Falling Man constitutes a work of Cultural Trauma Fiction in that its structure and narrative strategies move beyond the scope of the novel’s plot, offering insight into the cultural response to 9/11 and countering hegemonic narratives. Works of Cultural Trauma Fiction like Falling Man highlight the collective hidden transcript of traumatic events and challenge official narratives that oversimplify cultural traumas. Falling Man complicates and enriches the collective understanding of 9/11 by challenging, revising, and reconstructing its cultural narratives.
OfWRKY17-OfC3H49 module responding to high ambient temperature delays flowering via inhibiting OfSOC1B expression in Osmanthus fragrans
Authors: Ye Yong , Lu Xinke , Kong En , Wang Qianqian , Shen Lixiao , Zhong Shiwei , Wang Yiguang , Xiao Zheng , Deng Jinping , Zhao Hongbo , Dong Bin
Published: September 2024

Ambient temperature is a pivotal factor in the regulation of the flowering process in plants. In this study, we found that high ambient temperature exerts an inhibitory effect on the flowering of Osmanthus fragrans “Sjigui”. However, the underlying molecular mechanisms remain not fully understood. Through transcriptome analysis, a differently expressed C3H gene OfC3H49 was identified, which is induced by high ambient temperature. OfC3H49 was demonstrated to delay the flowering process of Arabidopsis and downregulate the expression of flowering-related genes in O. fragrans calli. Further investigation indicates that OfC3H49 as a transcriptional repressor directly suppresses the expression of the OfSOC1B thereby causing a delay in flowering time. Furthermore, a WRKY transcription factor, OfWRKY17, was identified to be responsive to high ambient temperature, directly binding to the OfC3H49 promoter and enhance OfC3H49 expression. Overexpression of OfWRKY17 in Arabidopsis resulted in a significant delay in flowering and induced the expression of OfC3H49 in O. fragrans calli. Collectively, our findings delineate a regulatory module, OfWRKY17-OfC3H49, which is activated by high ambient temperature and functions as a negative regulator of flowering by suppressing the expression of OfSOC1B in O. fragrans. This study provides novel insights into the molecular mechanisms involved in ambient temperature-mediated flowering control and contributes to the development of molecular breeding strategies for O. fragrans.
Opportunities and Challenges in Applying AI to Evolutionary Morphology
Authors: He Y , Mulqueeney J M , Watt E C , Salili-James A , Barber N S , Camaiti M , Hunt E S E , Kippax-Chui O , Knapp A , Lanzetti A , Rangel-de Lázaro G , McMinn J K , Minus J , Mohan A V , Roberts L E , Adhami D , Grisan E , Gu Q , Herridge V , Poon S T S , West T , Goswami A
Published: September 2024

Synopsis

Artificial intelligence (AI) is poised to revolutionize many aspects of science, including the study of evolutionary morphology. While classical AI methods such as principal component analysis and cluster analysis have been commonplace in the study of evolutionary morphology for decades, recent years have seen increasing application of deep learning to ecology and evolutionary biology. As digitized specimen databases become increasingly prevalent and openly available, AI is offering vast new potential to circumvent long-standing barriers to rapid, big data analysis of phenotypes. Here, we review the current state of AI methods available for the study of evolutionary morphology, which are most developed in the area of data acquisition and processing. We introduce the main available AI techniques, categorizing them into 3 stages based on their order of appearance: (1) machine learning, (2) deep learning, and (3) the most recent advancements in large-scale models and multimodal learning. Next, we present case studies of existing approaches using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, and phylogenetics. We then discuss the prospectus for near-term advances in specific areas of inquiry within this field, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. In particular, we note key areas where AI remains underutilized and could be used to enhance studies of evolutionary morphology. This combination of current methods and potential developments has the capacity to transform the evolutionary analysis of the organismal phenotype into evolutionary phenomics, leading to an era of “big data” that aligns the study of phenotypes with genomics and other areas of bioinformatics.
Organelles in the ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses
Authors: Sonett Dylan , Brown Tanya , Bengtsson-Palme Johan , Padilla-Gamiño Jacqueline L , Zaneveld Jesse R
Published: September 2024

