bluuebunny/crossref_metadata_2025_split huggingface dataset:
Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues
Authors: Abelin Jennifer G. , Bergstrom Erik J. , Rivera Keith D. , Taylor Hannah B. , Klaeger Susan , Xu Charles , Verzani Eva K. , Jackson White C. , Woldemichael Hilina B. , Virshup Maya , Olive Meagan E. , Maynard Myranda , Vartany Stephanie A. , Allen Joseph D. , Phulphagar Kshiti , Harry Kane M. , Rachimi Suzanna , Mani D. R. , Gillette Michael A. , Satpathy Shankha , Clauser Karl R. , Udeshi Namrata D. , Carr Steven A. 
Published: April 2023

AbstractSerial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each ‘ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.
Effectiveness of BNT162b2 after extending the primary series dosing interval in children and adolescents aged 5–17
Authors: Lai Francisco Tsz Tsun , Fan Min , Huang Caige , Chui Celine Sze Ling , Wan Eric Yuk Fai , Li Xue , Wong Carlos King Ho , Cheung Ching-Lung , Wong Ian Chi Kei , Chan Esther Wai Yin 
Published: April 2023

AbstractExtended intervals between the first and second doses of mRNA Covid-19 vaccines may reduce the risk of myocarditis in children and adolescents. However, vaccine effectiveness after this extension remains unclear. To examine this potential variable effectiveness, we conducted a population-based nested case-control study of children and adolescents aged 5–17 years who had received two doses of BNT162b2 in Hong Kong. From January 1 to August 15, 2022, 5396 Covid-19 cases and 202 Covid-19 related hospitalizations were identified and matched with 21,577 and 808 controls, respectively. For vaccine recipients with extended intervals [≥28 days, adjusted odds ratio 0.718, 95% Confidence Interval: 0.619, 0.833] there was a 29.2%-reduced risk of Covid-19 infection compared to those with regular intervals (21–27 days). If the threshold was set at eight weeks, the risk reduction was estimated at 43.5% (aOR 0.565, 95% CI: 0.456, 0.700). In conclusion, longer dosing intervals for children and adolescents should be considered.
Heavy tails and pruning in programmable photonic circuits for universal unitaries
Authors: Yu Sunkyu , Park Namkyoo 
Published: April 2023

AbstractDeveloping hardware for high-dimensional unitary operators plays a vital role in implementing quantum computations and deep learning accelerations. Programmable photonic circuits are singularly promising candidates for universal unitaries owing to intrinsic unitarity, ultrafast tunability and energy efficiency of photonic platforms. Nonetheless, when the scale of a photonic circuit increases, the effects of noise on the fidelity of quantum operators and deep learning weight matrices become more severe. Here we demonstrate a nontrivial stochastic nature of large-scale programmable photonic circuits—heavy-tailed distributions of rotation operators—that enables the development of high-fidelity universal unitaries through designed pruning of superfluous rotations. The power law and the Pareto principle for the conventional architecture of programmable photonic circuits are revealed with the presence of hub phase shifters, allowing for the application of network pruning to the design of photonic hardware. For the Clements design of programmable photonic circuits, we extract a universal architecture for pruning random unitary matrices and prove that “the bad is sometimes better to be removed” to achieve high fidelity and energy efficiency. This result lowers the hurdle for high fidelity in large-scale quantum computing and photonic deep learning accelerators.
Intrinsic timescales in the visual cortex change with selective attention and reflect spatial connectivity
Authors: Zeraati Roxana , Shi Yan-Liang , Steinmetz Nicholas A. , Gieselmann Marc A. , Thiele Alexander , Moore Tirin , Levina Anna , Engel Tatiana A. 
Published: April 2023

