bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phylogeny-informed characterisation of global tetrapod traits addresses data gaps and biases
Authors: Moura Mario R. , Ceron Karoline , Guedes Jhonny J. M. , Chen-Zhao Rosana , Sica Yanina V. , Hart Julie , Dorman Wendy , Portmann Julia M. , Gonzalez-del-Pliego Pamela , Ranipeta Ajay , Catenazzi Alessandro , Werneck Fernanda P. , Toledo Luís Felipe , Upham Nathan S. , Tonini João F. R. , Colston Timothy J. , Guralnick Robert , Bowie Rauri C. K. , Pyron R. Alexander , Jetz Walter 
Published: March 2023

AbstractTetrapods (amphibian, reptiles, birds and mammals) are model systems for global biodiversity science, but continuing data gaps, limited data standardisation, and ongoing flux in taxonomic nomenclature constrain integrative research on this group and potentially cause biased inference. We combined and harmonised taxonomic, spatial, phylogenetic, and attribute data with phylogeny-based multiple imputation to provide a comprehensive data resource (TetrapodTraits 1.0.0) that includes values, predictions, and sources for body size, activity time, micro- and macrohabitat, ecosystem, threat status, biogeography, insularity, environmental preferences and human influence, for all 33,281 tetrapod species covered in recent fully sampled phylogenies. We assess gaps and biases across taxa and space, finding that shared data missing in attribute values increased with taxon-level completeness and richness across clades. Prediction of missing attribute values using multiple imputation revealed substantial changes in estimated macroecological patterns. These results highlight biases incurred by non-random missingness and strategies to best address them. While there is an obvious need for further data collection and updates, our phylogeny--informed database of tetrapod traits can support a more comprehensive representation of tetrapod species and their attributes in ecology, evolution, and conservation research.
Subjective sleep onset latency is influenced by sleep structure and body heat loss in human subjects
Authors: Iijima Ryusei , Kadooka Akari , Sugawara Kairi , Fushimi Momo , Hosoe Mizuki , Aritake-Okada Sayaka 
Published: March 2023

ABSTRACTObjectivesThe current study examined the relationship between subjective SOL, sleep structure, changes in skin and body temperature, and subjective evaluation in healthy young adults to elucidate the pathophysiological mechanisms of insomnia.MethodsTwenty-eight participants (mean age: 21.5 ± 0.5 years) with no sleep problems participated in a 1-hour polysomnographic recording that obtained objective sleep parameters during the daytime while skin and body temperatures were recorded. The distal–proximal skin temperature gradient (DPG) was calculated. Subjective parameters, such as subjective SOL, sleep time, and restorative sleepiness, were evaluated before and after sleep.ResultsMost participants estimated their sleep latency as being longer than their actual SOL (13.7 min vs. 7.6 min). Objective SOL was significantly correlated with each sleep stage parameter whereas subjective SOL was negatively correlated with stage N2 sleep duration (Rho = −0.454, p = 0.020), slow-wave activity and delta power (Rho = −0.500, p = 0.011, Rho = −0.432, p = 0.031, respectively), and ΔDPG (the degree of reduction of heat loss before and after lights-off). Stepwise regression analysis showed that ΔDPG was the strongest predictive factor in explaining the length of subjective SOL.ConclusionsThe degree of heat dissipation before falling asleep contributed most to the sensation of falling asleep in healthy young adults. This finding may be helpful for elucidating the physiological mechanisms of insomnia and its treatment.STATEMENT OF SIGNIFICANCEThe time estimate ability is also activated during sleep. However, some insomniacs have abnormalities in this function and suffer from sleep state misperception, which is a discrepancy between subjective and objective sleep time. They often overestimate the sleep onset latency. We investigated the relationship between subjective sleep onset latency, sleep structure, EEG frequency components, and body temperature during the process of falling asleep in healthy adults. It was suggested that the Stage N2 duration, the amounts of slow wave activity around after lights-out, and the degree of heat dissipation before falling asleep may be related to the perception of falling asleep. These results are expected to contribute to the understanding of the pathophysiological mechanisms and to the treatment of insomnia.
Visual field asymmetries vary between adolescents and adults
Authors: Carrasco Marisa , Myers Caroline , Roberts Mariel 
Published: March 2023