The genomes of mitochondria and chloroplasts contain ribosomal RNA (rRNA) genes, reflecting their ancestry as free-living bacteria. These organellar rRNAs are often amplified in microbiome studies of animals and plants. If identified, they can be discarded, merely reducing sequencing depth. However, we identify certain high-abundance organeller RNAs not identified by common pipelines, which may compromise statistical analysis of microbiome structure and diversity. We quantified this by reanalyzing 7459 samples from seven 16S rRNA studies, including microbiomes from 927 unique animal genera. We find that under-annotation of cryptic mitochondrial and chloroplast reads affects multiple of these large-scale cross-species microbiome comparisons, and varies between host species, biasing comparisons. We offer a straightforward solution: supplementing existing taxonomies with diverse organelle rRNA sequences. This resolves up to 97% of unique unclassified sequences in some entire studies as mitochondrial (14% averaged across all studies), without increasing false positive annotations in mitochondria-free mock communities. Improved annotation decreases the proportion of unknown sequences by ≥10-fold in 2262 of 7459 samples (30%), spanning five of seven major studies examined. We recommend leveraging organelle sequence diversity to better identify organelle gene sequences in microbiome studies, and provide code, data resources and tutorials that implement this approach.
Prescribing Information: Elizabeth B. Connell, the Pill, and the (Woman) Patient’s Peace of Mind
Authors: Wei Jiemin Tina
Published: September 2024

Throughout the 1970s and 1980s, commercialized reproductive technologies experienced a reputational crisis as news about the hormonal birth control pill’s possible side effects reportedly caused 18–30% of women to stop taking it. While secondary literature has followed patients’ and legislatures’ actions, few histories have focused on physicians’ responses. How did physicians manage this public crisis of confidence? This article contributes to existing literature through a backstage look at the work of Elizabeth B. Connell (1925–2018), whose wide-ranging career in medicine, academia, government, industry consulting, and popular writing embroiled her at the center of these controversies. To counter critique from legislatures and consumer reformers, Connell became a mediator for medicine in the public sphere, dispensing select information and arguing for limits on others — for the patient’s sake. If legislative inquiry’s primary havoc was unleashing information, Connell would help the profession moderate it. Because Connell was a woman doctor whom health feminists who were her contemporaries denied was a feminist doctor, the existing scholarship has occluded her. This article reconstructs the contributions of this important and flawed doctor, illuminating how she contorted herself to suit her various public messages, constrained by her conflicting, dual identities as woman and doctor.
Benchmarking the spectroscopic masses of 249 evolved stars using asteroseismology with TESS
Authors: Malla Sai Prathyusha , Stello Dennis , Montet Benjamin T , Huber Daniel , Hon Marc , Bedding Timothy R , Reyes Claudia , Hey Daniel R
Published: September 2024

One way to understand planet formation is through studying the correlations between planet occurrence rates and stellar mass. However, measuring stellar mass in the red giant regime is very difficult. In particular, the spectroscopic masses of certain evolved stars, often referred to as ‘retired A-stars’, have been questioned in the literature. Efforts to resolve this mass controversy using spectroscopy, interferometry, and asteroseismology have so far been inconclusive. A recent ensemble study found a mass-dependent mass offset, but the result was based on only 16 stars. With NASA’s Transiting Exoplanet SurveySatellite (TESS), we expand the investigation of the mass discrepancy to a total of 92 low-luminosity stars, synonymous with the retired A-stars. We measure their characteristic oscillation frequency, $\mathrm{\nu }_{\mathrm{max}}$, and the large frequency separation, $\mathrm{\Delta \nu }$, from their TESS photometric time series. Using these measurements and asteroseismic scaling relations, we derive asteroseismic masses and compare them with spectroscopic masses from five surveys, to comprehensively study the alleged mass-dependent mass offset. We find a mass offset between spectroscopy and seismology that increases with stellar mass. However, we note that adopting the seismic mass scale does not have a significant effect on the planet occurrence-mass-metallicity correlation for the so-called retired A-stars. We also report seismic measurements and masses for 157 higher luminosity giants (mostly helium-core-burning) from the spectroscopic surveys.
INSPIRE: INvestigating Stellar Population In RElics – VII. The local environment of ultra-compact massive galaxies
Authors: Scognamiglio Diana , Spiniello Chiara , Radovich Mario , Tortora Crescenzo , Napolitano Nicola R , Li Rui , Maturi Matteo , Maksymowicz-Maciata Michalina , Cappellari Michele , Arnaboldi Magda , Bevacqua Davide , Coccato Lodovico , D’Ago Giuseppe , Feng Hai-Cheng , Ferré-Mateu Anna , Hartke Johanna , Martín-Navarro Ignacio , Pulsoni Claudia
Published: September 2024

