bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of clinical phenotypes for Alzheimer’s disease dementia from clinical notes using natural language processing
Authors: Oh Inez Y , Schindler Suzanne E , Ghoshal Nupur , Lai Albert M , Payne Philip R O , Gupta Aditi 
Published: February 2023

AbstractObjectivesThere is much interest in utilizing clinical data for developing prediction models for Alzheimer’s disease (AD) risk, progression, and outcomes. Existing studies have mostly utilized curated research registries, image analysis, and structured electronic health record (EHR) data. However, much critical information resides in relatively inaccessible unstructured clinical notes within the EHR.Materials and MethodsWe developed a natural language processing (NLP)-based pipeline to extract AD-related clinical phenotypes, documenting strategies for success and assessing the utility of mining unstructured clinical notes. We evaluated the pipeline against gold-standard manual annotations performed by 2 clinical dementia experts for AD-related clinical phenotypes including medical comorbidities, biomarkers, neurobehavioral test scores, behavioral indicators of cognitive decline, family history, and neuroimaging findings.ResultsDocumentation rates for each phenotype varied in the structured versus unstructured EHR. Interannotator agreement was high (Cohen’s kappa = 0.72–1) and positively correlated with the NLP-based phenotype extraction pipeline’s performance (average F1-score = 0.65–0.99) for each phenotype.DiscussionWe developed an automated NLP-based pipeline to extract informative phenotypes that may improve the performance of eventual machine learning predictive models for AD. In the process, we examined documentation practices for each phenotype relevant to the care of AD patients and identified factors for success.ConclusionSuccess of our NLP-based phenotype extraction pipeline depended on domain-specific knowledge and focus on a specific clinical domain instead of maximizing generalizability.
Transcription-wide impact by RESCUE-induced off-target single-nucleotide variants in mammalian cells
Authors: Li Guo , Zhu Xiaoning , Wang Yihan , Ma Hongru , Wang Yuzhe , Wu Hanyu , Li Xiangyang , Wang Yiling , Gao Jianen , Chen Xuexin , Huang Xingxu , Yao Yuan , Hu Xiaoxiang 
Published: February 2023

Abstract
RNA base editing is a promising tool in precise molecular therapy. Currently, there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions. Thus, RESCUE can generate twice the number of mutations compared to REPAIR. However, transcription-wide impact due to RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully appreciated. Therefore, to determine the off-target effects of RESCUE-mediated editing, we employed transcription-wide sequencing on cells edited by RESCUE. The SNVs showed different off-target effects on mRNA, circRNA, lncRNA, and miRNA expression patterns and their interacting networks. Our results illustrate the transcription-wide impact of RESCUE-induced off-target SNVs and highlight the need for careful characterization of the off-target impact by this editing platform.
Development of a specific real-time PCR assay for simultaneous detection and differentiation ofCoxiella burnetiistrains from environmental soil samples
Authors: Fernández-Carrillo Juan , del Olmo-Monge Javier , Sellek Ricela E , Ortega-García María Victoria , Cabria-Ramos Juan Carlos , Bassy Olga 
Published: February 2023

AbstractCoxiella burnetii, the causative agent of Q fever, is a small, coccoid, Gram-negative strict intracellular pathogen. One of the most common ways of acquiring Q fever is through inhalation of aerosols containing the bacteria. Because C. burnetii is highly infectious, spreads easily through the air, and is very resistant to environmental conditions, it is considered a biological threat. This paper presents the development and validation of a specific real-time polymerase chain reaction (real-time PCR or qPCR) assay for the detection of C. burnetii, based on the amplification of a fragment of the isocitrate dehydrogenase (icd) encoding gene. This real-time PCR is highly specific, reproducible, and sensitive, allowing the detection of as few as 5 genome equivalents (GEs) of C. burnetii per reaction. The method enables a rapid preliminary differentiation among strains, based on a point mutation at nucleotide 745 of the icd gene. The assay was successfully evaluated in environmental soil samples; a limit of detection of 3 × 104 colony forming units per 0.5 g of soil (∼3 GEs per reaction) was achieved. The newly developed real-time PCR offers a valuable tool for differential detection of C. burnetii strains in environmental soil samples.
The status of the Jewish temple in modern Hebrew literature (1848–1948): A big-data analysis
Authors: Hershkowitz Isaac 
Published: February 2023

