bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole exome sequencing in Alopecia Areata identifies rare variants in KRT82
Authors: Erjavec Stephanie O. , Gelfman Sahar , Abdelaziz Alexa R. , Lee Eunice Y. , Monga Isha , Alkelai Anna , Ionita-Laza Iuliana , Petukhova Lynn , Christiano Angela M. 
Published: February 2022

AbstractAlopecia areata is a complex genetic disease that results in hair loss due to the autoimmune-mediated attack of the hair follicle. We previously defined a role for both rare and common variants in our earlier GWAS and linkage studies. Here, we identify rare variants contributing to Alopecia Areata using a whole exome sequencing and gene-level burden analyses approach on 849 Alopecia Areata patients compared to 15,640 controls. KRT82 is identified as an Alopecia Areata risk gene with rare damaging variants in 51 heterozygous Alopecia Areata individuals (6.01%), achieving genome-wide significance (p = 2.18E−07). KRT82 encodes a hair-specific type II keratin that is exclusively expressed in the hair shaft cuticle during anagen phase, and its expression is decreased in Alopecia Areata patient skin and hair follicles. Finally, we find that cases with an identified damaging KRT82 variant and reduced KRT82 expression have elevated perifollicular CD8 infiltrates. In this work, we utilize whole exome sequencing to successfully identify a significant Alopecia Areata disease-relevant gene, KRT82, and reveal a proposed mechanism for rare variant predisposition leading to disrupted hair shaft integrity.
Shaping lightwaves in time and frequency for optical fiber communication
Authors: Cho Junho , Chen Xi , Raybon Greg , Che Di , Burrows Ellsworth , Olsson Samuel , Tkach Robert 
Published: February 2022

AbstractIn optical communications, sphere shaping is used to limit the energy of lightwaves to within a certain value over a period. This minimizes the energy required to contain information, allowing the rate of information transmission to approach the theoretical limit if the transmission medium is linear. However, when shaped lightwaves are transmitted through optical fiber, Kerr nonlinearity manifests itself as nonlinear interference in a peculiar way, potentially lowering communications capacity. In this article, we show that the impact of sphere shaping on Kerr nonlinearity varies with chromatic dispersion, shaping block length and symbol rate, and that this impact can be predicted using a novel statistical measure of light energy. As a practical consequence, by optimally controlling the parameters of sphere-shaped lightwaves, it is experimentally demonstrated that the information rate can be increased by up to 25% in low-dispersion channels on a 2824 km dispersion-managed wavelength-division multiplexed optical fiber link.
Direct assessment of confinement effect in zeolite-encapsulated subnanometric metal species
Authors: Liu Lichen , Lopez-Haro Miguel , Perez-Omil Jose Antonio , Boronat Mercedes , Calvino Jose J. , Corma Avelino 
Published: February 2022

AbstractSubnanometric metal species confined inside the microporous channels/cavities of zeolites have been demonstrated as stable and efficient catalysts. The confinement interaction between the metal species and zeolite framework has been proposed to play the key role for stabilization, though the confinement interaction is elusive to be identified and measured. By combining theoretical calculations, imaging simulation and experimental measurements based on the scanning transmission electron microscopy-integrated differential phase contrast imaging technique, we have studied the location and coordination environment of isolated iridium atoms and clusters confined in zeolite. The image analysis results indicate that the local strain is intimately related to the strength of metal-zeolite interaction and a good correlation is found between the zeolite deformation energy, the charge state of the iridium species and the local absolute strain. The direct observation of confinement with subnanometric metal species encapsulated in zeolites provides insights to understand their structural features and catalytic consequences.
Associative detachment in anion-atom reactions involving a dipole-bound electron
Authors: Hassan Saba Zia , Tauch Jonas , Kas Milaim , Nötzold Markus , Carrera Henry López , Endres Eric S. , Wester Roland , Weidemüller Matthias 
Published: February 2022

