bluuebunny/crossref_metadata_2025_split huggingface dataset:
The location of the Fisher zeros and estimates of y
T = 1/ν are found for the Baxter–Wu model
Authors: Monroe James L 
Published: July 2022

Abstract
The Fisher zeros of the Baxter–Wu model are examined for the first time and for two series of finite-sized systems, with ‘spherical’ boundary conditions, their location is found to be extremely simple. They lie on the unit circle in the complex sinh[2βJ
3] plane. This is the same location as the Fisher zeros of the square lattice Ising model with nearest neighbour interactions and Brascamp–Kunz boundary conditions. The Baxter–Wu model is an Ising model with three-site interactions, J
3, on the triangle lattice. From the leading Fisher zeros, using finite-size scaling, accurate estimates of the critical exponent 1/ν are obtained and emphasis is placed on using different variables such as exp[−2βJ
3], exp[−4βJ
3], and sinh[2βJ
3] to enhance the accuracy of estimates. Furthermore, using the imaginary parts of the leading zeros versus the real part of the leading zeros, yields different results. This is similar to results of Janke and Kenna for the nearest neighbour, Ising model on the square lattice and extends this behaviour to a multisite interaction system in a different universality class than the pair-interaction cases.
Temperature sensing using bulk and nanoparticles of Ca0.79Er0.01Yb0.2MoO4 phosphor
Authors: Singh Sachin , Kachhap Santosh , Singh Akhilesh Kumar , Pattnaik Sasank , Singh Sunil Kumar 
Published: July 2022

Abstract
Optical temperature sensing is widely realized by using upconversion (UC) emission in lanthanide-doped phosphors. There are various parameters that are responsible for UC intensity of the phosphor like particle shape and size, type of symmetry that exist at the site position, distribution of lanthanide ions in the phosphor, and so on. However, a comparative study of the bulk and nanostructure on the temperature sensing ability of such phosphor is rare. In the present work, we have taken Ca0.79Er0.01Yb0.2MoO4 phosphors as a model system and synthesized its bulk (via solid-state reaction method, named SCEY) and nanostructures (via solution combustion route, named CCEY). We further studied their phase, crystal structure, phonon frequency, optical excitation, and emission (upconversion & downshifting) properties. Finally, the optical temperature sensing behavior of SCEY and CCEY, in the range 305 K–573 K, have been compared. The maximum relative sensitivity of the phosphor SCEY and CCEY are 0.0061 K−1 at 305 K and 0.0094 K−1 at 299 K, respectively, while, the maximum absolute sensitivities are 0.0150 K−1 at 348 K, and 0.0170 K−1 at 398 K, respectively. We thus conclude that the temperature sensing ability of nanoparticle-based Ca0.79Er0.01Yb0.2MoO4 phosphor is better compared to its bulk phosphor.
Optimising correlative super resolution and atomic force microscopies for investigating the cellular cytoskeleton
Authors: Hargreaves Riley B , Rozario Ashley M , McCoy Thomas M , Meaney Shane P , Funston Alison M , Tabor Rico F , Whelan Donna R , Bell Toby D M 
Published: July 2022

Abstract
Correlative imaging methods can provide greater information for investigations of cellular ultra-structure, with separate analysis methods complementing each other's strengths and covering for deficiencies. Here we present a method for correlative applications of super resolution and atomic force microscopies, optimising the sample preparation for correlative imaging of the cellular cytoskeleton in COS-7 cells. This optimisation determined the order of permeabilisation and fixation, the concentration of Triton X-100 surfactant used and time required for sufficient removal of the cellular membrane while maintaining the microtubule network. Correlative SMLM/AFM imaging revealed the different information that can be obtained through each microscopy. The widths of microtubules and microtubule clusters were determined from both AFM height measurements and Gaussian fitting of SMLM intensity cross sections, these were then compared to determine the orientation of microtubules within larger microtubule bundles. The ordering of microtubules at intersections was determined from the AFM height profiles as each microtubule crosses the other. The combination of both microtubule diameter measurements enabled greater information on their structure to be found than either measurement could individually.
Improvement in white light emission of Dy3+ doped CaMoO4 via Zn2+ co-doping
Authors: Dixit Prashant , Pandey Prashant Kumar , Chauhan Vaibhav , Deshmukh Pratik , Satapathy S , Pandey Praveen C 
Published: July 2022