AbstractIntrinsic timescales characterize dynamics of endogenous fluctuations in neural activity. Variation of intrinsic timescales across the neocortex reflects functional specialization of cortical areas, but less is known about how intrinsic timescales change during cognitive tasks. We measured intrinsic timescales of local spiking activity within columns of area V4 in male monkeys performing spatial attention tasks. The ongoing spiking activity unfolded across at least two distinct timescales, fast and slow. The slow timescale increased when monkeys attended to the receptive fields location and correlated with reaction times. By evaluating predictions of several network models, we found that spatiotemporal correlations in V4 activity were best explained by the model in which multiple timescales arise from recurrent interactions shaped by spatially arranged connectivity, and attentional modulation of timescales results from an increase in the efficacy of recurrent interactions. Our results suggest that multiple timescales may arise from the spatial connectivity in the visual cortex and flexibly change with the cognitive state due to dynamic effective interactions between neurons.
The kidney, volume homeostasis and osmoregulation in space: current perspective and knowledge gaps
Authors: Olde Engberink Rik H. G. , van Oosten Paula J. , Weber Tobias , Tabury Kevin , Baatout Sarah , Siew Keith , Walsh Stephen B. , Valenti Giovanna , Chouker Alexander , Boutouyrie Pierre , Heer Martina , Jordan Jens , Goswami Nandu 
Published: April 2023

AbstractAlthough we have sent humans into space for more than 50 years crucial questions regarding kidney physiology, volume regulation and osmoregulation remain unanswered. The complex interactions between the renin-angiotensin-aldosterone system, the sympathetic nervous system, osmoregulatory responses, glomerular function, tubular function, and environmental factors such as sodium and water intake, motion sickness and ambient temperature make it difficult to establish the exact effect of microgravity and the subsequent fluid shifts and muscle mass loss on these parameters. Unfortunately, not all responses to actual microgravity can be reproduced with head-down tilt bed rest studies, which complicates research on Earth. Better understanding of the effects of microgravity on kidney function, volume regulation and osmoregulation are needed with the advent of long-term deep space missions and planetary surface explorations during which orthostatic intolerance complaints or kidney stone formation can be life-threatening for astronauts. Galactic cosmic radiation may be a new threat to kidney function. In this review, we summarise and highlight the current understandings of the effects of microgravity on kidney function, volume regulation and osmoregulation and discuss knowledge gaps that future studies should address.
PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships
Authors: Mills Caitlin , Marconett Crystal N. , Lewinger Juan Pablo , Mi Huaiyu 
Published: April 2023

AbstractThe vast majority of disease-associated variants identified in genome-wide association studies map to enhancers, powerful regulatory elements which orchestrate the recruitment of transcriptional complexes to their target genes’ promoters to upregulate transcription in a cell type- and timing-dependent manner. These variants have implicated thousands of enhancers in many common genetic diseases, including nearly all cancers. However, the etiology of most of these diseases remains unknown because the regulatory target genes of the vast majority of enhancers are unknown. Thus, identifying the target genes of as many enhancers as possible is crucial for learning how enhancer regulatory activities function and contribute to disease. Based on experimental results curated from scientific publications coupled with machine learning methods, we developed a cell type-specific score predictive of an enhancer targeting a gene. We computed the score genome-wide for every possible cis enhancer-gene pair and validated its predictive ability in four widely used cell lines. Using a pooled final model trained across multiple cell types, all possible gene-enhancer regulatory links in cis (~17 M) were scored and added to the publicly available PEREGRINE database (www.peregrineproj.org). These scores provide a quantitative framework for the enhancer-gene regulatory prediction that can be incorporated into downstream statistical analyses.
An effective live-attenuated Zika vaccine candidate with a modified 5′ untranslated region
Authors: Nazneen Farzana , Thompson E. Ashley , Blackwell Claire , Bai Jonathan S. , Huang Faqing , Bai Fengwei 
Published: April 2023