AbstractAssociative electronic detachment (AED) between anions and neutral atoms leads to the detachment of the anion’s electron resulting in the formation of a neutral molecule. It plays a key role in chemical reaction networks, like the interstellar medium, the Earth’s ionosphere and biochemical processes. Here, a class of AED involving a closed-shell anion (OH−) and alkali atoms (rubidium) is investigated by precisely controlling the fraction of electronically excited rubidium. Reaction with the ground state atom gives rise to a stable intermediate complex with an electron solely bound via dipolar forces. The stability of the complex is governed by the subtle interplay of diabatic and adiabatic couplings into the autodetachment manifold. The measured rate coefficients are in good agreement with ab initio calculations, revealing pronounced steric effects. For excited state rubidium, however, a lower reaction rate is observed, indicating dynamical stabilization processes suppressing the coupling into the autodetachment region. Our work provides a stringent test of ab initio calculations on anion-neutral collisions and constitutes a generic, conceptual framework for understanding electronic state dependent dynamics in AEDs.
Mark-release-recapture experiment in Burkina Faso demonstrates reduced fitness and dispersal of genetically-modified sterile malaria mosquitoes
Authors: Yao Franck Adama , Millogo Abdoul-Azize , Epopa Patric Stephane , North Ace , Noulin Florian , Dao Koulmaga , Drabo Mouhamed , Guissou Charles , Kekele Souleymane , Namountougou Moussa , Ouedraogo Robert Kossivi , Pare Lea , Barry Nourou , Sanou Roger , Wandaogo Haida , Dabire Roch K. , McKemey Andrew , Tripet Frederic , Diabaté Abdoulaye 
Published: February 2022

AbstractEvery year, malaria kills approximately 405,000 people in Sub-Saharan Africa, most of them children under the age of five years. In many countries, progress in malaria control has been threatened by the rapid spread of resistance to antimalarial drugs and insecticides. Novel genetic mosquito control approaches could play an important role in future integrated malaria control strategies. In July 2019, the Target Malaria consortium proceeded with the first release of hemizygous genetically-modified (GM) sterile and non-transgenic sibling males of the malaria mosquito Anopheles coluzzii in Burkina Faso. This study aimed to determine the potential fitness cost associated to the transgene and gather important information related to the dynamic of transgene-carrying mosquitoes, crucial for next development steps. Bayesian estimations confirmed that GM males had lower survival and were less mobile than their wild type (WT) siblings. The estimated male population size in Bana village, at the time of the release was 28,000 - 37,000. These results provide unique information about the fitness and behaviour of released GM males that will inform future releases of more effective strains of the A. gambiae complex.
Machine learning-based integration develops an immune-derived lncRNA signature for improving outcomes in colorectal cancer
Authors: Liu Zaoqu , Liu Long , Weng Siyuan , Guo Chunguang , Dang Qin , Xu Hui , Wang Libo , Lu Taoyuan , Zhang Yuyuan , Sun Zhenqiang , Han Xinwei 
Published: February 2022

AbstractLong noncoding RNAs (lncRNAs) are recently implicated in modifying immunology in colorectal cancer (CRC). Nevertheless, the clinical significance of immune-related lncRNAs remains largely unexplored. In this study, we develope a machine learning-based integrative procedure for constructing a consensus immune-related lncRNA signature (IRLS). IRLS is an independent risk factor for overall survival and displays stable and powerful performance, but only demonstrates limited predictive value for relapse-free survival. Additionally, IRLS possesses distinctly superior accuracy than traditional clinical variables, molecular features, and 109 published signatures. Besides, the high-risk group is sensitive to fluorouracil-based adjuvant chemotherapy, while the low-risk group benefits more from bevacizumab. Notably, the low-risk group displays abundant lymphocyte infiltration, high expression of CD8A and PD-L1, and a response to pembrolizumab. Taken together, IRLS could serve as a robust and promising tool to improve clinical outcomes for individual CRC patients.
Pluripotency factors determine gene expression repertoire at zygotic genome activation
Authors: Gao Meijiang , Veil Marina , Rosenblatt Marcus , Riesle Aileen Julia , Gebhard Anna , Hass Helge , Buryanova Lenka , Yampolsky Lev Y. , Grüning Björn , Ulianov Sergey V. , Timmer Jens , Onichtchouk Daria 
Published: February 2022