Abstract
The research in developing a single ingredient phosphor for white-light emission is progressively increasing. It is well known that the 4F9/2 → 6H13/2 (yellow) and 4F9/2 → 6H15/2 (blue) transitions of Dy3+ ions give near-white light emission. The white light emission of Dy3+ ions can be enhanced via improving the crystallinity of the host phosphor via co-doping of transition metal ions. In this paper, we report a significant improvement in the white light emission of Dy3+ doped CaMoO4 by co-doping Zn2+ ions. The x-ray diffraction pattern confirms the tetragonal phase of pure and doped CaMoO4 phosphor. The peak broadening and a red-shift in the absorption peak are observed by UV–vis absorption analysis of Zn2+/Dy3+ doped CaMoO4. From Photoluminescence studies, we have observed that in Dy3+ doped CaMoO4, the 4% Dy3+ doped CaMoO4 exhibits maximum emission. The Zn2+ ions are co-doped to further increase the luminescence intensity of CaMoO4:4%Dy3+ and the maximum luminescence is obtained for 0.25% Zn2+ concentration. Two intense emission peaks centered at 484 nm and 574 nm related to transitions 4F9/2 → 6H15/2 and 4F9/2 → 6H13/2 of Dy3+ ion are observed for Dy3+ doped phosphor. The 4F9/2 → 6H13/2 transition is the forced electric dipole transition which is affected by its chemical environment. After Zn2+ co-doping, the 4F9/2 → 6H13/2 transition is affected due to a change in asymmetricity around the Dy3+ ions. The 0.25% co-doping of Zn2+ gives 34% enhancement in luminescence emission of 4% Dy3+ doped CaMoO4. As a result, the CIE coordinates of chromaticity diagram and the color purity of the 0.25% Zn2+ co-doped CaMoO4:4Dy3+ show improvement in the overall white light emission. We have shown that with Zn2+ co-doping, the non-radiative relaxations are reduced which results in improved white light emission of Dy3+ions.
Comparison of heating mechanisms of argon helicon plasma in different wave modes with and without blue core
Authors: CUI Ruilin , ZHANG Tianliang , YUAN Qian , HE Feng , HAN Ruoyu , OUYANG Jiting 
Published: July 2022

Abstract
In this work, we investigated the discharge characteristics and heating mechanisms of argon helicon plasma in different wave coupled modes with and without blue core. Spatially resolved spectroscopy and emission intensity of argon atom and ion lines were measured via local optical emission spectroscopy, and electron density was measured experimentally by an RF-compensated Langmuir probe. The relation between the emission intensity and the electron density was obtained and the wavenumbers of helicon and ‘Trivelpiece-Gould’ (TG) waves were calculated by solving the dispersion relation in wave modes. The results show that at least two distinct wave coupled modes appear in argon helicon plasma at increasing RF power, i.e. blue core (or BC) mode with a significant bright core of blue lights and a normal wave (NW) mode without blue core. The emission intensity of atom line 750.5 nm (I
ArI750.5nm) is related to the electron density and tends to be saturated in wave coupled modes due to the neutral depletion, while the intensity of ion line 480.6 nm (I
ArII480.6nm) is a function of the electron density and temperature, and increases dramatically as the RF power is increased. Theoretical analysis shows that TG waves are strongly damped at the plasma edge in NW and/or BC modes, while helicon waves are the dominant mechanism of power deposition or central heating of electrons in both modes. The formation of BC column mainly depends on the enhanced central electron heating by helicon waves rather than TG waves since the excitation of TG waves would be suppressed in this special anti-resonance region.
Development of miniaturized SAF-LIBS with high repetition rate acousto-optic gating for quantitative analysis
Authors: CHEN Fei , HOU Jiajia , WANG Gang , ZHAO Yang , LI Jiaxuan , WANG Shuqing , ZHANG Lei , ZHANG Wanfei , MA Xiaofei , LIU Zhenrong , LUO Xuebin , YIN Wangbao , JIA Suotang 
Published: July 2022

