bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical investigation of effects of tongue articulation and velopharyngeal closure on the production of sibilant [s]
Authors: Lu HsuehJui , Yoshinaga Tsukasa , Li ChungGang , Nozaki Kazunori , Iida Akiyoshi , Tsubokura Makoto 
Published: September 2022

AbstractA numerical simulation of sibilant /s/ production with the realistically moving vocal tract was conducted to investigate the flow and acoustic characteristics during the articulation process of velopharyngeal closure and tongue movement. The articulation process was simulated from the end of /u/ to the middle of /s/ in the Japanese word /usui/, including the tongue elevation and the velopharyngeal valve closure. The time-dependent vocal tract geometry was reconstructed from the computed tomography scan. The moving immersed boundary method with the hierarchical structure grid was adopted to approach the complex geometry of the human speech organs. The acoustic characteristics during the co-articulation process were observed and consistent with the acoustic measurement for the subject of the scan. The further simulations with the different closing speeds of the velopharyngeal closure showed that the far-field sound during the co-articulation process was amplified with the slower closing case, and the velum closure speed was inverse proportional to the sound amplitude with the slope value of − 35.3 dB s/m. This indicates possible phonation of indistinguishable aeroacoustics sound between /u/ and /s/ with slower velopharyngeal closure.
The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness
Authors: Kim Kyumin , Calabrese Peter , Wang Shanshan , Qin Chao , Rao Youliang , Feng Pinghui , Chen Xiaojiang S. 
Published: September 2022

AbstractDuring COVID-19 pandemic, mutations of SARS-CoV-2 produce new strains that can be more infectious or evade vaccines. Viral RNA mutations can arise from misincorporation by RNA-polymerases and modification by host factors. Analysis of SARS-CoV-2 sequence from patients showed a strong bias toward C-to-U mutation, suggesting a potential mutational role by host APOBEC cytosine deaminases that possess broad anti-viral activity. We report the first experimental evidence demonstrating that APOBEC3A, APOBEC1, and APOBEC3G can edit on specific sites of SARS-CoV-2 RNA to produce C-to-U mutations. However, SARS-CoV-2 replication and viral progeny production in Caco-2 cells are not inhibited by the expression of these APOBECs. Instead, expression of wild-type APOBEC3 greatly promotes viral replication/propagation, suggesting that SARS-CoV-2 utilizes the APOBEC-mediated mutations for fitness and evolution. Unlike the random mutations, this study suggests the predictability of all possible viral genome mutations by these APOBECs based on the UC/AC motifs and the viral genomic RNA structure.
Spin-textures of medium-body boson systems with trapped spin-f cold atoms
Authors: He Y. Z. , Bao C. G. , Li Z. B. 
Published: September 2022

AbstractThe spin-textures of bound medium-body systems with spin-$$\mathfrak {f}$$
f
atoms ($$\mathfrak {f}\ge 3$$

f
≥
3

) have been studied. The Hamiltonian is assumed to be dominated by the two-body interaction favoring parallel spins. The system with particle number $$N=8$$

N
=
8

and $$\mathfrak {f}=3$$

f
=
3

is first chosen, and the Hamiltonian is exactly diagonalized by using Fock-states as basis-states, thereby all the eigenenergies and eigenstates are obtained and a detailed analysis is made. Then the cases with $$N=13$$

N
=
13

and $$\mathfrak {f}=4$$

f
=
4

are further studied. Since the total spin S is conserved, the eigenstates having the same S form an S-group. Let the lowest (highest) energy state of an S-group be called a bottom-state (top-state). We found that all the bottom-states are bipartite product states with constituent states describing fully polarized subsystems containing $$N_1$$

N
1

and $$N_2$$

N
2

($$\le N_1$$

≤

N
1

) particles, respectively. For two bottom-states different in $$N_2$$

N
2

, the one with a larger $$N_2$$

N
2

is higher. For two having the same $$N_2$$

N
2

, the one with a smaller S is higher. Whereas all the top-states are found to be essentially a product state of the pairs, in each pair the two spins are coupled to $$\lambda$$
λ
if the strength of the $$\lambda$$
λ
-channel is more repulsive than the others. For the states belonging to an S-group, the higher one would contain more pieces. As the energy goes up, larger pieces (those containing more than two particles) will disappear.
Deep learning-based quantitative estimation of lymphedema-induced fibrosis using three-dimensional computed tomography images
Authors: Son Hyewon , Lee Suwon , Kim Kwangsoo , Koo Kyo-in , Hwang Chang Ho 
Published: September 2022

