bluuebunny/crossref_metadata_2025 huggingface dataset:
Multisensory healing: transformative service encounters in nonpharmacological therapies for cancer patients’ well-being
Authors: Rezaee Vessal Saeedeh , El Euch Maalej Mariem , Partouche-Sebban Judith , Toledano Alain
Published: October 2024

Purpose

This study aims to explore the impact of nonpharmacological therapies on cancer patients’ daily illness management and long-term well-being. It focuses on the design and effects of immersive multisensory workshops, including therapies such as yoga, music therapy and visual imagery. By examining individuals’ experiences before, during and after the service experience, the study aims to provide comprehensive insights into the transformative effects of these immersive multisensorial experiences from the individuals’ perspectives.

Design/methodology/approach

From November 2021 to March 2023, the authors conducted 13 interviews and 3 focus groups (10 participants in total) among cancer patients. Thematic analysis of recorded interviews and focus groups revealed recurring patterns, key themes and meaningful insights from participants’ narratives.

Findings

The findings provide insights into individuals’ journey of service experiences among cancer patients from a user perspective. By framing the results within the service encounters model, individuals’ journey of this immersive multisensory experience is studied in three different periods: the pre-core, the core and the post-core service encounter. The pre-core service encounter includes activities such as information gathering to answer concerns and setting expectations, with the therapy. The core service encounter encompasses the immersive environmental experience, which includes multisensory integration and activity immersion, body-mind reconnection, as well as engaging interactive experiences with service providers, other patients and internal engagement. The post-core service encounter reflects the cognitive, psychological, behavioral and spiritual outcomes of the service.

Originality/value

This paper sheds light on the design of immersive multisensory workshops as nonpharmacological therapy. Adopting a user-focused approach using the service encounters framework helps clarify various aspects of this therapy and its effects on patients’ reconnection with their bodies and well-being. This research offers valuable insights for designing effective multisensory therapeutic environments for chronic patients to improve the quality of health-care services.
Arginine metabolism is a biomarker of red blood cell and human aging
Authors: Reisz Julie A. , Earley Eric J. , Nemkov Travis , Key Alicia , Stephenson Daniel , Keele Gregory R. , Dzieciatkowska Monika , Spitalnik Steven L. , Hod Eldad A. , Kleinman Steven , Roubinian Nareg H. , Gladwin Mark T. , Hansen Kirk C. , Norris Philip J. , Busch Michael P. , Zimring James C. , Churchill Gary A. , Page Grier P. , D'Alessandro Angelo
Published: October 2024

Increasing global life expectancy motivates investigations of molecular mechanisms of aging and age‐related diseases. This study examines age‐associated changes in red blood cells (RBCs), the most numerous host cell in humans. Four cohorts, including healthy individuals and patients with sickle cell disease, were analyzed to define age‐dependent changes in RBC metabolism. Over 15,700 specimens from 13,757 humans were examined, a major expansion over previous studies of RBCs in aging. Multi‐omics approaches identified chronological age‐related alterations in the arginine pathway with increased arginine utilization in RBCs from older individuals. These changes were consistent across healthy and sickle cell disease cohorts and were influenced by genetic variation, sex, and body mass index. Integrating multi‐omics data and metabolite quantitative trait loci (mQTL) in humans and 525 diversity outbred mice functionally linked metabolism of arginine during RBC storage to increased vesiculation—a hallmark of RBC aging—and lower post‐transfusion hemoglobin increments. Thus, arginine metabolism is a biomarker of RBC and organismal aging, suggesting potential new targets for addressing sequelae of aging.
Neurological dysfunction and fatal encephalitis due to Halicephalobus gingivalis in two horses in Belgium
Authors: Calewaert A. , Dufourni A. , Stee K. , Hiltrop R. , Raes E. , van Loon G.
Published: October 2024

Two horses kept on different farms at a geographical distance of 150 km were presented with acute neurological dysfunction. Ante‐mortem diagnostic tests including bloodwork, CT scan and cerebrospinal fluid analysis did not provide a diagnosis in either case. Due to rapid deterioration, both horses were euthanised shortly after admission. Postmortem histopathological examination revealed granulomatous meningoencephalitis with intralesional nematodes that were morphologically identified as Halicephalobus gingivalis. This is the first documentation of central nervous system infestation by H. gingivalis in horses residing in Belgium, emphasising the importance of considering aberrant parasitic migration in the differential diagnosis of acute neurological dysfunction.
Characterisation of δ142Ce/140Ce Isotope Ratios in Geological Reference Materials using an SSB+Sm Doping and MC‐ICP‐MS Method
Authors: Wu Jiaojiao , An Yajun , Li Xin , Liu Fang , Xu Jianbing , Ling Mingxing , Zhang Zhaofeng
Published: October 2024

