bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bosonic spinons in anisotropic triangular antiferromagnets
Authors: Choi Youngsu , Lee Suheon , Lee Je-Ho , Lee Seungyeol , Seong Maeng-Je , Choi Kwang-Yong 
Published: November 2021

AbstractAnisotropic triangular antiferromagnets can host two primary spin excitations, namely, spinons and triplons. Here, we utilize polarization-resolved Raman spectroscopy to assess the statistics and dynamics of spinons in Ca3ReO5Cl2. We observe a magnetic Raman continuum consisting of one- and two-pair spinon-antispinon excitations as well as triplon excitations. The twofold rotational symmetry of the spinon and triplon excitations are distinct from magnons. The strong thermal evolution of spinon scattering is compatible with the bosonic spinon scenario. The quasilinear spinon hardening with decreasing temperature is envisaged as the ordering of one-dimensional topological defects. This discovery will enable a fundamental understanding of novel phenomena induced by lowering spatial dimensionality in quantum spin systems.
CSC software corrects off-target mediated gRNA depletion in CRISPR-Cas9 essentiality screens
Authors: Perez Alexendar R. , Sala Laura , Perez Richard K. , Vidigal Joana A. 
Published: November 2021

AbstractOff-target effects are well established confounders of CRISPR negative selection screens that impair the identification of essential genomic loci. In particular, non-coding regulatory elements and repetitive regions are often difficult to target with specific gRNAs, effectively precluding the unbiased screening of a large portion of the genome. To address this, we developed CRISPR Specificity Correction (CSC), a computational method that corrects for the effect of off-targeting on gRNA depletion. We benchmark CSC with data from the Cancer Dependency Map and show that it significantly improves the overall sensitivity and specificity of viability screens while preserving known essentialities, particularly for genes targeted by highly promiscuous gRNAs. We believe this tool will further enable the functional annotation of the genome as it represents a robust alternative to the traditional filtering strategy of discarding unspecific guides from the analysis. CSC is an open-source software that can be seamlessly integrated into current CRISPR analysis pipelines.
Unsupervised deep learning identifies semantic disentanglement in single inferotemporal face patch neurons
Authors: Higgins Irina , Chang Le , Langston Victoria , Hassabis Demis , Summerfield Christopher , Tsao Doris , Botvinick Matthew 
Published: November 2021

AbstractIn order to better understand how the brain perceives faces, it is important to know what objective drives learning in the ventral visual stream. To answer this question, we model neural responses to faces in the macaque inferotemporal (IT) cortex with a deep self-supervised generative model, β-VAE, which disentangles sensory data into interpretable latent factors, such as gender or age. Our results demonstrate a strong correspondence between the generative factors discovered by β-VAE and those coded by single IT neurons, beyond that found for the baselines, including the handcrafted state-of-the-art model of face perception, the Active Appearance Model, and deep classifiers. Moreover, β-VAE is able to reconstruct novel face images using signals from just a handful of cells. Together our results imply that optimising the disentangling objective leads to representations that closely resemble those in the IT at the single unit level. This points at disentangling as a plausible learning objective for the visual brain.
Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders
Authors: Pagliaroli Luca , Porazzi Patrizia , Curtis Alyxandra T. , Scopa Chiara , Mikkers Harald M. M. , Freund Christian , Daxinger Lucia , Deliard Sandra , Welsh Sarah A. , Offley Sarah , Ott Connor A. , Calabretta Bruno , Brugmann Samantha A. , Santen Gijs W. E. , Trizzino Marco 
Published: November 2021

