bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil
Authors: Naslavsky Michel S. , Scliar Marilia O. , Yamamoto Guilherme L. , Wang Jaqueline Yu Ting , Zverinova Stepanka , Karp Tatiana , Nunes Kelly , Ceroni José Ricardo Magliocco , de Carvalho Diego Lima , da Silva Simões Carlos Eduardo , Bozoklian Daniel , Nonaka Ricardo , dos Santos Brito Silva Nayane , da Silva Souza Andreia , de Souza Andrade Heloísa , Passos Marília Rodrigues Silva , Castro Camila Ferreira Bannwart , Mendes-Junior Celso T. , Mercuri Rafael L. V. , Miller Thiago L. A. , Buzzo Jose Leonel , Rego Fernanda O. , Araújo Nathalia M. , Magalhães Wagner C. S. , Mingroni-Netto Regina Célia , Borda Victor , Guio Heinner , Rojas Carlos P. , Sanchez Cesar , Caceres Omar , Dean Michael , Barreto Mauricio L. , Lima-Costa Maria Fernanda , Horta Bernardo L. , Tarazona-Santos Eduardo , Meyer Diogo , Galante Pedro A. F. , Guryev Victor , Castelli Erick C. , Duarte Yeda A. O. , Passos-Bueno Maria Rita , Zatz Mayana 
Published: March 2022

AbstractAs whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still scarce. Here, we present a high-coverage WGS dataset of 1,171 highly admixed elderly Brazilians from a census-based cohort, providing over 76 million variants, of which ~2 million are absent from large public databases. WGS enables identification of ~2,000 previously undescribed mobile element insertions without previous description, nearly 5 Mb of genomic segments absent from the human genome reference, and over 140 alleles from HLA genes absent from public resources. We reclassify and curate pathogenicity assertions for nearly four hundred variants in genes associated with dominantly-inherited Mendelian disorders and calculate the incidence for selected recessive disorders, demonstrating the clinical usefulness of the present study. Finally, we observe that whole-genome and HLA imputation could be significantly improved compared to available datasets since rare variation represents the largest proportion of input from WGS. These results demonstrate that even smaller sample sizes of underrepresented populations bring relevant data for genomic studies, especially when exploring analyses allowed only by WGS.
The molecular basis of FimT-mediated DNA uptake during bacterial natural transformation
Authors: Braus Sebastian A. G. , Short Francesca L. , Holz Stefanie , Stedman Matthew J. M. , Gossert Alvar D. , Hospenthal Manuela K. 
Published: March 2022

AbstractNaturally competent bacteria encode sophisticated protein machinery for the uptake and translocation of exogenous DNA into the cell. If this DNA is integrated into the bacterial genome, the bacterium is said to be naturally transformed. Most competent bacterial species utilise type IV pili for the initial DNA uptake step. These proteinaceous cell-surface structures are composed of thousands of pilus subunits (pilins), designated as major or minor according to their relative abundance in the pilus. Here, we show that the minor pilin FimT plays an important role in the natural transformation of Legionella pneumophila. We use NMR spectroscopy, in vitro DNA binding assays and in vivo transformation assays to understand the molecular basis of FimT’s role in this process. FimT binds to DNA via an electropositive patch, rich in arginines, several of which are well-conserved and located in a conformationally flexible C-terminal tail. FimT orthologues from other Gammaproteobacteria share the ability to bind to DNA. Our results suggest that FimT plays an important role in DNA uptake in a wide range of competent species.
Evolution of the SARS-CoV-2 spike protein in the human host
Authors: Wrobel Antoni G. , Benton Donald J. , Roustan Chloë , Borg Annabel , Hussain Saira , Martin Stephen R. , Rosenthal Peter B. , Skehel John J. , Gamblin Steven J. 
Published: March 2022

AbstractRecently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.
Active label cleaning for improved dataset quality under resource constraints
Authors: Bernhardt Mélanie , Castro Daniel C. , Tanno Ryutaro , Schwaighofer Anton , Tezcan Kerem C. , Monteiro Miguel , Bannur Shruthi , Lungren Matthew P. , Nori Aditya , Glocker Ben , Alvarez-Valle Javier , Oktay Ozan 
Published: March 2022