ABSTRACTFor human adults, visual perception varies around isoeccentric locations (with polar angle at a constant distance from the center of gaze). The same visual information yields better performance along the horizontal than vertical meridian (horizontal vertical anisotropy, HVA) and along the lower than upper vertical meridian (vertical meridian asymmetry, VMA). For children, performance is better along the horizontal than vertical meridian (HVA) but does not differ between the lower and the upper vertical meridian. Here, we investigated whether the extent of the HVA varies and the VMA emerges and fully develops during adolescence, or whether the VMA only emerges in adulthood. We found that for adolescents, performance yields both HVA and VMA, but both are less pronounced than those for adults.
Cannabis and cannabinoids in dermatology: protocol for a systematic review and meta-analysis of quantitative outcomes
Authors: Sermsaksasithorn Pim , Nopsopon Tanawin , Samuthpongtorn Chatpol , Chotirosniramit Korn , Pongpirul Krit 
Published: March 2023

AbstractFollowing the discovery of various effects on skin function by modifying endocannabinoid systems, multiple preclinical studies have revealed the promise of cannabis and cannabinoids in the treatment of a variety of skin diseases. However, its clinical efficacy is still debated. This systematic review aims to evaluate the therapeutic efficacy of cannabis and cannabinoids in dermatological conditions and diseases. The protocol has been prepared using the Preferred Items for Systematic Review and Meta-analysis Protocols (PRISMA-P) guidelines and has been registered with the International Prospective Register of Systematic Reviews (PROSPERO: CRD42023397189). PubMed, EMBASE, SCOPUS, Cochrane Central Register of Controlled Trials (CENTRAL), and Web of Science will be used for the systemic search. The outcomes will be an improvement in dermatological characteristics, including disease-specific composite scores and objective and subjective outcomes of skin conditions. This systematic review will provide valuable information on dermatological therapy of cannabis and cannabinoids and could be the start of future research and medicinal applications.
Modelling the association between neutralizing antibody levels and SARS-CoV-2 viral dynamics : implications to define correlates of protection against infection
Authors: Lingas Guillaume , Planas Delphine , Péré Hélène , Duffy Darragh , Staropoli Isabelle , Porrot Françoise , Guivel-Benhassine Florence , Chapuis Nicolas , Gobeaux Camille , Veyer David , Delaugerre Constance , Goff Jérôme Le , Getten Prunelle , Hadjadj Jérôme , Bellino Adèle , Parfait Béatrice , Treluyer Jean-Marc , Schwartz Olivier , Guedj Jérémie , Kernéis Solen , Terrier Benjamin 
Published: March 2023

AbstractBackgroundWhile anti-SARS-CoV-2 antibody kinetics have been well described in large populations of vaccinated individuals, we still poorly understand how they evolve during a natural infection and how this impacts viral clearance.MethodsFor that purpose, we analyzed the kinetics of both viral load and neutralizing antibody levels in a prospective cohort of individuals during acute infection by Alpha variant.ResultsUsing a mathematical model, we show that the progressive increase in neutralizing antibodies leads to a shortening of the half-life of both infected cells and infectious viral particles. We estimated that the neutralizing activity reached 90% of its maximal level within 8 days after symptoms onset and could reduce the half-life of both infected cells and infectious virus by a 6-fold factor, thus playing a key role to achieve rapid viral clearance. Using this model, we conducted a simulation study to predict in a more general context the protection conferred by the existence of pre-existing neutralization, due to either vaccination or prior infection. We predicted that a neutralizing activity, as measured by ED50>103, could reduce by 50% the risk of having viral load detectable by standard PCR assays and by 99% the risk of having viral load above the threshold of cultivable virus.ConclusionsThis threshold value for the neutralizing activity could be used to identify individuals with poor protection against disease acquisition.
LINC01117 inhibits invasion and migration of lung adenocarcinoma through influencing EMT process
Authors: Liu Linjun , Ren Wenjia , Du Licheng , Xu Ke , Zhou Yubai 
Published: March 2023

