bluuebunny/crossref_metadata_2025 huggingface dataset:
Lsm7 phase-separated condensates trigger stress granule formation
Authors: Lindström Michelle , Chen Lihua , Jiang Shan , Zhang Dan , Gao Yuan , Zheng Ju , Hao Xinxin , Yang Xiaoxue , Kabbinale Arpitha , Thoma Johannes , Metzger Lisa C. , Zhang Deyuan Y. , Zhu Xuefeng , Liu Huisheng , Gustafsson Claes M. , Burmann Björn M. , Winderickx Joris , Sunnerhagen Per , Liu Beidong
Published: June 2022

Stress granules (SGs) are non-membranous organelles facilitating stress responses and linking the pathology of age-related diseases. In a genome-wide imaging-based phenomic screen, we identify Pab1 co-localizing proteins under 2-deoxy-D-glucose (2-DG) induced stress in Saccharomyces cerevisiae. We find that deletion of one of the Pab1 co-localizing proteins, Lsm7, leads to a significant decrease in SG formation. Under 2-DG stress, Lsm7 rapidly forms foci that assist in SG formation. The Lsm7 foci form via liquid-liquid phase separation, and the intrinsically disordered region and the hydrophobic clusters within the Lsm7 sequence are the internal driving forces in promoting Lsm7 phase separation. The dynamic Lsm7 phase-separated condensates appear to work as seeding scaffolds, promoting Pab1 demixing and subsequent SG initiation, seemingly mediated by RNA interactions. The SG initiation mechanism, via Lsm7 phase separation, identified in this work provides valuable clues for understanding the mechanisms underlying SG formation and SG-associated human diseases.
Compositional dependence of the fragility in metallic glass forming liquids
Authors: Kube Sebastian A. , Sohn Sungwoo , Ojeda-Mota Rodrigo , Evers Theo , Polsky William , Liu Naijia , Ryan Kevin , Rinehart Sean , Sun Yong , Schroers Jan
Published: June 2022

The viscosity and its temperature dependence, the fragility, are key properties of a liquid. A low fragility is believed to promote the formation of metallic glasses. Yet, the fragility remains poorly understood, since experimental data of its compositional dependence are scarce. Here, we introduce the film inflation method (FIM), which measures the fragility of metallic glass forming liquids across wide ranges of composition and glass-forming ability. We determine the fragility for 170 alloys ranging over 25 at.% in Mg–Cu–Y. Within this alloy system, large fragility variations are observed. Contrary to the general understanding, a low fragility does not correlate with high glass-forming ability here. We introduce crystallization complexity as an additional contribution, which can potentially become significant when modeling glass forming ability over many orders of magnitude.
Immunogenicity and reactogenicity of SARS-CoV-2 vaccines BNT162b2 and CoronaVac in healthy adolescents
Authors: Rosa Duque Jaime S. , Wang Xiwei , Leung Daniel , Cheng Samuel M. S. , Cohen Carolyn A. , Mu Xiaofeng , Hachim Asmaa , Zhang Yanmei , Chan Sau Man , Chaothai Sara , Kwan Kelvin K. H. , Chan Karl C. K. , Li John K. C. , Luk Leo L. H. , Tsang Leo C. H. , Wong Wilfred H. S. , Cheang Cheuk Hei , Hung Timothy K. , Lam Jennifer H. Y. , Chua Gilbert T. , Tso Winnie W. Y. , Ip Patrick , Mori Masashi , Kavian Niloufar , Leung Wing Hang , Valkenburg Sophie , Peiris Malik , Tu Wenwei , Lau Yu Lung
Published: June 2022

We present an interim analysis of a registered clinical study (NCT04800133) to establish immunobridging with various antibody and cellular immunity markers and to compare the immunogenicity and reactogenicity of 2-dose BNT162b2 and CoronaVac in healthy adolescents as primary objectives. One-dose BNT162b2, recommended in some localities for risk reduction of myocarditis, is also assessed. Antibodies and T cell immune responses are non-inferior or similar in adolescents receiving 2 doses of BNT162b2 (BB,N = 116) and CoronaVac (CC,N = 123) versus adults after 2 doses of the same vaccine (BB,N = 147; CC,N = 141) but not in adolescents after 1-dose BNT162b2 (B,N = 116). CC induces SARS-CoV-2 N and N C-terminal domain seropositivity in a higher proportion of adolescents than adults. Adverse reactions are mostly mild for both vaccines and more frequent for BNT162b2. We find higher S, neutralising, avidity and Fc receptor-binding antibody responses in adolescents receiving BB than CC, and a similar induction of strong S-specific T cells by the 2 vaccines, in addition to N- and M-specific T cells induced by CoronaVac but not BNT162b2, possibly implying differential durability and cross-variant protection by BNT162b2 and CoronaVac, the 2 most used SARS-CoV-2 vaccines worldwide. Our results support the use of both vaccines in adolescents.
Network-based machine learning approach to predict immunotherapy response in cancer patients
Authors: Kong JungHo , Ha Doyeon , Lee Juhun , Kim Inhae , Park Minhyuk , Im Sin-Hyeog , Shin Kunyoo , Kim Sanguk
Published: June 2022