AbstractAwakening of zygotic transcription in animal embryos relies on maternal pioneer transcription factors. The interplay of global and specific functions of these proteins remains poorly understood. Here, we analyze chromatin accessibility and time-resolved transcription in single and double mutant zebrafish embryos lacking pluripotency factors Pou5f3 and Sox19b. We show that two factors modify chromatin in a largely independent manner. We distinguish four types of direct enhancers by differential requirements for Pou5f3 or Sox19b. We demonstrate that changes in chromatin accessibility of enhancers underlie the changes in zygotic expression repertoire in the double mutants. Pou5f3 or Sox19b promote chromatin accessibility of enhancers linked to the genes involved in gastrulation and ventral fate specification. The genes regulating mesendodermal and dorsal fates are primed for activation independently of Pou5f3 and Sox19b. Strikingly, simultaneous loss of Pou5f3 and Sox19b leads to premature expression of genes, involved in regulation of organogenesis and differentiation.
Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants
Authors: Yu Huihui , Li Mu , Sandhu Jaspreet , Sun Guangchao , Schnable James C. , Walia Harkamal , Xie Weibo , Yu Bin , Mower Jeffrey P. , Zhang Chi 
Published: February 2022

AbstractIt is challenging to identify the smallest microexons (≤15-nt) due to their small size. Consequently, these microexons are often misannotated or missed entirely during genome annotation. Here, we develop a pipeline to accurately identify 2,398 small microexons in 10 diverse plant species using 990 RNA-seq datasets, and most of them have not been annotated in the reference genomes. Analysis reveals that microexons tend to have increased detained flanking introns that require post-transcriptional splicing after polyadenylation. Examination of 45 conserved microexon clusters demonstrates that microexons and associated gene structures can be traced back to the origin of land plants. Based on these clusters, we develop an algorithm to genome-wide model coding microexons in 132 plants and find that microexons provide a strong phylogenetic signal for plant organismal relationships. Microexon modeling reveals diverse evolutionary trajectories, involving microexon gain and loss and alternative splicing. Our work provides a comprehensive view of microexons in plants.
Optical van-der-Waals forces in molecules: from electronic Bethe-Salpeter calculations to the many-body dispersion model
Authors: Ambrosetti Alberto , Umari Paolo , Silvestrelli Pier Luigi , Elliott Joshua , Tkatchenko Alexandre 
Published: February 2022

AbstractMolecular forces induced by optical excitations are connected to a wide range of phenomena, from chemical bond dissociation to intricate biological processes that underpin vision. Commonly, the description of optical excitations requires the solution of computationally demanding electronic Bethe-Salpeter equation (BSE). However, when studying non-covalent interactions in large-scale systems, more efficient methods are desirable. Here we introduce an effective approach based on coupled quantum Drude oscillators (cQDO) as represented by the many-body dispersion model. We find that the cQDO Hamiltonian yields semi-quantitative agreement with BSE calculations and that both attractive and repulsive optical van der Waals (vdW) forces can be induced by light. These optical-vdW interactions dominate over vdW dispersion in the long-distance regime, showing a complexity that grows with system size. Evidence of highly non-local forces in the human formaldehyde dehydrogenase 1MC5 protein suggests the ability to selectively activate collective molecular vibrations by photoabsorption, in agreement with recent experiments.
Dissolving salt is not equivalent to applying a pressure on water
Authors: Zhang Chunyi , Yue Shuwen , Panagiotopoulos Athanassios Z. , Klein Michael L. , Wu Xifan 
Published: February 2022

AbstractSalt water is ubiquitous, playing crucial roles in geological and physiological processes. Despite centuries of investigations, whether or not water’s structure is drastically changed by dissolved ions is still debated. Based on density functional theory, we employ machine learning based molecular dynamics to model sodium chloride, potassium chloride, and sodium bromide solutions at different concentrations. The resulting reciprocal-space structure factors agree quantitatively with neutron diffraction data. Here we provide clear evidence that the ions in salt water do not distort the structure of water in the same way as neat water responds to elevated pressure. Rather, the computed structural changes are restricted to the ionic first solvation shells intruding into the hydrogen bond network, beyond which the oxygen radial-distribution function does not undergo major change relative to neat water. Our findings suggest that the widely cited pressure-like effect on the solvent in Hofmeister series ionic solutions should be carefully revisited.
Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic
Authors: Izdebski A. , Guzowski P. , Poniat R. , Masci L. , Palli J. , Vignola C. , Bauch M. , Cocozza C. , Fernandes R. , Ljungqvist F. C. , Newfield T. , Seim A. , Abel-Schaad D. , Alba-Sánchez F. , Björkman L. , Brauer A. , Brown A. , Czerwiński S. , Ejarque A. , Fiłoc M. , Florenzano A. , Fredh E. D. , Fyfe R. , Jasiunas N. , Kołaczek P. , Kouli K. , Kozáková R. , Kupryjanowicz M. , Lagerås P. , Lamentowicz M. , Lindbladh M. , López-Sáez J. A. , Luelmo-Lautenschlaeger R. , Marcisz K. , Mazier F. , Mensing S. , Mercuri A. M. , Milecka K. , Miras Y. , Noryśkiewicz A. M. , Novenko E. , Obremska M. , Panajiotidis S. , Papadopoulou M. L. , Pędziszewska A. , Pérez-Díaz S. , Piovesan G. , Pluskowski A. , Pokorny P. , Poska A. , Reitalu T. , Rösch M. , Sadori L. , Sá Ferreira C. , Sebag D. , Słowiński M. , Stančikaitė M. , Stivrins N. , Tunno I. , Veski S. , Wacnik A. , Masi A. 
Published: February 2022