AbstractIn lymphedema, proinflammatory cytokine-mediated progressive cascades always occur, leading to macroscopic fibrosis. However, no methods are practically available for measuring lymphedema-induced fibrosis before its deterioration. Technically, CT can visualize fibrosis in superficial and deep locations. For standardized measurement, verification of deep learning (DL)-based recognition was performed. A cross-sectional, observational cohort trial was conducted. After narrowing window width of the absorptive values in CT images, SegNet-based semantic segmentation model of every pixel into 5 classes (air, skin, muscle/water, fat, and fibrosis) was trained (65%), validated (15%), and tested (20%). Then, 4 indices were formulated and compared with the standardized circumference difference ratio (SCDR) and bioelectrical impedance (BEI) results. In total, 2138 CT images of 27 chronic unilateral lymphedema patients were analyzed. Regarding fibrosis segmentation, the mean boundary F1 score and accuracy were 0.868 and 0.776, respectively. Among 19 subindices of the 4 indices, 73.7% were correlated with the BEI (partial correlation coefficient: 0.420–0.875), and 13.2% were correlated with the SCDR (0.406–0.460). The mean subindex of Index 2 $$\left( {\frac{{P_{Fibrosis\, in\, Affected} - P_{Fibrosis\, in\, Unaffected} }}{{P_{Limb\, in\, Unaffected} }}} \right)$$

P

F
i
b
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o
s
i
s

i
n

A
f
f
e
c
t
e
d

-

P

F
i
b
r
o
s
i
s

i
n

U
n
a
f
f
e
c
t
e
d

P

L
i
m
b

i
n

U
n
a
f
f
e
c
t
e
d

presented the highest correlation. DL has potential applications in CT image-based lymphedema-induced fibrosis recognition. The subtraction-type formula might be the most promising estimation method.
Towards robust in vivo quantification of oscillating biomagnetic fields using Rotary Excitation based MRI
Authors: Gram Maximilian , Albertova P. , Schirmer V. , Blaimer M. , Gamer M. , Herrmann M. J. , Nordbeck P. , Jakob P. M. 
Published: September 2022

AbstractSpin-lock based functional magnetic resonance imaging (fMRI) has the potential for direct spatially-resolved detection of neuronal activity and thus may represent an important step for basic research in neuroscience. In this work, the corresponding fundamental effect of Rotary EXcitation (REX) is investigated both in simulations as well as in phantom and in vivo experiments. An empirical law for predicting optimal spin-lock pulse durations for maximum magnetic field sensitivity was found. Experimental conditions were established that allow robust detection of ultra-weak magnetic field oscillations with simultaneous compensation of static field inhomogeneities. Furthermore, this work presents a novel concept for the emulation of brain activity utilizing the built-in MRI gradient system, which allows REX sequences to be validated in vivo under controlled and reproducible conditions. Via transmission of Rotary EXcitation (tREX), we successfully detected magnetic field oscillations in the lower nano-Tesla range in brain tissue. Moreover, tREX paves the way for the quantification of biomagnetic fields.
Transfontanelle photoacoustic imaging for in-vivo cerebral oxygenation measurement
Authors: Manwar Rayyan , McGuire Laura S. , Islam Md. Tarikul , Shoo Anthony , Charbel Fady T. , Pillers De-Ann M. , Avanaki Kamran 
Published: September 2022

AbstractThe capability of photoacoustic (PA) imaging to measure oxygen saturation through a fontanelle has been demonstrated in large animals in-vivo. We called this method, transfontanelle photoacoustic imaging (TFPAI). A surgically induced 2.5 cm diameter cranial window was created in an adult sheep skull to model the human anterior fontanelle. The performance of the TFPAI has been evaluated by comparing the PA-based predicted results against the gold standard of blood gas analyzer measurements.
Self-supervised classification of subcellular morphometric phenotypes reveals extracellular matrix-specific morphological responses
Authors: Wong Kin Sun , Zhong Xueying , Low Christine Siok Lan , Kanchanawong Pakorn 
Published: September 2022