Immune checkpoint inhibitors (ICIs) have substantially improved the survival of cancer patients over the past several years. However, only a minority of patients respond to ICI treatment (~30% in solid tumors), and current ICI-response-associated biomarkers often fail to predict the ICI treatment response. Here, we present a machine learning (ML) framework that leverages network-based analyses to identify ICI treatment biomarkers (NetBio) that can make robust predictions. We curate more than 700 ICI-treated patient samples with clinical outcomes and transcriptomic data, and observe that NetBio-based predictions accurately predict ICI treatment responses in three different cancer types—melanoma, gastric cancer, and bladder cancer. Moreover, the NetBio-based prediction is superior to predictions based on other conventional ICI treatment biomarkers, such as ICI targets or tumor microenvironment-associated markers. This work presents a network-based method to effectively select immunotherapy-response-associated biomarkers that can make robust ML-based predictions for precision oncology.
Anionic polymerization of nonaromatic maleimide to achieve full-color nonconventional luminescence
Authors: Ji Xin , Tian Weiguo , Jin Kunfeng , Diao Huailing , Huang Xin , Song Guangjie , Zhang Jun
Published: June 2022

Nonconventional or nonconjugated luminophore without polycyclic aromatics or extended π-conjugation is a rising star in the area of luminescent materials. However, continuously tuning the emission color within a broad visible region via rational molecular design remains quite challenging because the mechanism of nonconventional luminescence is not fully understood. Herein, we present a new class of nonconventional luminophores, poly(maleimide)s (PMs), with full-color emission that can be finely regulated by anionic polymerization even at ambient temperature. Interestingly, the general characteristics of nonconventional luminescence, cluster-triggered emission, e.g., concentration-enhanced emission, are not observed in PMs. Instead, PMs have features similar to aggregation-caused quenching due to boosted intra/inter-molecular charge transfer. Such a biocompatible luminescent material synthesized from a low-cost monomer shows great prospects in large-scale production and applications, including security printing, fingerprint identification, metal ion recognition, etc. It also provides a new platform of rational molecular design to achieve full-color nonconventional luminescence without any aromatics.
Machine learning for the discovery of molecular recognition based on single-walled carbon nanotube corona-phases
Authors: Gong Xun , Renegar Nicholas , Levi Retsef , Strano Michael S.
Published: June 2022

Nanoparticle corona phase (CP) design offers a unique approach toward molecular recognition (MR) for sensing applications. Single-walled carbon nanotube (SWCNT) CPs can additionally transduce MR through its band-gap photoluminescence (PL). While DNA oligonucleotides have been used as SWCNT CPs, no generalized scheme exists for MR prediction de novo due to their sequence-dependent three-dimensional complexity. This work generated the largest DNA-SWCNT PL response library of 1408 elements and leveraged machine learning (ML) techniques to understand MR and DNA sequence dependence through local (LFs) and high-level features (HLFs). Out-of-sample analysis of our ML model showed significant correlations between model predictions and actual sensor responses for 6 out of 8 experimental conditions. Different HLF combinations were found to be uniquely correlated with different analytes. Furthermore, models utilizing both LFs and HLFs show improvement over that with HLFs alone, demonstrating that DNA-SWCNT CP engineering is more complex than simply specifying molecular properties.
A high-resolution climate simulation dataset for the past 540 million years
Authors: Li Xiang , Hu Yongyun , Guo Jiaqi , Lan Jiawenjing , Lin Qifan , Bao Xiujuan , Yuan Shuai , Wei Mengyu , Li Zhibo , Man Kai , Yin Zihan , Han Jing , Zhang Jian , Zhu Chenguang , Zhao Zhouqiao , Liu Yonggang , Yang Jun , Nie Ji
Published: June 2022

The Phanerozoic Eon has witnessed considerable changes in the climate system as well as abundant animals and plant life. Therefore, the evolution of the climate system in this Eon is worthy of extensive research. Only by studying climate changes in the past can we understand the driving mechanisms for climate changes in the future and make reliable climate projections. Apart from observational paleoclimate proxy datasets, climate simulations provide an alternative approach to investigate past climate conditions of the Earth, especially for long time span in the deep past. Here we perform 55 snapshot simulations for the past 540 million years, with a 10-million-year interval, using the Community Earth System Model version 1.2.2 (CESM1.2.2). The climate simulation dataset includes global distributions of monthly surface temperatures and precipitation, with a 1° horizontal resolution of 0.9° × 1.25° in latitude and longitude. This open access climate dataset is useful for multidisciplinary research, such as paleoclimate, geology, geochemistry, and paleontology.
Equivocal evidence for a link between megalencephaly-related genes and primate brain size evolution
Authors: DeCasien Alex R. , Trujillo Amber E. , Janiak Mareike C. , Harshaw Etta P. , Caes Zosia N. , Galindo Gabriela A. , Petersen Rachel M. , Higham James P.
Published: June 2022

A large brain is a defining feature of modern humans, and much work has been dedicated to exploring the molecular underpinnings of this trait. Although numerous studies have focused on genes associated with human microcephaly, no studies have explicitly focused on genes associated with megalencephaly. Here, we investigate 16 candidate genes that have been linked to megalencephaly to determine if: (1) megalencephaly-associated genes evolved under positive selection across primates; and (2) selection pressure on megalencephaly-associated genes is linked to primate brain size. We found evidence for positive selection for only one gene,OFD1, with 1.8% of the sites estimated to have dN/dSvalues greater than 1; however, we did not detect a relationship between selection pressure on this gene and brain size across species, suggesting that selection for changes to non-brain size traits drove evolutionary changes to this gene. In fact, our primary analyses did not identify significant associations between selection pressure and brain size for any candidate genes. While we did detect positive associations for two genes (GPC3andTBC1D7) when two phyletic dwarfs (i.e., species that underwent recent evolutionary decreases in brain size) were excluded, these associations did not withstand FDR correction. Overall, these results suggest that sequence alterations to megalencephaly-associated genes may have played little to no role in primate brain size evolution, possibly due to the highly pleiotropic effects of these genes. Future comparative studies of gene expression levels may provide further insights. This study enhances our understanding of the genetic underpinnings of brain size evolution in primates and identifies candidate genes that merit further exploration.
Environmental variables and genome-environment interactions predicting IBD diagnosis in large UK cohort
Authors: Yang Alan Z. , Jostins-Dean Luke
Published: June 2022

