bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pseudorandomness of primes at large scales
Authors: Leung Sun-kai 
Published: January 2025

ABSTRACT
Assuming a q-variant of the prime k-tuple conjecture uniformly, we compute mixed moments of the number of primes in disjoint short intervals and progressions. This involves estimating the mean of singular series along products of lattices, which is of independent interest. As a consequence, we establish the convergence of both sequences of suitably normalized primes to a standard Poisson point process.
Complement proteins in axial spondyloarthritis: associations with disease activity and TNFi treatment response in a multicentre RCT
Authors: Mistegaard Clara , Troldborg Anne , Torgutalp Murat , Loft Anne Gitte , Thiel Steffen , Muche Burkhard , Rios Rodriguez Valeria , Protopopov Mikhail , Listing Joachim , Sieper Joachim , Poddubnyy Denis , Proft Fabian 
Published: January 2025

Abstract

Objectives
To investigate lectin pathway proteins (LPPs) and complement activation marker C3dg as biomarkers for disease activity and treatment response in a multicentre, randomized controlled trial of axial spondyloarthritis (axSpA) patients initiating TNF inhibitor (TNFi) therapy.

Methods
Serum samples from 108 patients with active radiographic axSpA from the CONSUL study, collected before and after 12 weeks of TNFi therapy, were measured using immunoassays for LPPs (MBL, CL-L1, M-, L-, and H-ficolin, MASP-1, -2, and -3, MAp44) and the complement activation marker C3dg.

Results
After 12 weeks of TNFi therapy, serum levels of LPPs L-ficolin, M-ficolin, and MASP-2 decreased, while MASP-3 increased after adjustment for baseline CRP. Baseline L-ficolin levels correlated positively with baseline ASDAS-CRP and BASFI. C3dg correlated positively with ASDAS-CRP. Conversely, MASP-1 and MAp44 correlated negatively with ASDAS-CRP. Assessed by univariate logistic regression, C3dg and MASP-1 were associated with treatment response of clinically important improvement (ΔASDAS-CRP ≥1.1) and inactive disease (ASDAS-CRP &lt;1.3) at week 12, respectively. Only C3dg remained significant in a multivariate regression analysis.

Conclusion
In this study, complement LPPs L-ficolin, M-ficolin, and MASP-2 levels decrease following initiation of TNFi therapy, whereas alternative pathway critical component MASP-3 increases. Baseline L-ficolin and C3dg correlated positively with ASDAS-CRP, potentially by CRP influence. Nevertheless, baseline C3dg levels were associated with treatment response (ASDAS-CRP &lt;1.3) at week 12. Our results provide important perspectives on the inflammatory processes in axSpA, shedding light on the involvement of the complement system related to disease activity, treatment response, and potentially to prognosis.
matvis: a matrix-based visibility simulator for fast forward modelling of many-element 21 cm arrays
Authors: Kittiwisit Piyanat , Murray Steven G , Garsden Hugh , Bull Philip , Wilensky Michael J , Cain Christopher , Parsons Aaron R , Sipple Jackson , Adams Tyrone , Aguirre James E , Baartman Rushelle , Beardsley Adam P , Berkhout Lindsay M , Bernardi Gianni , Billings Tashalee S , Bowman Judd D , Bradley Richard F , Burba Jacob , Carey Steven , Carilli Chris L , Chen Kai-Feng , Choudhuri Samir , Cox Tyler , DeBoer David R , Acedo Eloy de Lera , Dexter Matt , Dillon Joshua S , Eksteen Nico , Ely John , Ewall-Wice Aaron , Fagnoni Nicolas , Furlanetto Steven R , Gale-Sides Kingsley , Gehlot Bharat Kumar , Glendenning Brian , Gorce Adelie , Gorthi Deepthi , Greig Bradley , Grobbelaar Jasper , Halday Ziyaad , Hazelton Bryna J , Hewitt Jacqueline N , Hickish Jack , Jacobs Daniel C , Josaitis Alec , Kern Nicholas S , Kerrigan Joshua , Kim Honggeun , Kolopanis Matthew , Lanman Adam , Plante Paul La , Liu Adrian , Ma Yin-Zhe , MacMahon David H E , Malan Lourence , Malgas Cresshim , Malgas Keith , Marero Bradley , Martinot Zachary E , McBride Lisa , Mesinger Andrei , Molewa Mathakane , Morales Miguel F , Mosiane Tshegofalang , Nunhokee Chuneeta Devi , Nuwegeld Hans , Pascua Robert , Qin Yuxiang , Rath Eleanor , Razavi-Ghods Nima , Robnett James , Santos Mario G , Sims Peter , Singh Saurabh , Storer Dara , Swarts Hilton , Tan Jianrong , Thyagarajan Nithyanandan , van Wyngaarden Pieter , Xu Zhilei , Zheng Haoxuan 
Published: January 2025