AbstractCell morphology is profoundly influenced by cellular interactions with microenvironmental factors such as the extracellular matrix (ECM). Upon adhesion to specific ECM, various cell types are known to exhibit different but distinctive morphologies, suggesting that ECM-dependent cell morphological responses may harbour rich information on cellular signalling states. However, the inherent morphological complexity of cellular and subcellular structures has posed an ongoing challenge for automated quantitative analysis. Since multi-channel fluorescence microscopy provides robust molecular specificity important for the biological interpretations of observed cellular architecture, here we develop a deep learning-based analysis pipeline for the classification of cell morphometric phenotypes from multi-channel fluorescence micrographs, termed SE-RNN (residual neural network with squeeze-and-excite blocks). We demonstrate SERNN-based classification of distinct morphological signatures observed when fibroblasts or epithelial cells are presented with different ECM. Our results underscore how cell shapes are non-random and established the framework for classifying cell shapes into distinct morphological signature in a cell-type and ECM-specific manner.
Longitudinal investigation of a xenograft tumor zebrafish model using polarization-sensitive optical coherence tomography
Authors: Lichtenegger Antonia , Tamaoki Junya , Licandro Roxane , Mori Tomoko , Mukherjee Pradipta , Bian Lixuan , Greutter Lisa , Makita Shuichi , Wöhrer Adelheid , Matsusaka Satoshi , Kobayashi Makoto , Baumann Bernhard , Yasuno Yoshiaki 
Published: September 2022

AbstractBreast cancer is a leading cause of death in female patients worldwide. Further research is needed to get a deeper insight into the mechanisms involved in the development of this devastating disease and to find new therapy strategies. The zebrafish is an established animal model, especially in the field of oncology, which has shown to be a promising candidate for pre-clinical research and precision-based medicine. To investigate cancer growth in vivo in zebrafish, one approach is to explore xenograft tumor models. In this article, we present the investigation of a juvenile xenograft zebrafish model using a Jones matrix optical coherence tomography (JM-OCT) prototype. Immunosuppressed wild-type fish at 1-month post-fertilization were injected with human breast cancer cells and control animals with phosphate buffered saline in the tail musculature. In a longitudinal study, the scatter, polarization, and vasculature changes over time were investigated and quantified in control versus tumor injected animals. A significant decrease in birefringence and an increase in scattering signal was detected in tumor injected zebrafish in comparison to the control once. This work shows the potential of JM-OCT as a non-invasive, label-free, three-dimensional, high-resolution, and tissue-specific imaging tool in pre-clinical cancer research based on juvenile zebrafish models.
Factors, associated with elevated concentration of soluble carbonic anhydrase IX in plasma of women with cervical dysplasia
Authors: Grincevičienė Švitrigailė , Vaitkienė Daiva , Kanopienė Daiva , Vansevičiūtė Rasa , Tykvart Jan , Sukovas Artūras , Celiešiūtė Joana , Ivanauskaitė Didžiokienė Ernesta , Čižauskas Arvydas , Laurinavičienė Aida , Král Vlastimil , Hlavačková Anna , Zemanová Jitka , Stravinskienė Dovilė , Sližienė Aistė , Petrošiūtė Agnė , Petrauskas Vytautas , Balsytė Renata , Grincevičius Jonas , Navratil Vaclav , Jahn Ullrich , Konvalinka Jan , Žvirblienė Aurelija , Matulis Daumantas , Matulienė Jurgita 
Published: September 2022