We report the δ142/140Ce values for thirty‐three widely available geological reference materials (RMs), including igneous rocks, metamorphic rocks, sediments and soils. The Ce isotope ratios of twenty‐two Chinese RMs are reported for the first time. After chemical purification using TODGA resin (50–100 μm, Eichrom, USA), Ce isotope measurements of these RMs were conducted by multi‐collector inductively coupled plasma‐mass spectrometry (MC‐ICP‐MS) with a combined standard‐sample bracketing (SSB) and Sm‐doping technique. The data quality of the Ce isotope results was assessed by repeated measurement of pure Ce reference solutions (NIST SRM 3110, JMC304, CDUT‐Ce) and well‐characterised geological RMs (BHVO‐2, BCR‐2, Nod‐A‐1, Nod‐P‐1, etc.). Our results are in excellent agreement with previously reported values within intermediate measurement precision (±0.04‰, 2s). The igneous rock and soil RMs showed limited variations in δ142/140Ce values, which ranged from ‐0.036 ± 0.018‰ to 0.062 ± 0.046‰ and ‐0.015 ± 0.015‰ to 0.029 ± 0.009‰, respectively. The river/marine sediments and Mn nodules displayed variable Ce isotope ratios ranging from ‐0.005 ± 0.018‰ to 0.141 ± 0.023‰, suggesting detectable Ce isotopic fractionation during low‐temperature processes.
Hypothalamic–pituitary–adrenal axis plasticity across life‐history stages of a free‐living subtropical finch, Amandava amandava amandava
Authors: Mohanty Banalata
Published: October 2024

The alterations of phenotypic traits (morphology, endocrine physiology, and behavior) in response to predictable environmental cues across life‐history stages in seasonally breeding birds enable successful culmination of reproduction. The present study elucidated the plasticity of the hypothalamic–pituitary–adrenal (HPA) axis in a subtropical free‐living finch, Amandava amandava amandava, and suggests the crucial role of the baseline corticosterone (CORT) to coordinate energetic readiness across life‐history stages. Birds were captured monthly from an area (25.1337° N 82.5644° E) in Uttar Pradesh, India, from June 2014 to May 2015. Only male birds were included in this study corresponding to different life‐history stages (6/life‐history stage; 2/month): pre‐breeding (June–August), breeding (September–November), post‐breeding (December–February), and quiescent phases (March–May). The pituitary expression of adrenocorticotropic hormone (ACTH), adrenal interrenal cell morphometry, and plasma level of the CORT showed varied patterns across life‐history stages. The density and immunointensity of the ACTH‐immunoreactive corticotropes and the interrenal cell number increased along with the significant plasma CORT elevation during the breeding cycle (both pre‐breeding and breeding phases). CORT might facilitate the energy demand for the display of sexual behavior (nest‐building, courtship), testicular recrudescence, and foraging of food for offspring during the breeding cycle. On the contrary, plasma CORT decrease in the post‐breeding and quiescent phases might enable the bird to molt avoiding the protein catabolic effect of the hormone. Given the complexity involved in the study of baseline CORT in free‐living birds, more studies are needed to better understand the crucial role of the HPA axis in the modulation of life‐history stages in this and other subtropical avian species.
Menstrual blood‐derived mesenchymal stem cells combining with platelet‐rich plasma infusion in endometrium repair
Authors: Wang Yang , Liu Wenxin , Xu Hui , Dong Liyuan , Jiao Yalou , Qiao Zhe
Published: October 2024

Objective

Thin endometrium caused by various factors affects the conception rate of females worldwide; however, current medications are still insufficient. Therefore, a novel approach is needed. We previously reported the effect of menstrual blood‐derived mesenchymal stem cells (MenSCs) in ameliorating ethanol‐induced endometrial injuries. In the present study, we aimed to investigate whether the effect of MenSCs is enhanced by a combination of platelet‐rich plasma (PRP) infusion.

Methods

An endometrial injury mouse model was established by infiltrating 95% ethanol for 15 s into the uterus, followed by MenSCs, PRP, or MenSCs + PRP treatment. Pathological changes were observed by HE staining. The expression of CK18, vimentin, ItgαVβ3, and VEGF was determined using IHC staining and WB blotting.

Results

Compared with the model, MenSCs, PRP, and MenSCs + PRP treatments significantly improved endometrial damage and thickness, with the combined therapy displaying the most pronounced efficacy. The density of CK18‐, vimentin‐, and ItgαVβ3 positive cells increased most significantly in the MenSCs + PRP group of mice. In addition, the protein expression of CK18, vimentin, and VEGF was significantly upregulated after MenSCs + PRP, MenSCs, and PRP treatment, with MenSCs + PRP therapy showing the best efficacy.

Conclusion

MenSCs + PRP therapy is more beneficial for ameliorating ethanol‐induced endometrial damage than MenSCs or PRP alone, providing a basis for the investigation of novel approaches for treating thin endometria.
Clozapine and objective assessment of hypersomnolence in patients with schizophrenia: a systematic review
Authors: Quiles Clélia , Taillard Jacques , Lopez Régis , Geoffroy Pierre Alexis , Salvo Francesco , Micoulaud‐Franchi Jean‐Arthur
Published: October 2024

Clozapine is effective in treatment‐resistant schizophrenia but with adverse effects including sedation. Excessive daytime sleepiness, a symptom of hypersomnolence, is the most frequently reported subjective side‐effect. The aim of this systematic review was to synthesise the literature evaluating the impact of clozapine on the objective assessment of hypersomnolence in people with schizophrenia. We systematically searched databases for articles evaluating hypersomnolence with electrophysiological or psychomotor/cognitive measures in clozapine‐treated patients with schizophrenia. Objective assessment of hypersomnolence was evaluated in six studies. All studies using polysomnography (PSG) found significantly longer total sleep time and shorter sleep onset latency in patients treated with clozapine at initiation of clozapine. The study with the multiple sleep latency test (MSLT) also found a shorter sleep onset latency. These observations did not persist 4–6 weeks after treatment initiation. Further investigations are needed. Longer total sleep time should be investigated with standardised long‐term PSG to investigate excessive sleep quantity. Shorter sleep onset latency should be investigated with the MSLT or the maintenance of wakefulness test to investigate the excessive propensity to fall asleep or ability to stay awake. Lastly, sleep inertia should be investigated specifically in the morning.
Do pregnant women with restless legs syndrome experience better sleep with physical activity?
Authors: Esteves Andrea Maculano , Hackethal Sandra , Riccardi Silvia , Garbazza Corrado , Manconi Mauro
Published: October 2024

