bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets
Authors: Mihalič Filip , Benz Caroline , Kassa Eszter , Lindqvist Richard , Simonetti Leandro , Inturi Raviteja , Aronsson Hanna , Andersson Eva , Chi Celestine N. , Davey Norman E. , Överby Anna K. , Jemth Per , Ivarsson Ylva 
Published: September 2023

AbstractThe virus life cycle depends on host-virus protein-protein interactions, which often involve a disordered protein region binding to a folded protein domain. Here, we used proteomic peptide phage display (ProP-PD) to identify peptides from the intrinsically disordered regions of the human proteome that bind to folded protein domains encoded by the SARS-CoV-2 genome. Eleven folded domains of SARS-CoV-2 proteins were found to bind 281 peptides from human proteins, and affinities of 31 interactions involving eight SARS-CoV-2 protein domains were determined (KD ∼ 7-300 μM). Key specificity residues of the peptides were established for six of the interactions. Two of the peptides, binding Nsp9 and Nsp16, respectively, inhibited viral replication. Our findings demonstrate how high-throughput peptide binding screens simultaneously identify potential host-virus interactions and peptides with antiviral properties. Furthermore, the high number of low-affinity interactions suggest that overexpression of viral proteins during infection may perturb multiple cellular pathways.
Single neuron responses underlying face recognition in the human midfusiform face-selective cortex
Authors: Quian Quiroga Rodrigo , Boscaglia Marta , Jonas Jacques , Rey Hernan G. , Yan Xiaoqian , Maillard Louis , Colnat-Coulbois Sophie , Koessler Laurent , Rossion Bruno 
Published: September 2023

AbstractFaces are critical for social interactions and their recognition constitutes one of the most important and challenging functions of the human brain. While neurons responding selectively to faces have been recorded for decades in the monkey brain, face-selective neural activations have been reported with neuroimaging primarily in the human midfusiform gyrus. Yet, the cellular mechanisms producing selective responses to faces in this hominoid neuroanatomical structure remain unknown. Here we report single neuron recordings performed in 5 human subjects (1 male, 4 females) implanted with intracerebral microelectrodes in the face-selective midfusiform gyrus, while they viewed pictures of familiar and unknown faces and places. We observed similar responses to faces and places at the single cell level, but a significantly higher number of neurons responding to faces, thus offering a mechanistic account for the face-selective activations observed in this region. Although individual neurons did not respond preferentially to familiar faces, a population level analysis could consistently determine whether or not the faces (but not the places) were familiar, only about 50 ms after the initial recognition of the stimuli as faces. These results provide insights into the neural mechanisms of face processing in the human brain.
Chiral recognition of neutral guests by chiral naphthotubes with a bis-thiourea endo-functionalized cavity
Authors: Wang Song-Meng , Wang Yan-Fang , Huang Liping , Zheng Li-Shuo , Nian Hao , Zheng Yu-Tao , Yao Huan , Jiang Wei , Wang Xiaoping , Yang Liu-Pan 
Published: September 2023

AbstractDeveloping chiral receptors with an endo-functionalized cavity for chiral recognition is of great significance in the field of molecular recognition. This study presents two pairs of chiral naphthotubes containing a bis-thiourea endo-functionalized cavity. Each chiral naphthotube has two homochiral centers which were fixed adjacent to the thiourea groups, causing the skeleton and thiourea groups to twist enantiomerically through chiral transfer. These chiral naphthotubes are highly effective at enantiomerically recognizing various neutral chiral molecules with an enantioselectivity up to 17.0. Furthermore, the mechanism of the chiral recognition has been revealed to be originated from differences in multiple non-covalent interactions. Various factors, such as the shape of cavities, substituents of guests, flexibility of host and binding modes are demonstrated to contribute to creating differences in the non-covalent interactions. Additionally, the driving force behind enantioselectivity is mainly attributed to enthalpic differences, and enthalpy -entropy compensation has also been observed to influence enantioselectivity.
Surface-immobilized cross-linked cationic polyelectrolyte enables CO2 reduction with metal cation-free acidic electrolyte
Authors: Qin Hai-Gang , Du Yun-Fan , Bai Yi-Yang , Li Fu-Zhi , Yue Xian , Wang Hao , Peng Jian-Zhao , Gu Jun 
Published: September 2023