Abstract
The self-absorption effect in laser-induced breakdown spectroscopy (LIBS) reduces the accuracy of quantitative measurement results. The self-absorption-free LIBS (SAF-LIBS) has been proved to directly capture the optically thin plasma spectra by setting an appropriate exposure time. In this work, a novel SAF-LIBS technique with high repetition rate acousto-optic gating is developed, in which an acousto-optic modulator is used as the shutter to diffract the optically thin fluorescence, and a high repetition rate laser is used to produce quasi-continuous plasmas to enhance the integral spectral intensity, so that the CCD spectrometer can replace an intensified CCD (ICCD) and echelle spectrometer in SAF-LIBS. Experimental results show that the average absolute prediction error of aluminum is reduced to 0.18%, which is equivalent to that of traditional SAF-LIBS. This technique not only effectively shields continuous background radiation and broadened spectral lines in optically thick plasma, but also has advantages of miniaturization, low cost, convenience and reliability.
A biology-informed similarity metric for simulated patches of human cell membrane
Authors: Bhatia Harsh , Thiagarajan Jayaraman J , Anirudh Rushil , Jayram T S , Oppelstrup Tomas , Ingólfsson Helgi I , Lightstone Felice C , Bremer Peer-Timo 
Published: July 2022

Abstract
Complex scientific inquiries rely increasingly upon large and autonomous multiscale simulation campaigns, which fundamentally require similarity metrics to quantify ‘sufficient’ changes among data and/or configurations. However, subject matter experts are often unable to articulate similarity precisely or in terms of well-formulated definitions, especially when new hypotheses are to be explored, making it challenging to design a meaningful metric. Furthermore, the key to practical usefulness of such metrics to enable autonomous simulations lies in in situ inference, which requires generalization to possibly substantial distributional shifts in unseen, future data. Here, we address these challenges in a cancer biology application and develop a meaningful similarity metric for ‘patches’—regions of simulated human cell membrane that express interactions between certain proteins of interest and relevant lipids. In the absence of well-defined conditions for similarity, we leverage several biology-informed notions about data and the underlying simulations to impose inductive biases on our metric learning framework, resulting in a suitable similarity metric that also generalizes well to significant distributional shifts encountered during the deployment. We combine these intuitions to organize the learned embedding space in a multiscale manner, which makes the metric robust to incomplete and even contradictory intuitions. Our approach delivers a metric that not only performs well on the conditions used for its development and other relevant criteria, but also learns key spatiotemporal relationships without ever being exposed to any such information during training.
Learning torsional eye movements through active efficient coding
Authors: Zhu Qingpeng , Zhang Chong , Triesch Jochen , Shi Bertram E 
Published: July 2022

Abstract
The human eye has three rotational degrees of freedom: azimuthal, elevational, and torsional. Although torsional eye movements have the most limited excursion, Hering and Helmholtz have argued that they play an important role in optimizing visual information processing. In humans, the relationship between gaze direction and torsional eye angle is described by Listing’s law. However, it is still not clear how this behavior initially develops and remains calibrated during growth. Here we present the first computational model that enables an autonomous agent to learn and maintain binocular torsional eye movement control. In our model, two neural networks connected in series: one for sensory encoding followed by one for torsion control, are learned simultaneously as the agent behaves in the environment. Learning is based on the active efficient coding (AEC) framework, a generalization of Barlow’s efficient coding hypothesis to include action. Both networks adapt by minimizing the prediction error of the sensory representation, subject to a sparsity constraint on neural activity. The policies that emerge follow the predictions of Listing’s law. Because learning is driven by the sensorimotor contingencies experienced by the agent as it interacts with the environment, our system can adapt to the physical configuration of the agent as it changes. We propose that AEC provides the most parsimonious expression to date of Hering’s and Helmholtz’s hypotheses. We also demonstrate that it has practical implications in autonomous artificial vision systems, by providing an automatic and adaptive mechanism to correct orientation misalignments between cameras in a robotic active binocular vision head. Our system’s use of fairly low resolution (100 × 100 pixel) image windows and perceptual representations amenable to event-based input paves a pathway towards the implementation of adaptive self-calibrating robot control on neuromorphic hardware.
Further Characterization of Clinicopathologic Features of Cystic Neutrophilic Granulomatous Mastitis
Authors: Liang Yuanxin , Zhan Haiying , Krishnamurti Uma , Harigopal Malini , Sun Tong 
Published: July 2022