Pregnant women benefit greatly from exercise due to its powerful impact on maternal and perinatal outcomes. The purpose of our study was to assess whether exercise improves objective sleep quality in pregnant women suffering from restless legs syndrome. This cross‐sectional study is based on data from a large, naturalistic, consecutive cohort study in pregnant women recruited by four sleep centres, in Bologna, Milan and Turin (Italy), and Lugano (Switzerland), named the Life‐ON study. Objective sleep parameters of 316 pregnant women were measured using polysomnographic recordings during the second trimester of pregnancy, and a self‐reported assessment was used to evaluate physical activity. Pregnant women with restless legs syndrome (n = 91) who engaged in physical activity (n = 28) experienced better sleep efficiency (84.20% versus 82.10%, p = 0.01), less stage 1 sleep (10.50% versus 11.40%, p = 0.04) and wake after sleep onset (52.20 min versus 76.40 min, p ≤ 0.001), as well as reduced periodic leg movements during sleep (5.50 per hr versus 16.40 per hr, p < 0.001) when compared with the sedentary restless legs syndrome group (n = 63). Sleep structure was also better conserved in physically active pregnant women without restless legs syndrome compared with the inactive restless legs syndrome negative group. Overall, this study provides further evidence of the benefits of physical activity in pregnant women by illustrating its positive impact on sleep structure.
Management of 10 Children With Inflammatory Rosacea With Topical Ivermectin
Authors: Dall'Oglio Federica , Nasca Maria Rita , Tedeschi Aurora , Nicotra Francesco , Micali Giuseppe
Published: October 2024

Rosacea diagnosis and treatment in children are challenging, due to its rarity and to the lack of approved pharmacological agents for its treatment in this age group. In this case series, response to treatment with once daily applications of ivermectin (IVM) 1% cream for 12 weeks in 10 children affected by mild to severe inflammatory rosacea was evaluated clinically by Investigator Erythema Severity Assessment (IESA), Investigator Global Assessment of Severity (IGA‐S), Investigator Global Assessment score of Global Efficacy (IGA‐GE), and instrumentally by dermoscopy and Erythema‐Directed Digital Photography (EDDP). Clinical improvement was achieved at the end of treatment compared to baseline (IESA: 2.3 vs. 0.5; IGA‐S: 2.1 vs. 0.3) and confirmed by IGA‐GE (0 = 55%, 1 = 33%, 3 = 11%) and instrumental monitoring (EDDP: 2.7 vs. 0.6). Once daily IVM application may be an effective therapeutic option for children with rosacea.
Deciphering the role of growth regulators in enhancing plant immunity against herbivory
Authors: Singh Archana , Yajnik Kalpesh Nath , Mogilicherla Kanakachari , Singh Indrakant K.
Published: October 2024

Plants are central to global food production, and the pursuit of sustainability aims to enhance or preserve food quality while safeguarding the environment. Due to their immobility, plants are unable to evade unfavourable climatic setups or interactions with other living creatures. Upon their interaction with insect herbivores, plants face biotic stress, which is a constant challenge for plants, causing molecular, physiological, and biochemical changes and reducing their productivity. To combat biotic stress caused by herbivores, plants have evolved intricate defence mechanisms through growth regulators such as auxins, cytokinins, gibberellins, salicylic acid (SA), jasmonic acid (JA), ethylene (ET), abscisic acid (ABA), strigolactones and brassinosteroids. The intricate network of specific proteins, metabolites and certain phytohormones orchestrates plant defensive reactions, leading to their skilful coordination in responding to insect attacks. Comprehending the defence mechanisms holds the key to mitigating significant crop and economic losses. This review entails a comprehensive analysis of the role of growth regulators in enhancing plant immunity against herbivory, highlighting the substantial efforts by the scientific community to manage and mitigate damages from biotic stress in plants, ultimately contributing to the advancement of sustainable agriculture.
Allele‐specific micro‐RNA‐mediated regulation of ADAM33 in childhood allergic asthma
Authors: Wen Xiang , Zhou Juan , Fang Heping , Li Juan , Wang Run , Zeng Dan , Xie Xiaohong , Deng Yu , Ren Luo , Liu Enmei
Published: October 2024

Background and Objective

A disintegrin and metalloprotease 33 (ADAM33) is associated with asthma susceptibility, and its genetic variations impact susceptibility and disease severity. However, the mechanisms remain unclear. This study aimed to investigate ADAM33 single nucleotide polymorphisms (SNPs) in childhood asthma susceptibility and explore their regulatory mechanisms.

Methods

Eleven selected SNPs in ADAM33 were genotyped and identified the association with asthma susceptibility. In the validation cohort, we measured plasma sADAM33 levels and compared them with disease severity among children with different SNP genotypes. Computational predictions identified miRNAs targeting the SNP, and the impact of the SNP on miRNA regulation was confirmed using a dual luciferase reporter system. Finally, we validated the regulatory role of miRNAs on ADAM33 expression using an in vitro model with upregulated ADAM33 expression.