AbstractSubunit switches in the BAF chromatin remodeler are essential during development. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause neurodevelopmental disorders, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we leveraged ARID1B+/− Coffin-Siris patient-derived iPSCs and modeled cranial neural crest cell (CNCC) formation. We discovered that ARID1B is active only during the first stage of this process, coinciding with neuroectoderm specification, where it is part of a lineage-specific BAF configuration (ARID1B-BAF). ARID1B-BAF regulates exit from pluripotency and lineage commitment by attenuating thousands of enhancers and genes of the NANOG and SOX2 networks. In iPSCs, these enhancers are maintained active by ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A- to ARID1B-BAF, eliciting attenuation of the NANOG/SOX2 networks and triggering pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at the pluripotency enhancers throughout all stages of CNCC formation. This leads to persistent NANOG/SOX2 activity which impairs CNCC formation. Despite showing the typical neural crest signature (TFAP2A/SOX9-positive), ARID1B-haploinsufficient CNCCs are also aberrantly NANOG-positive. These findings suggest a connection between ARID1B mutations, neuroectoderm specification and a pathogenic mechanism for Coffin-Siris syndrome.
Defect detection in atomic-resolution images via unsupervised learning with translational invariance
Authors: Guo Yueming , Kalinin Sergei V. , Cai Hui , Xiao Kai , Krylyuk Sergiy , Davydov Albert V. , Guo Qianying , Lupini Andrew R. 
Published: November 2021

AbstractCrystallographic defects can now be routinely imaged at atomic resolution with aberration-corrected scanning transmission electron microscopy (STEM) at high speed, with the potential for vast volumes of data to be acquired in relatively short times or through autonomous experiments that can continue over very long periods. Automatic detection and classification of defects in the STEM images are needed in order to handle the data in an efficient way. However, like many other tasks related to object detection and identification in artificial intelligence, it is challenging to detect and identify defects from STEM images. Furthermore, it is difficult to deal with crystal structures that have many atoms and low symmetries. Previous methods used for defect detection and classification were based on supervised learning, which requires human-labeled data. In this work, we develop an approach for defect detection with unsupervised machine learning based on a one-class support vector machine (OCSVM). We introduce two schemes of image segmentation and data preprocessing, both of which involve taking the Patterson function of each segment as inputs. We demonstrate that this method can be applied to various defects, such as point and line defects in 2D materials and twin boundaries in 3D nanocrystals.
On the evaluation of hydrogen evolution reaction performance of metal-nitrogen-doped carbon electrocatalysts using machine learning technique
Authors: Baghban Alireza , Habibzadeh Sajjad , Zokaee Ashtiani Farzin 
Published: November 2021

AbstractSingle-atom catalysts (SACs) introduce as a promising category of electrocatalysts, especially in the water-splitting process. Recent studies have exhibited that nitrogen-doped carbon-based SACs can act as a great HER electrocatalyst. In this regard, Adaptive Neuro-Fuzzy Inference optimized by Gray Wolf Optimization (GWO) method was used to predict hydrogen adsorption energy (ΔG) obtained from density functional theory (DFT) for single transition-metal atoms including Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, Hf, Ta, W, Re, Os, Ir, Pt, and Au embedded in N-doped carbon of different sizes. Various descriptors such as the covalent radius, Zunger radius of the atomic d-orbital, the formation energy of the single-atom site, ionization energy, electronegativity, the d-band center from − 6 to 6 eV, number of valence electrons, Bader charge, number of occupied d states from 0 to − 2 eV, and number of unoccupied d states from 0 to 2 eV were chosen as input parameters based on sensitivity analysis. The R-squared and MSE of the developed model were 0.967 and 0.029, respectively, confirming its great accuracy in determining hydrogen adsorption energy of metal/NC electrocatalysts.
Reporting the epidemiology of aural haematoma in dogs and proposing a novel aetiopathogenetic pathway
Authors: O’Neill Dan G. , Lee Yan Hui , Brodbelt Dave C. , Church David B. , Pegram Camilla , Halfacree Zoë 
Published: November 2021

