bluuebunny/crossref_metadata_2025_split huggingface dataset:
BET bromodomain inhibition rescues PD-1-mediated T-cell exhaustion in acute myeloid leukemia
Authors: Zhong Mengjun , Gao Rili , Zhao Ruocong , Huang Youxue , Chen Cunte , Li Kehan , Yu Xibao , Nie Dingrui , Chen Zheng , Liu Xin , Liu Zhuandi , Chen Shaohua , Lu Yuhong , Yu Zhi , Wang Liang , Li Peng , Zeng Chengwu , Li Yangqiu 
Published: August 2022

AbstractSustained expression of programmed cell death receptor-1 (PD-1) is correlated with the exhaustion of T cells, and blockade of the PD-1 pathway is an effective immunotherapeutic strategy for treating various cancers. However, response rates are limited, and many patients do not achieve durable responses. Thus, it is important to seek additional strategies that can improve anticancer immunity. Here, we report that the bromodomain and extraterminal domain (BET) inhibitor JQ1 inhibits PD-1 expression in Jurkat T cells, primary T cells, and T-cell exhaustion models. Furthermore, JQ1 dramatically impaired the expression of PD-1 and T-cell immunoglobulin mucin-domain-containing-3 (Tim-3) and promoted the secretion of cytokines in T cells from patients with acute myeloid leukemia (AML). In line with that, BET inhibitor-treated CD19-CAR T and CD123-CAR T cells have enhanced anti-leukemia potency and resistant to exhaustion. Mechanistically, BRD4 binds to the NFAT2 and PDCD1 (encoding PD-1) promoters, and NFAT2 binds to the PDCD1 and HAVCR2 (encoding Tim-3) promoters. JQ1-treated T cells showed downregulated NFAT2, PD-1, and Tim-3 expression. In addition, BET inhibitor suppressed programmed death-ligand 1 (PD-L1) expression and cell growth in AML cell lines and in primary AML cells. We also demonstrated that JQ1 treatment led to inhibition of leukemia progression, reduced T-cell PD-1/Tim-3 expression, and prolonged survival in MLL-AF9 AML mouse model and Nalm6 (B-cell acute lymphoblastic leukemia cell)-bearing mouse leukemia model. Taken together, BET inhibition improved anti-leukemia immunity by regulating PD-1/PD-L1 expression, and also directly suppressed AML cells, which provides novel insights on the multiple effects of BET inhibition for cancer therapy.
A common deletion at BAK1 reduces enhancer activity and confers risk of intracranial germ cell tumors
Authors: Sonehara Kyuto , Kimura Yui , Nakano Yoshiko , Ozawa Tatsuya , Takahashi Meiko , Suzuki Ken , Fujii Takashi , Matsushita Yuko , Tomiyama Arata , Kishikawa Toshihiro , Yamamoto Kenichi , Naito Tatsuhiko , Suzuki Tomonari , Yamaguchi Shigeru , Miwa Tomoru , Sasaki Hikaru , Kitagawa Masashi , Ohe Naoyuki , Fukai Junya , Ogiwara Hideki , Kawamura Atsufumi , Miyawaki Satoru , Matsuda Fumihiko , Kiyokawa Nobutaka , Ichimura Koichi , Nishikawa Ryo , Okada Yukinori , Terashima Keita 
Published: August 2022

AbstractIntracranial germ cell tumors (IGCTs) are rare brain neoplasms that mainly occur in children and adolescents with a particularly high incidence in East Asian populations. Here, we conduct a genome-wide association study (GWAS) of 133 patients with IGCTs and 762 controls of Japanese ancestry. A common 4-bp deletion polymorphism in an enhancer adjacent to BAK1 is significantly associated with the disease risk (rs3831846; P = 2.4 × 10−9, odds ratio = 2.46 [95% CI: 1.83–3.31], minor allele frequency = 0.43). Rs3831846 is in strong linkage disequilibrium with a testicular GCTs susceptibility variant rs210138. In-vitro reporter assays reveal rs3831846 to be a functional variant attenuating the enhancer activity, suggesting its contribution to IGCTs predisposition through altering BAK1 expression. Risk alleles of testicular GCTs derived from the European GWAS show significant positive correlations in the effect sizes with the Japanese IGCTs GWAS (P = 1.3 × 10−4, Spearman’s ρ = 0.48). These results suggest the shared genetic susceptibility of GCTs beyond ethnicity and primary sites.
Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis
Authors: Dupuy Pierre , Ghosh Shreya , Adefisayo Oyindamola , Buglino John , Shuman Stewart , Glickman Michael S. 
Published: August 2022