ABSTRACT
Detection of the faint 21 cm line emission from the Cosmic Dawn and Epoch of Reionization will require not only exquisite control over instrumental calibration and systematics to achieve the necessary dynamic range of observations but also validation of analysis techniques to demonstrate their statistical properties and signal loss characteristics. A key ingredient in achieving this is the ability to perform high-fidelity simulations of the kinds of data that are produced by the large, many-element, radio interferometric arrays that have been purpose-built for these studies. The large scale of these arrays presents a computational challenge, as one must simulate a detailed sky and instrumental model across many hundreds of frequency channels, thousands of time samples, and tens of thousands of baselines for arrays with hundreds of antennas. In this paper, we present a fast matrix-based method for simulating radio interferometric measurements (visibilities) at the necessary scale. We achieve this through judicious use of primary beam interpolation, fast approximations for coordinate transforms, and a vectorized outer product to expand per-antenna quantities to per-baseline visibilities, coupled with standard parallelization techniques. We validate the results of this method, implemented in the publicly available matvis code, against a high-precision reference simulator, and explore its computational scaling on a variety of problems.
Extinct scorpion family Chaerilobuthidae from Mid-Cretaceous Burmese amber reinterpreted as subfamily of extant family Pseudochactidae (Chelicerata: Scorpiones)
Authors: Xuan Qiang , Prendini Lorenzo , Engel Michael S , Cai Chenyang , Huang Diying 
Published: January 2025

Abstract
The extinct scorpion family Chaerilobuthidae Lourenço and Beigel, 2011, endemic to Burmese amber, was initially established due to its unique pedipalp trichobothrial pattern related to the Type A and Type B patterns of families Buthidae C.L. Koch, 1837 and Chaerilidae Pocock, 1893, respectively. The present contribution describes 11 new specimens, representing seven species of Chaerilobuthidae from Mid-Cretaceous Burmese amber, revealing their morphology using various imaging technologies. A revised diagnosis of Chaerilobuthus Lourenço and Beigel, 2011 is provided based on new morphological characters of the carapace, ocelli, chelicera, pedipalp trichobothria, coxapophyses, and leg tarsi. The other two genera of Chaerilobuthidae, Chaeriloiurus Lourenço, 2020 and Serratochaerilobuthus Lourenço, 2024, are synonymized with Chaerilobuthus based on a reassessment of their morphological characters and morphometric analysis, creating Chaerilobuthus brigittemuellerae (Lourenço and Velten, 2020), comb. nov. and Chaerilobuthus schmidti (Lourenço and Velten, 2024), comb. nov.. The systematic position of Chaerilobuthidae is clarified based on phylogenetic analyses of an updated morphological character matrix for Pseudochactidae Gromov, 1998, an extant family in Asia. Phylogenetic analysis placed Chaerilobuthidae sister to the pseudochactid subfamily Vietbocapinae Lourenço, 2012, justifying its transfer to Pseudochactidae, as Chaerilobuthinae Lourenço and Beigel, 2011, stat. nov.. This discovery confirms that Pseudochactidae date back 100 Mya and contributes to understanding the origin and evolutionary history of this relictual family.
Degree of Preoperative Bilateral Hearing Affects Patient-Reported Outcome in Primary Stapedotomy
Authors: Thunberg Ulrica , Tahir Taj , Redfors Ylva Dahlin , Finizia Caterina 
Published: January 2025

Objective
To investigate whether degree of asymmetric hearing impairment influences patient-reported outcome measures and objective hearing results in primary stapedotomy.

Study Design
Register study.

Setting
Data from the Swedish Quality Register for Otosclerosis Surgery consisting of 90% of stapes operations performed in Sweden

Main Outcome measure
The 984 patients eligible for inclusion were categorized on the basis of preoperative hearing impairment: unilateral, bilateral asymmetric, or bilateral symmetric. Pure-tone audiometry and patient-reported outcome measures were analyzed, and Glasgow benefit plots were constructed. Ordinal logistics regression analyses were performed to adjust for factors influencing PROMs associated with degree of asymmetric hearing.