AbstractTo evaluate the incidence and risk factors for aural haematoma in dogs under primary veterinary care in the UK. A cohort study design. Dogs diagnosed with aural haematoma during 2016 were identified from the VetCompass database. Univariable and multivariable logistic regression modelling were used for risk factor analysis. There were 2,249/905,554 dogs diagnosed with aural haematoma during 2016. The estimated one-year incidence risk for aural haematoma was 0.25% (95% confidence interval 0.24–0.26). After accounting for confounding factors, 14 breeds showed increased odds and 20 breeds showed reduced odds of aural haematoma compared with crossbred dogs. Breeds with the highest odds included Bull Terrier (OR 7.42, 95% confidence interval 4.39–12.54), Saint Bernard (OR 7.28, 95% confidence interval 3.58–14.81) and French Bulldog (OR 6.95, 95% confidence interval 5.55–8.70). Increasing age, increasing bodyweight and breeds with V-shaped drop and semi-erect ear carriage also showed increased odds of aural haematoma. Associations between ear carriage within breeds and the risk of aural haematoma suggest that trauma along the line of cartilage folding within V-shaped and semi-erect ears may trigger aural haematoma. New knowledge of key breed predispositions will contribute to improved breed health control strategies.
Improving water deficit tolerance of Salvia officinalis L. using putrescine
Authors: Mohammadi-Cheraghabadi Maryam , Modarres-Sanavy Seyed Ali Mohammad , Sefidkon Fatemeh , Rashidi-Monfared Sajad , Mokhtassi-Bidgoli Ali 
Published: November 2021

AbstractTo study the effects of foliar application of putrescine (distilled water (0), 0.75, 1.5, and 2.25 mM) and water deficit stress (20%, 40%, 60%, and 80% available soil water depletion (ASWD)) on the physiological, biochemical, and molecular attributes of Salvia officinalis L., a factorial experiment was performed in a completely randomized design with three replications in the growth chamber. The results of Real-Time quantitative polymerase chain reaction (qRT-PCR) analysis showed that putrescine concentration, irrigation regime, and the two-way interaction between irrigation regime and putrescine concentration significantly influenced cineole synthase (CS), sabinene synthase (SS), and bornyl diphosphate synthase (BPPS) relative expression. The highest concentration of 1,8-cineole, camphor, α-thujone, β-thujone, CS, SS, and BPPS were obtained in the irrigation regime of 80% ASWD with the application of 0.75 mM putrescine. There was high correlation between expression levels of the main monoterpenes synthase and the concentration of main monoterpenes. The observed correlation between the two enzyme activities of ascorbate peroxidase (APX) and catalase (CAT) strongly suggests they have coordinated action. On the other hand, the highest peroxidase (PO) and superoxide dismutase (SOD) concentrations were obtained with the application of 0.75 mM putrescine under the irrigation regime of 40% ASWD. Putrescine showed a significant increase in LAI and RWC under water deficit stress. There was an increasing trend in endogenous putrescine when putrescine concentration was increased in all irrigation regimes. Overall, the results suggest that putrescine may act directly as a stress-protecting compound and reduced H2O2 to moderate the capacity of the antioxidative system, maintain the membrane stability, and increase secondary metabolites under water deficit stress.
Objective and bias-free measures of candidate motivation during job applications
Authors: Kappen Mitchel , Naber Marnix 
Published: November 2021

AbstractSociety suffers from biases and discrimination, a longstanding dilemma that stems from ungrounded, subjective judgments. Especially unequal opportunities in labor remain a persistent challenge, despite the recent inauguration of top-down diplomatic measures. Here we propose a solution by using an objective approach to the measurement of nonverbal behaviors of job candidates that trained for a job assessment. First, we implemented and developed artificial intelligence, computer vision, and unbiased machine learning software to automatically detect facial muscle activity and emotional expressions to predict the candidates’ self-reported motivation levels. The motivation judgments by our model outperformed recruiters’ unreliable, invalid, and sometimes biased judgments. These findings mark the necessity and usefulness of novel, bias-free, and scientific approaches to candidate and employee screening and selection procedures in recruitment and human resources.
CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice
Authors: Achary V. Mohan Murali , Reddy Malireddy K. 
Published: November 2021