AbstractThe Black Death (1347–1352ce) is the most renowned pandemic in human history, believed by many to have killed half of Europe’s population. However, despite advances in ancient DNA research that conclusively identified the pandemic’s causative agent (bacteriumYersinia pestis), our knowledge of the Black Death remains limited, based primarily on qualitative remarks in medieval written sources available for some areas of Western Europe. Here, we remedy this situation by applying a pioneering new approach, ‘big data palaeoecology’, which, starting from palynological data, evaluates the scale of the Black Death’s mortality on a regional scale across Europe. We collected pollen data on landscape change from 261 radiocarbon-dated coring sites (lakes and wetlands) located across 19 modern-day European countries. We used two independent methods of analysis to evaluate whether the changes we see in the landscape at the time of the Black Death agree with the hypothesis that a large portion of the population, upwards of half, died within a few years in the 21 historical regions we studied. While we can confirm that the Black Death had a devastating impact in some regions, we found that it had negligible or no impact in others. These inter-regional differences in the Black Death’s mortality across Europe demonstrate the significance of cultural, ecological, economic, societal and climatic factors that mediated the dissemination and impact of the disease. The complex interplay of these factors, along with the historical ecology of plague, should be a focus of future research on historical pandemics.
Tropical larval and juvenile fish critical swimming speed (U-crit) and morphology data
Authors: Fisher Rebecca , Leis Jeffrey M. , Hogan J. Derek , Bellwood David R. , Wilson Shaun K. , Job Suresh D. 
Published: February 2022

AbstractFish swimming capacity is a key life history trait critical to many aspects of their ecology. U-crit (critical) swimming speeds provide a robust, repeatable relative measure of swimming speed that can serve as a useful surrogate for other measures of swimming performance. Here we collate and make available one the most comprehensive datasets on U-crit swimming abilities of tropical marine fish larvae and pelagic juveniles, most of which are reef associated as adults. The dataset includes U-crit speed measurements for settlement stage fishes across a large range of species and families obtained mostly from field specimens collected in light traps and crest nets; and the development of swimming abilities throughout ontogeny for a range of species using reared larvae. In nearly all instances, the size of the individual was available, and in many cases, data include other morphological measurements (e.g. “propulsive area”) useful for predicting swimming capacity. We hope these data prove useful for further studies of larval swimming performance and other broader syntheses.
From Himba indigenous knowledge to engineered Fe2O3 UV-blocking green nanocosmetics
Authors: Havenga D. , Akoba R. , Menzi L. , Azizi S. , Sackey J. , Swanepoel N. , Gibaud A. , Maaza M. 
Published: February 2022

AbstractThis contribution reports on the physical properties of the natural Namibian red Ochre used by the Himba Community in a form of a formulation, so called Otjize as a skin protective and beauty cream. The morphological and crystallographic studies of this red ochre validated its nano-scaled dominating phase of rhombohedral α-Fe2O3 nanocrystals with an additional hydrolized oxide component in a form of γ-FeOOH. The optical investigations showed that such a red ochre exhibits an exceptional UV filtration and a significant IR reflectivity substantiating its effectiveness as an effective UV-blocking & solar heat IR reflector in support of the low skin cancer rate within the Namibian Himba community. In addition, such nanocrystals exhibited a non-negligible antibacterial response against E. Coli & S. Aurus. This study seems confirming the effectiveness of the indigenous Otjize as an effective skin UV protection cream with a sound antimicrobial efficacy against e-Coli & S-Aurus.
Effect of magnetic field on improvement of photocatalytic performance of V2O5/TiO2 nanoheterostructure films prepared by sparking method
Authors: Pooseekheaw Porntipa , Thongpan Winai , Kantarak Ekkapong , sroila Wattikon , Kumpika Tewasin , Singjai Pisith 
Published: February 2022