Results

Only rs3918400 was associated with asthma susceptibility. In the validation cohort, children with allergic asthma exhibited higher plasma sADAM33 levels. Among asthmatic children, those with the rs3918400 CT/TT genotype had higher sADAM33 levels, poorer asthma control, more severe airway hyper‐responsiveness, lower FEV1% and higher dust mite‐specific IgE activity compared to those with the CC genotype. miR‐3928‐5p bound strongly to the rs3918400 C allele and effectively reduced ADAM33 protein expression in CC genotype cells. However, the binding affinity of miR‐3928‐5p to the T allele was weaker, resulting in diminished negative regulation of protein expression.

Conclusion

The rs3918400 SNP affects the negative regulation of ADAM33 by miR‐3928‐5p, potentially participating in a complex interplay of processes related to childhood asthma susceptibility.
New records and complementary description of four species of Phytoseiidae (Acari: Mesostigmata) from India
Authors: Jose Anna , Döker Ismail , Gowda Channegowda Chinnamade , Kreiter Serge , Bhullar Manmeet Brar , Mulimani Vidya
Published: October 2024

The study reports four new records of phytoseiid mites from the Indian subcontinent. Detailed description of all the four species viz., Cydnoseius negevi (Swirski & Amitai), Gynaeseius liturivorus (Ehara), Okiseius subtropicus Ehara, and Phytoseius haroldi Ueckermann & Kreiter is provided in this paper along with illustrations and comparison of specimens collected in the present study with those of the previous reports.
Resistance ratios and enzyme activity of Tetranychus urticae and Tetranychus turkestani (Acari: Tetranychidae) to commonly used acaricides on cotton in Aydin province, Türkiye
Authors: Güler Duran Selin , Özyılmaz Ümit , Ay Recep , Touray Mustapha , Kazak Cengiz , Saboori Alireza , Cakmak Ibrahim
Published: October 2024

This study aims to determine the resistance ratios of Tetranychus urticae Koch red form (RF) and Tetranychus turkestani (Ugarov & Nikolskii) populations collected from cotton fields in Soke, Germencik, Kocarli and Nazilli districts of Aydin province to commonly used acaricides (abamectin, hexythiazox, etoxazole, spiromesifen). The potential role of detoxification enzymes (esterase, glutathione-s-transferase (GST), P450 monooxygenase (P450)) in acaricide resistance was also assessed. Overall populations of T. urticae RF presented varying ratios of resistance to these acaricides with all three populations (G15R21, K24R21, S3R21) showing significant resistance to abamectin (187.1–223.66 fold), hexythiazox (156.31–168.25 fold), etoxazole (409.58–517.20 fold) and spiromesifen (981.77–1246.11 fold). In contrast, all five T. turkestani populations (G4G21, K16G21, N1G21, N11G21, S19G21) were susceptible to abamectin, etoxazole, and spiromesifen, but exhibited some resistance to hexythiazox (164.34–182.39 fold). The resistance ratios of T. turkestani were however lower compared to T. urticae RF. A relationship was also found between detoxification enzymes and resistance. Esterase activity varied among mite populations, with the highest levels recorded in resistant populations of T. urticae (G15R21 and K24R219) with rates ranging between 6.48 and 7 mOD/min/mg protein. GST activity was highest in resistant mite populations (T. urticae S3R21 and T. turkestani K16G21). T. turkestani N11G21 population exhibited the highest P450 enzyme activity, reaching 4.39 RFU/30 min/mg protein. This study was the first to determine the resistance ratios of T. turkestani to hexythiazox in Türkiye, and on a global scale.
First report of the genera Neotegonotus Newkirk & Keifer and Boczekiana Petanovic (Acari: Eriophyidae: Phyllocoptinae) from Saudi Arabia with the description of two new species
Authors: Khan Eid Muhammad , Kamran Muhammad , Alatawi Fahad
Published: October 2024

Two genera, Neotegonotus Newkirk & Keifer and Boczekiana Petanovic (Eriophyidae: Phyllocoptinae) are recorded for the first time from Saudi Arabia with two new species; N. saudiensis sp. nov. collected from Ficus carica L. (Moraceae) and B. bahahensis sp. nov. collected from Anthemis rascheyana Boiss (Asteraceae) described and illustrated based on females. Both species are vagrants on abaxial leaf surface causing no apparent damage to their host plants.
Group 2 innate lymphoid cells promote inhibitory synapse development and social behavior
Authors: Barron Jerika J. , Mroz Nicholas M. , Taloma Sunrae E. , Dahlgren Madelene W. , Ortiz-Carpena Jorge F. , Keefe Matthew G. , Escoubas Caroline C. , Dorman Leah C. , Vainchtein Ilia D. , Chiaranunt Pailin , Kotas Maya E. , Nowakowski Tomasz J. , Bender Kevin J. , Molofsky Ari B. , Molofsky Anna V.
Published: October 2024