AbstractEnhancing crop productivity and their nutritional quality are the key components and primary focus of crop improvement strategy for fulfilling future food demand and improving human health. Grain filling and endosperm development are the key determinants of grain yield and nutritional quality.GRAIN WIDTH and WEIGHT2(GW2) gene encodes a RING-type E3 ubiquitin ligase and determines the grain weight in cereal crops. Here we reportGW2knockout (KO) mutants in Indica (var. MTU1010) through CRISPR/Cas9 genome editing. The endosperm ofGW2-KO mutant seed displays a thick aleurone layer with enhanced grain protein content. Further the loss of function ofOsGW2results in improved accumulation of essential dietary minerals (Fe, Zn, K, P, Ca) in the endosperm of rice grain. Additionally, the mutants displayed an early growth vigour phenotype with an improved root and shoot architecture. The hull morphology ofGW2-KO lines also showed improved, grain filling thereby promoting larger grain architecture. Together, our findings indicate thatGW2may serve as a key regulator of improved grain architecture, grain nutritional quality and an important modulator of plant morphology. The study offers a strategy for the development of improved rice cultivars with enriched nutritional quality and its possible implementation in other cereals as well.
The importance of being heterozygote: effects of RHD-genotype-sex interaction on the physical and mental health of a non-clinical population
Authors: Flegr Jaroslav , Příplatová Lenka , Hlaváčová Jana , Šebánková Blanka , Žďárský Emanuel , Kaňková Šárka 
Published: November 2021

AbstractHuman populations, especially European, are polymorphic in theRHDgene. A significant fraction of their members carry no copy of the coding section ofRHDgene, which results in their Rh-negative blood type. Theoretically, this polymorphism should be unstable. Carriers of the less frequent allele are penalized by reduced fertility because of the immunization of RhD-negative mothers by their RhD-positive babies, which results in hemolytic disease of the fetus and newborn in their subsequent progeny. For about 90 years, some form of balancing selection has been suspected to sustain this polymorphism. Several recent studies showed that the RhD-positive heterozygotes express higher viability than both types of homozygotes. However, the genotype of subjects in these studies was estimated only by indirect methods. Here we compared the physical and mental health of 178 women and 86 men who were directly tested for theirRHDgenotype. The results showed that RhD-positive homozygotic women had worse and RhD-positive homozygotic men better physical health than RhD-negative homozygotes; the difference between RhD-negative homozygotes and heterozygotes was not significant. Our results confirmed that health of RhD-positive heterozygotes and homozygotes differ. Therefore, any result of the comparison of subjects with RhD-positive and RhD-negative phenotype depends on the heterozygote-to-homozygote ratio in the RhD-positive sample. It is, therefore, crucial to analyze the effects ofRHD-genotypes, not phenotypes in future studies.
Performance of different adiposity measures for predicting left ventricular remodeling in Chinese hypertensive youth
Authors: Cheng Hong , Xi Bo , Liu Junting , Yan Yinkun , Mi Jie 
Published: November 2021