Relic galaxies, the oldest ultra-compact massive galaxies (UCMGs), contain almost exclusively ‘pristine’ stars formed during an intense star formation (SF) burst at high redshift. As such, they allow us to study in detail the early mechanism of galaxy assembly in the Universe. Using the largest catalogue of spectroscopically confirmed UCMGs for which a degree of relicness (DoR) had been estimated, the INSPIRE catalogue, we investigate whether or not relics prefer dense environments. The objective of this study is to determine if the DoR, which measures how extreme the SF history was, and the surrounding environment are correlated. In order to achieve this goal, we employ the AMICO galaxy cluster catalogue to compute the probability for a galaxy to be a member of a cluster, and measure the local density around each UCMG using machine learning-based photometric redshifts. We find that UCMGs can reside both in clusters and in the field, but objects with very low DoR ($\lt 0.3$, i.e. a relatively extended SF history) prefer underdense environments. We additionally report a correlation between the DoR and the distance from the cluster centre: more extreme relics, when located in clusters, tend to occupy the more central regions of them. We finally outline potential evolution scenarios for UCMGs at different DoR to reconcile their presence in both clusters and field environments.
ExoMol line lists–LIX. High-temperature line list for N2O
Authors: Yurchenko Sergei N , Mellor Thomas M , Tennyson Jonathan
Published: September 2024

New hot line lists for five isotopologues of N$_2$O called TYM are presented, for the parent $^{14}$N$_2$$^{16}$O and 4 singly substituted species $^{14}$N$_2$$^{17}$O, $^{14}$N$_2$$^{18}$O, $^{14}$N$^{15}$N$^{16}$O and $^{15}$N$^{14}$N$^{16}$O. The line lists have been computed with the variational program TROVE (Theoretical ROVibrational Energies) using a new empirical potential energy surface (PES) and an accurate ab initio dipole moment surface of N$_2$O Ames-1. The PES was obtained by fitting to experimentally derived energies of N$_2$O compiled using the well established measured active rotation vibration energy levels (MARVEL) procedure. Here we also introduce an ‘artificial symmetry group’ $C_{n \text{s}}(\text{AEM})$ for an efficient construction of rotation-vibrational basis set of a linear non-symmetric triatomic molecule of the XYZ type. The line lists cover the rotational excitations up to $J=160$ and the wavenumber range up to 20000 cm$^{-1}$. MARVEL energies are also used to improve predicted line positions resulting in excellent agreement with the available experimental spectra, as demonstrated. An extensive comparison with existing line lists for N$_2$O HITRAN, HITEMP, NOSL-296, NOSD-1000, and Ames-296K is provided. The TYM line lists are freely accessible from www.exomol.com.
The chemical diversity of the metal-poor Milky Way
Authors: Buckley Nicole , Das Payel , Jofré Paula , Yates Robert M , Hawkins Keith
Published: September 2024

We present a detailed study of the chemical diversity of the metal-poor Milky Way using data from the GALAH DR3 survey. Considering 17 chemical abundances relative to iron ([X/Fe]) for 9923 stars, we employ principal component analysis (PCA) and extreme deconvolution (XD) to identify 10 distinct stellar groups. This approach, free from chemical or dynamical cuts, reveals known populations, including the accreted halo, thick disc, thin disc, and in situ halo. The thick disc is characterized by multiple substructures, suggesting it comprises stars formed in diverse environments. Our findings highlight the limited discriminatory power of magnesium in separating accreted and disc stars. Elements such as Ba, Al, Cu, and Sc are critical in distinguishing disc from accreted stars, while Ba, Y, Eu, and Zn differentiate disc and accreted stars from the in situ halo. This study demonstrates the potential power of combining a latent space representation of the data (PCA) with a clustering algorithm (XD) in Galactic archaeology, in providing new insights into the Galaxy’s assembly and evolutionary history.
Electron microscopy evidence of gadolinium toxicity being mediated through cytoplasmic membrane dysregulation
Authors: Arino Trevor , Faulkner David , Bustillo Karen C , An Dahlia D , Jorgens Danielle , Hébert Solène , McKinley Carla , Proctor Michael , Loguinov Alex , Vulpe Christopher , Abergel Rebecca J
Published: September 2024

