bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of Toxoplasma invasion machinery
Authors: Segev-Zarko Li-av , Dahlberg Peter D , Sun Stella Y , Pelt Daniël M , Kim Chi Yong , Egan Elizabeth S , Sethian James A , Chiu Wah , Boothroyd John C 
Published: September 2022

Abstract
Host cell invasion by intracellular, eukaryotic parasites within the phylum Apicomplexa is a remarkable and active process involving the coordinated action of apical organelles and other structures. To date, capturing how these structures interact during invasion has been difficult to observe in detail. Here, we used cryogenic electron tomography to image the apical complex of Toxoplasma gondii tachyzoites under conditions that mimic resting parasites and those primed to invade through stimulation with calcium ionophore. Through the application of mixed-scale dense networks for image processing, we developed a highly efficient pipeline for annotation of tomograms, enabling us to identify and extract densities of relevant subcellular organelles and accurately analyze features in 3-D. The results reveal a dramatic change in the shape of the anteriorly located apical vesicle upon its apparent fusion with a rhoptry that occurs only in the stimulated parasites. We also present information indicating that this vesicle originates from the vesicles that parallel the intraconoidal microtubules and that the latter two structures are linked by a novel tether. We show that a rosette structure previously proposed to be involved in rhoptry secretion is associated with apical vesicles beyond just the most anterior one. This result, suggesting multiple vesicles are primed to enable rhoptry secretion, may shed light on the mechanisms Toxoplasma employs to enable repeated invasion attempts. Using the same approach, we examine Plasmodium falciparum merozoites and show that they too possess an apical vesicle just beneath a rosette, demonstrating evolutionary conservation of this overall subcellular organization.
Are There Non-Propositional Implicatures?
Authors: Sullivan Arthur 
Published: September 2022

AbstractCould there be an implicature whose content is not propositional? Grice's canon is somewhat ambivalent on this question, but such figures as Sperber & Wilson, Davis, and Lepore & Stone presume that there cannot be, and argue that this causes glaring failures within the Gricean programme. Building on work by McDowell and Buchanan, I argue that, on the contrary, the notion of non-propositional implicature is very much worth investigating. I show how the notion has promise to illuminate the content of many sorts of complex utterance—from the cases of verbal irony, metaphorical usage, slurring, insinuation, and (some kinds of) humour, to various others which involve expressive or evaluative content.
Inferences from Utterance to Belief
Authors: Abreu Zavaleta Martín 
Published: September 2022

AbstractIf Amelia utters ‘Brad ate a salad in 2005’ assertorically, and she is speaking literally and sincerely, then I can infer that Amelia believes that Brad ate a salad in 2005. This paper discusses what makes this kind of inference truth-preserving. According to the baseline picture, my inference is truth-preserving because, if Amelia is a competent speaker, she believes that the sentence she uttered means that Brad ate a salad in 2005; thus, if Amelia believes that that sentence is true, then she must believe that Brad ate a salad in 2005. I argue that this view is not correct; on pain of irrationality, normal speakers can’t have specific beliefs about the meaning of the sentences they utter. I propose a new account, relying on the view that epistemically responsible speakers utter sentences assertorically only if they believe all the propositions which they think those sentences might mean.
Measurement of differential cross sections for Σ+p elastic scattering in the momentum range 0.44–0.80 GeV/c
Authors: Nanamura T , Miwa K , Ahn J K , Akazawa Y , Aramaki T , Ashikaga S , Callier S , Chiga N , Choi S W , Ekawa H , Evtoukhovitch P , Fujioka N , Fujita M , Gogami T , Harada T K , Hasegawa S , Hayakawa S H , Honda R , Hoshino S , Hosomi K , Ichikawa M , Ichikawa Y , Ieiri M , Ikeda M , Imai K , Ishikawa Y , Ishimoto S , Jung W S , Kajikawa S , Kanauchi H , Kanda H , Kitaoka T , Kang B M , Kawai H , Kim S H , Kobayashi K , Koike T , Matsuda K , Matsumoto Y , Nagao S , Nagatomi R , Nakada Y , Nakagawa M , Nakamura I , Naruki M , Ozawa S , Raux L , Rogers T G , Sakaguchi A , Sakao T , Sako H , Sato S , Shiozaki T , Shirotori K , Suzuki K N , Suzuki S , Tabata M , Taille C d L , Takahashi H , Takahashi T , Takahashi T N , Tamura H , Tanaka M , Tanida K , Tsamalaidze Z , Ukai M , Umetsu H , Wada S , Yamamoto T O , Yoshida J , Yoshimura K 
Published: September 2022