AbstractImperfections in data annotation, known as label noise, are detrimental to the training of machine learning models and have a confounding effect on the assessment of model performance. Nevertheless, employing experts to remove label noise by fully re-annotating large datasets is infeasible in resource-constrained settings, such as healthcare. This work advocates for a data-driven approach to prioritising samples for re-annotation—which we term “active label cleaning". We propose to rank instances according to estimated label correctness and labelling difficulty of each sample, and introduce a simulation framework to evaluate relabelling efficacy. Our experiments on natural images and on a specifically-devised medical imaging benchmark show that cleaning noisy labels mitigates their negative impact on model training, evaluation, and selection. Crucially, the proposed approach enables correcting labels up to 4 × more effectively than typical random selection in realistic conditions, making better use of experts’ valuable time for improving dataset quality.
The indirect effect of mRNA-based COVID-19 vaccination on healthcare workers’ unvaccinated household members
Authors: Salo Jussipekka , Hägg Milla , Kortelainen Mika , Leino Tuija , Saxell Tanja , Siikanen Markku , Sääksvuori Lauri 
Published: March 2022

AbstractMass vaccination is effective in reducing SARS-CoV-2 infections among vaccinated individuals. However, it remains unclear how effectively COVID-19 vaccines prevent people from spreading the virus to their close contacts. Using nationwide administrative datasets on SARS-CoV-2 infections, vaccination records, demographics, and unique household IDs, we conducted an observational cohort study to estimate the direct and indirect effectiveness of mRNA-based COVID-19 vaccines in reducing infections among vaccinated healthcare workers and their unvaccinated household members. Our estimates for adults imply indirect effectiveness of 39.1% (95% CI: −7.1% to 65.3%) two weeks and 39.0% (95% CI: 18.9% to 54.0%) eight weeks after the second dose. We find that the indirect effect of mRNA-based COVID-19 vaccines within households is smaller for unvaccinated children than for adults and statistically insignificant. Here, we show that mRNA-based COVID-19 vaccines are associated with a reduction in SARS-CoV-2 infections not only among vaccinated individuals but also among unvaccinated adult household members in a real-world setting.
Oxygen-sensitive methylation of ULK1 is required for hypoxia-induced autophagy
Authors: Li Jingyi , Zhang Tao , Ren Tao , Liao Xiaoyu , Hao Yilong , Lim Je Sun , Lee Jong-Ho , Li Mi , Shao Jichun , Liu Rui 
Published: March 2022

AbstractHypoxia is a physiological stress that frequently occurs in solid tissues. Autophagy, a ubiquitous degradation/recycling system in eukaryotic cells, renders cells tolerant to multiple stressors. However, the mechanisms underlying autophagy initiation upon hypoxia remains unclear. Here we show that protein arginine methyltransferase 5 (PRMT5) catalyzes symmetrical dimethylation of the autophagy initiation protein ULK1 at arginine 170 (R170me2s), a modification removed by lysine demethylase 5C (KDM5C). Despite unchanged PRMT5-mediated methylation, low oxygen levels decrease KDM5C activity and cause accumulation of ULK1 R170me2s. Dimethylation of ULK1 promotes autophosphorylation at T180, a prerequisite for ULK1 activation, subsequently causing phosphorylation of Atg13 and Beclin 1, autophagosome formation, mitochondrial clearance and reduced oxygen consumption. Further, expression of a ULK1 R170K mutant impaired cell proliferation under hypoxia. This study identifies an oxygen-sensitive methylation of ULK1 with an important role in hypoxic stress adaptation by promoting autophagy induction.
Landscape of adenosine-to-inosine RNA recoding across human tissues
Authors: Gabay Orshay , Shoshan Yoav , Kopel Eli , Ben-Zvi Udi , Mann Tomer D. , Bressler Noam , Cohen‐Fultheim Roni , Schaffer Amos A. , Roth Shalom Hillel , Tzur Ziv , Levanon Erez Y. , Eisenberg Eli 
Published: March 2022