Past functional toxicogenomic studies have indicated that genes relevant to membrane lipid synthesis are important for tolerance to the lanthanides. Moreover, previously reported imaging of patient's brains following administration of gadolinium-based contrast agents shows gadolinium lining the vessels of the brain. Taken together, these findings suggest the disruption of cytoplasmic membrane integrity as a mechanism by which lanthanides induce cytotoxicity. In the presented work we used scanning transmission electron microscopy and spatially resolved elemental spectroscopy to image the morphology and composition of gadolinium, europium, and samarium precipitates that formed on the outside of yeast cell membranes. In no sample did we find that the lanthanide contaminant had crossed the cell membrane, even in experiments using yeast mutants with disrupted genes for sphingolipid synthesis—the primary lipids found in yeast cytoplasmic membranes. Rather, we have evidence that lanthanides are co-located with phosphorus outside the yeast cells. These results lead us to hypothesize that the lanthanides scavenge or otherwise form complexes with phosphorus from the sphingophospholipid head groups in the cellular membrane, thereby compromising the structure or function of the membrane, and gaining the ability to disrupt membrane function without entering the cell.
Bile from the hemojuvelin-deficient mouse model of iron excess is enriched in iron and ferritin
Authors: Prajapati Milankumar , Chiu Lauren , Zhang Jared Z , Chong Grace S , DaSilva Nicholas A , Bartnikas Thomas B
Published: September 2024

Iron is an essential nutrient but is toxic in excess. Iron deficiency is the most prevalent nutritional deficiency and typically linked to inadequate intake. Iron excess is also common and usually due to genetic defects that perturb expression of hepcidin, a hormone that inhibits dietary iron absorption. Our understanding of iron absorption far exceeds that of iron excretion, which is believed to contribute minimally to iron homeostasis. Prior to the discovery of hepcidin, multiple studies showed that excess iron undergoes biliary excretion. We recently reported that wild-type mice raised on an iron-rich diet have increased bile levels of iron and ferritin, a multi-subunit iron storage protein. Given that genetic defects leading to excessive iron absorption are much more common causes of iron excess than dietary loading, we set out to determine if an inherited form of iron excess known as hereditary hemochromatosis also results in bile iron loading. We employed mice deficient in hemojuvelin, a protein essential for hepcidin expression. Mutant mice developed bile iron and ferritin excess. While lysosomal exocytosis has been implicated in ferritin export into bile, knockdown of Tfeb, a regulator of lysosomal biogenesis and function, did not impact bile iron or ferritin levels. Bile proteomes differed between female and male mice for wild-type and hemojuvelin-deficient mice, suggesting sex and iron excess impact bile protein content. Overall, our findings support the notion that excess iron undergoes biliary excretion in genetically determined iron excess.
Evolving Escherichia coli to use a tRNA with a non-canonical fold as an adaptor of the genetic code
Authors: Edelmann Martin P , Couperus Sietse , Rodríguez-Robles Emilio , Rivollier Julie , Roberts Tania M , Panke Sven , Marlière Philippe
Published: September 2024

All known bacterial tRNAs adopt the canonical cloverleaf 2D and L-shaped 3D structures. We aimed to explore whether alternative tRNA structures could be introduced in bacterial translation. To this end, we crafted a vitamin-based genetic system to evolve Escherichia coli toward activity of structurally non-canonical tRNAs. The system reliably couples (escape frequency <10−12) growth with the activities of a novel orthogonal histidine suppressor tRNA (HisTUAC) and of the cognate ARS (HisS) via suppression of a GTA valine codon in the mRNA of an enzyme in thiamine biosynthesis (ThiN). Suppression results in the introduction of an essential histidine and thereby confers thiamine prototrophy. We then replaced HisTUAC in the system with non-canonical suppressor tRNAs and selected for growth. A strain evolved to utilize mini HisT, a tRNA lacking the D-arm, and we identified the responsible mutation in an RNase gene (pnp) involved in tRNA degradation. This indicated that HisS, the ribosome, and EF-Tu accept mini HisT ab initio, which we confirmed genetically and through in vitro translation experiments. Our results reveal a previously unknown flexibility of the bacterial translation machinery for the accepted fold of the adaptor of the genetic code and demonstrate the power of the vitamin-based suppression system.
Kinetic mechanism and determinants of EF-P recruitment to translating ribosomes
Authors: Mudryi Vitalii , Frister Jan Ole , Peng Bee-Zen , Wohlgemuth Ingo , Peske Frank , Rodnina Marina V
Published: September 2024

