bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-omics and machine learning reveal context-specific gene regulatory activities of PML::RARA in acute promyelocytic leukemia
Authors: Villiers William , Kelly Audrey , He Xiaohan , Kaufman-Cook James , Elbasir Abdurrahman , Bensmail Halima , Lavender Paul , Dillon Richard , Mifsud Borbála , Osborne Cameron S. 
Published: February 2023

AbstractThe PML::RARA fusion protein is the hallmark driver of Acute Promyelocytic Leukemia (APL) and disrupts retinoic acid signaling, leading to wide-scale gene expression changes and uncontrolled proliferation of myeloid precursor cells. While known to be recruited to binding sites across the genome, its impact on gene regulation and expression is under-explored. Using integrated multi-omics datasets, we characterize the influence of PML::RARA binding on gene expression and regulation in an inducible PML::RARA cell line model and APL patient ex vivo samples. We find that genes whose regulatory elements recruit PML::RARA are not uniformly transcriptionally repressed, as commonly suggested, but also may be upregulated or remain unchanged. We develop a computational machine learning implementation called Regulatory Element Behavior Extraction Learning to deconvolute the complex, local transcription factor binding site environment at PML::RARA bound positions to reveal distinct signatures that modulate how PML::RARA directs the transcriptional response.
A method for an unbiased estimate of cross-ancestry genetic correlation using individual-level data
Authors: Momin Md. Moksedul , Shin Jisu , Lee Soohyun , Truong Buu , Benyamin Beben , Lee S. Hong 
Published: February 2023

AbstractCross-ancestry genetic correlation is an important parameter to understand the genetic relationship between two ancestry groups. However, existing methods cannot properly account for ancestry-specific genetic architecture, which is diverse across ancestries, producing biased estimates of cross-ancestry genetic correlation. Here, we present a method to construct a genomic relationship matrix (GRM) that can correctly account for the relationship between ancestry-specific allele frequencies and ancestry-specific allelic effects. Through comprehensive simulations, we show that the proposed method outperforms existing methods in the estimations of SNP-based heritability and cross-ancestry genetic correlation. The proposed method is further applied to anthropometric and other complex traits from the UK Biobank data across ancestry groups. For obesity, the estimated genetic correlation between African and European ancestry cohorts is significantly different from unity, suggesting that obesity is genetically heterogenous between these two ancestries.
Photonic Majorana quantum cascade laser with polarization-winding emission
Authors: Han Song , Chua Yunda , Zeng Yongquan , Zhu Bofeng , Wang Chongwu , Qiang Bo , Jin Yuhao , Wang Qian , Li Lianhe , Davies Alexander Giles , Linfield Edmund Harold , Chong Yidong , Zhang Baile , Wang Qi Jie 
Published: February 2023

AbstractTopological cavities, whose modes are protected against perturbations, are promising candidates for novel semiconductor laser devices. To date, there have been several demonstrations of topological lasers (TLs) exhibiting robust lasing modes. The possibility of achieving nontrivial beam profiles in TLs has recently been explored in the form of vortex wavefront emissions enabled by a structured optical pump or strong magnetic field, which are inconvenient for device applications. Electrically pumped TLs, by contrast, have attracted attention for their compact footprint and easy on-chip integration with photonic circuits. Here, we experimentally demonstrate an electrically pumped TL based on photonic analogue of a Majorana zero mode (MZM), implemented monolithically on a quantum cascade chip. We show that the MZM emits a cylindrical vector (CV) beam, with a topologically nontrivial polarization profile from a terahertz (THz) semiconductor laser.
Identification of potential biomarkers in Barrett’s esophagus derived esophageal adenocarcinoma
Authors: Yi Nan , Zhao Hailiang , He Juan , Xie Xike , Liang Liexin , Zuo Guowen , Xiong Mingyue , Liang Yunxiao , Yi Tingzhuang 
Published: February 2023