AbstractPrecancerous lesions of human cervix uteri have a tendency for regression or progression. In cervical intraepithelial neoplasia grade 2 (CINII) case there is an uncertainty if a lesion will progress or regress. The carbonic anhydrase IX (CAIX) enzyme is overexpressed in cervical cancer which is more sensitive to radiotherapy. CAIX is associated with poor prognosis in solid hypoxic tumors. The aim of this study was to determine factors related to elevated soluble CAIX (s-CAIX) in high-grade intraepithelial lesion (HSIL) cases. Methods. Patients diagnosed with HSIL (N = 77) were included into the research group whereas without HSIL (N = 72)—the control group. Concentration of the soluble CAIX (s-CAIX) in plasma was determined by the DIANA ligand-antibody-based method. C. trachomatis was detected from cervical samples by PCR. Primary outcomes were risk factors elevating s-CAIX level in HSIL group. Non-parametric statistical analysis methods were used to calculate correlations. Results. The s-CAIX level in patients with HSIL was elevated among older participants (rs = 0.27, p = 0.04) and with C. trachomatis infection (p = 0.028). Among heavy smokers with HSIL, the concentration of s-CAIX was higher in older women (rs = 0.52, p = 0.005), but was not related to the age of heavy smokers’ controls (τ = 0.18 p = 0.40). Conclusion. The concentration of s-CAIX was higher among older, heavy smoking and diagnosed with C. trachomatis patients. All these factors increased the risk for HSIL progression.
Impact of diurnal temperature range on hospital admissions for cerebrovascular disease among farmers in Northwest China
Authors: Zhai Guangyu , Zhang Jing , Zhang Kuan , Chai Guorong 
Published: September 2022

AbstractDiurnal temperature range (DTR) is an appropriate indicator for reflecting climate change. Many previous studies have examined the relationship between DTR and mortality. Cerebrovascular disease (CVD) have a higher mortality than other diseases, with mortality from CVD higher in rural areas than in urban areas. A distributed lag non-linear model (DLNM) was used to analyze the exposure-effect relationship between DTR and hospital admissions for CVD from 2018 to 2020 in the population living in rural areas of Tianshui, Gansu Province, China. We investigated the effects of extreme DTR in groups stratified according to gender and age. A U-shape relationship was observed between DTR and hospital admissions for CVD. Both high DTR (19 °C) and low DTR (3 °C) were significantly associated significantly with CVD hospital admissions. When the lag period was 0–21 days, the impact of high DTR (1.595 [95% CI 1.301–1.957]) was slightly more significant than that of a low DTR (1.579 [95% CI − 1.202 to 2.075]). The effect of DTR on CVD varied in different populations. Males and adults were more sensitive to DTR than females and elderly people. It is necessary to make preventive measures to protect vulnerable populations from the adverse effects of extreme DTR.
Ultra-Rare BRD9 Loss-of-Function Variants Limit the Antiviral Action of Interferon
Authors: Mair Nina K. , Hale Benjamin G. 
Published: September 2022

AbstractThe human type I interferon (IFN) system is central to innate immune defense, and is essential to protect individuals against severe viral disease. Consequently, genetic disruption of IFN signaling or effector mechanisms is extremely rare, as affected individuals typically suffer life-threatening infections at an early age. While loss-of-function (LOF) mutations in canonical JAK-STAT signaling genes (such as IFNAR2, TYK2, STAT1, STAT2 and IRF9) have previously been characterized, little is known about the consequences of mutations in other human factors required for IFN signaling. Here, we studied the impact of rare human genetic variants in the recently identified contributor to IFN-stimulated gene expression and antiviral activity, bromodomain-containing protein 9 (BRD9). Using a cell-based BRD9 knock-out and reconstitution model system, we functionally assessed 12 rare human BRD9 missense variants predicted to impair protein function, as well as 3 ultra-rare human BRD9 LOF variants that lead to truncated versions of BRD9. As compared to wild-type BRD9, none of the 12 BRD9 missense variants affected the ability of exogenous IFN to limit virus replication. In contrast, all 3 truncated BRD9 LOF variants failed to allow exogenous IFN to function efficiently, as evidenced by exacerbated replication of an IFN-sensitive virus and diminished IFN-stimulated gene expression. Thus, while no homozygous BRD9 LOF carriers have yet been identified, our results predict that such extremely rare individuals would exhibit a compromised ability to mount a fully protective IFN-mediated antiviral response. Genetic variation in BRD9 could be considered in future studies to understand the infection susceptibility of some individuals.
Estimating genetics of body dimensions and activity levels in pigs using automated pose estimation
Authors: Gorssen Wim , Winters Carmen , Meyermans Roel , D’Hooge Rudi , Janssens Steven , Buys Nadine 
Published: September 2022