EF-P is a translation factor that facilitates the formation of peptide bonds between consecutive prolines. Using FRET between EF-P and ribosomal protein bL33, we studied dynamics and specificity of EF-P binding to the ribosome. Our findings reveal that EF-P rapidly scans for a free E site and can bind to any ribosome containing a P-site tRNA, regardless of the ribosome's functional state. The interaction with uL1 is essential for EF-P binding, while the β-Lys modification of EF-P doubles the association rate. Specific interactions with the D-loop of tRNAPro or tRNAfMet and via the β-Lys group with the tRNA in the peptidyl transferase center reduce the rate of EF-P dissociation from the ribosome, providing the specificity for complexes that need help in catalyzing peptide bond formation. The nature of the E-site codon has little effect on EF-P binding kinetics. Although EF-P dissociation is reduced upon recognizing its correct tRNA substrate, it remains sufficiently rapid compared to tRNA translocation and does not affect the translocation rate. These results highlight the importance of EF-P’s scanning-engagement mechanism for dynamic substrate recognition during rapid translation.
GenomicLinks: deep learning predictions of 3D chromatin interactions in the maize genome
Authors: Schlegel Luca , Bhardwaj Rohan , Shahryary Yadollah , Demirtürk Defne , Marand Alexandre P , Schmitz Robert J , Johannes Frank
Published: September 2024

Gene regulation in eukaryotes is partly shaped by the 3D organization of chromatin within the cell nucleus. Distal interactions between cis-regulatory elements and their target genes are widespread, and many causal loci underlying heritable agricultural traits have been mapped to distal non-coding elements. The biology underlying chromatin loop formation in plants is poorly understood. Dissecting the sequence features that mediate distal interactions is an important step toward identifying putative molecular mechanisms. Here, we trained GenomicLinks, a deep learning model, to identify DNA sequence features predictive of 3D chromatin interactions in maize. We found that the presence of binding motifs of specific transcription factor classes, especially bHLH, is predictive of chromatin interaction specificities. Using an in silico mutagenesis approach we show the removal of these motifs from loop anchors leads to reduced interaction probabilities. We were able to validate these predictions with single-cell co-accessibility data from different maize genotypes that harbor natural substitutions in these TF binding motifs. GenomicLinks is currently implemented as an open-source web tool, which should facilitate its wider use in the plant research community.
Antimicrobial performance and instrumental analysis for hexagonal ZnO NPs biosynthesized via Ziziphus leaf extract
Authors: Al-Assaly Rafal , Abdulmunem Habeeb Saba , Hammadi Asmaa H , Fadhil Al-Jibouri Lena , Hameed Rusul , Al-Nafiey Amer
Published: September 2024

In this study, ZnO (NPs) were successfully biosynthesized using Zn(NO3)2·6H2O as the Zn+2 source and fresh Ziziphus leaf extract as the reductive and stabilizer regent. The pH and temperature of the reaction were controlled, and the NPs were calcinated at 500°C for 2 h to produce ZnO. FESEM, EDX, XRD, UV-visible, and FTIR were used to analyze ZnO NPs. UV–Vis spectroscopy confirmed the interaction of the biomolecule with the Zn precursors (λmax = 362 nm). FESEM revealed hexagonal NPs with a size of 41.7 nm. XRD analysis confirmed a hexagonal structure with an average particle size of 17.4 nm. In addition to this work, we use the Minimum Inhibitory Concentration MIC method using a Biotek 800ST plate reader (Biotek, USA) to examine the antimicrobial efficacy of biosynthesized nanoparticles against standard and clinical strains of Pseudomonas aeruginosa (ATCC PAO1), Streptococcus pneumoniae (ATCC BAA-334), and local isolate Candida albicans. The results of MIC explain that MIC value 125 µg/ml with IC50 = 56.2 µg/ml for Pseudomonas aeruginosa (ATCC PAO1), MIC value 125 µg/ml and IC50 = 38.9 µg/ml for Streptococcus pneumoniae (ATCC BAA-334) and MIC value 250 µg/ml with IC50 = 79.3 µg/ml for the local isolate Candida albicans. This green approach offers a potential strategy for developing eco-friendly antimicrobial agents.
Zambia’s Industrial Policy
Authors: Chiwele Dennis K. , Phiri Mwanda , Banda Bernard , Mumba Amos
Published: September 2024