Results
Over 90% of patients across all groups reported improved or much improved hearing ability post-surgery. Ninety-five percent of patients who rated their hearing as worse or much worse after surgery had an air-conductive gain of <20 dB PTA4. Individuals with unilateral hearing impairment were more likely to report lower satisfaction with hearing function and daily life activities after surgery compared with those with bilateral hearing impairment, especially bilateral symmetric hearing impairment. In terms of hearing function, the bilateral symmetric hearing impairment group showed a significant decrease in the log odds of reporting lower satisfaction with a coefficient of −0.71 (95% confidence interval, −1.13 to −0.33), whereas the bilateral asymmetric hearing impairment group showed a nonsignificant decrease with a coefficient of −0.14 (95% confidence interval, −0.41 to 0.14) compared with the unilateral hearing impairment group. Tinnitus was more frequent in those with unilateral hearing impairment.

Conclusion
Those with preoperative unilateral hearing impairment were more likely to express lower satisfaction with the results, compared with patients with bilateral impairment. Our findings suggest that the degree of bilateral hearing impairment should be considered in preoperative counseling, to better align with patient expectations regarding the benefit of surgery. An estimated air-conductive gain of at least 20 dB PTA4 was favorable for patient satisfaction.
Effect of Patient Positioning on CT Number Accuracy: A Phantom Study Comparing Energy Integrating and Deep Silicon Photon Counting Detector CT
Authors: Salyapongse Aria M. , Rose Sean D. , Pickhardt Perry J. , Lubner Meghan G. , Toia Giuseppe V. , Bujila Robert , Yin Zhye , Slavic Scott , Szczykutowicz Timothy P. 
Published: January 2025

Objective
Patient positioning during clinical practice can be challenging, and mispositioning leads to a change in CT number. CT number fluctuation was assessed in single-energy (SE) EID, dual-energy (DE) EID, and deep silicon photon-counting detector (PCD) CT over water-equivalent diameter (WED) with different mispositions.

Methods
A phantom containing five clinically relevant inserts (Mercury Phantom, Gammex) was scanned on a clinical EID CT and a deep silicon PCD CT prototype at vertical positions of 0, 4, 8, and 12 cm. EID scans used 120 kV and rapid kV-switching DE techniques. CT number was calculated for air, water, polystyrene, iodine 10 mg/mL, and bone. Ideal CT numbers were calculated using the NIST XCOM database toolkit. Comparison of measured to ideal CT number utilized relative root mean square error (RMSE). Trends in CT number versus WED were compared using linear regression and statistical comparisons to test for differences in slope.

Results
No statistical difference of CT number with mispositioning was seen between acquisition modes. CT number fluctuation was larger due to WED than mispositioning for all material inserts. Water, iodine, and bone, for deep silicon PCD CT had statistically significant (P < 0.05) smaller slopes compared to EIDof CT number over WED for all tested mispositions. The accuracy of deep silicon PCD CT was higher than either SE or DE EID CT for all materials at all mispositions except for polystyrene.

Conclusions
WED (ie, patient size) contributes to CT number fluctuation more than mispositioning. The change in CT number was significantly smaller, and CT number accuracy was higher for deep silicon PCD CT in this phantom study.
Pilot Study Examining the Use of DCE MRI With Pharmacokinetic Analysis to Evaluate Hypoxia in Prostate Cancer
Authors: Febronio Eduardo Miguel , Secaf André de Freitas , Chahud Fernando , Elias Jorge , Reis Rodolfo B. , Muglia Valdair F. 
Published: January 2025

Purpose:
This study aimed to investigate the association between tumor hypoxia, assessed through anti-HIF (hypoxia-inducible factor) staining, and aggressiveness in prostate cancer using a pharmacokinetic model, particularly those derived from the Tofts model, in predicting tumor aggressiveness.

Material and Methods:
From January 2019 to April 2021, we conducted a retrospective search of patients with confirmed prostate cancer and a previous magnetic resonance imaging (MRI) examination. After exclusions, a total of 57 consecutive patients were enrolled. Patient data, including demographic, laboratory, and pathologic variables, were collected. MRI acquisition followed PI-RADS guidelines, encompassing T2-weighted, diffusion-weighted imaging, and dynamic contrast-enhanced imaging. An experienced abdominal radiologist conducted both morphologic and quantitative MRI analyses, evaluating parameters such as lesion size, apparent diffusion coefficient values, and the Tofts pharmacokinetics (TF) model. The histopathologic analysis included the International Society of Uropathology (ISUP) score and hypoxia marker immunohistochemistry.

Results:
There were no significant demographic and imaging differences between hypoxic and nonhypoxic tumors, except for elevated prostate-specific antigen levels in the latter and decreased normalized apparent diffusion coefficient in the former. Morphologic assessments revealed larger lesions in the hypoxia group. While K
trans showed a positive association with hypoxia, it did not independently predict high-risk lesions.