Abstract
We performed a novel Σ+p scattering experiment at the J-PARC Hadron Experimental Facility. Approximately 2400 Σ+p elastic scattering events were identified from 4.9 × 107 tagged Σ+ particles in the Σ+ momentum range 0.44–0.80 GeV/c. The differential cross sections of the Σ+p elastic scattering were derived with much better precision than in previous experiments. The obtained differential cross sections were approximately 2 mb/sr or less, which were not as large as those predicted by the fss2 and FSS models based on the quark cluster model in the short-range region. By performing phase-shift analyses for the obtained differential cross sections, we experimentally derived the phase shifts of the 3S1 and 1P1 channels for the first time. The phase shift of the 3S1 channel, where a large repulsive core was predicted owing to the Pauli effect between quarks, was evaluated as $20^\circ \lt |\delta _{^3S_1}|\lt 35^\circ$. If the sign of $\delta _{^3S_1}$ is assumed to be negative, the interaction in this channel is moderately repulsive, as the Nijmegen extended-sort-core models predicted.
Safety of Human Embryonic Stem Cell-derived Mesenchymal Stem Cells for Treating Interstitial Cystitis: A Phase I Study
Authors: Shin Jung Hyun , Ryu Chae-Min , Yu Hwan Yeul , Park Juhyun , Kang Ah Reum , Shin Jeong Min , Hong Ki-Sung , Kim Eun Young , Chung Hyung-Min , Shin Dong-Myung , Choo Myung-Soo 
Published: September 2022

Abstract
There are still no definite treatment modalities for interstitial cystitis (IC). Meanwhile, stem cell therapy is rising as potential alternative for various chronic diseases. This study aimed to investigate the safety of the clinical-grade mesenchymal stem cells (MSCs) derived from human embryonic stem cells (hESCs), code name MR-MC-01 (SNU42-MMSCs), in IC patients. Three female IC patients with (1) symptom duration &gt;6 months, (2) visual pain analog scale (VAS) ≥4, and (3) one or two Hunner lesions &lt;2 cm in-office cystoscopy within 1 month were included. Under general anesthesia, participants received cystoscopic submucosal injection of SNU42-MMSCs (2.0 × 107/5 mL) at the center or margin of Hunner lesions and other parts of the bladder wall except trigone with each injection volume of 1 mL. Follow-up was 1, 3, 6, 9, and 12 months postoperatively. Patients underwent scheduled follow-ups, and symptoms were evaluated with validated questionnaires at each visit. No SNU42-MMSCs-related adverse events including immune reaction and abnormalities on laboratory tests and image examinations were reported up to 12-month follow-up. VAS pain was temporarily improved in all subjects. No de novo Hunner lesions were observed and one lesion of the first subject was not identifiable on 12-month cystoscopy. This study reports the first clinical application of transurethral hESC-derived MSC injection in three patients with IC. hESC-based therapeutics was safe and proved to have potential therapeutic efficacy in IC patients. Stem cell therapy could be a potential therapeutic option for treating IC.
Diagnostic Performance of 0.55 T MRI for Intracranial Aneurysm Detection
Authors: Osmanodja Filiz , Rösch Julie , Knott Michael , Doerfler Arnd , Grodzki David , Uder Michael , Heiss Rafael 
Published: September 2022

Objectives
Intracranial aneurysm (IA) is the main cause of subarachnoid hemorrhages. Time-of-flight (TOF) magnetic resonance angiography (MRA) at 1.5 T or 3 T magnetic resonance imaging (MRI) is a well-established method for the diagnosis of IA. The aim of this prospective study was to evaluate the performance of a modern 0.55 T MRI in the diagnosis of IAs in comparison to digital subtraction angiography (DSA) as a standard of reference.