This chapter is an appraisal of Zambia’s industrial policies from independence in 1964. It is found that Zambia’s policy landscape has evolved extensively, from when policy was laid down in national development plans and political pronouncements of the United Nations Independence Party (UNIP) that announced key reforms by public address. A standalone industrial policy was first adopted in 1994 after the Movement for Multi-party Development (MMD) came to power. Chief in policy goals was now to create a conducive environment for the private sector to thrive. In this fast liberalizing context, policy was backed by a wide range of legislation. Compared to countries with a similar industrial base in the 1960s—China, South Korea, and Malaysia—it is observed that Zambia’s three comparators underwent a classic economic transformation with labour moving from low productivity agriculture into higher and better rewarding manufacturing. Zambia’s initial success in industrial production was buttressed by protectionist measures and subsidies under the import substitution industrialization that made companies inefficient and therefore unable to compete against imports when trade liberalization came. Further, Zambia made little technology upgrading in its manufacturing. Whereas the comparators moved from resource-based and low technology manufactured exports, Zambia’s remained resource-based. Looking into the future, Zambia’s industrial policy would need to prepare the country to meet the challenges of the times, including the forthcoming digital revolution.
Development Finance in Zambia
Authors: Pamu Emmanuel Mulenga
Published: September 2024

The chapter discusses development finance in Zambia. We argue that government involvement is critical in mobilizing resources for economic development. Official development assistance was replaced by programme loans as Zambia gained access to international debt markets. More recently, the country acquired more project financing loans, contributing to a sharp increase in Zambia’s public external debt. In response to the financing challenges, efforts have been made to leverage resources from the private sector through public–private partnerships. The performance of development finance institutions in Zambia has been dismal, due to excessive risk-taking behaviour with widespread evidence of moral hazard. With reduced external financing, the country must enhance domestic resource mobilization. One strategy is to look again at the mining tax regime to improve collections from the mining sector.
Chinese Thinking on Geoeconomics and Economic Statecraft
Authors: Norris William J. , Xu Yaosheng , Hu Dora
Published: September 2024

This chapter discusses Chinese academic and policy-relevant approaches to the topic of economic statecraft and geoeconomics. The Chinese language literature on these subjects is largely derivative of English language scholarship, tends to focus more on empirical approaches over original theory, and is mainly interested in how to best harness Chinese economic power for political objectives. On the policy side, we note a clear shift toward a more confrontational paradigm, a departure from earlier themes of peaceful integration and win-win mutual benefit. This more assertive turn contrasts with the cooperative themes that had previously colored the way Chinese policy elites and many Chinese academics had traditionally thought of the intersection of economics and strategy. The chapter first examines how Chinese policy and academic communities think about geoeconomics and later the development of Chinese economic statecraft since the beginning of the twenty-first century, with a particular focus on the “New Era” under Xi Jinping. It finds that since the 2008 financial crisis, China’s economic statecraft has shifted away from a clear prioritization of opening up, commercial liberalization, and integrating China into global markets toward a resurgence of party-state mechanisms to guide and direct China’s economic activity. China’s contemporary economic statecraft has been increasingly characterized by a resurgence of Communist Party intervention domestically and the growing intensity of a great power competition abroad.
Communication between cancer cell subtypes by exosomes contributes to nasopharyngeal carcinoma metastasis and poor prognosis
Authors: Xie Hao-Jun , Jiang Ming-Jie , Jiang Ke , Tang Lin-Quan , Chen Qiu-Yan , Yang An-Kui , Mai Hai-Qiang
Published: September 2024

Background

Intratumor heterogeneity is common in cancers, with different cell subtypes supporting each other to become more malignant. Nasopharyngeal carcinoma (NPC), a highly metastatic cancer, shows significant heterogeneity among its cells. This study investigates how NPC cell subtypes with varying metastatic potentials influence each other through exosome-transmitted molecules.