Conclusions:
Our results suggest that pharmacokinetic analysis by the Tofts model was associated with tumors with hypoxia. However, this parameter was not an independent predictor of more aggressive tumors. Further studies, with a larger number of patients, multi-institutional and prospective, are needed to verify this possible association.
Dual-Split CT to Simulate Multiple Radiation Doses From a Single Scan—Liver Lesion Detection Compared With Dose-Matched Single-Energy CT
Authors: Racine Damien , Niemann Tilo , Nemeth Bence , Manzano Lucia Gallego , Alkadhi Hatem , Viry Anaïs , Kubik-Huch Rahel A. , Frauenfelder Thomas , Euler André 
Published: January 2025

Objectives
The aim of this study was to evaluate the potential use of simulated radiation doses from a dual-split CT scan for dose optimization by comparing their lesion detectability to dose-matched single-energy CT acquisitions at different radiation dose levels using a mathematical model observer.

Materials and Methods
An anthropomorphic abdominal phantom with liver lesions (5–10 mm, both hyperattenuating and hypoattenuating) was imaged using a third-generation dual-source CT in single-energy dual-source mode at 100 kVp and 3 radiation doses (5, 2.5, 1.25 mGy). The tube current was 67% for tube A and 33% for tube B. For each dose, 5 simulated radiation doses (100%, 67%, 55%, 45%, 39%, and 33%) were generated through linear image blending. The phantom was also imaged using traditional single-source single-energy mode at equivalent doses. Each setup was repeated 10 times. Image noise texture was evaluated by the average spatial frequency (fav) of the noise power spectrum. Liver lesion detection was measured by the area under the receiver operating curve (AUC), using a channelized Hotelling model observer with 10 dense Gaussian channels.

Results
Fav decreased at lower radiation doses and differed between simulated and single-energy images (eg, 0.16 mm−1 vs 0.14 mm−1 for simulated and single-energy images at 1.25 mGy), indicating slightly blotchier noise texture for dual-split CT. For hyperattenuating lesions, the mean AUC ranged between 0.92–0.99, 0.81–0.96, and 0.68–0.89 for single-energy, and between 0.91–0.99, 0.78–0.91, and 0.70–0.85 for dual-split at 5 mGy, 2.5 mGy, and 1.25 mGy, respectively. For hypoattenuating lesions, the AUC ranged between 0.90–0.98, 0.75–0.93, and 0.69–0.86 for the single-energy, and between 0.92–0.99, 0.76–0.87, and 0.67–0.81 for dual-split at 5 mGy, 2.5 mGy, and 1.25 mGy, respectively. AUC values were similar between both modes at 5 mGy, and slightly lower, albeit not significantly, for the dual-split mode at 2.5 and 1.25 mGy.

Conclusions
Lesion detectability was comparable between multiple simulated radiation doses from a dual-split CT scan and dose-matched single-energy CT. Noise texture was slightly blotchier in the simulated images. Simulated doses using dual-split CT can be used to assess the impact of radiation dose reduction on lesion detectability without the need for repeated patient scans.
Anin vitroplatform for characterizing axonal electrophysiology of individual human iPSC-derived nociceptors
Authors: Clément Blandine F. , Petrella Lorenzo , Wallimann Lea , Duru Jens , Tringides Christina M. , Vörös János , Ruff Tobias 
Published: January 2025

AbstractCurrent treatments against severe forms of neuropathic pain demonstrate insufficient efficacy or lead to unwanted side effects as they fail to specifically target the affected nociceptors - a specialized subclass of sensory neurons conveying potentially damaging stimuli information to the central nervous system. Neuropathic pain may involve different nociceptor subtypes in different patients. Tools that can distinguish nociceptive axons would enable a more targeted compound screening. Therefore, we developed anin vitroplatform combining a CMOS-based high-density microelectrode array with a polydimethylsiloxane (PDMS) guiding microstructure that captures the electrophysiological responses of nociceptors. Human induced pluripotent stem cell-derived (iPSC) nociceptors were cultured at low density with axons distributed through parallel 4 × 10 µm microchannels exiting the seeding well before converging to a bigger axon-collecting channel. This configuration allowed the measurement of stimulation-induced responses of individual axons. Nociceptors were found to exhibit a great diversity of electrophysiological response profiles that can be classified into different functional archetypes. Moreover, we show that some responses are affected by applying the TRPV1 agonist capsaicin. Overall, results using our platform demonstrate that we were able to distinguish nociceptive axons from different subtypes. The platform provides a promising tool for screening potential candidates for nociceptor-specific drugs.
Lithography-free Water Stable Conductive Polymer Nanowires
Authors: Hughes Damien , Mousa Abdelrazek H. , Musumeci Chiara , Larsson Malte , Shameem Muhammad Anwar , Aydemir Umut , Schmiderer Ludwig , Larsson Jonas , Berggren Magnus , Ek Fredrik , Olsson Roger , Hjort Martin 
Published: January 2025