AbstractPig breeding is changing rapidly due to technological progress and socio-ecological factors. New precision livestock farming technologies such as computer vision systems are crucial for automated phenotyping on a large scale for novel traits, as pigs’ robustness and behavior are gaining importance in breeding goals. However, individual identification, data processing and the availability of adequate (open source) software currently pose the main hurdles. The overall goal of this study was to expand pig weighing with automated measurements of body dimensions and activity levels using an automated video-analytic system: DeepLabCut. Furthermore, these data were coupled with pedigree information to estimate genetic parameters for breeding programs. We analyzed 7428 recordings over the fattening period of 1556 finishing pigs (Piétrain sire x crossbred dam) with two-week intervals between recordings on the same pig. We were able to accurately estimate relevant body parts with an average tracking error of 3.3 cm. Body metrics extracted from video images were highly heritable (61–74%) and significantly genetically correlated with average daily gain (rg = 0.81–0.92). Activity traits were low to moderately heritable (22–35%) and showed low genetic correlations with production traits and physical abnormalities. We demonstrated a simple and cost-efficient method to extract body dimension parameters and activity traits. These traits were estimated to be heritable, and hence, can be selected on. These findings are valuable for (pig) breeding organizations, as they offer a method to automatically phenotype new production and behavioral traits on an individual level.
Performance comparison of three deep learning models for impacted mesiodens detection on periapical radiographs
Authors: Jeon Kug Jin , Ha Eun-Gyu , Choi Hanseung , Lee Chena , Han Sang-Sun 
Published: September 2022

AbstractThis study aimed to develop deep learning models that automatically detect impacted mesiodens on periapical radiographs of primary and mixed dentition using the YOLOv3, RetinaNet, and EfficientDet-D3 algorithms and to compare their performance. Periapical radiographs of 600 pediatric patients (age range, 3–13 years) with mesiodens were used as a training and validation dataset. Deep learning models based on the YOLOv3, RetinaNet, and EfficientDet-D3 algorithms for detecting mesiodens were developed, and each model was trained 300 times using training (540 images) and validation datasets (60 images). The performance of each model was evaluated based on accuracy, sensitivity, and specificity using 120 test images (60 periapical radiographs with mesiodens and 60 periapical radiographs without mesiodens). The accuracy of the YOLOv3, RetinaNet, and EfficientDet-D3 models was 97.5%, 98.3%, and 99.2%, respectively. The sensitivity was 100% for both the YOLOv3 and RetinaNet models and 98.3% for the EfficientDet-D3 model. The specificity was 100%, 96.7%, and 95.0% for the EfficientDet-D3, RetinaNet, and YOLOv3 models, respectively. The proposed models using three deep learning algorithms to detect mesiodens on periapical radiographs showed good performance. The EfficientDet-D3 model showed the highest accuracy for detecting mesiodens on periapical radiographs.
Pile driving repeatedly impacts the giant scallop (Placopecten magellanicus)
Authors: Jézéquel Youenn , Cones Seth , Jensen Frants H. , Brewer Hannah , Collins John , Mooney T. Aran 
Published: September 2022

AbstractLarge-scale offshore wind farms are a critical component of the worldwide climate strategy. However, their developments have been opposed by the fishing industry because of concerns regarding the impacts of pile driving vibrations during constructions on commercially important marine invertebrates, including bivalves. Using field-based daily exposure, we showed that pile driving induced repeated valve closures in different scallop life stages, with particularly stronger effects for juveniles. Scallops showed no acclimatization to repetitive pile driving across and within days, yet quickly returned to their initial behavioral baselines after vibration-cessation. While vibration sensitivity was consistent, daily pile driving did not disrupt scallop circadian rhythm, but suggests serious impacts at night when valve openings are greater. Overall, our results show distance and temporal patterns can support future mitigation strategies but also highlight concerns regarding the larger impact ranges of impending widespread offshore wind farm constructions on scallop populations.