AbstractAlmost 50% of esophageal adenocarcinoma (EAC) patients progressed from Barrett’s esophagus (BE). EAC is often diagnosed at late stages and is related to dismal prognosis. However, there are still no effective methods for stratification and therapy in BE and EAC. Two public datasets (GSE26886 and GSE37200) were analyzed to identify differentially expressed genes (DEGs) between BE and EAC. Then, a series of bioinformatics analyses were performed to explore potential biomarkers associated with BE-EAC. 27 up- and 104 down-regulated genes were observed between GSE26886 and GSE37200. The GO and KEGG enrichment analysis indicated that the DEGs were highly involved in tumorigenesis. Subsequently, Weighted Gene Co-Expression Network Analysis (WGCNA) were performed to explore the potential genes related to BE-EAC, which were validated in The Cancer Genome Atlas (TCGA) database,and 5 up-regulated genes (MYO1A,ACE2,COL1A1,LGALS4, andADRA2A) and 3 down-regulated genes (AADAC,RAB27A, andP2RY14) were found in EAC. Meanwhile,ADRA2AandAADACcould contribute to EAC pathogenesis and progression.MYO1A,ACE2,COL1A1,LGALS4,ADRA2A, AADAC,RAB27A, andP2RY14could be potential novel diagnostic and prognostic biomarkers in BE-EAC.
Factors influencing satisfaction with male circumcision in Taiwan
Authors: Chen Chia Hung , Cheng Wei-Ming , Fan Yu-Hua , Chang Tung-Ping 
Published: February 2023

AbstractWe aimed to investigate patient satisfaction with male circumcision in Taiwan. An online, questionnaire-based, cross-sectional study involving 376 circumcised men 20 to 40 years of age in Taiwan was conducted. Circumcision-related satisfaction was defined as a visual analogue scale score ≥ 6 (range, 1–10). Pearson’s chi-square test was performed to compare differences between satisfied and unsatisfied participants. Factors predictive of participant satisfaction were analysed using multivariate logistic regression. Statistical significance was set at P < 0.05. Among 376 circumcised men, 249 (66.2%) reported satisfaction with circumcision. Satisfied participants had higher levels of education, underwent circumcision for phimosis or balanitis, underwent circumcision during adulthood, reported a larger penile size, and had fewer long-term complaints. Furthermore, 89.4% had various long-term complaints, including skin colour mismatch, changes in masturbation methods, hypertrophic scarring, excessive shortening of the prepuce, and redundant prepuce. Multivariate analysis revealed that adult circumcision and the absence of long-term conditions were predictive of satisfaction. Two-thirds of participants were satisfied with their circumcision outcome, especially those who underwent circumcision for phimosis or balanitis during adulthood. Proper preoperative patient selection and postoperative symptom prevention would improve patient satisfaction.
Sedimentary structures of microbial carbonates in the fourth member of the Middle Triassic Leikoupo Formation, Western Sichuan Basin, China
Authors: Wang Yuanchong , Shi Kaibo , Liu Bo 
Published: February 2023

AbstractIn recent years, abundant natural gas has been found in microbial carbonates in the fourth member of the Leikoupo Formation in Western Sichuan Basin. In this study, from the observation of 626 microbial thin sections, four types of microbial carbonates are classified based on the differences of mesostructures. Among them, thrombolites and stromatolites are subdivided into eight types based on the differences of microstructures. Six types of microbial microstructure association (MSA) are identified, and are mainly developed in microbial mounds. The energy of sedimentary environment and hydrodynamic conditions of them from low to high is MSA-5, MSA-1, MSA-6, MSA-3, MSA-4 and MSA-2. Because of the arid climate in the Annie Period, a restricted platform are developed in the upper sub-member of the Leikoupo Formation in Western Sichuan Basin, and the sedimentary facies are lagoon (gypsiferous lagoon or salt lake in evaporate conditions), microbial mounds, shoals, inner platform shoals and open sea from the east to the west. Microbial microstructures not only affect the pore evolution of microbial carbonate reservoirs, but also affect the diagenesis of microbial carbonate reservoirs of the fourth member of the Leikoupo Formation.
Agricultural spider decline: long-term trends under constant management conditions
Authors: Samu F. , Szita É. , Botos E. , Simon J. , Gallé-Szpisjak N. , Gallé R. 
Published: February 2023