AbstractAntibiotic resistance of Mycobacterium tuberculosis is exclusively a consequence of chromosomal mutations. Translesion synthesis (TLS) is a widely conserved mechanism of DNA damage tolerance and mutagenesis, executed by translesion polymerases such as DinBs. In mycobacteria, DnaE2 is the only known agent of TLS and the role of DinB polymerases is unknown. Here we demonstrate that, when overexpressed, DinB1 promotes missense mutations conferring resistance to rifampicin, with a mutational signature distinct from that of DnaE2, and abets insertion and deletion frameshift mutagenesis in homo-oligonucleotide runs. DinB1 is the primary mediator of spontaneous −1 frameshift mutations in homo-oligonucleotide runs whereas DnaE2 and DinBs are redundant in DNA damage-induced −1 frameshift mutagenesis. These results highlight DinB1 and DnaE2 as drivers of mycobacterial genome diversification with relevance to antimicrobial resistance and host adaptation.
Flexible-type ultrathin holographic endoscope for microscopic imaging of unstained biological tissues
Authors: Choi Wonjun , Kang Munkyu , Hong Jin Hee , Katz Ori , Lee Byunghak , Kim Guang Hoon , Choi Youngwoon , Choi Wonshik 
Published: August 2022

AbstractUltrathin lensless fibre endoscopes offer minimally invasive investigation, but they mostly operate as a rigid type due to the need for prior calibration of a fibre probe. Furthermore, most implementations work in fluorescence mode rather than label-free imaging mode, making them unsuitable for general medical diagnosis. Herein, we report a fully flexible ultrathin fibre endoscope taking 3D holographic images of unstained tissues with 0.85-μm spatial resolution. Using a bare fibre bundle as thin as 200-μm diameter, we design a lensless Fourier holographic imaging configuration to selectively detect weak reflections from biological tissues, a critical step for label-free endoscopic reflectance imaging. A unique algorithm is developed for calibration-free holographic image reconstruction, allowing us to image through a narrow and curved passage regardless of fibre bending. We demonstrate endoscopic reflectance imaging of unstained rat intestine tissues that are completely invisible to conventional endoscopes. The proposed endoscope will expedite a more accurate and earlier diagnosis than before with minimal complications.
Trafficked Malayan pangolins contain viral pathogens of humans
Authors: Shi Wenqiang , Shi Mang , Que Teng-Cheng , Cui Xiao-Ming , Ye Run-Ze , Xia Luo-Yuan , Hou Xin , Zheng Jia-Jing , Jia Na , Xie Xing , Wu Wei-Chen , He Mei-Hong , Wang Hui-Feng , Wei Yong-Jie , Wu Ai-Qiong , Zhang Sheng-Feng , Pan Yu-Sheng , Chen Pan-Yu , Wang Qian , Li Shou-Sheng , Zhong Yan-Li , Li Ying-Jiao , Tan Luo-Hao , Zhao Lin , Jiang Jia-Fu , Hu Yan-Ling , Cao Wu-Chun 
Published: August 2022

AbstractPangolins are the most trafficked wild animal in the world according to the World Wildlife Fund. The discovery of SARS-CoV-2-related coronaviruses in Malayan pangolins has piqued interest in the viromes of these wild, scaly-skinned mammals. We sequenced the viromes of 161 pangolins that were smuggled into China and assembled 28 vertebrate-associated viruses, 21 of which have not been previously reported in vertebrates. We named 16 members ofHunnivirus,PestivirusandCopiparvoviruspangolin-associated viruses. We report that thel-protein has been lost from all hunniviruses identified in pangolins. Sequences of four human-associated viruses were detected in pangolin viromes, including respiratory syncytial virus,Orthopneumovirus,RotavirusAandMammalian orthoreovirus. The genomic sequences of five mammal-associated and three tick-associated viruses were also present. Notably, a coronavirus related to HKU4-CoV, which was originally found in bats, was identified. The presence of these viruses in smuggled pangolins identifies these mammals as a potential source of emergent pathogenic viruses.
Muscle and adipose tissue segmentations at the third cervical vertebral level in patients with head and neck cancer
Authors: Wahid Kareem A. , Olson Brennan , Jain Rishab , Grossberg Aaron J. , El-Habashy Dina , Dede Cem , Salama Vivian , Abobakr Moamen , Mohamed Abdallah S. R. , He Renjie , Jaskari Joel , Sahlsten Jaakko , Kaski Kimmo , Fuller Clifton D. , Naser Mohamed A. 
Published: August 2022