Abstract

Objectives
Clinical and demographic features of cystic neutrophilic granulomatous mastitis (CNGM) have not been fully explored due to the rarity of the disease. Herein we studied clinicopathologic characteristics of CNGM in a sizable hospital-based cohort.

Methods
A case-control study was performed to compare clinicopathologic characteristics between patients with CNGM and granulomatous mastitis other than CNGM and between CNGM with and without Corynebacterium identification.

Results
Cases of CNGM (n = 31) and non-CNGM (n = 30) were included. Compared with the non-CNGM group, patients with CNGM were statistically significantly younger (median age: 38 vs 43 years), were less likely to be smokers (9% vs 40%), were more likely to have a painful lesion (97% vs 77%) or a larger mass-like lesion (median size: 4.6 vs 1.9 cm), and tended to have a higher Breast Imaging Reporting and Data System score in radiologic studies (score ≥4: 81% vs 53%), positive Corynebacterium identification results (36% vs 0%), and a longer resolving time (12 vs 6 months; all P values for above comparisons &lt;.05). Among CNGM cases, patients with and without Corynebacterium identification shared a similar clinicopathologic profile.

Conclusions
Our study further demonstrated that CNGM is a unique infectious disease with distinct clinicopathologic features.
Relationship Between Risks for Obstructive Sleep Apnea, Resistant Hypertension, and Aldosterone Among African American Adults in the Jackson Heart Study
Authors: Koo Patrick , Muntner Paul , Hall Michael E , Gjelsvik Annie , McCool Franklin Dennis , Eaton Charles B 
Published: July 2022

Abstract

BACKGROUND
African Americans have a higher prevalence of resistant hypertension compared with Caucasians. Racial differences in obstructive sleep apnea (OSA) and increased aldosterone level may explain the racial disparity in resistant hypertension prevalence. Therefore, the purpose of this study is to investigate if aldosterone level and hypertension status differ by risks for OSA (e.g., obesity, loud snoring, and daytime sleepiness) and how aldosterone level varies with hypertension severity and control among African Americans.

METHODS
A cross-sectional analysis was performed using baseline data on 5,052 African American adults in the Jackson Heart Study to investigate the relationships of interest using multivariable linear and multinomial logistic regression models adjusted for potential confounders. Risks for OSA were defined by a “risk score” consisting of the number of risks for OSA.

RESULTS
Of the 5,052 participants, 623 had no risks for OSA. Body mass index was the highest among those with a risk score of 6. About 39% of the sample had no hypertension, 29% had controlled hypertension, 26% had uncontrolled hypertension, and 6% had resistant hypertension. Higher odds of having uncontrolled hypertension or resistant hypertension were present in those with a higher risk score compared with those without risks for OSA. Log-aldosterone level increased with each additional risk for OSA (P-trend &lt;0.05). Similarly, log-aldosterone also increased with more severe hypertension (P-trend &lt;0.001). The highest aldosterone level was found in those with resistant hypertension that was inadequately controlled with medications.