A combination of genetic susceptibility and environmental exposure is thought to cause inflammatory bowel disease (IBD), but the non-genetic component remains poorly characterized. We therefore undertook a search for environmental variables and gene-environment interactions associated with future IBD diagnosis in a large UK cohort. Using self-report and electronic health records, we identified 1946 Crohn’s disease (CD) and 3715 ulcerative colitis (UC) patients after quality control in the UK Biobank. Based on prior literature and biological plausibility
, we tested 38 candidate environmental variables for association with CD, UC, and overall IBD using Cox proportional hazard regressions. We also tested whether these variables interacted with polygenic risk in predicting disease, following up significant (FDR < 0.05) results with tests for SNP-environment associations. We performed robustness analyses on all significant results. As in previous reports, appendectomy protected against UC, smoking (both current and previous) elevated risk for CD, current smoking protected against UC, and previous smoking imparted a risk for UC. Childhood antibiotic use associated with IBD, as did sun exposure during the winter. Socioeconomic deprivation was conferred a risk for IBD, CD, and UC. We uncovered negative interactions between polygenic risk and previous oral contraceptive use for IBD and UC. Polygenic risk also interacted negatively with previous smoking in predicting UC. There were no individually significant SNP-environment interactions. Thus, for a limited set of environmental variables, there was strong evidence of association with IBD diagnosis in the UK Biobank, and interaction with polygenic risk was minimal.
Anatomy-dependent lung doses from 3D-conformal breast-cancer radiotherapy
Authors: Kundrát Pavel , Rennau Hannes , Remmele Julia , Sebb Sabine , Simonetto Cristoforo , Kaiser Jan Christian , Hildebrandt Guido , Wolf Ulrich , Eidemüller Markus
Published: June 2022

This study aims to identify key anatomic features that govern the individual variability of lung doses from breast-cancer radiotherapy. 3D conformal, intensity-modulated and hybrid techniques with 50.4 Gy whole-breast dose were planned for 128 patients. From their CT images, 17 anatomic measures were assessed and tested as predictors for lung dose-volume characteristics. Tangential techniques yielded mean ipsilateral lung doses in the range of 3–11 Gy. This inter-patient variability was explained to almost 40% by central lung distance, and to almost 60% if this measure was complemented by midplane lung width and maximum heart distance. Also the variability in further dose-volume metrics such as volume fractions receiving 5, 20 or 40 Gy could be largely explained by the anatomy. Multi-field intensity-modulated radiotherapy reduced high-exposed lung volumes, but resulted in higher mean ipsilateral lung doses and larger low-dose burden. Contralateral lung doses ranged from 0.3 to 1 Gy. The results highlight that there are large differences in lung doses among breast-cancer patients. Most of this inter-individual variability can be explained by a few anatomic features. The results will be implemented in a dedicated software tool to provide personalized estimates of long-term health risks related to breast-cancer radiotherapy. The results may also be used to identify favourable as well as problematic anatomies, and serve as a quick quantitative benchmark for individual treatment plans.
Determination of lipid requirements in black soldier fly through semi-purified diets
Authors: Bellezza Oddon S. , Biasato I. , Resconi A. , Gasco L.
Published: June 2022

The insect market is still far from an effective upscale and, to achieve this goal, it is necessary to know the BSF dietary requirements for the production maximization. Worldwide, given the waste variability, is not always easy to identify the optimal waste-based mixture that can allow to reach the best production, in terms of quantity and quality. Due this reason, nutritional need ranges are the basic knowledge, affordable for everyone, to increase the profitability of the insect farming. The study aims to evaluate the effects of 6 semi-purified, isonitrogenous and isoenergetic diets (SPII) with increasing lipid levels (1%, L1; 1.5%, L1.5; 2.5%, L2.5; 3.5% L3.5; 4.5%, L4.5) on BSF life history traits (6 replicates/treatment and 100 larvae/replicate). The Gainesville diet was used as environmental control. Considering the whole larval stage, 4.5% lipid level guarantees better performance when compared to content lower than 2.5%. The L4.5 10-day-old larvae yielded greater when compared to the other dietary treatments. At 14 and 18 days of age, the larvae of the groups above 2.5% performed better than L1, while the L1.5 showed intermediate results. Lipid levels below 1.5% on DM, when compared to 4.5%, resulted in a smaller prepupa and pupa size. The results obtained on the adult stage do not allow the identification of a lipid levels ideal range, as in the larval stage. In conclusion, in the whole larval stage and in prepupae/pupae phases, lipid percentage lower than (or equal to) 1% have a negative effect on growth. Other research will be needed in order to evaluate lipid levels above 4.5% on DM.
Effects of animal-assisted psychotherapy incorporating mindfulness and self-compassion in neurorehabilitation: a randomized controlled feasibility trial
Authors: Künzi Pascale , Ackert Michael , grosse Holtforth Martin , Hund-Georgiadis Margret , Hediger Karin
Published: June 2022