Materials and Methods
Seventeen patients with suspicion of single or multiple IAs underwent TOF MRA at 0.55 T MRI 1 day before DSA. Two neuroradiologists independently measured the aneurysm neck, width, and height on 0.55 T, 1.5 T, and 3 T 3D-TOF MRA source images and 2D/3D rotational angiography. The main analysis assessed the intermodality agreement between 0.55 T TOF MRA and DSA using Bland-Altman plots, a Wilcoxon test, and the intraclass correlation coefficient (ICC). In a secondary analysis, aneurysm dimensions were compared between 0.55 T TOF MRA and 1.5/3 T TOF MRA. Interreader agreement was evaluated by ICC. A third neuroradiologist blinded to patient history screened 0.55 T TOF MRA data sets of the aforementioned 17 patients and 15 additional healthy patients for the presence and location of aneurysms.

Results
A total of 19 aneurysms in 16 patients were identified in both 0.55 T MRA and DSA. Measurements of the 2 nonblinded readers showed no significant differences between 0.55 T TOF MRA and DSA in the overall aneurysm size (calculated as the mean from height/width/neck) (P = 0.178), as well as in the mean width (P = 0.778) and neck values (P = 0.190). The mean height was significantly larger in 0.55 T TOF MRA in comparison to DSA (P = 0.020). Intermodality (1.5/3 T TOF MRA) and interrater agreement were excellent (ICC > 0.94). Of the 32 data sets of patients with and without IA, the blinded reader detected all aneurysms correctly by using 0.55 T images.

Conclusions
TOF-MRA acquired with a modern 0.55 T MRI is a reliable tool for the detection and initial assessment of IAs.
Hip Imaging in Children With Cerebral Palsy
Authors: Nosrati Reyhaneh , Zhang Da , Callahan Michael J. , Shore Benjamin J. , Tsai Andy 
Published: September 2022

Objectives
Hip displacement is the second most common orthopedic problem affecting children with cerebral palsy (CP). Routine radiographic hip surveillance typically involves an anteroposterior (AP) pelvis radiograph. Unfortunately, this imaging protocol is limited by its projectional technique and the positioning challenges in children with CP. Alternatively, hip low-dose computed tomography (LDCT) has been advocated as a more accurate strategy for imaging surveillance as it provides biofidelic details of the hip that is independent of patient positioning. However, the tradeoff is the (presumed) higher radiation dose to the patient. The goal of this study is to estimate patient-specific radiation doses of hip LDCTs and AP pelvis radiographs in CP patients, and perform an intrapatient dose comparison.

Materials and Methods
A search of our imaging database was performed to identify children with CP who underwent hip LDCT and AP pelvis radiograph within 6 months of each other. The LDCTs were performed using weight-adjusted kVp and tube current modulation, whereas the radiographs were obtained with age-/size-adjusted kVp/mAs. The patient-specific organ and effective doses for LDCT were estimated by matching the patients to a nonreference pediatric phantom library from the National Cancer Institute Dosimetry System for Computed Tomography database with Monte Carlo–based dosimetry. The patient-specific organ and effective doses for radiograph were estimated using the National Cancer Institute Dosimetry System for Radiography and Fluoroscopy with Monte Carlo–based dose calculation. Dose conversion k-factors of dose area product for radiography and dose length product for LDCT were adapted, and the estimation results were compared with patient-specific dosimetry.

Results
Our study cohort consisted of 70 paired imaging studies from 67 children (age, 9.1 ± 3.3 years). The patient-specific and dose length product–based effective doses for LDCT were 0.42 ± 0.21 mSv and 0.59 ± 0.28 mSv, respectively. The patient-specific and dose area product–based effective doses for radiography were 0.14 ± 0.09 mSv and 0.08 ± 0.06 mSv, respectively.