Abstract
Since its final destruction in antiquity, the memory of the temple in Jerusalem has served as the nexus of Jewish liturgy and messianic worldview. This article has sought to examine the ideological and cultural roles played by the image of the Jewish temple in the Hebrew literature of 1848–1948. Toward this end, I formulated a broad corpus comprised of homogeneous genres and authors, namely those which situate the temple as their main focus. The evidence arising from this corpus suggests that the conceptual role of the temple underwent no dramatic transformations; the temple in this literature, taken as a whole, is mostly indistinguishable from the historical, religious, and nationalistic symbol that featured in the Jewish tradition over nearly 2,000 years. The bulk of the present corpus places the temple in conceptual and historical contexts that are familiar and very similar to those of the historical temple in all its contexts, without removing it from the domains of Jewish nationalism or classical religiosity. These findings contravene my initial presupposition that the discourse of the temple had undergone a metamorphosis in the 19th and 20th centuries, the image of the temple had changed into an abstract symbol for world peace, moral perfection, and intellectual and scientific excellence.
The Thousand Pulsar Array program on MeerKAT – IX. The time-averaged properties of the observed pulsar population
Authors: Posselt B , Karastergiou A , Johnston S , Parthasarathy A , Oswald L S , Main R A , Basu A , Keith M J , Song X , Weltevrede P , Tiburzi C , Bailes M , Buchner S , Geyer M , Kramer M , Spiewak R , Krishnan V Venkatraman 
Published: February 2023

ABSTRACT
We present the largest single survey to date of average profiles of radio pulsars, observed and processed using the same telescope and data reduction software. Specifically, we present measurements for 1170 pulsars, observed by the Thousand Pulsar Array programme at the 64-dish SARAO MeerKAT radio telescope, in a frequency band from 856 to 1712 MHz. We provide rotation measures (RM), dispersion measures, flux densities, and polarization properties. The catalogue includes 254 new RMs that substantially increase the total number of known pulsar RMs. Our integration times typically span over 1000 individual rotations per source. We show that the radio (pseudo-) luminosity has a strong, shallow dependence on the spin-down energy, proportional to $\dot{E}^{0.15\pm 0.04}$, that contradicts some previous proposals of population synthesis studies. In addition, we find a significant correlation between the steepness of the observed flux density spectra and $\dot{E}$, and correlations of the fractional linear polarization with $\dot{E}$, the spectral index, and the pulse width, which we discuss in the context of what is known about pulsar radio emission and how pulsars evolve with time. On the whole, we do not see significant correlations with the estimated surface magnetic field strength, and the correlations with $\dot{E}$ are much stronger than those with the characteristic age. This finding lends support to the suggestion that magnetic dipole braking may not be the dominant factor for the evolution of pulsar rotation over the lifetimes of pulsars. A public data release of the high-fidelity time-averaged pulse profiles in full polarization accompanies our catalogue.
The EBLM project X. Benchmark masses, radii, and temperatures for two fully convective M-dwarfs using K2
Authors: Duck Alison , Martin David V , Gill Sam , Armitage Tayt , Rodríguez Martínez Romy , Maxted Pierre F L , Sebastian Daniel , Sethi Ritika , Swayne Matthew I , Cameron Andrew Collier , Dransfield Georgina , Gaudi B Scott , Gillon Michael , Hellier Coel , Kunovac Vedad , Lovis Christophe , McCormac James , Pepe Francesco A , Pollacco Don , Sairam Lalitha , Santerne Alexandre , Ségransan Damien , Standing Matthew R , Southworth John , Triaud Amaury H M J , Udry Stephane 
Published: February 2023