The innate immune system shapes brain development and is implicated in neurodevelopmental diseases. It is critical to define the relevant immune cells and signals and their impact on brain circuits. In this work, we found that group 2 innate lymphoid cells (ILC2s) and their cytokine interleukin-13 (IL-13) signaled directly to inhibitory interneurons to increase inhibitory synapse density in the developing mouse brain. ILC2s expanded and produced IL-13 in the developing brain meninges. Loss of ILC2s or IL-13 signaling to interneurons decreased inhibitory, but not excitatory, cortical synapses. Conversely, ILC2s and IL-13 were sufficient to increase inhibitory synapses. Loss of this signaling pathway led to selective impairments in social interaction. These data define a type 2 neuroimmune circuit in early life that shapes inhibitory synapse development and behavior.
Cooperative adsorbate binding catalyzes high-temperature hydrogen oxidation on palladium
Authors: Schwarzer Michael , Borodin Dmitriy , Wang Yingqi , Fingerhut Jan , Kitsopoulos Theofanis N. , Auerbach Daniel J. , Guo Hua , Wodtke Alec M.
Published: October 2024

Atomic-scale structures that account for the acceleration of reactivity by heterogeneous catalysts often form only under reaction conditions of high temperatures and pressures, making them impossible to observe with low-temperature, ultra-high-vacuum methods. We present velocity-resolved kinetics measurements for catalytic hydrogen oxidation on palladium over a wide range of surface concentrations and at high temperatures. The rates exhibit a complex dependence on oxygen coverage and step density, which can be quantitatively explained by a density functional and transition-state theory–based kinetic model involving a cooperatively stabilized configuration of at least three oxygen atoms at steps. Here, two oxygen atoms recruit a third oxygen atom to a nearby binding site to produce an active configuration that is far more reactive than isolated oxygen atoms. Thus, hydrogen oxidation on palladium provides a clear example of how reactivity can be enhanced on a working catalyst.
Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome
Authors: Rogalska Malgorzata E. , Mancini Estefania , Bonnal Sophie , Gohr André , Dunyak Bryan M. , Arecco Niccolò , Smith Peter G. , Vaillancourt Frédéric H. , Valcárcel Juan
Published: October 2024

The spliceosome is the complex molecular machinery that sequentially assembles on eukaryotic messenger RNA precursors to remove introns (pre-mRNA splicing), a physiologically regulated process altered in numerous pathologies. We report transcriptome-wide analyses upon systematic knock down of 305 spliceosome components and regulators in human cancer cells and the reconstruction of functional splicing factor networks that govern different classes of alternative splicing decisions. The results disentangle intricate circuits of splicing factor cross-regulation, reveal that the precise architecture of late-assembling U4/U6.U5 tri–small nuclear ribonucleoprotein (snRNP) complexes regulates splice site pairing, and discover an unprecedented division of labor among protein components of U1 snRNP for regulating exon definition and alternative 5′ splice site selection. Thus, we provide a resource to explore physiological and pathological mechanisms of splicing regulation.
Policy evaluation and the causal analysis of public support
Authors: Carattini Stefano , Dur Robert , List John
Published: October 2024

Support for initially unpopular policies may grow over time
A solution to the anti-Bredt olefin synthesis problem
Authors: McDermott Luca , Walters Zach G. , French Sarah A. , Clark Allison M. , Ding Jiaming , Kelleghan Andrew V. , Houk K. N. , Garg Neil K.
Published: October 2024

The π-bonds in unsaturated organic molecules are typically associated with having well-defined geometries that are conserved across diverse structural contexts. Nonetheless, these geometries can be distorted, leading to heightened reactivity of the π-bond. Although π-bond–containing compounds with bent geometries are well utilized in synthetic chemistry, the corresponding leveraging of π-bond–containing compounds that display twisting or pyramidalization remains underdeveloped. We report a study of perhaps the most notorious class of geometrically distorted molecules that contain π-bonds: anti-Bredt olefins (ABOs). ABOs have been known since 1924, and conventional wisdom maintains that ABOs are difficult or impossible to access. We provide a solution to this long-standing problem. Our study also highlights the strategic manipulation of compounds that display considerable distortion arising from the presence of geometrically constrained π-bonds.
Exploring structural diversity across the protein universe with The Encyclopedia of Domains
Authors: Lau Andy M. , Bordin Nicola , Kandathil Shaun M. , Sillitoe Ian , Waman Vaishali P. , Wells Jude , Orengo Christine A. , Jones David T.
Published: October 2024

The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enable many functional and evolutionary analyses but has remained challenging because of the sheer scale of the data. Using deep learning methods, we have detected and classified every domain in the AFDB, producing The Encyclopedia of Domains. We detected nearly 365 million domains, over 100 million more than can be found by sequence methods, covering more than 1 million taxa. Reassuringly, 77% of the nonredundant domains are similar to known superfamilies, greatly expanding representation of their domain space. We uncovered more than 10,000 new structural interactions between superfamilies and thousands of new folds across the fold space continuum.
Passive materials–based solutions for cool and “radiant” cities
Authors: Yin Xiaobo
Published: October 2024

Tokyo, the most populous city in the world and known for its mild northern climate, reached a record-high temperature of over 35°C in September 2024. Earlier this year, a heat wave swept through South America, with Rio de Janeiro, Brazil, experiencing a staggering heat index of 62.3°C. In May, Delhi, India, saw temperatures soar above 50°C. I recently moved to another densely populated city, Hong Kong, a gateway to mainland China. This high-density city has shattered its temperature records every summer for the past 3 years.
Population dynamics of defective viral genomes of tomato black ring virus during host-to-host transmission
Authors: Budzyńska Daria , Minicka Julia , Olmo-Uceda María J. , Elena Santiago F. , Hasiów-Jaroszewska Beata
Published: October 2024