AbstractBackgroundStudying the mechanism of action of LincRNAs in lung adenocarcinoma (LUAD) is of great importance for an in-depth understanding of the molecular mechanism of lung adeno carcinogenesis and development.ObjectiveTo identify long-stranded non-coding RNAs that are specifically highly expressed in LUAD cells and to investigate their function in LUAD cells to provide new potential targets for targeting LUAD therapy.MethodsThis study used publicly available data downloaded from The Cancer Genome Atlas (TCGA) database. Construction of siRNA and overexpression plasmid-packed lentiviral constructs were used to knock down and increase the expression of LINC01117 in LUAD cells. The effect of LINC01117 on LUAD cell migration and invasion was verified by scratch assays and Transwell assays. Western blot assays were performed to verify the effect of knocking down LINC01117 expression on key proteins of the EMT process.ResultsLINC01117 expression was upregulated in LUAD tissues and cell lines. Clinical correlation and prognostic analyses showed that LINC01117 was associated with poorer clinical features (staging and N classification) and poorer prognosis and could be analyzed as an independent prognostic factor. Cell migration and invasion were significantly inhibited in the knockdown group compared to the control group; in contrast, cell migration and invasion were promoted in the overexpression group. The expression of N-cadherin and vimentin, molecular markers of the EMT process, was elevated in the overexpression group, and the expression of E-cadherin was decreased. Conclusions: LINC01117 was highly expressed in LUAD cells, and inhibition of LINC01117 expression significantly inhibited the migration and invasion of LUAD cells, while overexpression of LINC01117 significantly promoted the migration and invasion of LUAD cells, and may affect the migration ability of LUAD cells through the EMT process. It suggests that LINC01117 may play a key role in the occurrence and development of LUAD.
Closely relatedBacteroidesof the murine intestinal microbiota affect each other’s growth positively or negatively
Authors: Fokt Hanna , Sakalyte Gabija , Unni Rahul , Abukhalaf Mohammad , Cassidy Liam , Marinos Georgios , Godfroid Maxime , Kinfu Birhanu M , Schmitz Ruth A , Kaleta Christoph , Tholey Andreas , Baines John F , Dagan Tal , Unterweger Daniel 
Published: March 2023

AbstractThe mammalian intestine is a unique ecosystem for thousands of bacterial species and strains. How naturally coexisting bacteria of the microbiota interact with each other is not yet fully understood. Here, we isolated formerly coexisting, closely related strains of the genusBacteroidesfrom the intestines of healthy, wild-derived mice. The effect of one strain on another strain’s growth was tested in 169 pairsin vitro. We find a vast diversity of growth promoting and growth inhibiting activities. A strong positive effect was observed between two strains with differing metabolisms. Growth inhibition among a subset of strains was associated with the known bacterial toxin bacteroidetocin B. Across all strains, we observed growth promotion more often than growth inhibition. The effects were independent of two strains belonging to the same or different species. In some cases, one species differed in its effect on another according to host origin. These findings on obligate host-associated bacteria demonstrate that closely related and naturally coexisting strains have the potential to affect each other’s growth positively or negatively. These results have implications for our basic understanding of host-associated microbes and the design of synthetic microbial communities.
In vivoreprogramming of wound-resident cells generates skin with hair
Authors: Moriwaki Yuta , Qi Shen , Okada Hiroyuki , Zening Du , Suga Shogo , Kato Motoi , Numahata Takao , Li Kexin , Kanayama Koji , Okazaki Mutsumi , Hirabayashi Yusuke , Belmonte Juan Carlos Izpisua , Hojo Hironori , Kurita Masakazu 
Published: March 2023