AbstractFree-standing nanowires can gain intracellular access without causing cellular stress or apoptosis. Current approaches to generate nanowires focus on lithographic patterning and inorganic materials (Si, GaAs, Al2O3, etc.) while organic materials are less explored. Use of organic conductive polymers allows for creation of soft mixed ion–electron conducting nanowires. Processing conductive polymers into nanowires is challenging due to the harsh chemicals and processing conditions used. Here, we demonstrate a lithography-free and scalable method to generate all-organic water-stable nanowires composed of conductive polymers. A nanoporous membrane is filled with conductive polymer in solution followed by a cross-linking step to make the polymer water stable. The surface of the membrane is anisotropically etched using a reactive ion etcher to reveal the polymer inside the pores, which extend from the membrane as nanowires. We interface the nanowires with model algal cells and human primary hematopoietic stem and progenitor cells.TOC Graphic
Minimally Invasive DNA-Mediated Photostabilization for Extended Single-Molecule and Super-resolution Imaging
Authors: Scheckenbach Michael , Close Cindy , Bauer Julian , Grabenhorst Lennart , Cole Fiona , Köhler Jens , Matikonda Siddharth S. , Zhang Lei , Cordes Thorben , Schnermann Martin J. , Herrmann Andreas , Tinnefeld Philip , Szalai Alan M. , Glembockyte Viktorija 
Published: January 2025

AbstractPhotobleaching of fluorescence labels poses a major limitation in single-molecule and super-resolution microscopy. Conventional photostabilization methods, such as oxygen removal and addition of high concentrations of photostabilization additives, often require careful fluorophore selection and can disrupt the biological environment. To address these limitations, we developed a modular and minimally invasive photostabilization approach that utilizes DNA-mediated delivery of a photostabilizer directly to the imaging site. Under lower excitation intensities, the DNA-mediated strategy outperformed solution-based approaches, achieving efficient photostabilization at significantly lower additive concentrations. However, at higher excitation intensities, the stability of a single photostabilizer molecule became the limiting factor. To overcome this and reduce the loss of localizations in DNA-PAINT experiments we have also implemented a recovery scheme where the photostabilizer is continuously replenished at the imaging site. We further extended the approach to cell imaging, demonstrating improved localization rate and precision in 3D-DNA PAINT measurements. DNA-mediated photostabilization offers a promising solution for imaging applications where high additive concentrations are prohibited. Its modularity enables adaptation to various imaging schemes and ultimately expands the repertoire of fluorophores suitable for single-molecule and super-resolution imaging.
Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression inArabidopsis thaliana
Authors: Zhong Ziming , Bailey Mark , Kim Yong-In , Afsharyan Nazanin P. , Parker Briony , Arathoon Louise , Li Xiaowei , Rundle Chelsea A. , Behrens Andrew , Nedialkova Danny , Slavov Gancho , Hassani-Pak Keywan , Lilley Kathryn S. , Theodoulou Frederica L. , Mott Richard 
Published: January 2025

AbstractBackgroundWe investigated the flow of information from genome sequence to protein expression implied by the Central Dogma, to determine the impact of intermediate genomic levels in plants.ResultsWe performed genomic profiling of rosettes in twoArabidopsisaccessions, Col-0 and Can-0, and assembled their genomes using long reads and chromatin interaction data. We measured gene and protein expression in biological replicates grown in a controlled environment, also measuring CpG methylation, ribosome-associated transcript levels and tRNA abundance. Each omic level is highly reproducible between biological replicates and between accessions despite their 0.5% sequence divergence; the single best predictor of any level in one accession is the corresponding level in the other. Within each accession, gene codon frequencies accurately model both mRNA and protein expression. The effects of a codon on mRNA and protein expression are highly correlated but are unrelated to genome-wide codon frequencies or to tRNA levels which instead match genome-wide amino acid frequencies. Ribosome-associated transcripts closely track mRNA levels.ConclusionsIn the absence of environmental perturbation, neither methylation, tRNA nor ribosome-associated transcript levels add appreciable information about constitutive protein abundance beyond that in DNA codon frequencies and mRNA expression levels. The impact of constitutive gbM is mostly explained by gene codon composition. tRNA abundance tracks overall amino acid demand. However, genetic differences between accessions associate with differential gbM by inflating differential expression variation. Our data show that the Central Dogma holds only if both sequence and abundance information in mRNA are considered.