AbstractThere is no consistent conclusion on which adiposity measure is best to predict cardiovascular risk factors in youth. The present study aims to assess the performance of body mass index (BMI), waist circumference (WC), and waist-to-height ratio (WHtR) in predicting abnormal left ventricular structure in Chinese hypertensive youth. A total of 1180 youth aged 6–17 years with hypertension from the China Child and Adolescent Cardiovascular Health Study were included in this study. Logistic regression model, receiver operator characteristic (ROC) curve analysis and net reclassification improvement (NRI) method were used to assess performance of BMI, WC, and WHtR in predicting left ventricular hypertrophy (LVH) and left ventricular geometry (LVG). A 1-standard deviation increment in any of three indexes in predicting LVH and LVG were similar, e.g., with the odds ratios and 95% confidence intervals of 1.34 (1.16–1.55), 1.25 (1.08–1.45) and 1.40 (1.20–1.62), respectively. In addition, ROC analysis and NRI method confirmed the similar performance of three adiposity indexes in predicting LVH and LVG. In conclusion, BMI, WC and WHtR had similar performance in predicting abnormal left ventricular structure in Chinese hypertensive youth, but all three indexes had limited value in prediction. WHtR is a simple and convenient adiposity index for screening youth at high risk of target organ damage.
Neuroprotection of retinal ganglion cells by the sigma-1 receptor agonist pridopidine in models of experimental glaucoma
Authors: Geva Michal , Gershoni-Emek Noga , Naia Luana , Ly Philip , Mota Sandra , Rego Ana Cristina , Hayden Michael R. , Levin Leonard A. 
Published: November 2021

AbstractOptic neuropathies such as glaucoma are characterized by retinal ganglion cell (RGC) degeneration and death. The sigma-1 receptor (S1R) is an attractive target for treating optic neuropathies as it is highly expressed in RGCs, and its absence causes retinal degeneration. Activation of the S1R exerts neuroprotective effects in models of retinal degeneration. Pridopidine is a highly selective and potent S1R agonist in clinical development. We show that pridopidine exerts neuroprotection of retinal ganglion cells in two different rat models of glaucoma. Pridopidine strongly binds melanin, which is highly expressed in the retina. This feature of pridopidine has implications to its ocular distribution, bioavailability, and effective dose. Mitochondria dysfunction is a key contributor to retinal ganglion cell degeneration. Pridopidine rescues mitochondrial function via activation of the S1R, providing support for the potential mechanism driving its neuroprotective effect in retinal ganglion cells.
Noninvasive detection of elevated ICP using spontaneous tympanic membrane pulsation
Authors: Dhar Rajkumar , Sandler Richard H. , Manwaring Kim , Kostick Nathan , Mansy Hansen A. 
Published: November 2021

AbstractNeurological conditions such as traumatic brain injury (TBI) and hydrocephalus may lead to intracranial pressure (ICP) elevation. Current diagnosis methods rely on direct pressure measurement, while CT, MRI and other expensive imaging may be used. However, these invasive or expensive testing methods are often delayed because symptoms of elevated ICP are non-specific. Invasive methods, such as intraventricular catheter, subdural screw, epidural sensor, lumbar puncture, are associated with an increased risk of infection and hemorrhage. On the other hand, noninvasive, low-cost, accurate methods of ICP monitoring can help avoid risks and reduce costs while expediting diagnosis and treatment. The current study proposes and evaluates a novel method for noninvasive ICP monitoring using tympanic membrane pulsation (TMp). These signals are believed to be transmitted from ICP to the auditory system through the cochlear aqueduct. Fifteen healthy subjects were recruited and TMp signals were acquired noninvasively while the subjects performed maneuvers that are known to change ICP. A custom made system utilizing a stethoscope headset and a pressure transducer was used to perform these measurements. Maneuvers included head-up-tilt, head-down-tilt and hyperventilation. When elevated ICP was induced, significant TMp waveform morphological changes were observed in each subject (p < 0.01). These changes include certain waveform slopes and high frequency wave features. The observed changes were reversed by the maneuvers that decreased ICP (p < .01). The study results suggest that TMp waveform measurement and analysis may offer an inexpensive, noninvasive, accurate tool for detection and monitoring of ICP elevations. Further studies are warranted to validate this technique in patients with pathologically elevated ICP.
Genome analyses revealed genetic admixture and selection signatures in Bos indicus
Authors: Dixit S. P. , Bhatia A. K. , Ganguly Indrajit , Singh Sanjeev , Dash Soumya , Sharma Anurodh , Anandkumar N. , Dang A. K. , Jayakumar S. 
Published: November 2021

AbstractThe genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.