AbstractOur porous V2O5/TiO2 nanoheterostructure films (with a Ti/V atomic ratio of 1:1) were fabricated via a single-step sparking method using a strong magnetic field (0.5 T) without annealing requirement for the first time. We found that the magnetic flux arrangement has effect on film crystallization, unique morphology, large specific surface area, and surprisingly controllable phase structure of the films. An amorphous TV film was transformed to the TiO2 (anatase/rutile) phase (for TVN) and V2O5–VO2 mixed-phase (for TVH) without destroying the mesopores from an annealing process. Moreover, the TVH sample able to improve the degradation rate up to 270% compared with pre-annealed TV films and up to 30% with post-annealed (400 °C) TVA films. In this paper, the influence of magnetic flux arrangement on structural, morphological, optical, and photocatalytic properties of prepared sample have been investigated and reported.
Verification of rebuild-up effect on superficial cardiac lesion of ventricular tachycardia using 3-D printed phantom in volumetric-modulated arc therapy planning
Authors: Roh Shiwon , Shin Jun-Bong , Bae Yong-Ki , Kim Jungmin , Hong Semie , Lee Jeong-Woo 
Published: February 2022

AbstractThe aim of the study was to evaluate dose distributions on the superficial cardiac lesion surrounded by low-density lungs. Volumetric modulated arc therapy (VMAT) technique was applied to optimize the dose distribution using the anisotropic analytic algorithm (AAA) and Acuros XB algorithm (AXB) using the 3-D printed cardiac phantom. We used four full and half arcs with 6-MV and 15-MV photons to investigate the rebuild-up effect near the planning target volume (PTV). Depending on the calculation algorithm (AAA vs. AXB) for full arcs plans, V95of PTV differed by 27% for 6-MV and 29% for 15-MV, and D95for 6-MV and 15-MV shows 24% and 30%, respectively. The maximum doses in the AXB plans on PTV were 5.1% higher than those in AAA plans at 6-MV, and 3.8% higher at 15-MV. In addition, half arcs treatment plans showed a very similar tendency with full arcs plans. Film dosimetry showed significant differences from the planned results in the AAA plans. Particularly, the dose mismatch occurred between the cardiac PTV and the left lung interface. In the case of 6-MV plans calculated by AAA, the maximum dose increased from 4.1 to 7.7% in the PTV. Furthermore, it showed that 50% of the width of dose profiles was reduced by 1.3 cm in the 6-MV plan. Conversely, in the case of the plans using the AXB algorithm, the maximum dose increased by 2.0–5.0%. In contrast to the AAA algorithm, the dose patterns at the interface demonstrated a good agreement with the plans. Dose fluctuation on the interface between superficial cardiac lesions and low-density lungs can lead to an error in the estimation of accurate dose delivery for the case of VT SBRT.
Raster plots machine learning to predict the seizure liability of drugs and to identify drugs
Authors: Matsuda N. , Odawara A. , Kinoshita K. , Okamura A. , Shirakawa T. , Suzuki I. 
Published: February 2022

AbstractIn vitro microelectrode array (MEA) assessment using human induced pluripotent stem cell (iPSC)-derived neurons holds promise as a method of seizure and toxicity evaluation. However, there are still issues surrounding the analysis methods used to predict seizure and toxicity liability as well as drug mechanisms of action. In the present study, we developed an artificial intelligence (AI) capable of predicting the seizure liability of drugs and identifying drugs using deep learning based on raster plots of neural network activity. The seizure liability prediction AI had a prediction accuracy of 98.4% for the drugs used to train it, classifying them correctly based on their responses as either seizure-causing compounds or seizure-free compounds. The AI also made concentration-dependent judgments of the seizure liability of drugs that it was not trained on. In addition, the drug identification AI implemented using the leave-one-sample-out scheme could distinguish among 13 seizure-causing compounds as well as seizure-free compound responses, with a mean accuracy of 99.9 ± 0.1% for all drugs. These AI prediction models are able to identify seizure liability concentration-dependence, rank the level of seizure liability based on the seizure liability probability, and identify the mechanism of the action of compounds. This holds promise for the future of in vitro MEA assessment as a powerful, high-accuracy new seizure liability prediction method.