AbstractElectrochemical CO2 reduction in acidic electrolytes is a promising strategy to achieve high utilization efficiency of CO2. Although alkali cations in acidic electrolytes play a vital role in suppressing hydrogen evolution and promoting CO2 reduction, they also cause precipitation of bicarbonate on the gas diffusion electrode (GDE), flooding of electrolyte through the GDE, and drift of the electrolyte pH. In this work, we realize the electroreduction of CO2 in a metal cation-free acidic electrolyte by covering the catalyst with cross-linked poly-diallyldimethylammonium chloride. This polyelectrolyte provides a high density of cationic sites immobilized on the surface of the catalyst, which suppresses the mass transport of H+ and modulates the interfacial field strength. By adopting this strategy, the Faradaic efficiency (FE) of CO reaches 95 ± 3% with the Ag catalyst and the FE of formic acid reaches 76 ± 3% with the In catalyst in a 1.0 pH electrolyte in a flow cell. More importantly, with the metal cation-free acidic electrolyte the amount of electrolyte flooding through the GDE is decreased to 2.5 ± 0.6% of that with alkali cation-containing acidic electrolyte, and the FE of CO maintains above 80% over 36 h of operation at −200 mA·cm−2.
Genetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo
Authors: Wong Jeffrey Y. K. , Ekanayake Arunika I. , Kharchenko Serhii , Kirberger Steven E. , Qiu Ryan , Kelich Payam , Sarkar Susmita , Li Jiaqian , Fernandez Kleinberg X. , Alvizo-Paez Edgar R. , Miao Jiayuan , Kalhor-Monfared Shiva , John J. Dwyer , Kang Hongsuk , Choi Hwanho , Nuss John M. , Vederas John C. , Lin Yu-Shan , Macauley Matthew S. , Vukovic Lela , Pomerantz William C. K. , Derda Ratmir 
Published: September 2023

AbstractPeptide-based therapeutics have gained attention as promising therapeutic modalities, however, their prevalent drawback is poor circulation half-life in vivo. In this paper, we report the selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine SNAr chemistry, with decafluoro-diphenylsulfone (DFS). Testing of the binding of the selected peptides to albumin identified SICRFFC as the lead sequence. We replaced DFS with isosteric pentafluorophenyl sulfide (PFS) and the PFS-SICRFFCGG exhibited KD = 4–6 µM towards human serum albumin. When injected in mice, the concentration of the PFS-SICRFFCGG in plasma was indistinguishable from the reference peptide, SA-21. More importantly, a conjugate of PFS-SICRFFCGG and peptide apelin-17 analogue (N3-PEG6-NMe17A2) showed retention in circulation similar to SA-21; in contrast, apelin-17 analogue was cleared from the circulation after 2 min. The PFS-SICRFFC is the smallest known peptide macrocycle with a significant affinity for human albumin and substantial in vivo circulation half-life. It is a productive starting point for future development of compact macrocycles with extended half-life in vivo.
Detection of diagnostic and prognostic methylation-based signatures in liquid biopsy specimens from patients with meningiomas
Authors: Herrgott Grayson A. , Snyder James M. , She Ruicong , Malta Tathiane M. , Sabedot Thais S. , Lee Ian Y. , Pawloski Jacob , Podolsky-Gondim Guilherme G. , Asmaro Karam P. , Zhang Jiaqi , Cannella Cara E. , Nelson Kevin , Thomas Bartow , deCarvalho Ana C. , Hasselbach Laura A. , Tundo Kelly M. , Newaz Rehnuma , Transou Andrea , Morosini Natalia , Francisco Victor , Poisson Laila M. , Chitale Dhananjay , Mukherjee Abir , Mosella Maritza S. , Robin Adam M. , Walbert Tobias , Rosenblum Mark , Mikkelsen Tom , Kalkanis Steven , Tirapelli Daniela P. C. , Weisenberger Daniel J. , Carlotti Carlos G. , Rock Jack , Castro Ana Valeria , Noushmehr Houtan 
Published: September 2023

AbstractRecurrence of meningiomas is unpredictable by current invasive methods based on surgically removed specimens. Identification of patients likely to recur using noninvasive approaches could inform treatment strategy, whether intervention or monitoring. In this study, we analyze the DNA methylation levels in blood (serum and plasma) and tissue samples from 155 meningioma patients, compared to other central nervous system tumor and non-tumor entities. We discover DNA methylation markers unique to meningiomas and use artificial intelligence to create accurate and universal models for identifying and predicting meningioma recurrence, using either blood or tissue samples. Here we show that liquid biopsy is a potential noninvasive and reliable tool for diagnosing and predicting outcomes in meningioma patients. This approach can improve personalized management strategies for these patients.
Laser-induced nitrogen fixation
Authors: Wang Huize , Seemakurthi Ranga Rohit , Chen Gao-Feng , Strauss Volker , Savateev Oleksandr , Hai Guangtong , Ding Liangxin , López Núria , Wang Haihui , Antonietti Markus 
Published: September 2023

AbstractFor decarbonization of ammonia production in industry, alternative methods by exploiting renewable energy sources have recently been explored. Nonetheless, they still lack yield and efficiency to be industrially relevant. Here, we demonstrate an advanced approach of nitrogen fixation to synthesize ammonia at ambient conditions via laser–induced multiphoton dissociation of lithium oxide. Lithium oxide is dissociated under non–equilibrium multiphoton absorption and high temperatures under focused infrared light, and the generated zero–valent metal spontaneously fixes nitrogen and forms a lithium nitride, which upon subsequent hydrolysis generates ammonia. The highest ammonia yield rate of 30.9 micromoles per second per square centimeter is achieved at 25 °C and 1.0 bar nitrogen. This is two orders of magnitude higher than state–of–the–art ammonia synthesis at ambient conditions. The focused infrared light here is produced by a commercial simple CO2 laser, serving as a demonstration of potentially solar pumped lasers for nitrogen fixation and other high excitation chemistry. We anticipate such laser-involved technology will bring unprecedented opportunities to realize not only local ammonia production but also other new chemistries .
Interplay of valley polarized dark trion and dark exciton-polaron in monolayer WSe2
Authors: Cong Xin , Mohammadi Parisa Ali , Zheng Mingyang , Watanabe Kenji , Taniguchi Takashi , Rhodes Daniel , Zhang Xiao-Xiao 
Published: September 2023

AbstractThe interactions between charges and excitons involve complex many-body interactions at high densities. The exciton-polaron model has been adopted to understand the Fermi sea screening of charged excitons in monolayer transition metal dichalcogenides. The results provide good agreement with absorption measurements, which are dominated by dilute bright exciton responses. Here we investigate the Fermi sea dressing of spin-forbidden dark excitons in monolayer WSe2. With a Zeeman field, the valley-polarized dark excitons show distinct p-doping dependence in photoluminescence when the carriers reach a critical density. This density can be interpreted as the onset of strongly modified Fermi sea interactions and shifts with increasing exciton density. Through valley-selective excitation and dynamics measurements, we also infer an intervalley coupling between the dark trions and exciton-polarons mediated by the many-body interactions. Our results reveal the evolution of Fermi sea screening with increasing exciton density and the impacts of polaron-polaron interactions, which lay the foundation for understanding electronic correlations and many-body interactions in 2D systems.
Clustering predicted structures at the scale of the known protein universe
Authors: Barrio-Hernandez Inigo , Yeo Jingi , Jänes Jürgen , Mirdita Milot , Gilchrist Cameron L. M. , Wein Tanita , Varadi Mihaly , Velankar Sameer , Beltrao Pedro , Steinegger Martin 
Published: September 2023