AbstractRNA editing by adenosine deaminases changes the information encoded in the mRNA from its genomic blueprint. Editing of protein-coding sequences can introduce novel, functionally distinct, protein isoforms and diversify the proteome. The functional importance of a few recoding sites has been appreciated for decades. However, systematic methods to uncover these sites perform poorly, and the full repertoire of recoding in human and other mammals is unknown. Here we present a new detection approach, and analyze 9125 GTEx RNA-seq samples, to produce a highly-accurate atlas of 1517 editing sites within the coding region and their editing levels across human tissues. Single-cell RNA-seq data shows protein recoding contributes to the variability across cell subpopulations. Most highly edited sites are evolutionary conserved in non-primate mammals, attesting for adaptation. This comprehensive set can facilitate understanding of the role of recoding in human physiology and diseases.
Macro- and atomic-scale observations of a one-dimensional heterojunction in a nickel and palladium nanowire complex
Authors: Wakizaka Masanori , Kumagai Shohei , Wu Hashen , Sonobe Takuya , Iguchi Hiroaki , Yoshida Takefumi , Yamashita Masahiro , Takaishi Shinya 
Published: March 2022

AbstractThe creation of low-dimensional heterostructures for intelligent devices is a challenging research topic; however, macro- and atomic-scale connections in one-dimensional (1D) electronic systems have not been achieved yet. Herein, we synthesize a heterostructure comprising a 1D Mott insulator [Ni(chxn)2Br]Br2 (1; chxn = 1R-2R-diaminocyclohexane) and a 1D Peierls or charge-density-wave insulator [Pd(chxn)2Br]Br2 (2) using stepwise electrochemical growth. It can be considered as the first example of electrochemical liquid-phase epitaxy applied to molecular-based heterostructures with a macroscopic scale. Moreover, atomic-resolution scanning tunneling microscopy images reveal a modulation of the electronic state in the heterojunction region with a length of five metal atoms (~ 2.5 nm), that is a direct evidence for the atomic-scale connection of 1 and 2. This is the first time that the heterojunction in the 1D chains has been shown and examined experimentally at macro- and atomic-scale. This study thus serves as proof of concept for heterojunctions in 1D electronic systems.
A top-down strategy for amorphization of hydroxyl compounds for electrocatalytic oxygen evolution
Authors: Liu Shangheng , Geng Shize , Li Ling , Zhang Ying , Ren Guomian , Huang Bolong , Hu Zhiwei , Lee Jyh-Fu , Lai Yu-Hong , Chu Ying-Hao , Xu Yong , Shao Qi , Huang Xiaoqing 
Published: March 2022

AbstractAmorphous materials have attracted increasing attention in diverse fields due to their unique properties, yet their controllable fabrications still remain great challenges. Here, we demonstrate a top-down strategy for the fabrications of amorphous oxides through the amorphization of hydroxides. The versatility of this strategy has been validated by the amorphizations of unitary, binary and ternary hydroxides. Detailed characterizations indicate that the amorphization process is realized by the variation of coordination environment during thermal treatment, where the M–OH octahedral structure in hydroxides evolves to M–O tetrahedral structure in amorphous oxides with the disappearance of the M–M coordination. The optimal amorphous oxide (FeCoSn(OH)6-300) exhibits superior oxygen evolution reaction (OER) activity in alkaline media, where the turnover frequency (TOF) value is 39.4 times higher than that of FeCoSn(OH)6. Moreover, the enhanced OER performance and the amorphization process are investigated with density functional theory (DFT) and molecule dynamics (MD) simulations. The reported top-down fabrication strategy for fabricating amorphous oxides, may further promote fundamental research into and practical applications of amorphous materials for catalysis.
Small symmetry-breaking triggering large chiroptical responses of Ag70 nanoclusters
Authors: Luo Xi-Ming , Gong Chun-Hua , Pan Fangfang , Si Yubing , Yuan Jia-Wang , Asad Muhammad , Dong Xi-Yan , Zang Shuang-Quan , Mak Thomas C. W. 
Published: March 2022