Summary ParagraphMammalian skin appendages, such as hair follicles and sweat glands, are complex mini-organs formed during skin development1, 2. As wounds heal, the resulting scar tissue lacks skin appendages. The clinical regeneration of skin appendages is an ongoing challenge3, 4. Skin epithelial tissues have been regeneratedin vivoby cellular reprogramming5, 6, but thede novogeneration of skin appendages has not previously been achieved. Here, we show that transplantation of a type of epithelial cell and two types of mesenchymal cells, reprogrammed from adult mouse subcutaneous mesenchymal cells to mimic developing skin cells, resulted in the generation of skin-appendage-like structures. Furthermore, with the development of a new AAV serotype,in vivoreprogramming of wound-resident cells with the same reprogramming factors generates skin withde novoappendages in adult mice. These findings may provide new therapeutic avenues for skin regeneration and frequent aging-associated skin appendage disorders, such as hair loss and dry skin, and may extend to other tissues and organs. This study also provides the potential forde novogeneration of complex organsin vivo.
Beyond the Genetic Code:A Tissue Code?
Authors: Boman Bruce M. , Dinh Thien-Nam , Decker Keith , Emerick Brooks , Modarai Shirin , Opdenaker Lynn , Fields Jeremy Z. , Raymond Christopher , Schleiniger Gilberto 
Published: March 2023

ABSTRACTThe genetic code determines how the precise amino acid sequence of proteins is specified by genomic information in cells. But what specifies the precise histologic organization of cells in plant and animal tissues is unclear. We now hypothesize that another code, thetissue code, exists at an even higher level of complexity which determines how tissue organization is dynamically maintained. Accordingly, we modeled spatial and temporal asymmetries of cell division and established that five simple mathematical laws (“the tissue code”) convey a set of biological rules that maintain the specific organization and continuous self-renewal dynamics of cells in tissues. These laws might even help us understand wound healing, and how tissue disorganization leads to birth defects and tissue pathology like cancer.
Phylogenetic analysis shows canine distemper virus outbreak in stray dogs possibly occurs through spillover from wild carnivore reservoirs
Authors: Manandhar Prajwol , Napit Rajindra , Pradhan Saman M , Rajbhandari Pragun G , Moravek Jessie A , Joshi Pranav R , Shrestha Rima D , Karmacharya Dibesh 
Published: March 2023

AbstractCanine distemper is a highly contagious, often fatal disease caused by canine distemper virus (CDV) in domestic dogs and wild carnivores. The virus has caused mass epidemics in wild carnivores of high conservation value such as tigers, lions and leopards in both wild and captivity. Hence, understanding and managing CDV outbreaks is particularly important in Nepal, which is home to many species of threatened wild carnivores including tigers, leopards, snow leopards, dholes and wolves, as well as a large population of stray dogs. Previous studies have suggested that CDV may pose a threat to wild carnivores, but there has not been any studies characterizing the genetic strains of the virus circulating in Nepal’s carnivores. We collected invasive and non-invasive biological samples from stray dogs in Kathmandu Valley and genetically characterized the strains of CDV in the dogs to belong to Asia-5 lineage by using phylogenetic analysis. The same lineage also contained CDV strains isolated from dogs, civets, red panda and lions in India. Based on our phylogenetic analysis, we think it is likely that in Nepal CDV is maintained through sylvatic cycle among small carnivore guilds allowing the recurring spillovers and outbreaks among free-ranging stray dogs and possibly large carnivores. It is crucial to prevent the virus transmission from reservoir hosts to other species, especially threatened populations of large carnivores in Nepal. Hence, we recommend for regular surveillance of CDV targeting small wild carnivores as well as vaccination programmes to control the disease spillover in stray dogs.
IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events
Authors: Fujiwara Rina , Zhai Si-Nan , Liang Dongming , Tracey Matthew , Ma Xu-Kai , Shah Aayushi P. , Fields Christopher J. , Mendoza-Figueroa María Saraí , Meline Michele C. , Tatomer Deirdre C. , Yang Li , Wilusz Jeremy E. 
Published: March 2023