AbstractZika virus (ZIKV) is a mosquito-transmitted flavivirus that has caused devastating congenital Zika syndrome (CZS), including microcephaly, congenital malformation, and fetal demise in human newborns in recent epidemics. ZIKV infection can also cause Guillain-Barré syndrome (GBS) and meningoencephalitis in adults. Despite intensive research in recent years, there are no approved vaccines or antiviral therapeutics against CZS and adult Zika diseases. In this report, we developed a novel live-attenuated ZIKV strain (named Z7) by inserting 50 RNA nucleotides (nt) into the 5′ untranslated region (UTR) of a pre-epidemic ZIKV Cambodian strain, FSS13025. We used this particular ZIKV strain as it is attenuated in neurovirulence, immune antagonism, and mosquito infectivity compared with the American epidemic isolates. Our data demonstrate that Z7 replicates efficiently and produces high titers without causing apparent cytopathic effects (CPE) in Vero cells or losing the insert sequence, even after ten passages. Significantly, Z7 induces robust humoral and cellular immune responses that completely prevent viremia after a challenge with a high dose of an American epidemic ZIKV strain PRVABC59 infection in type I interferon (IFN) receptor A deficient (Ifnar1−/−) mice. Moreover, adoptive transfer of plasma collected from Z7 immunized mice protects Ifnar1−/− mice from ZIKV (strain PRVABC59) infection. These results suggest that modifying the ZIKV 5′ UTR is a novel strategy to develop live-attenuated vaccine candidates for ZIKV and potentially for other flaviviruses.
Surgical polarimetric endoscopy for the detection of laryngeal cancer
Authors: Qi Ji , Tatla Taranjit , Nissanka-Jayasuriya Eranga , Yuan Alan Yilun , Stoyanov Danail , Elson Daniel S. 
Published: April 2023

AbstractThe standard-of-care for the detection of laryngeal pathologies involves distinguishing suspicious lesions from surrounding healthy tissue via contrasts in colour and texture captured by white-light endoscopy. However, the technique is insufficiently sensitive and thus leads to unsatisfactory rates of false negatives. Here we show that laryngeal lesions can be better detected in real time by taking advantage of differences in the light-polarization properties of cancer and healthy tissues. By measuring differences in polarized-light retardance and depolarization, the technique, which we named ‘surgical polarimetric endoscopy’ (SPE), generates about one-order-of-magnitude greater contrast than white-light endoscopy, and hence allows for the better discrimination of cancerous lesions, as we show with patients diagnosed with squamous cell carcinoma. Polarimetric imaging of excised and stained slices of laryngeal tissue indicated that changes in the retardance of polarized light can be largely attributed to architectural features of the tissue. We also assessed SPE to aid routine transoral laser surgery for the removal of a cancerous lesion, indicating that SPE can complement white-light endoscopy for the detection of laryngeal cancer.
First Peoples’ knowledge leads scientists to reveal ‘fairy circles’ and termite linyji are linked in Australia
Authors: Walsh Fiona , Bidu Gladys Karimarra , Bidu Ngamaru Karimarra , Evans Theodore A. , Judson Thelma Milangka , Kendrick Peter , Michaels Alice Nampijinpa , Moore Danae , Nelson Matilda , Oldham Carolyn , Schofield Josef , Sparrow Ashley , Taylor Muuki Karimarra , Taylor Desmond Purungu , Wayne Lee Nangala , Williams Carol Milangka ,   Martu elders and experts, Taylor Wokka , Taylor Karnu , Taylor Nola , Williams Wirnta , Simpson Muni Rita , Robinson Mayapi , Judson Junju , Oates Dawn , Biljabu Jakayu , Biljabu Daphne , Peterson Patricia , Robinson Nayapi , Mac Gardener Kirriwirri , Edwards Titikiya , Williams Rosie , Rogers Rena , Gibbs Dulcie , Chapman Nancy , Nyaju Rosie , James Jeffery Jangala 
Published: April 2023