ABSTRACT
M-dwarfs are the most abundant stars in the galaxy and popular targets for exoplanet searches. However, their intrinsic faintness and complex spectra inhibit precise characterization. We only know of dozens of M-dwarfs with fundamental parameters of mass, radius, and effective temperature characterized to better than a few per cent. Eclipsing binaries remain the most robust means of stellar characterization. Here we present two targets from the Eclipsing Binary Low Mass (EBLM) survey that were observed with K2: EBLM J0055-00 and EBLM J2217-04. Combined with HARPS and CORALIE spectroscopy, we measure M-dwarf masses with precisions better than 5 per cent, radii better than 3 per cent, and effective temperatures on order 1 per cent. However, our fits require invoking a model to derive parameters for the primary star and fitting the M-dwarf using the transit and radial velocity observations. By investigating three popular stellar models, we determine that the model uncertainty in the primary star is of similar magnitude to the statistical uncertainty in the model fits of the secondary M-dwarf. Therefore, whilst these can be considered benchmark M-dwarfs, we caution the community to consider model uncertainty when pushing the limits of precise stellar characterization.
Foreground removal of CO intensity mapping using deep learning
Authors: Zhou Xingchen , Gong Yan , Deng Furen , Zhang Meng , Yue Bin , Chen Xuelei 
Published: February 2023

ABSTRACTLine intensity mapping (LIM) is a promising probe to study star formation, the large-scale structure of the Universe, and the epoch of reionization (EoR). Since carbon monoxide (CO) is the second most abundant molecule in the Universe except for molecular hydrogen H2, it is suitable as a tracer for LIM surveys. However, just like other LIM surveys, CO intensity mapping also suffers strong foreground contamination that needs to be eliminated for extracting valuable astrophysical and cosmological information. In this work, we take 12CO($\it J$ = 1-0) emission line as an example to investigate whether deep learning method can effectively recover the signal by removing the foregrounds. The CO(1-0) intensity maps are generated by N-body simulations considering CO luminosity and halo mass relation, and we discuss two cases with median and low CO signals by comparing different relations. We add foregrounds generated from real observations, including thermal dust, spinning dust, free–free, synchrotron emission, and cosmic microwave background anisotropy. The beam with sidelobe effect is also considered. Our deep learning model is built upon ResUNet, which combines image generation algorithm UNet with the state-of-the-art architecture of deep learning, ResNet. The principal component analysis (PCA) method is employed to preprocess data before feeding it to the ResUNet. We find that, in the case of low instrumental noise, our UNet can efficiently reconstruct the CO signal map with correct line power spectrum by removing the foregrounds and recovering PCA signal loss and beam effects. Our method also can be applied to other intensity mappings like neutral hydrogen 21-cm surveys.
The spectra of IceCube Neutrino (SIN) candidate sources – III. Optical spectroscopy and source characterization of the full sample
Authors: Paiano Simona , Falomo Renato , Treves Aldo , Padovani Paolo , Giommi Paolo , Scarpa Riccardo , Bisogni Susanna , Marini Ester 
Published: February 2023

ABSTRACTA correlation between astrophysical high-energy neutrinos and blazars has been suggested by various authors. In particular, a likely association between IceCube events and intermediate- and high-energy peaked BL Lac objects has led to a sample of 47 objects having a high probability of being neutrino sources. In the first paper of this series we reported optical spectroscopy of 17 objects, which together with data taken from the literature covered 80 per cent of the sample. Here, we present spectroscopy obtained at large aperture telescopes of a further 17 objects (plus four additional targets), which completes the sample coverage. For 12 objects we are able to determine the redshift (0.07 &lt; z &lt; 1.6), while for the others we set a lower limit on it, based on either the robust detection of intervening absorption systems or on an estimation derived from the absence of spectral signatures of the host galaxy. With these new data we expand and reinforce the main results of our previous papers, namely the fact that in terms of their broad-band properties our sources appear to be indistinguishable from the rest of the blazar population and the relatively large (&gt;34 per cent and possibly as high as 80 per cent) fraction of masquerading BL Lac objects, for which the low equivalent width of the emission lines is due to the brightness of the boosted continuum, rather than being an intrinsic property, in our sample.
On the functional form of the radial acceleration relation
Authors: Desmond Harry , Bartlett Deaglan J , Ferreira Pedro G 
Published: February 2023