AbstractProteins are key to all cellular processes and their structure is important in understanding their function and evolution. Sequence-based predictions of protein structures have increased in accuracy1, and over 214 million predicted structures are available in the AlphaFold database2. However, studying protein structures at this scale requires highly efficient methods. Here, we developed a structural-alignment-based clustering algorithm—Foldseek cluster—that can cluster hundreds of millions of structures. Using this method, we have clustered all of the structures in the AlphaFold database, identifying 2.30 million non-singleton structural clusters, of which 31% lack annotations representing probable previously undescribed structures. Clusters without annotation tend to have few representatives covering only 4% of all proteins in the AlphaFold database. Evolutionary analysis suggests that most clusters are ancient in origin but 4% seem to be species specific, representing lower-quality predictions or examples of de novo gene birth. We also show how structural comparisons can be used to predict domain families and their relationships, identifying examples of remote structural similarity. On the basis of these analyses, we identify several examples of human immune-related proteins with putative remote homology in prokaryotic species, illustrating the value of this resource for studying protein function and evolution across the tree of life.
A foundation model for generalizable disease detection from retinal images
Authors: Zhou Yukun , Chia Mark A. , Wagner Siegfried K. , Ayhan Murat S. , Williamson Dominic J. , Struyven Robbert R. , Liu Timing , Xu Moucheng , Lozano Mateo G. , Woodward-Court Peter , Kihara Yuka ,   UK Biobank Eye & Vision Consortium, Allen Naomi , Gallacher John E. J. , Littlejohns Thomas , Aslam Tariq , Bishop Paul , Black Graeme , Sergouniotis Panagiotis , Atan Denize , Dick Andrew D. , Williams Cathy , Barman Sarah , Barrett Jenny H. , Mackie Sarah , Braithwaite Tasanee , Carare Roxana O. , Ennis Sarah , Gibson Jane , Lotery Andrew J. , Self Jay , Chakravarthy Usha , Hogg Ruth E. , Paterson Euan , Woodside Jayne , Peto Tunde , Mckay Gareth , Mcguinness Bernadette , Foster Paul J. , Balaskas Konstantinos , Khawaja Anthony P. , Pontikos Nikolas , Rahi Jugnoo S. , Lascaratos Gerassimos , Patel Praveen J. , Chan Michelle , Chua Sharon Y. L. , Day Alexander , Desai Parul , Egan Cathy , Fruttiger Marcus , Garway-Heath David F. , Hardcastle Alison , Khaw Sir Peng T. , Moore Tony , Sivaprasad Sobha , Strouthidis Nicholas , Thomas Dhanes , Tufail Adnan , Viswanathan Ananth C. , Dhillon Bal , Macgillivray Tom , Sudlow Cathie , Vitart Veronique , Doney Alexander , Trucco Emanuele , Guggeinheim Jeremy A. , Morgan James E. , Hammond Chris J. , Williams Katie , Hysi Pirro , Harding Simon P. , Zheng Yalin , Luben Robert , Luthert Phil , Sun Zihan , McKibbin Martin , O’Sullivan Eoin , Oram Richard , Weedon Mike , Owen Chris G. , Rudnicka Alicja R. , Sattar Naveed , Steel David , Stratton Irene , Tapp Robyn , Yates Max M. , Petzold Axel , Madhusudhan Savita , Altmann Andre , Lee Aaron Y. , Topol Eric J. , Denniston Alastair K. , Alexander Daniel C. , Keane Pearse A. 
Published: September 2023

AbstractMedical artificial intelligence (AI) offers great potential for recognizing signs of health conditions in retinal images and expediting the diagnosis of eye diseases and systemic disorders1. However, the development of AI models requires substantial annotation and models are usually task-specific with limited generalizability to different clinical applications2. Here, we present RETFound, a foundation model for retinal images that learns generalizable representations from unlabelled retinal images and provides a basis for label-efficient model adaptation in several applications. Specifically, RETFound is trained on 1.6 million unlabelled retinal images by means of self-supervised learning and then adapted to disease detection tasks with explicit labels. We show that adapted RETFound consistently outperforms several comparison models in the diagnosis and prognosis of sight-threatening eye diseases, as well as incident prediction of complex systemic disorders such as heart failure and myocardial infarction with fewer labelled data. RETFound provides a generalizable solution to improve model performance and alleviate the annotation workload of experts to enable broad clinical AI applications from retinal imaging.
Bile salts enhance the susceptibility of the peach allergenic lipid transfer protein, Pru p 3, to in vitro gastrointestinal proteolysis
Authors: Wang Kai , Gali-Moya Judit , Ruano-Zaragoza Maria , Cain Kathleen , D’Auria Giovanni , Daly Matthew , Barran Perdita , Crevel René , Mills E. N. Clare 
Published: September 2023

AbstractSensitisation to the lipid transfer protein Pru p 3 is associated with severe allergic reactions to peach, the proteins stability being thought to play a role in its allergenicity. Lipid binding increases susceptibility of Pru p 3 to digestion and so the impact of bile salts on the in vitro gastrointestinal digestibility of Pru p 3 was investigated and digestion products mapped by SDS-PAGE and mass spectrometry. Bile salts enhanced the digestibility of Pru p 3 resulting in an ensemble of around 100 peptides spanning the protein’s sequence which were linked by disulphide bonds into structures of ~ 5–6 kDa. IgE binding studies with a serum panel from peach allergic subjects showed digestion reduced, but did not abolish, the IgE reactivity of Pru p 3. These data show the importance of including bile salts in vitro digestion systems and emphasise the need to profile of digestion in a manner that allows identification of immunologically relevant disulphide-linked peptide aggregates.
Differential abundance of lipids and metabolites related to SARS-CoV-2 infection and susceptibility
Authors: Albóniga Oihane E. , Moreno Elena , Martínez-Sanz Javier , Vizcarra Pilar , Ron Raquel , Díaz-Álvarez Jorge , Rosas Cancio-Suarez Marta , Sánchez-Conde Matilde , Galán Juan Carlos , Angulo Santiago , Moreno Santiago , Barbas Coral , Serrano-Villar Sergio 
Published: September 2023