Transdiagnostic psychotherapeutic approaches are increasingly used in neurorehabilitation to address psychological distress. Animal-assistance is thought to increase efficacy. The present study evaluates a psychotherapeutic mindfulness- and self-compassion-based group intervention (MSCBI) with and without animal-assistance for patients with acquired brain injury. Patients (N = 31) were randomly assigned to the 6-week intervention with (n = 14) or without animal-assistance (n = 17). Primary outcome was psychological distress at post- and follow-up treatment, secondary outcomes were changes within-session of patients’ emotional states, adherence to treatment and attrition. Psychological distress significantly decreased in both groups from pre- to follow-up treatment with no difference between groups. Patients in the animal-assisted MSCBI group reported significantly higher increases in feeling secure, accepted, comforted, grateful, motivated and at ease during the sessions compared to patients in the MSCBI group without animal-assistance. Adherence to sessions was significantly higher in the animal-assisted MSCBI group. Attrition did not significantly differ between groups. Our results show that both MSCBIs with and without animal-assistance are feasible and effective in reducing psychological distress in patients with acquired brain injury. The significant changes within-sessions mainly in relationship-based emotional states and the higher treatment adherence suggest additional effects of animal-assistance. Animal-assistance might increase acceptability and patients’ commitment to psychotherapy.
Fully inkjet-printed flexible organic voltage inverters as a basic component in digital NOT gates
Authors: Luczak Adam , Mitra Kalyan Y. , Baumann Reinhard R. , Zichner Ralf , Luszczynska Beata , Jung Jaroslaw
Published: June 2022

In relation to conventional vacuum-based processing techniques inkjet printing enables upscaling fabrication of basic electronic elements, such as transistors and diodes. We present the fully inkjet printed flexible electronic circuits, including organic voltage inverter which can work as a NOT logic gate. For this purpose the special ink compositions were formulated to preparation of gate dielectric layer containing poly (4-vinylphenol) and of the semiconductor layer poly[2,5-(2-octyldodecyl)-3,6-diketopyrrolopyrrole-alt-5,5-(2,5-di(thien-2-yl)thieno [3,2-b]thiophene)]. A printed photoxidized poly (3-hexyltiophene) semiconductor was used as the active layer of the resistors. The operation of the printed inverters and NOT logic gates was analyzed based on the DC current–voltage characteristics of the devices. The resistance of the devices to atmospheric air was also tested. Not encapsulated samples stored for three years under ambient conditions. Followed by annealing to remove moisture showed unchanged electrical parameters in comparison to freshly printed samples.
Renal transcriptome profiles in mice reveal the need for sufficient water intake irrespective of the drinking water type
Authors: Shon Woo-Jeong , Park Mi-Na , Lee Jooyoung , Shin Ji-Hee , Shin Dong-Mi
Published: June 2022

This study sought to characterize the impact of long-term dehydration in terms of physiological and biochemical parameters, as well as renal transcriptomes. Furthermore, we assessed whether consumption of specific types of water elicit more beneficial effects on these health parameters. To this end, C57BL/6 mice were either provided water for 15 min/day over 2 and 4 weeks (water restricted; RES), or ad libitum access to distilled (CON), tap, spring, or purified water. Results show that water restriction decreases urine output and hematocrit levels while increasing brain vasopressin mRNA levels in RES mice compared to control mice (CON). Meanwhile, blood urea nitrogen and creatinine levels were higher in the RES group compared to the CON group. Kidney transcriptome analysis further identified kidney damage as the most significant biological process modulated by dehydration. Mechanistically, prolonged dehydration induces kidney damage by suppressing the NRF2-signaling pathway, which targets the cytoprotective defense system. However, type of drinking water does not appear to impact physiological or blood biochemical parameters, nor the renal transcriptome profile, suggesting that sufficient water consumption is critical, irrespective of the water type. Importantly, these findings also inform practical action for environmental sustainability by providing a theoretical basis for reducing bottled water consumption.
A model-specific simplification of the Mouse Grimace Scale based on the pain response of intraperitoneal CCl4 injections
Authors: Ernst Lisa , Bruch Stefan , Kopaczka Marcin , Merhof Dorit , Bleich André , Tolba René H. , Talbot Steven R.
Published: June 2022

Despite its long establishment and applicability in mice pain detection, the Mouse Grimace Scale still seems to be underused in acute pain detection during chronic experiments. However, broadening its applicability can identify possible refinement approaches such as cumulative severity and habituation to painful stimuli. Therefore, this study focuses on two main aspects: First, five composite MGS criteria were evaluated with two independent methods (the MoBPs algorithm and a penalized least squares regression) and ranked for their relative importance. The most important variable was used in a second analysis to specifically evaluate the context of pain after an i.p. injection (intervention) in two treatment groups (CCl4 and oil (control)) at fixed times throughout four weeks in 24 male C57BL/6 N mice. One hour before and after each intervention, video recordings were taken, and the MGS assessment was performed. In this study, the results indicate orbital tightening as the most important criterion. In this experimental setup, a highly significant difference after treatment between week 0 and 1 was found in the CCl4 group, resulting in a medium-sized effect (W = 62.5, p value < 0.0001, rCCl4 = 0.64). The oil group showed no significant difference (week 0 vs 1, W = 291.5, p value = 0.7875, rcontrol = 0.04). Therefore, the study showed that the pain caused by i.p. injections was only dependent on the applied substance, and no significant cumulation or habituation occurred due to the intervention. Further, the results indicated that the MGS system can be simplified.
Comparison of anxiety-like and social behaviour in medaka and zebrafish
Authors: Lucon-Xiccato Tyrone , Loosli Felix , Conti Francesca , Foulkes Nicholas S. , Bertolucci Cristiano
Published: June 2022