AbstractThere is widespread evidence for a worldwide trend of insect decline, but we have much fewer data about recent temporal trends in other arthropod groups, including spiders. Spiders can be hypothesised to similarly decline because of trophic dependence on insects and being equally sensitive to local and global environmental changes. Background trends in arthropod populations can be verified if we decouple large-scale environmental transitions, such as climate change, from local factors. To provide a case study on baseline spider community trends, we observed changes in the spider community of an unsprayed alfalfa field and its margin 23 years apart under largely unchanged local conditions. We aimed to determine whether there are changes in spider abundance, species richness and mean species characteristics. Spider abundance per unit effort decreased dramatically, by 45% in alfalfa and by 59% in the margin, but species richness and most characteristics remained unchanged. Community composition in both habitats shifted and became more similar by the current study period. The population decline was especially marked in certain farmland species. We propose that in the absence of local causative factors, spider abundance decline in our study indicates a reduction of spider populations at landscape and regional scales.
Experimenter familiarization is a crucial prerequisite for assessing behavioral outcomes and reduces stress in mice not only under chronic pain conditions
Authors: Segelcke Daniel , Talbot Steven R. , Palme Rupert , La Porta Carmen , Pogatzki-Zahn Esther , Bleich André , Tappe-Theodor Anke 
Published: February 2023

AbstractRodent behavior is affected by different environmental conditions. These do not only comprise experimental and housing conditions but also familiarization with the experimenter. However, specific effects on pain-related behavior and chronic pain conditions have not been examined. Therefore, we aimed to investigate the impact of different housing conditions, using individually ventilated and standard open top cages, inverted day-night cycles, and experimenter familiarization on male mice following peripheral neuropathy using the spared nerve injury (SNI) model. Using a multimodal approach, we evaluated evoked pain-related- using von Frey hair filaments, measured gait pattern with the CatWalk system, assessed anxiety- and depression-like behavior with the Elevated plus maze and tail suspension test, measured corticosterone metabolite levels in feces and utilized an integrative approach for relative-severity-assessment. Mechanical sensitivity differed between the cage systems and experimenter familiarization and was affected in both sham and SNI mice. Experimenter familiarization and an inverted day-night cycle reduced mechanical hypersensitivity in SNI and sham mice. SNI mice of the inverted day-night group displayed the slightest pronounced alterations in gait pattern in the Catwalk test. Anxiety-related behavior was only found in SNI mice of experimenter-familiarized mice compared to the sham controls. In addition, familiarization reduced the stress level measured by fecal corticosteroid metabolites caused by the pain and the behavioral tests. Although no environmental condition significantly modulated the severity in SNI mice, it influenced pain-affected phenotypes and is, therefore, crucial for designing and interpreting preclinical pain studies. Moreover, environmental conditions should be considered more in the reporting guidelines, described in more detail, and discussed as a potential influence on pain phenotypes.
Seroprevalence of four endemic human coronaviruses and, reactivity and neutralization capability against SARS-CoV-2 among children in the Philippines
Authors: Sayama Yusuke , Okamoto Michiko , Saito Mayuko , Saito-Obata Mariko , Tamaki Raita , Joboco Christine Dahlia , Lupisan Socorro , Oshitani Hitoshi 
Published: February 2023