Defective viral genomes (DVGs) emerge during error-prone replication of viral genomes and contain deletions, insertions, genomic rearrangements, and hypermutations. These large-effect mutations result in the inability of DVGs to complete an infectious cycle in the absence of a helper wild-type virus. It has been shown that
in vitro
DVGs usually accumulate in viral populations when a virus is serially passaged in the same host at a high multiplicity of infection. To investigate the impact of host-to-host transmission on DVG formation and population dynamics
in vivo
, we conducted evolution experiments with tomato black ring virus (TBRV). TBRV was sequentially passaged through a combination of four distinct host species: quinoa, tobacco, lettuce, and spinach. The host was changed every fifth passage. The diversity and population dynamics of DVGs were analyzed based on the RNA-Seq data obtained through sequencing of viral RNA after 20 passages. Our findings indicate the possibility of TBRV DVGs generation when the virus was passaged through different host species. The level of DVG abundance varied across host plant combinations, with a weak indication that the host species past sequence may play a role in DVGs generation. Most abundant DVGs in the TBRV evolved populations were derived from RNA1. Deletions were the most prevalent class of DVGs, followed by insertions. The deletion DVG subpopulation exhibited substantial diversity in species composition and the richness of the deletions species was correlated with their abundance. Longer DVGs characterized by small deletions were predominant, whereas those shorter than 1,000 nucleotides constituted less than 2%.

IMPORTANCE

Defective viral genomes (DVGs) have been identified
in vivo
and
in vitro
for different virus species infecting humans, animals, and plants. The ability to form DVGs during the passaging of virus in one host has been demonstrated, i.e., for tomato black ring virus (TBRV). In our research, RNA-Seq data obtained after TBRV passaging through a combination of four distinct host species were analyzed. Our results indicate that the level of DVG abundance varied across host plant combinations. Deletions were the most prevalent class of DVGs, with the domination of longer species. Additionally, the conserved junction sites in the TBRV genome were identified, resulting in the generation of identical deletions in independently evolved viral lineages. In summary, our findings provide significant insights into the origin and structure of DVGs of plant viruses. The obtained results will help in understanding viral evolution and host-virus interactions.
Host species-specific activity of the poxvirus PKR inhibitors E3 and K3 mediate host range function
Authors: Haller Sherry L. , Park Chorong , Bruneau Ryan C. , Megawati Dewi , Zhang Chi , Vipat Sameera , Peng Chen , Senkevich Tatiana G. , Brennan Greg , Tazi Loubna , Rothenburg Stefan
Published: October 2024

The antiviral protein kinase R (PKR) is activated by viral double-stranded RNA and phosphorylates translation initiation factor eIF2α, thereby inhibiting translation and virus replication. Most poxviruses contain two PKR inhibitors, called E3 and K3 in vaccinia virus (VACV), which are determinants of viral host range. The prevailing model for E3 function is that it inhibits PKR through the non-specific sequestration of double-stranded (ds) RNA. Our data revealed that Syrian hamster PKR was resistant to E3, which is at odds with the sequestration model. However, Syrian hamster PKR was still sensitive to K3 inhibition. In contrast, Armenian hamster PKR showed opposite sensitivities, being sensitive to E3 and resistant to K3 inhibition. Mutational analyses of hamster PKRs showed that sensitivity to E3 inhibition was largely determined by the region linking the dsRNA-binding domains and the kinase domain of PKR, whereas two amino acid residues in the kinase domain (helix αG) determined sensitivity to K3. The expression of PKRs in congenic cells showed that Syrian hamster PKR containing the two Armenian hamster PKR residues in helix αG was resistant to wild-type VACV infection and that cells expressing either hamster PKR recapitulated the phenotypes observed in species-derived cell lines. The observed resistance of Syrian hamster PKR to E3 explains its host range function and challenges the paradigm that dsRNA-binding PKR inhibitors mainly act by the sequestration of dsRNA.

IMPORTANCE

The molecular mechanisms that govern the host range of viruses are incompletely understood. We show that the host range functions of E3 and K3, two host range factors from vaccinia virus, are a result of species-specific interactions with the antiviral protein kinase R (PKR) and that PKR from closely related species displayed dramatic differences in their sensitivities to these viral inhibitors. The current model for E3-mediated PKR inhibition is that E3 non-specifically sequesters double-stranded (ds) RNA to prevent PKR activation. This model does not predict species-specific sensitivity to E3; therefore, our data suggest that the current model is incomplete and that dsRNA sequestration is not the primary mechanism for E3 activity.
IGFBP6 Modulates Proteostasis by Activating ATF4 Targets and Reducing ER Retrotranslocon Expression
Authors: Kolodeeva O. E. , Kolodeeva O. E. , Antipenko I. D. , Fatkulin A. A. , Yakhina M. R. , Makarova J. A.
Published: October 2024