AbstractThe accurate determination of sarcopenia is critical for disease management in patients with head and neck cancer (HNC). Quantitative determination of sarcopenia is currently dependent on manually-generated segmentations of skeletal muscle derived from computed tomography (CT) cross-sectional imaging. This has prompted the increasing utilization of machine learning models for automated sarcopenia determination. However, extant datasets currently do not provide the necessary manually-generated skeletal muscle segmentations at the C3 vertebral level needed for building these models. In this data descriptor, a set of 394 HNC patients were selected from The Cancer Imaging Archive, and their skeletal muscle and adipose tissue was manually segmented at the C3 vertebral level using sliceOmatic. Subsequently, using publicly disseminated Python scripts, we generated corresponding segmentations files in Neuroimaging Informatics Technology Initiative format. In addition to segmentation data, additional clinical demographic data germane to body composition analysis have been retrospectively collected for these patients. These data are a valuable resource for studying sarcopenia and body composition analysis in patients with HNC.
Chromosome-level assembly of Gymnocypris eckloni genome
Authors: Wang Fayan , Wang Lihan , Liu Dan , Gao Qiang , Nie Miaomiao , Zhu Shihai , Chao Yan , Yang Chaojie , Zhang Cunfang , Yi Rigui , Ni Weilin , Tian Fei , Zhao Kai , Qi Delin 
Published: August 2022

AbstractGymnocypris eckloni is widely distributed in isolated lakes and the upper reaches of the Yellow River and play significant roles in the trophic web of freshwater communities. In this study, we generated a chromosome-level genome of G. eckloni using PacBio, Illumina and Hi-C sequencing data. The genome consists of 23 pseudo-chromosomes that contain 918.68 Mb of sequence, with a scaffold N50 length of 43.54 Mb. In total, 23,157 genes were annotated, representing 94.80% of the total predicted protein-coding genes. The phylogenetic analysis showed that G. eckloni was most closely related to C. carpio with an estimated divergence time of ~34.8 million years ago. For G. eckloni, we identified a high-quality genome at the chromosome level. This genome will serve as a valuable genomic resource for future research on the evolution and ecology of the schizothoracine fish in the Qinghai-Tibetan Plateau.
Computational models predicting the early development of the COVID-19 pandemic in Sweden: systematic review, data synthesis, and secondary validation of accuracy
Authors: Gerlee Philip , Jöud Anna , Spreco Armin , Timpka Toomas 
Published: August 2022

AbstractComputational models for predicting the early course of the COVID-19 pandemic played a central role in policy-making at regional and national levels. We performed a systematic review, data synthesis, and secondary validation of studies that reported on prediction models addressing the early stages of the COVID-19 pandemic in Sweden. A literature search in January 2021 based on the search triangle model identified 1672 peer-reviewed articles, preprints and reports. After applying inclusion criteria 52 studies remained out of which 12 passed a Risk of Bias Opinion Tool. When comparing model predictions with actual outcomes only 4 studies exhibited an acceptable forecast (mean absolute percentage error, MAPE < 20%). Models that predicted disease incidence could not be assessed due to the lack of reliable data during 2020. Drawing conclusions about the accuracy of the models with acceptable methodological quality was challenging because some models were published before the time period for the prediction, while other models were published during the prediction period or even afterwards. We conclude that the forecasting models involving Sweden developed during the early stages of the COVID-19 pandemic in 2020 had limited accuracy. The knowledge attained in this study can be used to improve the preparedness for coming pandemics.
Impact of substerilizing dose on histological changes in gonads and ovaries of Ephestia cautella (Lepidoptera: Pyralidae) by gamma radiation
Authors: Hamza Ali , Zahran Nagwan , Sawires Sameh 
Published: August 2022

AbstractTo investigate the effect of Gamma radiation on the reproductive systems of emerged female and male of Ephestia cautella (Walker) moths, mature pupae of both sexes were irradiated with doses of 50, 100 and 150 Gy. Histological study of the treated individuals showed in females that the ovaries appear sever damage in the follicular epithelium at all doses, which become thinness and separated from developing oocytes, moreover, some of the nurse cells were rupture. In males which treated with 150 Gy, it was noticed retardation in the stages of spermatogenesis and few numbers of sperm bundles and their dispersion in the testicular follicles’ adults, on the other hand, the doses of 50 and 100 Gy showed little or moderate effects on the structure of the testis contents.
A conditional random field based feature learning framework for battery capacity prediction
Authors: Wang Hai-Kun , Zhang Yang , Huang Mohong 
Published: August 2022

AbstractThis paper proposes a network model framework based on long and short-term memory (LSTM) and conditional random field (CRF) to promote Li-ion battery capacity prediction results. The model uses LSTM to extract temporal features from the data and CRF to build a transfer matrix to enhance temporal feature learning for long serialization prediction of lithium battery feature sequence data. The NASA PCOE lithium battery dataset is selected for the experiments, and control tests on LSTM temporal feature extraction modules, including recurrent neural network (RNN), gated recurrent unit (GRU), bi-directional gated recurrent unit (BiGRU) and bi-directional long and short term memory (BiLSTM) networks, are designed to test the adaptability of the CRF method to different temporal feature extraction modules. Compared with previous Li-ion battery capacity prediction methods, the network model framework proposed in this paper achieves better prediction results in terms of root mean square error (RMSE) and mean absolute percentage error (MAPE) metrics.
Sand dust image visibility enhancement algorithm via fusion strategy
Authors: Si Yazhong , Yang Fan , Liu Zhao 
Published: August 2022

AbstractThe outdoor images captured in sand dust weather often suffer from poor contrast and color distortion, which seriously interfere with the performance of intelligent information processing systems. To solve the issues, a novel enhancement algorithm based on fusion strategy is proposed in this paper. It includes two components in sequence: sand removal via the improved Gaussian model-based color correction algorithm and dust elimination using the residual-based convolutional neural network (CNN). Theoretical analysis and experimental results show that compared with the prior sand dust image enhancement methods, the proposed fusion strategy can effectively correct the overall yellowing hue and remove the dust haze disturbance, which provides a constructive idea for the future development of sand dust image enhancement.
Evaluation of liver function tests to identify hepatotoxicity among acute lymphoblastic leukemia patients who are receiving chemotherapy induction
Authors: Mekonnen Ayal Tsegaye , Wondmeneh Temesgen Gebeyehu 
Published: August 2022

AbstractThe effect of induction chemotherapy on liver function in patients with acute lymphoblastic leukemia is not well documented in Ethiopia. This study assessed hepatotoxicity in patients with acute lymphoblastic leukemia who were undergoing induction chemotherapy in Ethiopia. A 1-month cohort study was undertaken in forty patients with acute lymphoblastic leukemia, with measurements taken at the baseline, second, and fourth weeks. A Log 10 transformation was done because of the skewed distribution of liver function tests. Descriptive statistics such as mean and proportion were calculated. A mixed model ANOVA and Bonferroni post hoc test were computed. A p value < 0.05 was declared to determine statistical significance. Clinically significant hepatotoxicity was observed in 15% of patients. Mild liver injury occurred in 5% of patients. The mean of all liver function tests increased significantly from pre-induction to post-induction. ALT levels were significantly higher in patients who received blood transfusions, but not in those who did not. Regardless of other factors, ALP level in children is significantly higher than in adults, although total bilirubin in adults is higher than in children. A significant proportion of patients had hepatotoxicity. During chemotherapy induction, the mean of all liver function tests rose significantly, but this elevation of serum liver function tests may be transient. Chemotherapy drugs should be given without causing a significant alteration in serum liver function tests. Continuous monitoring of patients should be required.
Design of a machine learning model for the precise manufacturing of green cementitious composites modified with waste granite powder
Authors: Czarnecki Sławomir , Hadzima-Nyarko Marijana , Chajec Adrian , Sadowski Łukasz 
Published: August 2022

AbstractIn this study, a machine learning model for the precise manufacturing of green cementitious composites modified with granite powder sourced from quarry waste was designed. For this purpose, decision tree, random forest and AdaBoost ensemble models were used and compared. A database was created containing 216 sets of data based on an experimental study. The database consists of parameters such as the percentage of cement substituted with granite powder, time of testing and curing conditions. It was shown that this method for designing green cementitious composite mixes, in terms of predicting compressive strength using ensemble models and only three input parameters, can be more accurate and much more precise than the conventional approach. Moreover, to the best of the authors' knowledge, artificial intelligence has been one of the most effective and precise methods used in the design and manufacturing industry in recent decades. The simplicity of this method makes it more suitable for construction practice due to the ease of evaluating the input variables. As the push towards decreasing carbon emissions increases, a method for designing green cementitious composites without producing waste that is more precise than traditional tests performed in a laboratory is essential.
Combined improved A* and greedy algorithm for path planning of multi-objective mobile robot
Authors: Xiang Dan , Lin Hanxi , Ouyang Jian , Huang Dan 
Published: August 2022

AbstractWith the development of artificial intelligence, path planning of Autonomous Mobile Robot (AMR) has been a research hotspot in recent years. This paper proposes the improved A* algorithm combined with the greedy algorithm for a multi-objective path planning strategy. Firstly, the evaluation function is improved to make the convergence of A* algorithm faster. Secondly, the unnecessary nodes of the A* algorithm are removed, meanwhile only the necessary inflection points are retained for path planning. Thirdly, the improved A* algorithm combined with the greedy algorithm is applied to multi-objective point planning. Finally, path planning is performed for five target nodes in a warehouse environment to compare path lengths, turn angles and other parameters. The simulation results show that the proposed algorithm is smoother and the path length is reduced by about 5%. The results show that the proposed method can reduce a certain path length.
Sound Localization of Listeners With Normal Hearing, Impaired Hearing, Hearing Aids, Bone-Anchored Hearing Instruments, and Cochlear Implants: A Review
Authors: Zheng Yunfang , Swanson Jacob , Koehnke Janet , Guan Jianwei 
Published: August 2022

Purpose:
This review article reviews the contemporary studies of localization ability for different populations in different listening environments and provides possible future research directions.

Conclusions:
The ability to accurately localize a sound source relying on three cues (interaural time difference, interaural level difference, and spectral cues) is important for communication, learning, and safety. Confounding effects including noise and reverberation, which exist in common listening environments, mask or alter localization cues and negatively affect localization performance. Hearing loss, a common public health issue, also affects localization accuracy. Although hearing devices have been developed to provide excellent audibility of speech signals, less attention has been paid to preserving and replicating crucial localization cues. Unique challenges are faced by users of various hearing devices, including hearing aids, bone-anchored hearing instruments, and cochlear implants. Hearing aids have failed to consistently improve localization performance and, in some cases, significantly impair sound localization. Bone-conduction hearing instruments show little to no benefit for sound localization performance in most cases, although some improvement is seen in binaural users. Although cochlear implants provide great hearing benefit to individuals with severe-to-profound sensorineural hearing loss, cochlear implant users have significant difficulty localizing sound, even with two implants. However, technologies in each of these areas are advancing to reduce interference with desired sound signals and preserve localization cues to help users achieve better hearing and sound localization in real-life environments.
Validation of an Automated Procedure for Calculating Core Lexicon From Transcripts
Authors: Dalton Sarah Grace , Stark Brielle C. , Fromm Davida , Apple Kristen , MacWhinney Brian , Rensch Amanda , Rowedder Madyson 
Published: August 2022

Purpose:
The aim of this study was to advance the use of structured, monologic discourse analysis by validating an automated scoring procedure for core lexicon (CoreLex) using transcripts.

Method:
Forty-nine transcripts from persons with aphasia and 48 transcripts from persons with no brain injury were retrieved from the AphasiaBank database. Five structured monologic discourse tasks were scored manually by trained scorers and via automation using a newly developed CLAN command based upon previously published lists for CoreLex. Point-to-point (or word-by-word) accuracy and reliability of the two methods were calculated. Scoring discrepancies were examined to identify errors. Time estimates for each method were calculated to determine if automated scoring improved efficiency.

Results:
Intraclass correlation coefficients for the tasks ranged from .998 to .978, indicating excellent intermethod reliability. Automated scoring using CLAN represented a significant time savings for an experienced CLAN user and for inexperienced CLAN users following step-by-step instructions.

Conclusions:

Automated scoring of CoreLex is a valid and reliable alternative to the current gold standard of manually scoring CoreLex from transcribed monologic discourse samples. The downstream time saving of this automated analysis may allow for more efficient and broader utilization of this discourse measure in aphasia research. To further encourage the use of this method, go to
https://aphasia.talkbank.org/discourse/CoreLexicon/
for materials and the step-by-step instructions utilized in this project.

Supplemental Material:

https://doi.org/10.23641/asha.20399304