CONCLUSIONS
Risks for OSA were positively associated with resistant hypertension and higher aldosterone level in African American adults.
Trail Making Test Could Predict Impairment in Cognitive Domains in Patients with Multiple Sclerosis: A Study of Diagnostic Accuracy
Authors: Kabiri Samaneh , Jameie Melika , Balali Pargol , Adib Moradi Sahand , Sanjari Moghaddam Hossein , Aghamollaii Vajiheh , Harirchian Mohammad Hossein 
Published: July 2022

AbstractObjectiveCognitive impairment (CI) and executive dysfunction (ED) are prevalent in patients with multiple sclerosis (PwMS). The Minimal Assessment of Cognitive Function in Multiple Sclerosis (MACFIMS) is the gold standard neuropsychological battery (NPB) for detecting CI. Delis-Kaplan Executive Function System (DKEFS) NPB evaluates ED. We aimed to find practical test(s) from DKEFS with acceptable diagnostic utility for early detection of impairment in cognitive and executive domains.MethodsCognitive and executive tasks, physical disability, and depression scores of 30 PwMS were assessed (17 women, age: 38.1). Symbol Digit Modalities Test (SDMT), Paced Auditory Serial Addition Test (PASAT), and Controlled Oral Word Association Test (COWAT) from MACFIMS and Trail Making Test (TMT), Design Fluency Test (DFT), and Verbal Fluency Test (VFT) from DKEFS were selected. The association between patients' characteristics and performance in tests, and diagnostic accuracy of DKEFS tests in detecting impairment in cognitive tasks were evaluated, using Pearson correlation and receiver operator characteristic curve analyses, respectively.ResultsA significant correlation was found between disease duration and SDMT and TMT subtests. Expanded Disability Status Scale was significantly related to SDMT, VFT-switching, and TMT subtests. Beck Depression Inventory was significantly related to DFT. TMT-switching detected abnormalities in SDMT and PASAT with 100% sensitivity, 93.3% (for SDMT), and 85.7% specificity (for PASAT). TMT-letter showed 100% sensitivity and 90% specificity in identifying abnormalities in COWAT.ConclusionsTMT, particularly the switching condition, is a practical paper-based test that could predict impairment in cognitive tasks. Clinicians may use TMT as a screening tool among PwMS.
EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets
Authors: Xie Gui-Yan , Liu Chun-Jie , Guo An-Yuan 
Published: July 2022

Abstract
Extracellular vesicles (EVs) carrying various small non-coding RNAs (sncRNAs) play a vital roles in cell communication and diseases. Correct quantification of multiple sncRNA biotypes simultaneously in EVs is a challenge due to the short reads (&lt;30 bp) could be mapped to multiple sncRNA types. To address this question, we developed an optimized reads assignment algorithm (ORAA) to dynamically map multi-mapping reads to the sncRNA type with a higher proportion. We integrated ORAA with reads processing steps into EVAtool Python-package (http://bioinfo.life.hust.edu.cn/EVAtool) to quantify sncRNAs, especially for sncRNA-seq from EV samples. EVAtool allows users to specify interested sncRNA types in advanced mode or use default seven sncRNAs (microRNA, small nucleolar RNA, PIWI-interacting RNAs, small nuclear RNA, ribosomal RNA, transfer RNA and Y RNA). To prove the utilities of EVAtool, we quantified the sncRNA expression profiles for 200 samples from cognitive decline and multiple sclerosis. We found that more than 20% of short reads on average were mapped to multiple sncRNA biotypes in multiple sclerosis. In cognitive decline, the proportion of Y RNA is significantly higher than other sncRNA types. EVAtool is a flexible and extensible tool that would benefit to mine potential biomarkers and functional molecules in EVs.
Learning representations for gene ontology terms by jointly encoding graph structure and textual node descriptors
Authors: Zhao Lingling , Sun Huiting , Cao Xinyi , Wen Naifeng , Wang Junjie , Wang Chunyu 
Published: July 2022

Abstract
Measuring the semantic similarity between Gene Ontology (GO) terms is a fundamental step in numerous functional bioinformatics applications. To fully exploit the metadata of GO terms, word embedding-based methods have been proposed recently to map GO terms to low-dimensional feature vectors. However, these representation methods commonly overlook the key information hidden in the whole GO structure and the relationship between GO terms. In this paper, we propose a novel representation model for GO terms, named GT2Vec, which jointly considers the GO graph structure obtained by graph contrastive learning and the semantic description of GO terms based on BERT encoders. Our method is evaluated on a protein similarity task on a collection of benchmark datasets. The experimental results demonstrate the effectiveness of using a joint encoding graph structure and textual node descriptors to learn vector representations for GO terms.