The medaka, Oryzias latipes, is rapidly growing in importance as a model in behavioural research. However, our knowledge of its behaviour is still incomplete. In this study, we analysed the performance of medaka in 3 tests for anxiety-like behaviour (open-field test, scototaxis test, and diving test) and in 3 sociability tests (shoaling test with live stimuli, octagonal mirror test, and a modified shoaling test with mirror stimulus). The behavioural response of medaka was qualitatively similar to that observed in other teleosts in the open-field test (thigmotaxis), and in 2 sociability tests, the shoaling test and in the octagonal mirror test (attraction towards the social stimulus). In the remaining tests, medaka did not show typical anxiety (i.e., avoidance of light environments and preference for swimming at the bottom of the aquarium) and social responses (attraction towards the social stimulus). As a reference, we compared the behaviour of the medaka to that of a teleost species with well-studied behaviour, the zebrafish, tested under the same conditions. This interspecies comparison indicates several quantitative and qualitative differences across all tests, providing further evidence that the medaka responds differently to the experimental settings compared to other fish models.
Immediate impact of yogic breathing on pulsatile cerebrospinal fluid dynamics
Authors: Yildiz Selda , Grinstead John , Hildebrand Andrea , Oshinski John , Rooney William D. , Lim Miranda M. , Oken Barry
Published: June 2022

Cerebrospinal fluid (CSF), a clear fluid bathing the central nervous system (CNS), undergoes pulsatile movements. Together with interstitial fluid, CSF plays a critical role for the removal of waste products from the brain, and maintenance of the CNS health. As such, understanding the mechanisms driving CSF movement is of high scientific and clinical impact. Since pulsatile CSF dynamics is sensitive and synchronous to respiratory movements, we are interested in identifying potential integrative therapies such as yogic breathing to regulate CSF dynamics, which has not been reported before. Here, we investigated the pre-intervention baseline data from our ongoing randomized controlled trial, and examined the impact of four yogic breathing patterns: (i) slow, (ii) deep abdominal, (iii) deep diaphragmatic, and (iv) deep chest breathing with the last three together forming a yogic breathing called three-part breath. We utilized our previously established non-invasive real-time phase contrast magnetic resonance imaging approach using a 3T MRI instrument, computed and tested differences in single voxel CSF velocities (instantaneous, respiratory, cardiac 1st and 2nd harmonics) at the level of foramen magnum during spontaneous versus yogic breathing. In examinations of 18 healthy participants (eight females, ten males; mean age 34.9 ± 14 (SD) years; age range: 18–61 years), we observed immediate increase in cranially-directed velocities of instantaneous-CSF 16–28% and respiratory-CSF 60–118% during four breathing patterns compared to spontaneous breathing, with the greatest changes during deep abdominal breathing (28%, p = 0.0008, and 118%, p = 0.0001, respectively). Cardiac pulsation was the primary source of pulsatile CSF motion except during deep abdominal breathing, when there was a comparable contribution of respiratory and cardiac 1st harmonic power [0.59 ± 0.78], suggesting respiration can be the primary regulator of CSF depending on the individual differences in breathing techniques. Further work is needed to investigate the impact of sustained training yogic breathing on pulsatile CSF dynamics for CNS health.
Subclinical infection occurs frequently following low dose exposure to prions by blood transfusion
Authors: Salamat M. Khalid F. , Stewart Paula , Brown Helen , Tan Kyle B. C. , Smith Allister , de Wolf Christopher , Alejo Blanco A. Richard , Turner Marc , Manson Jean C. , McCutcheon Sandra , Houston E. Fiona
Published: June 2022

Infectious prion diseases have very long incubation periods, and the role that subclinical infections play in transmission, persistence and re-emergence of these diseases is unclear. In this study, we used a well-established model of vCJD (sheep experimentally infected with bovine spongiform encephalopathy, BSE) to determine the prevalence of subclinical infection following exposure by blood transfusion from infected donors. Many recipient sheep survived for years post-transfusion with no clinical signs and no disease-associated PrP (PrPSc) found in post mortem tissue samples by conventional tests. Using a sensitive protein misfolding cyclic amplification assay (PMCA), we found that the majority of these sheep had detectable PrPSc in lymph node samples, at levels approximately 105–106 times lower than in equivalent samples from clinically positive sheep. Further testing revealed the presence of PrPSc in other tissues, including brain, but not in blood samples. The results demonstrate that subclinical infection is a frequent outcome of low dose prion infection by a clinically relevant route for humans (blood transfusion). The long term persistence of low levels of infection has important implications for prion disease control and the risks of re-emergent infections in both humans and animals.
Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces
Authors: Leung Kevin , Greathouse Jeffery A.
Published: June 2022

Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu2+-OH− bonds, yielding three local minima in the free energy profiles associated with 0-2 OH− bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH− hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu2+ dimer formation on silica surfaces over monomer adsorption.
Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer
Authors: Boehm Kevin M. , Aherne Emily A. , Ellenson Lora , Nikolovski Ines , Alghamdi Mohammed , Vázquez-García Ignacio , Zamarin Dmitriy , Long Roche Kara , Liu Ying , Patel Druv , Aukerman Andrew , Pasha Arfath , Rose Doori , Selenica Pier , Causa Andrieu Pamela I. , Fong Chris , Capanu Marinela , Reis-Filho Jorge S. , Vanguri Rami , Veeraraghavan Harini , Gangai Natalie , Sosa Ramon , Leung Samantha , McPherson Andrew , Gao JianJiong ,   MSK MIND Consortium, Lakhman Yulia , Shah Sohrab P.
Published: June 2022