Methods

Exosomes were purified and characterized. MicroRNA expression was analyzed via sequencing and qRT-PCR. The effects of miR-30a-5p on migration, invasion, and metastasis were evaluated in vitro and in vivo. Its impact on desmoglein glycoprotein (DSG2) was assessed using dual-luciferase assays and Western blotting. Immunohistochemistry (IHC) and statistical models linked miR-30a-5p/DSG2 levels to patient prognosis.

Results

Different NPC cell subtypes transmit metastatic potential via exosomes. High-metastatic cells enhance the migration, invasion, and metastasis of low-metastatic cells through exosome-transmitted miR-30a-5p. Plasma levels of exosomal miR-30a-5p are reliable indicators of NPC prognosis. miR-30a-5p may promote metastasis by targeting DSG2 and modulating Wnt signaling. Plasma exosomal miR-30a-5p inversely correlates with DSG2 levels, predicting patient outcomes.

Conclusion

High-metastatic NPC cells can increase the metastatic potential of low-metastatic cells through exosome-transmitted miR-30a-5p, which is a valuable prognostic marker assessable via liquid biopsy.
Fecal microbiota and metabolites in the pathogenesis and precision medicine for inflammatory bowel disease
Authors: Ju Long , Suo Zhimin , Lin Jian , Liu Zhanju
Published: September 2024

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract, and its pathogenesis is believed to be associated with an imbalance between commensal organisms and the intestinal immune system. This imbalance is significantly influenced by the intestinal microbiota and metabolites and plays a critical role in maintaining intestinal mucosal homeostasis. However, disturbances in the intestinal microbiota cause dysregulated immune responses and consequently induce intestinal inflammation. Recent studies have illustrated the roles of the intestinal microbiota in the pathogenesis of IBD and underscored the potential of precision diagnosis and therapy. This work summarises recent progress in this field and particularly focuses on the application of the intestinal microbiota and metabolites in the precision diagnosis, prognosis assessment, treatment effectiveness evaluation, and therapeutic management of IBD.
The potential impact of AI innovations on US occupations
Authors: Septiandri Ali Akbar , Constantinides Marios , Quercia Daniele
Published: September 2024

An occupation is comprised of interconnected tasks, and it is these tasks, not occupations themselves, that are affected by Artificial Intelligence (AI). To evaluate how tasks may be impacted, previous approaches utilized manual annotations or coarse-grained matching. Leveraging recent advancements in machine learning, we replace coarse-grained matching with more precise deep learning approaches. Introducing the AI Impact measure, we employ Deep Learning Natural Language Processing to automatically identify AI patents that may impact various occupational tasks at scale. Our methodology relies on a comprehensive dataset of 17,879 task descriptions and quantifies AI’s potential impact through analysis of 24,758 AI patents filed with the United States Patent and Trademark Office between 2015 and 2022. Our results reveal that some occupations will potentially be impacted, and that impact is intricately linked to specific skills. These include not only routine tasks (codified as a series of steps), as previously thought but also nonroutine ones (e.g. diagnosing health conditions, programming computers, and tracking flight routes). However, AI’s impact on labor is limited by the fact that some of the occupations affected are augmented rather than replaced (e.g. neurologists, software engineers, air traffic controllers), and the sectors affected are experiencing labor shortages (e.g. IT, Healthcare, Transport).
Heavy metals and probabilistic risk assessment via Prunella vulgaris (food and medicine homology) consumption in Guangdong Province, China
Authors: Huang Rui , Chen Shaowei , Wang Ping , Zhu Pan , Xu Xiumin , Chen Zihui , Peng Jiewen
Published: September 2024