ABSTRACTThe metazoan-specific Integrator complex catalyzes 3’ end processing of small nuclear RNAs (snRNAs) as well as premature transcription termination events that attenuate expression of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are always required for complex function. Here, we show that IntS6 (Integrator subunit 6) over-expression is sufficient to block Integrator function at a subset ofDrosophilaprotein-coding genes, while having no effect on snRNA processing or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits from the rest of the Integrator complex and thus the only loci affected are those where the phosphatase module is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not associate with Integrator, are also sufficient to inhibit Integrator function at select loci. Altogether, these results show that the phosphatase module is critical and limiting at only a subset of Integrator regulated genes and point to recruitment of PP2A via IntS6 as a tunable step that can be used to modulate transcription termination efficiency.
MAUDGAN: Motion Artifact Unsupervised Disentanglement Generative Adversarial Network of Multicenter MRI Data with Different Brain tumors
Authors: Safari Mojtaba , Fatemi Ali , Archambault Louis 
Published: March 2023

AbstractPurposeThis study proposed a novel retrospective motion reduction method named motion artifact unsupervised disentanglement generative adversarial network (MAUDGAN) that reduces the motion artifacts from brain images with tumors and metastases. The MAUDGAN was trained using a mutlimodal multicenter 3D T1-Gd and T2-fluid attenuated inversion recovery MRI images.ApproachThe motion artifact with different artifact levels were simulated ink-space for the 3D T1-Gd MRI images. The MAUDGAN consisted of two generators, two discriminators and two feature extractor networks constructed using the residual blocks. The generators map the images from content space to artifact space and vice-versa. On the other hand, the discriminators attempted to discriminate the content codes to learn the motion-free and motion-corrupted content spaces.ResultsWe compared the MAUDGAN with the CycleGAN and Pix2pix-GAN. Qualitatively, the MAUDGAN could remove the motion with the highest level of soft-tissue contrasts without adding spatial and frequency distortions. Quantitatively, we reported six metrics including normalized mean squared error (NMSE), structural similarity index (SSIM), multi-scale structural similarity index (MS-SSIM), peak signal-to-noise ratio (PSNR), visual information fidelity (VIF), and multi-scale gradient magnitude similarity deviation (MS-GMSD). The MAUDGAN got the lowest NMSE and MS-GMSD. On average, the proposed MAUDGAN reconstructed motion-free images with the highest SSIM, PSNR, and VIF values and comparable MS-SSIM values.ConclusionsThe MAUDGAN can disentangle motion artifacts from the 3D T1-Gd dataset under a multimodal framework. The motion reduction will improve automatic and manual post-processing algorithms including auto-segmentations, registrations, and contouring for guided therapies such as radiotherapy and surgery.
Relapse timing is associated with distinct evolutionary dynamics in DLBCL
Authors: Hilton Laura K. , Ngu Henry S. , Collinge Brett , Dreval Kostiantyn , Ben-Neriah Susana , Rushton Christopher K. , Wong Jasper C.H. , Cruz Manuela , Roth Andrew , Boyle Merrill , Meissner Barbara , Slack Graham W. , Farinha Pedro , Craig Jeffrey W. , Gerrie Alina S. , Freeman Ciara L. , Villa Diego , Crump Michael , Shepherd Lois , Hay Annette E. , Kuruvilla John , Savage Kerry J. , Kridel Robert , Karsan Aly , Marra Marco A. , Sehn Laurie H. , Steidl Christian , Morin Ryan D. , Scott David W. 
Published: March 2023

AbstractDiffuse large B-cell lymphoma (DLBCL) is cured in over 60% of patients, but outcomes are poor for patients with relapsed or refractory disease (rrDLBCL). Here, we performed whole genome/exome sequencing (WGS/WES) on tumors from 73 serially-biopsied patients with rrDLBCL. Based on the observation that outcomes to salvage therapy/autologous stem cell transplantation are related to time-to-relapse, we stratified patients into groups according to relapse timing to explore the relationship to genetic divergence and sensitivity to salvage immunochemotherapy. The degree of mutational divergence increased with time between biopsies, yet tumor pairs were mostly concordant for cell-of-origin, oncogene rearrangement status and genetics-based subgroup. In patients with highly divergent tumors, several genes acquired exclusive mutations independently in each tumor, which, along with concordance of genetics-based subgroups, suggests that the earliest mutations in a shared precursor cell constrain tumor evolution. These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease.