bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classification of brain tumours in MR images using deep spatiospatial models
Authors: Chatterjee Soumick , Nizamani Faraz Ahmed , Nürnberger Andreas , Speck Oliver 
Published: January 2022

AbstractA brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning, and magnetic resonance imaging is the principal imaging modality for diagnosing brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models, and the improvements in the model architectures yield better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating one spatial dimension separately or by considering the slices as a sequence of images over time, spatiotemporal models can be employed as “spatiospatial” models for this task. These models have the capabilities of learning specific spatial and temporal relationships while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.9345 and a test accuracy of 96.98%, while at the same time being the model with the least computational cost.
Reliability and validity of ultrasound to measure of muscle mass following allogeneic hematopoietic stem cell transplantation
Authors: Hashida Nao , Tada Yuma , Suzuki Masayuki , Ito Kumiko , Kato Yuji , Tamiya Hironari , Ishikawa Jun 
Published: January 2022

AbstractAllogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients frequently show physical dysfunction due to loss of muscle mass. This study aimed to clarify the reliability and validity of ultrasound in evaluating muscle mass and to analyze the patterns of change in muscle mass before and after allo-HSCT. We conducted a prospective observational study using data from 68 patients who had undergone their first allo-HSCT. We evaluated the thickness of the quadriceps, biceps, and suprahyoid muscle. Three individual evaluators underwent this examination for each muscle before transplantation and on days 30, 90, and 180 after allo-HSCT. Inter-rater reliability was calculated using the interclass correlation (ICC), and the level of correlation between muscle mass measured by ultrasound and psoas muscle mass assessed using computed tomography (CT) was assessed using Pearson correlation. ICC values ranged from 0.897 to 0.977 in the measurement. The correlation scores were 0.730, 0.546 and 0.579 between psoas muscle and the biceps, quadriceps, and suprahyoid muscle. The thickness of the biceps and quadriceps muscle were both significantly decreased after allo-HSCT from baseline. These results showed that the ultrasound technique was a reliable tool for evaluating muscle mass and detecting changes in muscle mass following allo-HSCT.
Effect of subjective vertical perception on lateral flexion posture of patients with Parkinson’s disease
Authors: Mikami Kyohei , Shiraishi Makoto , Kamo Tsutomu 
Published: January 2022

AbstractIn a retrospective study we tested our hypothesis that the subjective postural vertical ratio (SPV ratio), i.e., the subjective postural vertical measured in relation to the lateral flexion axis, is predictive of lateral trunk flexion in patients with Parkinson's disease (PD). Twenty-five patients were included. The SPV angle, i.e., the subjective perception of a vertical position with reference to the vertical axis, and the SPV ratio, i.e., the SPV angle with reference to the axis of lateral flexion, were calculated. The SPV ratio (r = 0.698, P = 0.001) and LTF angle (r =  − 0.601, P = 0.001) correlated with change in the LTF angle at 1 year. The SPV ratio was significantly smaller in patients for whom lateral trunk flexion improved (n = 12) than in those for whom it did not improve (n = 13) (0.99 ± 0.78 vs 1.66 ± 0.71, P = 0.011). The AUC under the ROC curve of the SPV ratio for discrimination of improvement was 0.795 (95% confidence interval: 0.61–0.98). We found that the SPV ratio is associated with change in the LTF and that it can conceivably be used to predict the likelihood of improvement in PD-associated lateral trunk flexion.
Precision cancer genome testing needs proficiency testing involving all stakeholders
Authors: Maekawa Masato , Taniguchi Terumi , Nishio Kazuto , Sakai Kazuko , Matsushita Kazuyuki , Nakatani Kaname , Ishige Takayuki , Ikejiri Makoto , Nishihara Hiroshi , Sunami Kuniko , Yatabe Yasushi , Hatanaka Kanako C. , Hatanaka Yutaka , Yamamoto Yoshihiro , Fukuyama Keita , Oda Shinya , Saito Kayoko , Yokomura Mamoru , Kubo Yuji , Sato Hiroko , Tanaka Yoshinori , Fuchioka Misa , Yamasaki Tadashi , Matsuda Koichiro , Kurachi Kiyotaka , Funai Kazuhiro , Baba Satoshi , Iwaizumi Moriya 
Published: January 2022

AbstractTo implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared genomic DNA from the cancer tissue and peripheral blood of 5 cancer patients and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants and 25 bp delins in EGFR. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. By conducting this pilot study using patient samples, we were able to obtain a glimpse of the current status of cancer genome testing at participating laboratories. To enhance domestic cancer genome testing, it is important to conduct local PT and to involve the parties concerned as organizers and participants.
Barrier removal and dynamics of intermittent stream habitat regulate persistence and structure of fish community
Authors: Kukuła Krzysztof , Bylak Aneta 
Published: January 2022

AbstractBarrier effects observed in the presence of weirs are exacerbated by low water levels. We conducted a 10-year study to assess the ecological effects of stream restoration while analysing the possibility of a seasonal lack of hydrological continuity, with multiple measurements before and after restoring stream structural continuity. The research hypothesis assumes that in intermittent streams, there would be little or no change in the fish community downstream the barrier before vs. after barrier removal, and a significant change upstream the barrier before vs. after. Our results indicate, that by removing small barriers, their detrimental effects on the longitudinal passage of riverine fishes and fish assemblages can be rehabilitated. In the wet season, fish migrants from the mainstem river appeared in the downstream section of the stream. Stream intermittency, however, placed a habitat filter over the assemblage. Thus, after barrier removal, only two small-bodied fish species that tolerate periodic oxygen deficiencies and rising water temperatures gradually shifted upstream and formed stable populations. We emphasize, that we should not refrain from restoring the longitudinal continuity of intermittent streams, because they periodically provide fish valuable refugia and can also be a source of new generations and strengthen fish populations in mainstem river.
Genomic landscape and immune-related gene expression profiling of epithelial ovarian cancer after neoadjuvant chemotherapy
Authors: Lodewijk I. , Bernardini A. , Suárez-Cabrera C. , Bernal E. , Sánchez R. , Garcia J. L. , Rojas K. , Morales L. , Wang S. , Han X. , Dueñas M. , Paramio J. M. , Manso L. 
Published: January 2022

AbstractPlatinum-based neoadjuvant chemotherapy followed by interval debulking surgery is an accepted treatment for patients with stage III or IV epithelial ovarian cancer who are not suitable for primary debulking surgery. The identification of suitable adjuvant treatments in these patients is an unmet need. Here, we explore potential genomic characteristics (mutational and immune-associated expression profiles) in a series of patients undergoing neoadjuvant chemotherapy. Tumor samples from biopsy and interval debulking surgery were analyzed for mutational landscape and immune profiling, together with detailed immunohistochemistry using different immune cell markers, and correlated with clinicopathological characteristics and potential response to neoadjuvant chemotherapy. No major differences in the mutational landscape were observed in paired biopsy and surgery samples. Genomic loss of heterozygosity was found to be higher in patients with total/near-total tumor response. The immune gene expression profile after neoadjuvant chemotherapy revealed activation of several immune regulation-related pathways in patients with no/minimal or partial response. In parallel, neoadjuvant therapy caused a significant increase of tumor-infiltrating lymphocyte population abundance, primarily due to an augmentation of the CD8+ T cell population. Remarkably, these changes occurred irrespective of potential homologous recombination defects, such as those associated with BRCA1/2 mutations. Our study strengthens the use of loss of heterozygosity as a biomarker of homologous repair deficiency. The changes of immune states during neoadjuvant chemotherapy reveal the dynamic nature of tumor-host immune interactions and suggest the potential use of immune checkpoint inhibitors or their combination with poly-ADP polymerase inhibitors in high stage and grade epithelial ovarian cancer patients undergoing neoadjuvant therapy.
PhenoPad: Building AI enabled note-taking interfaces for patient encounters
Authors: Wang Jixuan , Yang Jingbo , Zhang Haochi , Lu Helen , Skreta Marta , Husić Mia , Arbabi Aryan , Sultanum Nicole , Brudno Michael 
Published: January 2022

AbstractCurrent clinical note-taking approaches cannot capture the entirety of information available from patient encounters and detract from patient-clinician interactions. By surveying healthcare providers’ current note-taking practices and attitudes toward new clinical technologies, we developed a patient-centered paradigm for clinical note-taking that makes use of hybrid tablet/keyboard devices and artificial intelligence (AI) technologies. PhenoPad is an intelligent clinical note-taking interface that captures free-form notes and standard phenotypic information via a variety of modalities, including speech and natural language processing techniques, handwriting recognition, and more. The output is unobtrusively presented on mobile devices to clinicians for real-time validation and can be automatically transformed into digital formats that would be compatible with integration into electronic health record systems. Semi-structured interviews and trials in clinical settings rendered positive feedback from both clinicians and patients, demonstrating that AI-enabled clinical note-taking under our design improves ease and breadth of information captured during clinical visits without compromising patient-clinician interactions. We open source a proof-of-concept implementation that can lay the foundation for broader clinical use cases.
Importance of CSF-based Aβ clearance with age in humans increases with declining efficacy of blood-brain barrier/proteolytic pathways
Authors: Elbert Donald L. , Patterson Bruce W. , Lucey Brendan P. , Benzinger Tammie L. S. , Bateman Randall J. 
Published: January 2022

AbstractThe kinetics of amyloid beta turnover within human brain is still poorly understood. We previously found a dramatic decline in the turnover of Aβ peptides in normal aging. It was not known if brain interstitial fluid/cerebrospinal fluid (ISF/CSF) fluid exchange, CSF turnover, blood-brain barrier function or proteolysis were affected by aging or the presence of β amyloid plaques. Here, we describe a non-steady state physiological model developed to decouple CSF fluid transport from other processes. Kinetic parameters were estimated using: (1) MRI-derived brain volumes, (2) stable isotope labeling kinetics (SILK) of amyloid-β peptide (Aβ), and (3) lumbar CSF Aβ concentration during SILK. Here we show that changes in blood-brain barrier transport and/or proteolysis were largely responsible for the age-related decline in Aβ turnover rates. CSF-based clearance declined modestly in normal aging but became increasingly important due to the slowing of other processes. The magnitude of CSF-based clearance was also lower than that due to blood-brain barrier function plus proteolysis. These results suggest important roles for blood-brain barrier transport and proteolytic degradation of Aβ in the development Alzheimer’s Disease in humans.
Strain and pseudo-magnetic fields in optical lattices from density-assisted tunneling
Authors: Jamotte Maxime , Goldman Nathan , Di Liberto Marco 
Published: January 2022

AbstractApplying time-periodic modulations is routinely used to control and design synthetic matter in quantum-engineered settings. In lattice systems, this approach is explored to engineer band structures with non-trivial topological properties, but also to generate exotic interaction processes. A prime example is density-assisted tunneling, by which the hopping amplitude of a particle between neighboring sites explicitly depends on their respective occupations. Here, we show how density-assisted tunneling can be tailored in view of simulating the effects of strain in synthetic graphene-type systems. Specifically, we consider a mixture of two atomic species on a honeycomb optical lattice: one species forms a Bose-Einstein condensate in an anisotropic harmonic trap, whose inhomogeneous density profile induces an effective uniaxial strain for the second species through density-assisted tunneling processes. In direct analogy with strained graphene, the second species experiences a pseudo-magnetic field, hence exhibiting relativistic Landau levels and the valley Hall effect. Our proposed scheme introduces a unique platform for the investigation of strain-induced gauge fields, opening the door to future studies of their possible interplay with quantum fluctuations and collective excitations.
Reasonable design of NIR AIEgens for fluorescence imaging and effective photothermal/photodynamic cancer therapy
Authors: Wang Hongsen , Wang Yu , Zheng Zhaohui , Yang Fang , Ding Xiaobin , Wu Aiguo 
Published: January 2022

On the basis of this molecular design, we obtained a TCF-SS-TPA compound. TCF-SS-TPA NPs showed a NIR fluorescence and excellent 1O2 generation ability. Notably, the photothermal conversion efficiency of TCF-SS-TPA NPs is as high as 84.5%.
The HDAC2/SP1/miR-205 feedback loop contributes to tubular epithelial cell extracellular matrix production in diabetic kidney disease
Authors: Zheng Zongji , Zhang Shuting , Chen Jiaqi , Zou Meina , Yang Yanlin , Lu Wen , Ren Shijing , Wang Xiangyu , Dong Wenhui , Zhang Zikun , Wang Ling , Guan Meiping , Cheing Gladys L.Y. , Xue Yaoming , Jia Yijie 
Published: January 2022

Abstract
Extracellular matrix (ECM) accumulation is considered an important pathological feature of diabetic kidney disease (DKD). Histone deacetylase (HDAC) inhibitors protect against kidney injury. However, the potential mechanisms of HDACs in DKD are still largely unknown. Here, we describe a novel feedback loop composed of HDAC2 and miR-205 that regulates ECM production in tubular epithelial cells in individuals with DKD. We found that HDAC2 mRNA expression in peripheral blood was markedly higher in patients with DKD than in patients with diabetes. Nuclear HDAC2 protein expression was increased in TGFβ1-stimulated tubular epithelial cells and db/db mice. We also found that miR-205 was regulated by HDAC2 and down-regulated in TGFβ1-treated HK2 cells and db/db mice. In addition, HDAC2 reduced histone H3K9 acetylation in the miR-205 promoter region to inhibit its promoter activity and subsequently suppressed miR-205 expression through an SP1-mediated pathway. Furthermore, miR-205 directly targeted HDAC2 and inhibited HDAC2 expression. Intriguingly, miR-205 also regulated its own transcription by inhibiting HDAC2 and increasing histone H3K9 acetylation in its promoter, forming a feedback regulatory loop. Additionally, the miR-205 agonist attenuated ECM production in HK2 cells and renal interstitial fibrosis in db/db mice. In conclusion, the HDAC2/SP1/miR-205 feedback loop may be crucial for the pathogenesis of DKD.
Judicious Arrangement of Symbols on a Simulated Augmentative and Alternative Communication Display Optimizes Visual Attention by Individuals With Down Syndrome
Authors: Wilkinson Krista M. , Gilmore Rick , Qian Yiming 
Published: January 2022

Purpose:
Aided augmentative and alternative communication (AAC) displays are often designed as symmetrical row–column grids, with each square in the grid containing a symbol. To maximize vocabulary on displays, symbols are often placed close to one another, and background color cuing is used to signal/differentiate symbols across different grammatical categories. However, from a visual and developmental standpoint, these display features (close-set symbols and use of background color cues) may not be optimal. In particular, placing symbols quite close together may result in visual crowding, in which individual symbols cannot be distinguished due to the presence of many neighbors, or flankers. This research sought to examine the role of display arrangement and background color cuing on the efficiency of visual attention during search.

Method:
Ten adolescents and adults with Down syndrome underwent a visual search task while a research-based eye tracking system recorded their patterns of visual attention. Participants searched for symbol targets on displays with varying levels of visual crowding and background color cuing.

Results:
Spatial arrangements that reduced visual crowding and that used the spatial organization to cue the grammatical category of symbols resulted in significantly fewer fixations to nonrelevant distracters during search and reduced the likelihood of fixations away from the target once it was located. Background color was helpful in reducing the latency to find the target.

Discussion:
Spatial cues may offer a powerful means to maximize the efficiency of search within AAC displays. Background color cuing may facilitate speed to locate targets in these older individuals. Implications for AAC design, as well as future avenues for maximizing (growing) vocabulary, are discussed.
Completing the X-ray view of the recently discovered supernova remnant G53.41+0.03
Authors: Domček V. , Vink J. , Zhou P. , Sun L. , Driessen L. 
Published: January 2022

Aims.We present a detailed X-ray study of the recently discovered supernova remnant (SNR) G53.41+0.03, which follows up and further expands on the previous, limited analysis of archival data covering a small portion of the SNR.Methods.With the new dedicated 70 ksXMM-Newtonobservation we investigate the morphological structure of the SNR in X-rays, search for a presence of a young neutron star, and characterise the plasma conditions in the selected regions by means of spectral fitting.Results.The first full view of SNR G53.41+0.03 shows an X-ray emission region well aligned with the reported half-shell radio morphology. We find two distinct regions of the remnant that differ in terms of the brightness and hardness of the spectra, and both regions are best characterised by a hot plasma model in a non-equilibrium ionisation state. Of the two regions, the brighter one contains the most mature plasma, with ionisation ageτ≈ 4 × 1010s cm−3(whereτ=net), a lower electron temperature ofkTe≈ 1 keV, and the highest estimated gas density,nH≈ 0.87 cm−3. The second, fainter but spectrally harder, region reveals a younger plasma (τ≈ 1.7 × 1010s cm−3) with a higher temperature (kTe≈ 2 keV) and a two to three times lower density (nH≈ 0.34 cm−3). No clear evidence of X-ray emission was found for emission from a complete shell, the southern part appearing to be absent. Employing several methods for age estimation, we find the remnant to bet≈ 1000–5000 yr old, confirming earlier reports of a relatively young age. The environment of the remnant also contains a number of point sources, most of which are expected to be positioned in the foreground. Of the two point sources in the geometrical centre of the remnant, one is consistent with the characteristics of a young neutron star.
Photometric signatures of corotating magnetospheres of hot stars governed by higher-order magnetic multipoles
Authors: Krtička J. , Mikulášek Z. , Kurfürst P. , Oksala M. E. 
Published: January 2022

Context. The light curves of magnetic, chemically peculiar stars typically show periodic variability due to surface spots that in most cases can be modeled by low-order harmonic expansion. However, high-precision satellite photometry reveals tiny complex features in the light curves of some of these stars that are difficult to explain as caused by a surface phenomenon under reasonable assumptions. These features might originate from light extinction in corotating magnetospheric clouds supported by a complex magnetic field dominated by higher-order multipoles.
Aims. We aim to understand the photometric signatures of corotating magnetospheres that are governed by higher-order multipoles.
Methods. We determined the location of magnetospheric clouds from the minima of the effective potential along the magnetic field lines for different orders of multipoles and their combination. From the derived magnetospheric density distribution, we calculated light curves accounting for absorption and subsequent emission of light.
Results. For axisymmetric multipoles, the rigidly rotating magnetosphere model is able to explain the observed tiny features in the light curves only when the higher-order multipoles dominate the magnetic field not only at the stellar surface, but even at the Kepler radius. However, even a relatively weak nonaxisymmetric component leads to warping of equilibrium surfaces. This introduces structures that can explain the tiny features observed in the light curves of chemically peculiar stars. The light emission contributes to the light variability only if a significant fraction of light is absorbed in the magnetosphere.