Prunella vulgaris is widely used as the main ingredient of herb tea in Southeast Asia, as well as a traditional Chinese medicine. However, the heavy metal contaminations such as arsenic, cadmium, mercury and lead in P. vulgaris may be a cause for concern due to the environment pollution around, plantation and processing contamination. Thus, this study intented to assess both non-carcinogenic risks and carcinogenic risks attributed to cumulative exposure to the four heavy metals in P. vulgaris. The contaminations levels of heavy metals were determined in 90 batches of P. vulgaris. And the consumption level was obtained through a questionnaire survey among a total of 6,235 adult participants in Guangdong province. This study estimated the probabilistic health risks using Monte Carlo simulation, and found that the estimated mean and the 95th percentile values for cumulative noncarcinogenic risk (HI value) and carcinogenic risk (TCR value) of P. vulgaris were all within the acceptable risk. And the assessment results indicated that arsenic was the primary contributors to both noncarcinogenic and carcinogenic risks through P. vulgaris consumption. These findings and continuing the surveillance of heavy metals in P. vulgaris will be particularly relevant to both consumers and policy makers.
Implications of breast density for breast cancer screening
Authors: Watkins Elyse , Jackson Toni
Published: September 2024

Extremely dense breasts can be an independent risk factor for breast cancer. A new FDA rule requires that patients be notified of their breast density and the possible benefits of additional imaging to screen for breast cancer. Clinicians should be cognizant of the data about breast cancer risk, breast density, and recommendations to change screening techniques if patients, particularly premenopausal females, have extremely dense breasts but no other known risk factors.
Using ultrasound to identify adnexal masses
Authors: McConnell Michael , Strelow Brittany
Published: September 2024

This article describes the use of ultrasound in the initial diagnosis of a patient with a pelvic mass. CT commonly is used to detect ovarian cancer, especially when the patient has nonspecific symptoms; ultrasound also can be used as a follow-up procedure after an abdominal ultrasound reveals suspicious findings.
Early combined arthroscopic and open management of combined ACL and PCL tibial spine avulsion in a knee dislocation: A case report
Authors: Davis Ashton , Lindeman Robert W.
Published: September 2024

A 35-year-old man presented with right knee pain following a tree stump landing on his leg two days prior. Evaluation revealed a knee dislocation injury (KD III M) with displaced avulsion fractures of the anterior cruciate ligament and posterior cruciate ligament, with the fragments flipped 180 degrees. Additional injuries identified through preoperative imaging (computer tomography, magnetic resonance imaging) and physical examination included bony medial patellofemoral ligament tear, bony posterolateral corner injury, complete medial collateral ligament tear, and medial/lateral meniscus root bony avulsions. The injury was treated utilizing a single-staged arthroscopic and open ligament repair and reconstruction. Bicruciate avulsion fractures in the setting of a knee dislocation injury is a challenging surgical problem in which arthroscopic management of bicruciate tibial spine injuries can be utilized successfully.
Global burden of lung cancer in 2022 and projected burden in 2050
Authors: Guo Lanwei , Zhu Chenxin , Cai Lin , Zhang Xinglong , Fang Yi , Chen Hongda , Yang Haiyan
Published: September 2024

Background:

Lung cancer is the most common cancer and a leading cause of cancer-related deaths globally. The aim of this study was to evaluate the incidence and mortality of lung cancer worldwide in 2022 and to project the number of new cases and deaths due to lung cancer in China and the United States in 2050.

Methods:

In this study, data from the GLOBCAN 2022 database were used to analyze lung cancer incidence and mortality. The current status of lung cancer incidence and deaths was described by country/region, sex, age, and the human development index (HDI), and future lung cancer incidence and deaths in China and the United States were projected for 2050.

Results:

Globally, an estimated 2,480,675 new lung cancer cases and 1,817,469 lung cancer-related deaths occurred in 2022, with age-standardized incidence rates (ASIRs) and age-standardized mortality rates (ASMRs) of 23.6/100,000 and 16.8/100,000, respectively. In China, the ASIR and ASMR for male lung cancer patients were approximately 1.7 times and 2.7 times greater than those for female lung cancer patients, respectively. The ASIR and ASMR in high-HDI countries were approximately 8.5 times and 6.5 times those in low-HDI countries, respectively. It is estimated that in 2050, there will be approximately 1120 thousand new cases and 960 thousand deaths among Chinese men, 680 thousand new cases and 450 thousand deaths among Chinese women, approximately 170 thousand new cases and 110 thousand deaths among American men, and 160 thousand new cases and 90 thousand deaths among American women.

Conclusions:

There are significant differences in the incidence and mortality of lung cancer among different regions and sexes. Therefore, sex factors need to be considered in the prevention, screening, and treatment strategies of lung cancer, and the implementation of tertiary prevention measures for lung cancer, especially primary and secondary prevention, needs to be actively promoted.