AbstractIn the past, when scientists encountered and studied ‘new’ environmental phenomena, they rarely considered the existing knowledge of First Peoples (also known as Indigenous or Aboriginal people). The scientific debate over the regularly spaced bare patches (so-called fairy circles) in arid grasslands of Australian deserts is a case in point. Previous researchers used remote sensing, numerical modelling, aerial images and field observations to propose that fairy circles arise from plant self-organization. Here we present Australian Aboriginal art and narratives, and soil excavation data, that suggest these regularly spaced, bare and hard circles in grasslands are pavement nests occupied by Drepanotermes harvester termites. These circles, called linyji (Manyjilyjarra language) or mingkirri (Warlpiri language), have been used by Aboriginal people in their food economies and for other domestic and sacred purposes across generations. Knowledge of the linyji has been encoded in demonstration and oral transmission, ritual art and ceremony and other media. While the exact origins of the bare circles are unclear, being buried in deep time and Jukurrpa, termites need to be incorporated as key players in a larger system of interactions between soil, water and grass. Ecologically transformative feedbacks across millennia of land use and manipulation by Aboriginal people must be accounted for. We argue that the co-production of knowledge can both improve the care and management of those systems and support intergenerational learning within and across diverse cultures.
Live-attenuated vaccine sCPD9 elicits superior mucosal and systemic immunity to SARS-CoV-2 variants in hamsters
Authors: Nouailles Geraldine , Adler Julia M. , Pennitz Peter , Peidli Stefan , Teixeira Alves Luiz Gustavo , Baumgardt Morris , Bushe Judith , Voss Anne , Langenhagen Alina , Langner Christine , Martin Vidal Ricardo , Pott Fabian , Kazmierski Julia , Ebenig Aileen , Lange Mona V. , Mühlebach Michael D. , Goekeri Cengiz , Simmons Szandor , Xing Na , Abdelgawad Azza , Herwig Susanne , Cichon Günter , Niemeyer Daniela , Drosten Christian , Goffinet Christine , Landthaler Markus , Blüthgen Nils , Wu Haibo , Witzenrath Martin , Gruber Achim D. , Praktiknjo Samantha D. , Osterrieder Nikolaus , Wyler Emanuel , Kunec Dusan , Trimpert Jakob 
Published: April 2023

AbstractVaccines play a critical role in combating the COVID-19 pandemic. Future control of the pandemic requires improved vaccines with high efficacy against newly emerging SARS-CoV-2 variants and the ability to reduce virus transmission. Here we compare immune responses and preclinical efficacy of the mRNA vaccine BNT162b2, the adenovirus-vectored spike vaccine Ad2-spike and the live-attenuated virus vaccine candidate sCPD9 in Syrian hamsters, using both homogeneous and heterologous vaccination regimens. Comparative vaccine efficacy was assessed by employing readouts from virus titrations to single-cell RNA sequencing. Our results show that sCPD9 vaccination elicited the most robust immunity, including rapid viral clearance, reduced tissue damage, fast differentiation of pre-plasmablasts, strong systemic and mucosal humoral responses, and rapid recall of memory T cells from lung tissue after challenge with heterologous SARS-CoV-2. Overall, our results demonstrate that live-attenuated vaccines offer advantages over currently available COVID-19 vaccines.
A relay velocity model infers cell-dependent RNA velocity
Authors: Li Shengyu , Zhang Pengzhi , Chen Weiqing , Ye Lingqun , Brannan Kristopher W. , Le Nhat-Tu , Abe Jun-ichi , Cooke John P. , Wang Guangyu 
Published: April 2023

AbstractRNA velocity provides an approach for inferring cellular state transitions from single-cell RNA sequencing (scRNA-seq) data. Conventional RNA velocity models infer universal kinetics from all cells in an scRNA-seq experiment, resulting in unpredictable performance in experiments with multi-stage and/or multi-lineage transition of cell states where the assumption of the same kinetic rates for all cells no longer holds. Here we present cellDancer, a scalable deep neural network that locally infers velocity for each cell from its neighbors and then relays a series of local velocities to provide single-cell resolution inference of velocity kinetics. In the simulation benchmark, cellDancer shows robust performance in multiple kinetic regimes, high dropout ratio datasets and sparse datasets. We show that cellDancer overcomes the limitations of existing RNA velocity models in modeling erythroid maturation and hippocampus development. Moreover, cellDancer provides cell-specific predictions of transcription, splicing and degradation rates, which we identify as potential indicators of cell fate in the mouse pancreas.
Phase engineering of layered anode materials during ion-intercalation in Van der Waal heterostructures
Authors: Parida Shayani , Dobley Arthur , Carter C. Barry , Dongare Avinash M. 
Published: April 2023