Reduced expression of the IGFBP6 protein leads to an increase in the metastatic potential of breast cancer (BC) cells. The level of protein synthesis in tumor cells is increased, leading to a compensatory adjustment of proteostasis. One of the tools used to study proteostasis is protein toxins of the RIP-II family, which irreversibly inactivate ribosomes (particularly, viscumin). We investigated the effect of IGFBP6 gene knockdown on the proteostasis in the BC cell line MDA-MB-231. Ribosomes from MDA-MB-231IGFBP6 cells, knockdown for the IGFBP6 gene, are less efficiently modified by the toxin. This is probably due to the reduced transport of the viscumin catalytic subunit from the ER to the cytoplasm. MDA-MB-231IGFBP6 cells showed reduced expression of the retrotranslocon HRD1/Derlin subunit, which is a component of the ER-associated protein degradation system (ERAD). For ATF4 transcription factor, which is a part of the ER unfolded protein response (UPR) pathway, an increased expression of its targets was found.
Effects of Silver Citrate Prolonged Exposure on Behavioral and Cognitive Functions of Mice
Authors: Antsiferova A. A. , Kopaeva M. Yu. , Kashkarov P. K.
Published: October 2024

Pure silver as well as silver compounds have been used as antiseptics for centuries. Nowadays, the most frequently applied silver compounds are silver nanoparticles. Several studies demonstrate the ability of silver nanoparticles and silver salts to accumulate in the brain of laboratory animals as well as the ability of silver nanoparticles to influence behavioral and cognitive functions of laboratory mammals. For the first time, the influence of silver citrate on the change dynamics of behavioral and cognitive functions of laboratory mice at the daily oral exposure during 30, 60, 120, and 180 days were investigated in the present research. We observed the anxiety increase after 30 days of the exposure as well as the ability of mice to adapt to the prolonged oral exposure of silver citrate manifested in the anxiety decrease, increase of locomotor activity and the tendency of long-term contextual memory improvement at the further stages of the experiment. Increase of locomotor activity and memory improvement might be associated with the sensitivity increase and regarded as compensatory mechanism to anxiety increase. The observed phenomenon is classified as a hormetic effect. A comparison with the analogous study, which implemented polyvinylpyrrolidone coated silver nanoparticles, is carried out. It was concluded that the nanoscale impacts into the toxicity of silver compound.
Fusions in salivary gland neoplasms: a review of practical diagnostic applications
Authors: Bishop Justin A
Published: October 2024

There is an ongoing explosion of new information regarding the underlying molecular alterations driving a variety of salivary gland neoplasms. The volume of this emerging data makes it difficult to keep up with and may cause pathologists to believe that salivary gland neoplasms cannot be diagnosed without genetic analysis. This review focuses on the practical diagnostic applications of molecular tools in surgical pathology specimens.
Assessment of the quality of full-depth reclamation (FDR) using a dynamic cone penetrometer (DCP): a case study
Authors: Lamothe Sébastien , Rinieri Manon , Vaillancourt Michel , Lachance-Tremblay Éric
Published: October 2024

The full-depth reclamation with no stabilization (FDR-NS) is widely used as a pavement rehabilitation technique. It is important to evaluate the on-site characteristics of FDR-NS materials to avoid short-term underperformance. The need for performance-based testing could then be supported by in situ and non-destructive testing, such as dynamic cone penetrometer (DCP). DCP allows to estimate the bearing capacity of the pavement structure and to verify its homogeneity according to the depth. The objective of this research is to evaluate the applicability of using DCP to assess the quality of FDR-NS. Overall, DCP results showed a good reliability, allows to measure the effective depth of reclamation and to observe a significant reduction (average of 75%), in terms of DCP values, between before and after the reclamation (FDR) process. Thus, the potential of using DCP for FDR-NS rehabilitation was confirmed. The results from this research provide a rational basis for establishing specifications.
Progress in Trapped-Ion Quantum Simulation
Authors: Foss-Feig Michael , Pagano Guido , Potter Andrew C. , Yao Norman Y.
Published: October 2024

Trapped ions offer long coherence times and high fidelity, programmable quantum operations, making them a promising platform for quantum simulation of condensed matter systems, quantum dynamics, and problems related to high-energy physics. We review selected developments in trapped-ion qubits and architectures and discuss quantum simulation applications that utilize these emerging capabilities. This review emphasizes developments in digital (gate-based) quantum simulations that exploit trapped-ion hardware capabilities, such as flexible qubit connectivity, selective mid-circuit measurement, and classical feedback, to simulate models with long-range interactions, explore nonunitary dynamics, compress simulations of states with limited entanglement, and reduce the circuit depths required to prepare or simulate long-range entangled states.
Effects of two carbonic anhydrase inhibitors on exercise performance in acute hypoxia
Authors: Chang Jou-Chung , Thompson Benjamin P. , Doherty Connor J. , Mann Leah M. , Berdeklis Antonia N. , Foster Glen E. , Tupling A. Russell , Swenson Erik R. , Dominelli Paolo B.
Published: October 2024

Administration of acetazolamide (AZ) and methazolamide (MZ) both resulted in a significantly slower 5-km time trial in acute normobaric hypoxia compared with a placebo. Both drugs lead to a partially compensated metabolic acidosis, but ventilation and oxyhemoglobin saturation were not different across the conditions. Overall, acetazolamide and methazolamide both impaired whole body exercise performance in acute normobaric hypoxia but potentially have different mechanisms of action.
Disparities in Cancer Stage Shifts Associated with the COVID-19 Pandemic in California, 2020 to 2021
Authors: Wang Katarina , Canchola Alison J. , McKinley Meg , Guan Alice , Vu Annie , Lin Katherine , Meltzer Dan , Dixit Niharika , Chu Janet N. , Idossa Dame , Van Blarigan Erin L. , Cheng Iona , Shariff-Marco Salma , Gomez Scarlett Lin
Published: October 2024

Background:

The COVID-19 pandemic and associated shutdowns disrupted healthcare access and resulted in decreased cancer screenings. Cancer diagnosis delays have concerning downstream effects on late-stage cancer, especially for marginalized populations.