AbstractThe mechanisms driving SARS-CoV-2 susceptibility remain poorly understood, especially the factors determining why unvaccinated individuals remain uninfected despite high-risk exposures. To understand lipid and metabolite profiles related with COVID-19 susceptibility and disease progression. We collected samples from an exceptional group of unvaccinated healthcare workers heavily exposed to SARS-CoV-2 but not infected (‘non-susceptible’) and subjects who became infected during the follow-up (‘susceptible’), including non-hospitalized and hospitalized patients with different disease severity providing samples at early disease stages. Then, we analyzed their plasma metabolomic profiles using mass spectrometry coupled with liquid and gas chromatography. We show specific lipids profiles and metabolites that could explain SARS-CoV-2 susceptibility and COVID-19 severity. More importantly, non-susceptible individuals show a unique lipidomic pattern characterized by the upregulation of most lipids, especially ceramides and sphingomyelin, which could be interpreted as markers of low susceptibility to SARS-CoV-2 infection. This study strengthens the findings of other researchers about the importance of studying lipid profiles as relevant markers of SARS-CoV-2 pathogenesis.
The fructose-bisphosphate, Aldolase A (ALDOA), facilitates DNA-PKcs and ATM kinase activity to regulate DNA double-strand break repair
Authors: Sobanski Thais , Suraweera Amila , Burgess Joshua T. , Richard Iain , Cheong Chee Man , Dave Keyur , Rose Maddison , Adams Mark N. , O’Byrne Kenneth J. , Richard Derek J. , Bolderson Emma 
Published: September 2023

AbstractGlucose metabolism and DNA repair are fundamental cellular processes frequently dysregulated in cancer. In this study, we define a direct role for the glycolytic Aldolase A (ALDOA) protein in DNA double-strand break (DSB) repair. ALDOA is a fructose biphosphate Aldolase that catalyses fructose-1,6-bisphosphate to glyceraldehyde 3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP), during glycolysis. Here, we show that upon DNA damage induced by ionising radiation (IR), ALDOA translocates from the cytoplasm into the nucleus, where it partially co-localises with the DNA DSB marker γ-H2AX. DNA damage was shown to be elevated in ALDOA-depleted cells prior to IR and following IR the damage was repaired more slowly. Consistent with this, cells depleted of ALDOA exhibited decreased DNA DSB repair via non-homologous end-joining and homologous recombination. In support of the defective repair observed in its absence, ALDOA was found to associate with the major DSB repair effector kinases, DNA-dependent Protein Kinase (DNA-PK) and Ataxia Telangiectasia Mutated (ATM) and their autophosphorylation was decreased when ALDOA was depleted. Together, these data establish a role for an essential metabolic protein, ALDOA in DNA DSB repair and suggests that targeting ALDOA may enable the concurrent targeting of cancer metabolism and DNA repair to induce tumour cell death.
IBA and melatonin increase trigonelline and caffeine during the induction and initiation of adventitious roots in Coffea arabica L. cuttings
Authors: de Andrade Francisco Hélio Alves , Ferreira Ana Maria Oliveira , Azevedo Lillian Magalhães , de Oliveira Santos Meline , Carvalho Gladyston Rodrigues , de Resende Mário Lucio Vilela , Bicalho Elisa Monteze , Silva Vânia Aparecida 
Published: September 2023

AbstractCaffeine and trigonelline are found in Coffea arabica, and show antioxidant roles and growth and development functions. However, there are no reports on trigonelline and caffeine in relation to coffee rooting. The aim was to evaluate the impact of application of indole-3-butyric acid (IBA) and melatonin on caffeine and trigonelline at different stages of adventitious rooting in cuttings. In addition, to study the correlation between these metabolites and H2O2, phenols, and antioxidant enzymes. Four treatments (Control, melatonin 21 µM (M21), melatonin 43 µM (M43), and IBA 7380 µM (IBA)) were used, with four replications. The growth and biochemical parameters of the antioxidant system were performed in induction, initiation, and extension rooting stages. Higher concentrations of trigonelline and caffeine quantified in the induction and initiation stages were positively correlated with higher percentage of rooted cuttings. Trigonelline and caffeine were positively correlated with H2O2 in all stages of development of adventitious roots. The correlations of trigoneline and caffeine with phenols and antioxidant enzymes reveal different profiles, depending on the phases. The results indicate that IBA and melatonin increase trigonelline and caffeine during the induction and initiation of adventitious roots in Coffea arabica cuttings, which is correlated with a higher percentage of rooted cuttings.