Patients with high-grade serous ovarian cancer suffer poor prognosis and variable response to treatment. Known prognostic factors for this disease include homologous recombination deficiency status, age, pathological stage and residual disease status after debulking surgery. Recent work has highlighted important prognostic information captured in computed tomography and histopathological specimens, which can be exploited through machine learning. However, little is known about the capacity of combining features from these disparate sources to improve prediction of treatment response. Here, we assembled a multimodal dataset of 444 patients with primarily late-stage high-grade serous ovarian cancer and discovered quantitative features, such as tumor nuclear size on staining with hematoxylin and eosin and omental texture on contrast-enhanced computed tomography, associated with prognosis. We found that these features contributed complementary prognostic information relative to one another and clinicogenomic features. By fusing histopathological, radiologic and clinicogenomic machine-learning models, we demonstrate a promising path toward improved risk stratification of patients with cancer through multimodal data integration.
Symptomatic lithospheric drips triggering fast topographic rise and crustal deformation in the Central Andes
Authors: Andersen Julia , Göğüş Oguz H. , Pysklywec Russell N. , Santimano Tasca , Şengül Uluocak Ebru
Published: June 2022

The basin and plateau regions of the Central Andes have undergone phases of rapid subsidence and uplift during the last ~20 Myr in addition to internal tectonic deformation. Paleoelevation data and the presence of high seismic wave speed anomalies beneath the Puna Plateau suggest that these tectonic events may be related to lithospheric foundering. Here, we study the geodynamic processes in the region using three dimensional, scaled, analogue models and high-resolution optical image correlation techniques. The analogue experiments show how a gravitational instability of the mantle lithosphere developing into a lithospheric drip may form a circular sedimentary basin in the crust that undergoes subsidence and subsequently reverses to uplift, while simultaneously undergoing internal crustal shortening. The model results reveal that drips may be “symptomatic” where the crust is well coupled to the sinking mantle lithosphere and manifests tectonic deformation at the surface, or poorly coupled “asymptomatic” drips with weak crustal surface manifestations. Overall, the physical models suggest that the formation of the Arizaro Basin and nearby Central Andean basins are caused by symptomatic lithospheric dripping events and highlight the significant role of non-subduction geodynamic mechanisms in driving surface tectonics.
Leveraging genomics to understand the broader role of fungal small secreted proteins in niche colonization and nutrition
Authors: Plett Jonathan M , Plett Krista L
Published: June 2022

The last few years have seen significant advances in the breadth of fungi for which we have genomic resources and our understanding of the biological mechanisms evolved to enable fungi to interact with their environment and other organisms. One field of research that has seen a paradigm shift in our understanding concerns the role of fungal small secreted proteins (SSPs) classified as effectors. Classically thought to be a class of proteins utilized by pathogenic microbes to manipulate host physiology in support of colonization, comparative genomic studies have demonstrated that mutualistic fungi and fungi not associated with a living host (i.e., saprotrophic fungi) also encode inducible effector and candidate effector gene sequences. In this review, we discuss the latest advances in understanding how fungi utilize these secreted proteins to colonize a particular niche and affect nutrition and nutrient cycles. Recent studies show that candidate effector SSPs in fungi may have just as significant a role in modulating hyphosphere microbiomes and in orchestrating fungal growth as they do in supporting colonization of a living host. We conclude with suggestions on how comparative genomics may direct future studies seeking to characterize and differentiate effector from other more generalized functions of these enigmatic secreted proteins across all fungal lifestyles.
N-Methyl deuterated rhodamines for protein labelling in sensitive fluorescence microscopy
Authors: Roßmann Kilian , Akkaya Kerem C. , Poc Pascal , Charbonnier Corentin , Eichhorst Jenny , Gonschior Hannes , Valavalkar Abha , Wendler Nicolas , Cordes Thorben , Dietzek-Ivanšić Benjamin , Jones Ben , Lehmann Martin , Broichhagen Johannes
Published: June 2022

Deuteration enhances photophysical and chemical properties of fluorescent rhodamine dyes for higher brightness in sensitive microscopy.
Smart contact lens containing hyaluronate–rose bengal conjugate for biophotonic myopia vision correction
Authors: Mun Jonghwan , Kim Tae Yeon , Myung David , Hahn Sei Kwang
Published: June 2022

We develop a smart contact lens to deliver hyaluronate–rose bengal conjugates for the corneal collagen crosslinking possibly for myopia vision correction.
A chemical biology toolbox to overcome the hypoxic tumor microenvironment for photodynamic therapy: a review
Authors: Zheng Xuwei , Sun Wen , Ju Minzi , Wu Jichun , Huang He , Shen Baoxing
Published: June 2022

A summary of strategies for overcoming hypoxia in the tumor microenvironment during photodynamic therapy.
Functionalization of carbon nanotubes with bovine plasma biowaste by forming a protein corona enhances copper removal from water and ecotoxicity mitigation
Authors: Martins Carlos Henrique Zanini , Côa Francine , Da Silva Gabriela Helena , Bettini Jefferson , De Farias Marcelo Alexandre , Portugal Rodrigo Villares , Umbuzeiro Gisela de Aragão , Alves Oswaldo Luiz , Martinez Diego Stéfani Teodoro
Published: June 2022