Methods:

The study population included 349,458 adults in the California Cancer Registry diagnosed with cancer between January 2019 and December 2021, during which California experienced two stay-at-home orders. We examined the percentage of late-stage (III–IV) cancer diagnoses across five periods: Pre-pandemic (January 2019–February 2020), Shutdown #1 (March–June 2020), Post-shutdown #1 (July–November 2020), Post-shutdown #2 (December 2020–March 2021), and Post-vaccine rollout (April–December 2021). To examine the association between time period and late-stage diagnoses, we conducted a multivariable log-binomial regression model adjusted for sociodemographic and neighborhood factors.

Results:

The percentage of late-stage cancer diagnoses increased during Shutdown #1 (+5.2%) and returned to baseline Post-vaccine rollout. Groups with notably higher increases in the percentage of late-stage cancer (vs. overall population) during Shutdown #1 include Pacific Islander (+13.7%), Thai (+11.2%), Chinese (+8.1%), Native Hawaiian (+7.4%), Filipino (+6.6%), and uninsured (+7.4%). Uninsured [vs. private insurance; prevalence ratio (PR), 1.41], low neighborhood socioeconomic status (nSES; vs. high; PR, 1.19), and racial and ethnic minoritized groups (vs. non-Hispanic White; PR, 1.04–1.19) had higher likelihood for late-stage cancer diagnosis.

Conclusions:

The pandemic exacerbated late-stage cancer disparities for racial and ethnic minoritized groups, underinsured, and low nSES communities in California (2020–2021).

Impact:

Interventions to improve cancer screening must be focused on racial and ethnic minoritized, underinsured, and low nSES communities, as they are likely to be more vulnerable to healthcare disruptions like the pandemic.
Supplementary Table S9 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

Table S9. Variable Importance for predicting BCLM CD68+ using primary tumor clusters.
Supplementary Table S6 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

Table S6. Variable Importance for predicting BCLM CD31+ using primary tumor clusters.
Supplementary Table S3 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

Table S3. Variable Importance for predicting BCLM CD163+ using primary tumor clusters.
Supplementary Table S2 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

Table S2. Variable Importance for predicting BCLM CD14+ using primary tumor clusters.
Supplementary Table S11 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

Supplementary Table S11
Supplementary Figure S4 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

S4. Example of mapping of the annotated phenotype to corresponding segmented cells based on the markers identified by IMC for paired primary tumor and BCLM (patient 15).
Supplementary Figure S2 from Characterization of the Breast Cancer Liver Metastasis Microenvironment via Machine Learning Analysis of the Primary Tumor Microenvironment
Authors: Goodin Dylan A. , Chau Eric , Zheng Junjun , O’Connell Cailin , Tiwari Anjana , Xu Yitian , Niravath Polly , Chen Shu-Hsia , Godin Biana , Frieboes Hermann B.
Published: October 2024

S2. Heatmap of IMC cluster densities originating from BCLM (top) and primary breast tumors (bottom) after mean aggregation of ROIs.
The Blindness Series and Experimental Media Art of the 1990s
Authors: Tran Kim-Trang T.
Published: October 2024

At the March 2022 College Art Association’s meeting, a roundtable convened by Liz Kim discussed the topic: Intersectionality and the Video Art of Asian American Women Artists. Kim-Trang T. Tran’s video kore (1994), part of her Blindness Series, was one of the featured works. The Blindness Series, consisting of eight short-format experimental videos, focused on physical blindness and its metaphors to address intersectional issues of race, gender, and sexuality. While the specific topics and approaches of the videos in the series were products of their time, revisiting them today, we can see that contemporary concerns were already reflected in Asian American women artists’ works from the 1990s.
Vahlia capensis (Vahliaceae): first record of a possibly invasive species and genus in the Americas
Authors: SALOMÓN-MONTIJO BLADIMIR , DÍAZ JOSÉ SATURNINO , MÁRQUEZ-SALAZAR GILBERTO , PÍO-LEÓN JUAN FERNANDO
Published: October 2024

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On the Brazilian Exocnophila stick insects (Insecta: Phasmatodea), with the description of a new species
Authors: GHIROTTO VICTOR MORAIS , CONLE OSKAR , HENNEMANN FRANK , VALERO PABLO , CANCELLO ELIANA M.
Published: October 2024

Several stick insects occurring in Brazil belong to the Diapheromerinae. Before this work, the Brazilian genus Exocnophila contained three species known only from females, Exocnophila exintegra Zompro, 2001, Exocnophila tuberculata (Brunner von Wattenwyl, 1907) and Exocnophila cornuta (Brunner von Wattenwyl, 1907). Based on recently collected material, we found that the males of Exocnophila are assigned to another genus in the Diapheromerinae, the heterogeneous Bacteria. Here we show that the type species Exocnophila exintegra Zompro, 2001 syn. nov. is a junior synonym of Bacteria brevitarsata Brunner von Wattenwyl, 1907, which is transferred and redescribed as Exocnophila brevitarsata comb. nov.. We also transfer and redescribe Bacteria hastata as Exocnophila hastata comb. nov. and propose a new species, Exocnophila ovifuscum sp. nov., from Rio de Janeiro state, Brazil, with descriptions of females, males and eggs. We provide the first biological observations for the genus and a short discussion about its relationships.