AbstractThe origins of the chiroptical activities of inorganic nanostructures have perplexed scientists, and deracemization of high-nuclearity metal nanoclusters (NCs) remains challenging. Here, we report a single-crystal structure of Rac-Ag70 that contains enantiomeric pairs of 70-nuclearity silver clusters with 20 free valence electrons (Ag70), and each of these clusters is a doubly truncated tetrahedron with pseudo-T symmetry. A deracemization method using a chiral metal precursor not only stabilizes Ag70 in solution but also enables monitoring of the gradual enlargement of the electronic circular dichroism (CD) responses and anisotropy factor gabs. The chiral crystals of R/S-Ag70 in space group P21 containing a pseudo-T-symmetric enantiomeric NC show significant kernel-based and shell-based CD responses. The small symmetry breaking of Td symmetry arising from local distortion of Ag−S motifs and rotation of the apical Ag3 trigons results in large chiroptical responses. This work opens an avenue to construct chiral medium/large-sized NCs and nanoparticles, which are promising for asymmetric catalysis, nonlinear optics, chiral sensing, and biomedicine.
Waning of SARS-CoV-2 booster viral-load reduction effectiveness
Authors: Levine-Tiefenbrun Matan , Yelin Idan , Alapi Hillel , Herzel Esma , Kuint Jacob , Chodick Gabriel , Gazit Sivan , Patalon Tal , Kishony Roy 
Published: March 2022

AbstractThe BNT162b2 COVID-19 vaccine has been shown to reduce viral load of breakthrough infections (BTIs), an important factor affecting infectiousness. This viral-load protective effect has been waning with time post the second vaccine and later restored with a booster shot. It is currently unclear though for how long this regained effectiveness lasts. Analyzing Ct values of SARS-CoV-2 qRT-PCR tests of over 22,000 infections during a Delta-variant-dominant period in Israel, we find that this viral-load reduction effectiveness significantly declines within months post the booster dose. Adjusting for age, sex and calendric date, Ct values of RdRp gene initially increases by 2.7 [CI: 2.3-3.0] relative to unvaccinated in the first month post the booster dose, yet then decays to a difference of 1.3 [CI: 0.7-1.9] in the second month and becomes small and insignificant in the third to fourth months. The rate and magnitude of this post-booster decline in viral-load reduction effectiveness mirror those observed post the second vaccine. These results suggest rapid waning of the booster’s effectiveness in reducing infectiousness, possibly affecting community-level spread of the virus.
Comparative treatments of a green tattoo ink with Ruby, Nd:YAG nano- and picosecond lasers in normal and array mode
Authors: Cecchetti Daniele , Bauer Elvira Maria , Guerriero Ettore , Sennato Simona , Tagliatesta Pietro , Tagliaferri Marco , Cerri Luca , Carbone Marilena 
Published: March 2022

AbstractThe tattoos removal has become an issue upon spread of the tattooing practice worldwide and hindsight regrets. Lasers are typically used for the purpose, though some colours such as green are considered “recalcitrant” to the treatment. In the current investigation, we aim at determining the efficacy of removal of a green ink water dispersion, using 5 laser treatments: Nd:YAG nano- and picosecond lasers in normal and array mode and Ruby nanosecond laser, keeping the total irradiated energy constant. The UV–Vis spectroscopy of the treated samples indicate that Nd:YAG picosecond laser is most effective, and the Ruby nanosecond laser is the least efficient. Fragment compounds generated from the pigment and siloxanes are common to all treatments, whereas hydrocarbon emerge by a larger amount upon Nd:YAG nanosecond treatment. Fibres are formed upon picosecond treatments and when operating in array mode, and lamellae are achieved by Ruby nanosecond laser treatment. Residual particles suspensions are very heterogeneous upon nanosecond treatments.
Non-local correlation dynamics in two-dimensional graphene
Authors: Mohamed Abdel-Baset A. , Abdel-Aty Abdel-Haleem , Qasymeh Montasir , Eleuch Hichem 
Published: March 2022