ABSTRACTWe apply a new method for learning equations from data – Exhaustive Symbolic Regression (ESR) – to late-type galaxy dynamics as encapsulated in the radial acceleration relation (RAR). Relating the centripetal acceleration due to baryons, gbar, to the total dynamical acceleration, gobs, the RAR has been claimed to manifest a new law of nature due to its regularity and tightness in agreement with Modified Newtonian Dynamics (MOND). Fits to this relation have been restricted by prior expectations to particular functional forms, while ESR affords an exhaustive and nearly prior-free search through functional parameter space to identify the equations optimally trading accuracy with simplicity. Working with the SPARC data, we find the best functions typically satisfy gobs ∝ gbar at high gbar, although the coefficient of proportionality is not clearly unity and the deep-MOND limit $g_\text{obs}\propto \sqrt{g_\text{bar}}$ as gbar → 0 is little evident at all. By generating mock data according to MOND with or without the external field effect, we find that symbolic regression would not be expected to identify the generating function or reconstruct successfully the asymptotic slopes. We conclude that the limited dynamical range and significant uncertainties of the SPARC RAR preclude a definitive statement of its functional form, and hence that this data alone can neither demonstrate nor rule out law-like gravitational behaviour.
Nephrolithiasis and/or nephrocalcinosis is significantly related to renal dysfunction in patients with primary Sjögren’s syndrome
Authors: Fujisawa Yuhei , Mizushima Ichiro , Suzuki Yasunori , Kawano Mitsuhiro 
Published: February 2023

ABSTRACT

Objective
The present study compared the clinical features of patients with primary Sjögren’s syndrome (pSS) with and without nephrolithiasis and/or nephrocalcinosis to determine factors related to renal dysfunction.

Methods
The clinical features of 68 patients with anti-Sjogren's syndrome antigen A (SSA)/Ro-antibody–positive pSS with and without nephrolithiasis and/or nephrocalcinosis who underwent abdominal computed tomography and/or ultrasonography were retrospectively analysed.

Results
Of the 68 patients with anti-SSA-antibody–positive pSS, 23 (33%) had renal nephrolithiasis and/or nephrocalcinosis, whereas 45 (67%) did not. Fourteen (20%) patients had renal dysfunction at diagnostic imaging. Among five patients who underwent renal biopsy, four patients with renal nephrolithiasis and/or nephrocalcinosis were diagnosed with tubulointerstitial nephritis, and one without nephrolithiasis and/or nephrocalcinosis was diagnosed with minimal change nephrotic syndrome. Estimated glomerular filtration rate at diagnostic imaging was significantly lower in patients with than without nephrolithiasis and/or nephrocalcinosis group (P = 0.010). In addition to nephrolithiasis and/or nephrocalcinosis (odds ratio [OR], 3.467; P = 0.045), the gap between serum sodium and chloride concentrations (OR, 10.400; P = 0.012) and increased urinary β2-microglobulin (OR, 5.444; P = 0.033) were associated with renal dysfunction at the time of diagnostic imaging.