AbstractTransition metal dichalcogenides (TMDs) are a class of 2D materials demonstrating promising properties, such as high capacities and cycling stabilities, making them strong candidates to replace graphitic anodes in lithium-ion batteries. However, certain TMDs, for instance, MoS2, undergo a phase transformation from 2H to 1T during intercalation that can affect the mobility of the intercalating ions, the anode voltage, and the reversible capacity. In contrast, select TMDs, for instance, NbS2 and VS2, resist this type of phase transformation during Li-ion intercalation. This manuscript uses density functional theory simulations to investigate the phase transformation of TMD heterostructures during Li-, Na-, and K-ion intercalation. The simulations suggest that while stacking MoS2 layers with NbS2 layers is unable to limit this 2H → 1T transformation in MoS2 during Li-ion intercalation, the interfaces effectively stabilize the 2H phase of MoS2 during Na- and K-ion intercalation. However, stacking MoS2 layers with VS2 is able to suppress the 2H → 1T transformation of MoS2 during the intercalation of Li, Na, and K-ions. The creation of TMD heterostructures by stacking MoS2 with layers of non-transforming TMDs also renders theoretical capacities and electrical conductivities that are higher than that of bulk MoS2.
Onchocerciasis transmission status in some endemic communities of Cross River State, Nigeria after two decades of mass drug administration with ivermectin
Authors: Chikezie Friday Maduka , Opara Kenneth Nnamdi , Ubulom Peace Mayen Edwin , Yaro Clement Ameh , Al-Akeel Rasha Khalifah , Osei-Atweneboana Mike Yaw , Alexiou Athanasios , Papadakis Marios , Batiha Gaber El-Saber 
Published: April 2023

AbstractOnchocerciasis is a parasitic disease transmitted by black flies. Human onchocerciasis is a public health and socioeconomic problem in Nigeria. Its prevalence and morbidity have reduced over the years because of control efforts especially, Mass Drug Administration with ivermectin. The current goal is to eliminate the disease transmission by 2030. Understanding the changes in transmission patterns in Cross River State is critical to elimination of onchocerciasis in Nigeria. This study was designed to determine the transmission dynamics of onchocerciasis in Cross River State after over two decades of mass ivermectin distribution in endemic communities. Agbokim, Aningeje, Ekong Anaku and Orimekpang are four endemic communities from three Local Government Areas of the State selected for this study. Transmission indices such as infectivity rates, biting rates and transmission potentials, parity rates and diurnal biting activities were determined. A total of 15,520 adult female flies were caught on human baits, Agbokim (2831), Aningeje (6209), Ekong Anaku (4364) and Orimekpang (2116). A total of 9488 and 5695 flies were collected during the rainy and dry seasons respectively in the four communities studied. The differences in relative abundance among the communities were statistically significant (P < 0.001). Monthly and seasonal fly numbers varied significantly (P < 0.008). There were differences in diurnal biting activities of flies in this study at different hours of the day and different months. The peak monthly biting rates were 5993 (Agbokim, October), 13,134 (Aningeje, October), 8680 (Ekong Anaku, October) and 6120 (Orimekpang, September) bites/person/month while the lowest monthly biting rates were 400 (Agbokim, November), 2862 (Aningeje, August), 1405 (Ekong Anaku, January) and 0.0 (Orimekpang, November and December) bites/person/month. Differences in biting rates among the study communities were significant (P < 0.001). The peak monthly transmission potential in Aningeje was 160 infective bites/person/month in the month of February while the lowest (except for months with no transmission) was 42 infective bites/person/month in the month of April. All other study sites had no ongoing transmission in this study. Transmission studies showed that there is progress toward transmission interruption especially in 3 out of the four studied areas. Molecular O-150 poolscreen studies is required to confirm the true transmission situation in the areas.