Conclusions
The radiation dose for a hip LDCT is ~4 times higher than pelvis radiograph, but it is still very low and poses minimal risk to the patient.
Thermoluminescence Dosimetry in Abdominal CT for Urinary Stone Detection
Authors: Grunz Jan-Peter , Halt Daniel , Schüle Simone , Beer Meinrad , Hackenbroch Carsten 
Published: September 2022

Objectives
Spectral shaping via tin prefiltration has gained recognition for dose saving in high-contrast imaging tasks. The aim of this phantom dosimetry study was to investigate whether the use of tin filters can also reduce the effective radiation dose in 100 kVp abdominal computed tomography (CT) compared with standard low-dose scans for suspected urolithiasis.

Methods
Using a third-generation dual-source CT scanner, 4 scan protocols each were used on a standard (P1–P4) and a modified obese Alderson-Rando phantom (P5–P8), in which 11 urinary stones of different compositions were placed. Hereby 1 scan protocol represented standard low-dose settings (P1/P5: 110 kVp/120 kVp), whereas 3 experimental protocols used low-kilovoltage spectral shaping (P2/P3/P4 and P6/P7/P8: 100 kVp with tin prefiltration). Radiation dose was recorded by thermoluminescent dosimeters at 24 measurement sites. For objective assessment of image quality, dose-weighted contrast-to-noise ratios were calculated and compared between scan protocols. Additional subjective image quality analysis was performed by 2 radiologists using equidistant 5-point scales for estimation image noise, artifacts, kidney stone detectability, and delineation of bone and soft tissue.

Results
Both conventional low-dose protocols without tin prefiltration were associated with the highest individual equivalent doses and the highest effective radiation dose in the experimental setup (P1: 0.29–6.43 mGy, 1.45–1.83 mSv; P5: 0.50–9.35 mGy, 2.33–2.79 mSv). With no false-positive diagnoses, both readers correctly detected each of the 11 urinary calculi irrespective of scan protocol and phantom configuration. Protocols using spectral shaping via tin prefiltration allowed for effective radiation dose reduction of up to 38% on the standard phantom and 18% on the modified obese phantom, while maintaining overall diagnostic image quality. Effective dose was approximately 10% lower in a male versus female anatomy and could be reduced by another 10% if gonadal protection was used (P < 0.001).

Conclusions
Spectral shaping via tin prefiltration at 100 kVp is a suitable means to reduce the effective radiation dose in abdominal CT imaging of patients with suspected urolithiasis. The dose reduction potential is slightly less pronounced in a modified phantom emulating an obese body composition compared with a standard phantom.
High diversity of arthropod colour vision: from genes to ecology
Authors: Yilmaz Ayse , Hempel de Ibarra Natalie , Kelber Almut 
Published: September 2022

Colour vision allows animals to use the information contained in the spectrum of light to control important behavioural decisions such as selection of habitats, food or mates. Among arthropods, the largest animal phylum, we find completely colour-blind species as well as species with up to 40 different opsin genes or more than 10 spectral types of photoreceptors, we find a large diversity of optical methods shaping spectral sensitivity, we find eyes with different colour vision systems looking into the dorsal and ventral hemisphere, and species in which males and females see the world in different colours. The behavioural use of colour vision shows an equally astonishing diversity. Only the neural mechanisms underlying this sensory ability seems surprisingly conserved—not only within the phylum, but even between arthropods and the other well-studied phylum, chordates. The papers in this special issue allow a glimpse into the colourful world of arthropod colour vision, and besides giving an overview this introduction highlights how much more research is needed to fill in the many missing pieces of this large puzzle.
This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Colour vision in stomatopod crustaceans
Authors: Cronin Thomas W. , Porter Megan L. , Bok Michael J. , Caldwell Roy L. , Marshall Justin 
Published: September 2022