Conclusion
Nephrolithiasis and/or nephrocalcinosis, normal anion gap metabolic acidosis, and tubulointerstitial damage are associated with renal dysfunction in patients with pSS.
Evaluating the intensity, duration and frequency of flexible energy resources needed in a zero-emission, hydropower reliant power system
Authors: Doering Kenji , Anderson C Lindsay , Steinschneider Scott 
Published: February 2023

Abstract
Rapid increases in global temperature are motivating governments to restructure the energy sector towards emissions-free electricity generation. One of the key factors affecting the viability of emissions-free power systems is the joint variability of renewable resources and drivers of energy demand across spatiotemporal scales. This study evaluates the impact of multi-scale hydroclimatic variability on the reliability of a zero-emissions power system in a case study of New York State (NYS), which recently passed the Climate Leadership and Community Protection Act (CLCPA) requiring zero-emissions electricity generation by 2040. We first analyze covariation between renewable energy generation and energy demand, including large-scale hydropower generation on the Great Lakes, and develop a stochastic generator to simulate an ensemble of plausible realizations of this joint variability. Using a simplified energy balance model of the NYS power system, we then quantify resource gaps across spatiotemporal scales that emerge under load and generation scenarios projected under the CLCPA. We focus on the intensity, duration, and frequency of these gaps, which will have to be filled with carbon-free, dispatchable resources not prescribed under the CLCPA. We show that the covariability between load and wind can lead to major short-term resource gaps, which is exacerbated by transmission constraints. We also show that long-duration hydropower droughts increase the likelihood of co-occurring renewable resource deficits and extended periods (weeks to months) of energy shortage. We conclude by discussing the implications of these results on the need for alternative, carbon-free, and dispatchable resources to support zero emission, hydropower-reliant electric grids.
Job Matching with Subsidy and Taxation
Authors: Kojima Fuhito , Sun Ning , Yu Ning Neil 
Published: February 2023

Abstract
In markets for indivisible resources such as workers and objects, subsidy and taxation for an agent may depend on the set of acquired resources and prices. This paper investigates how such transfer policies interfere with the substitutes condition, which is critical for market equilibrium existence and auction mechanism performance among other important issues. For environments where the condition holds in the absence of policy intervention, we investigate which transfer policies preserve the substitutes condition in various economically meaningful settings, establishing a series of characterisation theorems. For environments where the condition may fail without policy intervention, we examine how to use transfer policies to re-establish it, finding exactly when transfer policies based on scales are effective for that purpose. These results serve to inform policymakers, market designers, and market participants of how transfer policies may impact markets, so more informed decisions can be made.
Impact of COVID-19 on hand surgery transfers at a level-1 trauma center
Authors: Stearns Stephen A. , Beagles Clay B. , Hegermiller Katherine , Harper Carl M. 
Published: February 2023

Background:
The COVID-19 pandemic significantly impacted elective surgical volume across the country; however, its effect on urgent transfers is unclear. This study sought to understand the impact of COVID-19 on transfers for hand surgery evaluation at a single quaternary referral center during the initial 3 mo of state mandated restrictions.

Methods:
A retrospective analysis was performed comparing the rate and character of transfers for hand surgery evaluation from March to June of 2020 to a temporally matched cohort averaged across 2018 and 2019. The primary outcome of this study was transfer frequency, with secondary outcomes of treatment rendered and type of disposition.

Results:
The rate of transfer between emergency departments for hand surgery evaluation was not statistically different from before to during COVID (ED-to-ED transfer rate: 4.3% and 5.1% respectively, P=0.68). Patient demographics were similar, with no difference in age (pre-COVID-19 mean 48.6 yr vs. intra-COVID-19 mean 53.2 yr, P=0.31) or type of insurance (P=0.99). Regarding reason for transfer, both cohorts were similar in the number of transfers for trauma versus infection (pre-COVID-19 infection: 11 trauma: 20.5 vs. intra-COVID-19 infection: 4 trauma: 17 P=0.99). We observed similar rates of transfers requiring procedural intervention (pre-COVID-19 69.8% vs. intra-COVID-19 57.1% P=0.19). Lastly, there was no difference in admission patterns, with pre-COVID-19 rates (71.4%) similar to those during COVID-19 (52%) P=0.15.

Conclusions:
Despite the many changes to healthcare in the US during the COVID-19 pandemic, the practice of transferring for evaluation to a Level 1 hand surgery center was similar to pre-pandemic years.

Level VI Evidence:
Presenting a single descriptive study.