Functionalization of carbon nanotubes through protein corona formation with bovine plasma is a novel waste-to-wealth approach in agri-environmental nanoscience towards remediation of pollutants from water.
Synergetic effect of photocatalysis and peroxymonosulfate activation by CoTiO3/SBA-15, NiTiO3/SBA-15 and Fe2TiO5/SBA-15 for efficient photocatalytic removal of oxytetracycline hydrochloride
Authors: Li Di , Long Mingyang , Zhao Qianqian , Li Hongmiao , Wen Qi , Song Fang
Published: June 2022

Peroxymonosulfate was activated by photogenerated e−, Co, Ni and Fe.
Injectable macromolecule-based calcium phosphate bone substitutes
Authors: Moussi Hilel , Weiss Pierre , Le Bideau Jean , Gautier Hélène , Charbonnier Baptiste
Published: June 2022

Injectable bone substitutes (IBS) represent compelling options for bone regenerative medicine as they can be used to optimally fill a complex bone defect through minimally invasive intervention.
A solution-derived bismuth aluminum gallium tin oxide film constructed by a brush coating method for spontaneous liquid crystal alignment
Authors: Lee Dong Wook , Kim Eun Mi , Heo Gi Seok , Kim Dong Hyun , Oh Jin Young , Kim Dae-Hyun , Liu Yang , Seo Dae-Shik
Published: June 2022

The directional structure of a solution-derived bismuth aluminum gallium tin oxide film is achieved by a brush coating method. This structure is used for spontaneous and uniform liquid crystal alignment.
Multivalent stimulation of β1-, but not β2-receptors by adrenaline functionalised gold nanoparticles
Authors: Mattern Annabelle , Claßen Rebecca , Wolf Annemarie , Pouokam Ervice , Schlüter Klaus-Dieter , Wickleder Mathias S. , Diener Martin
Published: June 2022

Adrenaline functionalised gold nanoparticles had no influence on respiratory smooth muscle cells which are regulated by β2-receptors, while the stimulation of β1-receptors led to an increased contractility of cardiomyocytes.
Bandgap tuning of a CsPbBr3 perovskite with synergistically improved quality via Sn2+ doping for high-performance carbon-based inorganic perovskite solar cells
Authors: Wang Guiqiang , Bi Jiayu , Chang Jiarun , Lei Miao , Zheng Huiling , Yan Yu
Published: June 2022

Partially substituting Pb2+ with an appropriate amount of Sn2+ simultaneously reduces the bandgap and improves the quality and morphology of a CsPbBr3 perovskite film.
Silver-catalyzed radical ring-opening of cycloalkanols for the synthesis of distal acylphosphine oxides
Authors: Li Cheng-Kun , Shoberu Adedamola , Zou Jian-Ping
Published: June 2022

This article reports a novel silver-catalyzed ring-opening approach for the regioselective synthesis of distal acylphosphine oxides; the mechanistic studies reveal the cross-coupling of alkyl and phosphorous-centered radicals.
Synthesis of γ-amino acids via photocatalyzed intermolecular carboimination of alkenes
Authors: Wang Xinhua , Chen Yi , Liang Ping , Chen Jian-Qiang , Wu Jie
Published: June 2022

We report a direct approach to achieve the energy transfer-driven carboimination of alkenes for the synthesis of a diverse collection of valuable γ-amino acids.
A facile imine-linked covalent organic framework doped with a carbon dot composite for the detection and removal of Hg2+ in surface water
Authors: Shili Q. I. N. , Xudong H. E. , Fenglong J. I. N. , Ying W. A. N. G. , Hongtao C. H. U. , Shuang H. A. N. , Yangyang S. U. N. , Lidi G. A. O.
Published: June 2022

TpPa-1 COF@CDs as a fluorescent composite exhibited good detection and removal performance for Hg2+. The simple functional monomer, short reaction time and metal-free raw material made TpPa-1 COF@CDs reliable, cost effective and eco-friendly.
Photocatalytic dye-degradation activity of nano-crystalline Ti1−xMxO2−δ (M =Ag, Pd, Fe, Ni and x = 0, 0.01) for water pollution abatement
Authors: Soni Vaishali , Singh Abhay Narayan , Singh Preetam , Gupta Asha
Published: June 2022

Redox-pair stabilization in TiO2 lattice by doping of Ag+ and Pd2+ ions play a defining role in enhancing the photocatalytic activity of the catalyst by scavenging electrons generated through UV-irradiation on the catalyst.
Impact of dipole–dipole interactions on motility-induced phase separation
Authors: Sesé-Sansa Elena , Liao Guo-Jun , Levis Demian , Pagonabarraga Ignacio , Klapp Sabine H. L.
Published: June 2022

We present a hydrodynamic theory for systems of dipolar active Brownian particles which, in the regime of weak dipolar coupling, predicts the onset of motility-induced phase separation (MIPS), consistent with Brownian dynamics (BD) simulations.
A new order of liquids: polar order in nematic liquid crystals
Authors: Mandle Richard J.
Published: June 2022

Given the widespread adoption of display technology based on nematic liquid crystals, the discovery of new nematic phases at thermodynamic equilibrium, although extremely rare, generates much excitement.
Elastically-mediated collective organisation of magnetic microparticles
Authors: Junot Gaspard , Wei Xuefeng , Ortín Jordi , Golestanian Ramin , Wang Yanting , Tierno Pietro , Meng Fanlong
Published: June 2022