The stomatopod crustaceans, or mantis shrimps, are colourful marine invertebrate predators. Their unusual compound eyes have dorsal and ventral regions resembling typical crustacean apposition designs separated by a unique region called the midband that consists of from two to six parallel rows of ommatidia. In species with six-row midbands, the dorsal four rows are themselves uniquely specialized for colour analysis. Rhabdoms of ommatidia in these rows are longitudinally divided into three distinct regions: an apical ultraviolet (UV) receptor, a shorter-wavelength middle tier receptor and a longer-wavelength proximal tier receptor. Each of the total of 12 photoreceptors has a different spectral sensitivity, potentially contributing to a colour-vision system with 12 channels. Mantis shrimps can discriminate both human-visible and UV colours, but with limited precision compared to other colour-vision systems. Here, we review the structure and function of stomatopod colour vision, examining the types of receptors present in a species, the spectral tuning of photoreceptors both within and across species, the neural analysis of colour and the genetics underlying the multiple visual pigments used for colour vision. Even today, after many decades of research into the colour vision of stomatopods, much of its operation and its use in nature remain a mystery.This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Exploiting colour space geometry for visual stimulus design across animals
Authors: Christenson Matthias P. , Mousavi S. Navid , Oriol Elie , Heath Sarah L. , Behnia Rudy 
Published: September 2022

Colour vision represents a vital aspect of perception that ultimately enables a wide variety of species to thrive in the natural world. However, unified methods for constructing chromatic visual stimuli in a laboratory setting are lacking. Here, we present stimulus design methods and an accompanying programming package to efficiently probe the colour space of any species in which the photoreceptor spectral sensitivities are known. Our hardware-agnostic approach incorporates photoreceptor models within the framework of the principle of univariance. This enables experimenters to identify the most effective way to combine multiple light sources to create desired distributions of light, and thus easily construct relevant stimuli for mapping the colour space of an organism. We include methodology to handle uncertainty of photoreceptor spectral sensitivity as well as to optimally reconstruct hyperspectral images given recent hardware advances. Our methods support broad applications in colour vision science and provide a framework for uniform stimulus designs across experimental systems.
This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
Colour vision in thrips (Thysanoptera)
Authors: Lopez-Reyes Karla , Armstrong Karen F. , van Tol Robert W. H. M. , Teulon David A. J. , Bok Michael J. 
Published: September 2022

Insects are an astonishingly successful and diverse group, occupying the gamut of habitats and lifestyle niches. They represent the vast majority of described species and total terrestrial animal biomass on the planet. Their success is in part owed to their sophisticated visual systems, including colour vision, which drive a variety of complex behaviours. However, the majority of research on insect vision has focused on only a few model organisms including flies, honeybees and butterflies. Especially understudied are phytophagous insects, such as diminutive thrips (Thysanoptera), in spite of their damage to agriculture. Thrips display robust yet variable colour-specific responses despite their miniaturized eyes, but little is known about the physiological and ecological basis of their visual systems. Here, we review the known visual behavioural information about thrips and the few physiological studies regarding their eyes. Eye structure, spectral sensitivity, opsin genes and the presence of putative colour filters in certain ommatidia strongly imply dynamic visual capabilities. Finally, we discuss the major gaps in knowledge that remain for a better understanding of the visual system of thrips and why bridging these gaps is important for expanding new possibilities for applied pest management strategies for these tiny insects.
This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.
A model for colour preference behaviour of spring migrant aphids
Authors: Döring Thomas F. , Kirchner Sascha M. 
Published: September 2022

Aphids are economically and ecologically important herbivorous insects. A critical step in their life cycle is the visually guided host finding behaviour. To elucidate the role of colour in host finding of aphid spring migrants we conducted large colour trap experiments in the field and analysed aphid catch data, using trap spectral reflectance data as input. Based on known and putative photoreceptor sensitivities we developed and optimized a simple empirical colour choice model for spring migrants of different aphid species which confirmed and explained the yellow preference of these insects. In a further step, we applied multivariate statistical methods to behavioural and reflectance data, but without data on photoreceptor sensitivities, to find the wavelengths of greatest importance for the aphids' behavioural responses. This analysis confirmed the position of the green photoreceptor peak previously obtained independently with electrophysiological methods. In a final step, we applied the colour preference model to a dataset of leaf spectra. This showed that aphid visual preference would be dependent on the plants’ nutritional status, with lower nitrogen input being associated with stronger preference, despite known benefits of high nitrogen levels for aphid reproduction and fitness. Ecological and evolutionary implications of these results are discussed.This article is part of the theme issue ‘Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods’.