AbstractWe explore the non-local correlation dynamics in a Graphene sheet of disordered electrons in a two-dimensional honeycomb lattice, containing two sublattices, induced by the interaction range of impurity potentials of two Dirac points. The Bell function, uncertainty-induced non-locality, and concurrence are used to investigate the formation and robustness of the non-local correlation between the honeycomb lattice and the Dirac point. The generated lattice-point non-local correlations are explored when the lattice-point system is initially in the uncorrelated state. Due to the lattice-point interaction, the resulting Bell-function non-locality and entanglement concurrence satisfy the hierarchy principle. The generated uncertainty-induced non-locality correlation has a higher degree of stability and robustness than the Bell non-locality and concurrence. We analyze the robustness of the initial maximal non-local correlations under the effects of the band parameter, the intravalley scattering processes, the wave numbers, and the intrinsic decoherence. The formation and stability of lattice-point correlations are highly dependent on the honeycomb lattice and Dirac point characteristics.
An online cursive handwritten medical words recognition system for busy doctors in developing countries for ensuring efficient healthcare service delivery
Authors: Tabassum Shaira , Abedin Nuren , Rahman Md Mahmudur , Rahman Md Moshiur , Ahmed Mostafa Taufiq , Islam Rafiqul , Ahmed Ashir 
Published: March 2022

AbstractDoctors in developing countries are too busy to write digital prescriptions. Ninety-seven percent of Bangladeshi doctors write handwritten prescriptions, the majority of which lack legibility. Prescriptions are harder to read as they contain multiple languages. This paper proposes a machine learning approach to recognize doctors’ handwriting to create digital prescriptions. A ‘Handwritten Medical Term Corpus’ dataset is developed containing 17,431 samples of 480 medical terms. In order to improve the recognition efficiency, this paper introduces a data augmentation technique to widen the variety and increase the sample size. A sequence of line data is extracted from the augmented images of 1,591,100 samples and fed to a Bidirectional Long Short-Term Memory (LSTM) network. Data augmentation includes pattern Rotating, Shifting, and Stretching (RSS). Eight different combinations are applied to evaluate the strength of the proposed method. The result shows 93.0% average accuracy (max: 94.5%, min: 92.1%) using Bidirectional LSTM and RSS data augmentation. This accuracy is 19.6% higher than the recognition result with no data expansion. The proposed handwritten recognition technology can be installed in a smartpen for busy doctors which will recognize the writings and digitize them in real-time. It is expected that the smartpen will contribute to reduce medical errors, save medical costs and ensure healthy living in developing countries.
A compact two elements MIMO antenna for 5G communication
Authors: Ahmad Ashfaq , Choi Dong-you , Ullah Sadiq 
Published: March 2022

AbstractThis study presents a simple, miniaturized, and low-profile multiple-input multiple-output (MIMO) antenna operating at 29 GHz with reduced mutual coupling between the antenna elements for futuristic 5G communication. The proposed design employs two radiating elements with slits in the radiators to produce high isolation among the antenna radiators. The MIMO antenna maintains a compact structure of 11.4 × 5.3 mm2, which is the smallest size compared to previous 5G antennas. Roger’s 4350B laminate was employed as a substrate material. At 29 GHz, low mutual coupling of − 36 dB, low envelope correlation coefficient (ECC < 0.001), and high diversity gain (DG > 9.8 dB) are achieved. The proposed design is examined in terms of the S-parameters, diversity gain, radiation pattern, and envelope correlation. Compared to the straight antenna element, an improvement of − 20 dB is observed in the isolation for both the simulated and measured results.
Deep learning based sarcopenia prediction from shear-wave ultrasonographic elastography and gray scale ultrasonography of rectus femoris muscle
Authors: Yi Jisook , Shin YiRang , Hahn Seok , Lee Young Han 
Published: March 2022

AbstractWe aim to evaluate the performance of a deep convolutional neural network (DCNN) in predicting the presence or absence of sarcopenia using shear-wave elastography (SWE) and gray-scale ultrasonography (GSU) of rectus femoris muscle as an imaging biomarker. This retrospective study included 160 pair sets of GSU and SWE images (n = 160) from December 2018 and July 2019. Two radiologists scored the echogenicity of muscle on GSU (4-point score). Among them, 141 patients underwent CT and their L3 skeletal muscle index (SMI) were measured to categorize the presence or absence of sarcopenia. For DCNN, we used three CNN architectures (VGG19, ResNet-50, DenseNet 121). The accuracies of DCNNs for sarcopenia classification were 70.0–80.0% (based on SWE) and 65.0–75.0% (based on GSU). The DCNN application to SWE images highlights the utility of deep-learning base SWE for sarcopenia prediction. DCNN application to SWE images might be a potentially useful biomarker to predict sarcopenic status.