We combine theory and experiments to investigate how gels mediate the organization of embedded magnetic microparticles when driven by an external field.
Entropy-stabilized metal oxide nanoparticles supported on reduced graphene oxide as a highly active heterogeneous catalyst for selective and solvent-free oxidation of toluene: a combined experimental and numerical investigation
Authors: Mehrabi-Kalajahi Seyedsaeed , Moghaddam Ahmad Ostovari , Hadavimoghaddam Fahimeh , Varfolomeev Mikhail A. , Zinnatullin Almaz L. , Vakhitov Iskander , Minnebaev Kamil R. , Emelianov Dmitrii A. , Uchaev Daniil , Cabot Andreu , Il'yasov Il'dar R. , Davletshin Rustam R. , Trofimov Evgeny , Khasanova Nailia M. , Vagizov Farit G.
Published: June 2022

Noble metal-free heterogeneous catalysts are highly desired for selective and solvent-free oxidation reactions. However, their practical application has been greatly restricted by their moderate activity.
Improved H2O2 photogeneration and stability on rational tailored polymeric carbon nitride via enhanced O2 adsorption
Authors: Li Zehao , Chen Tianxiang , Chen Yufei , Chen Xiaoyuan , Li Le , Kuang Siya , Gao Jing , Guo Yuxuan , Lo Tsz Woon Benedict , Du Jimin
Published: June 2022

Owing to the excellent oxygen-capture ability, the modified PCN presents excellent photocatalytic activity and stability for H2O2 production.
Nanomaterials and paper-based electrochemical devices: merging strategies for fostering sustainable detection of biomarkers
Authors: Caratelli Veronica , Di Meo Erika , Colozza Noemi , Fabiani Laura , Fiore Luca , Moscone Danila , Arduini Fabiana
Published: June 2022

This review aims to analyze how the paper material offers unique and polyvalent properties to bridge together multiple uses of nanomaterials and develop electrochemical biosensors for application in the biomedical field.
An organic transistor for the selective detection of tropane alkaloids utilizing a molecularly imprinted polymer
Authors: Zhou Qi , Sasaki Yui , Ohshiro Kohei , Fan Haonan , Montagna Valentina , Gonzato Carlo , Haupt Karsten , Minami Tsuyoshi
Published: June 2022

An organic transistor functionalized with a molecularly imprinted polymer (MIP) succeeded in the highly selective detection of chiral tropane alkaloids owing to the optimized internal molecular recognition sites in the MIP.
Back to the future: taking enzymes to the next level of sustainability
Authors: Padrosa David Roura , Benítez-Mateos Ana I. , Paradisi Francesca
Published: June 2022

The use of enzymes (protein catalysts from biological origin) has been key to the development of our society and daily life since the dawn of humanity. Nowadays, the better understanding of how enzymes work and their manipulation has enabled enzymes to become a crucial technology in the current biotechnological revolution. In this sense, while enzymes in their naturally occurring form are excellent biocatalysts, they are not yet broadly implemented in industry due to their instability and poor reusability. As a solution, enzyme immobilization is a strategy that enables the preparation of more resistant, reusable and more cost-efficient biocatalysts that, combined with continuous flow technologies, have the potential to make their promise true: transition towards more cost-efficient, sustainable, and environmental friendly chemical manufacturing.
Biocatalysis for future sustainable manufacturing
Authors: Woodley John M.
Published: June 2022

Enzymes are the catalytically active proteins, responsible for carrying out biochemistry in nature. Today, they are also finding use as catalysts in organic chemistry, both in the laboratory as well as in large-scale manufacturing of chemicals in industry. Their special properties enable sustainable syntheses, supported by tools such as protein engineering so they can be tuned to operate efficiently, thereby meeting industrial requirements.
Examining the Prevalence of Intervention Approaches Internationally: The Use of Nonspeech Oral Motor Exercises in Guatemala
Authors: Baigorri Miriam , Crowley Catherine J. , Sommer Chelsea L. , Blackwell Amanda , Miranda Anny J. , Moya-Galé Gemma
Published: June 2022

Purpose:

Little is known about the use of nonspeech oral motor exercises (NSOMEs) to treat Speech Sound Disorders (SSDs) in low- and middle-income countries, such as Guatemala, where the field of speech-language pathology is less well established. The purpose of this study is to examine clinical practices for SSDs in Guatemala. The authors then compare these findings with previous literature on the use of NSOMEs in countries with developed fields of speech-language pathology.

Method:

Nonmembers and members of the professional association for speech providers, Asociación de Terapistas del Lenguaje de Guatemala (SomosTLgt;
n
= 65), completed an online survey regarding the use of NSOMEs.

Results:

Although approximately half of the clinicians in Guatemala reported using NSOMEs in therapy, the time spent in therapy sessions using these exercises was limited to 25% of the time. Very few clinicians (19.8%) reported to use NSOMEs almost always or 50%–75% of the time. NSOMEs were not reportedly used by 33.8% of the clinicians when treating SSDs. A significant positive correlation was found between years of experience and use of NSOME in clinical practice. Nearly all respondents specified learning about NSOMEs at university.

Conclusions:

Contrary to previous studies from high-income countries that indicate that NSOMEs are commonly used by speech-language pathologists when targeting SSDs, the use of NSOMEs across speech therapists from Guatemala in this current investigation is less. Future studies should explore the rationale behind the use of NSOME across different countries.