AbstractFour endemic human coronaviruses (HCoV), HCoV-229E, HCoV-NL63, HCoV-HKU1, and HCoV-OC43, are closely related to SARS-CoV-2. These coronaviruses are known to infect humans living in temperate areas, including children under 5 years old; however, the seroprevalence of four HCoVs among children in tropical areas, including the Philippines, remains unclear. This study aimed to assess the prevalence of antibodies against four HCoVs and to determine the reactivity and neutralization of these antibodies against SARS-CoV-2 among children in the Philippines. A total of 315 serum samples collected from 2015 to 2018, before the emergence of SARS-CoV-2, in Biliran island, Philippines, were tested for the presence of antibodies against four HCoVs and SARS-CoV-2 using recombinant spike ectodomain proteins by IgG-enzyme-linked immunosorbent assay (ELISA). Reactivity to and neutralization of SARS-CoV-2 were also investigated. The seroprevalence of the four HCoVs was 63.8% for HCoV-229E, 71.4% for HCoV-NL63, 76.5% for HCoV-HKU1, and 83.5% for HCoV-OC43 by ELISA. Age group analysis indicated that seropositivity to all HCoVs reached 80% by 2–3 years of age. While 69/315 (21.9%) of the samples showed reactive to SARS-CoV-2, almost no neutralization against SARS-CoV-2 was detected using neutralization assay. Reactivity of antibodies against SARS-CoV-2 spike protein obtained by ELISA may not correlate with neutralization capability.
Electron tomography unravels new insights into fiber cell wall nanostructure; exploring 3D macromolecular biopolymeric nano-architecture of spruce fiber secondary walls
Authors: Fernando Dinesh , Kowalczyk Michael , Guindos Pablo , Auer Manfred , Daniel Geoffrey 
Published: February 2023

AbstractLignocellulose biomass has a tremendous potential as renewable biomaterials for fostering the “bio-based society” and circular bioeconomy paradigm. It requires efficient use and breakdown of fiber cell walls containing mainly cellulose, hemicellulose and lignin biopolymers. Despite their great importance, there is an extensive debate on the true structure of fiber walls and knowledge on the macromolecular nano-organization is limited and remains elusive in 3D. We employed dual-axis electron tomography that allows visualization of previously unseen 3D macromolecular organization/biopolymeric nano-architecture of the secondary S2 layer of Norway spruce fiber wall. Unprecedented 3D nano-structural details with novel insights into cellulose microfibrils (~ 2 nm diameter), macrofibrils, nano-pore network and cell wall chemistry (volume %) across the S2 were explored and quantified including simulation of structure related permeability. Matrix polymer association with cellulose varied between microfibrils and macrofibrils with lignin directly associated with MFs. Simulated bio-nano-mechanical properties revealed stress distribution within the S2 and showed similar properties between the idealized 3D model and the native S2 (actual tomogram). Present work has great potential for significant advancements in lignocellulose research on nano-scale understanding of cell wall assembly/disassembly processes leading to more efficient industrial processes of functionalization, valorization and target modification technologies.
Compositional changes and ecological characteristics of earthworm mucus under different electrical stimuli
Authors: Huan Huihui , Wang Xingming , Chu Zhaoxia , Yu Xiaokun , Fan Tingyu , Li Gang , Xu Xiaoping , Zhen Quan , Sun Luntao , Dong Zhongbing , Zha Shijiao 
Published: February 2023

AbstractEarthworm mucus is rich in nutrients that can initiate the mineralization and humification of organic matter and is of great importance for contaminated soil remediation and sludge reutilization. In this study, six voltage and current combinations were utilized to promote earthworm mucus production (5 V and 6 V at 10, 20 and 30 mA, respectively), to explore the compositional changes of the mucus produced under different electrical stimuli, and to propose the best electrical stimulation group and mucus fraction applicable to soil heavy metal pollution remediation and sludge reutilization. The results showed that the mucus produced by the six electrical stimuli was mainly composed of proteins, amino acids, carbohydrates, fatty acids, and polysaccharides, with small amounts of alcohol, phenol, and ester organic substances. Under different electrical stimuli, each component changed significantly (P < 0.05). pH and conductivity were higher at 6 V 20 mA, total nitrogen and phosphorus contents reached their maximum at 5 V 30 mA, and total potassium at 6 V 10 mA. Protein, amino acids, and carbohydrates were most abundant in the mucus produced at 5 V 10 mA, while trace metal elements reached their lowest values at 5 V 10 mA. Finally, based on principal component analysis and combined with previous studies, it was concluded that the mucus produced at 5 V 10 mA was weakly alkaline, high in amino acids and nutrients and low in trace metal elements, and most suitable for sludge and straw composting experiments, soil remediation and amendment experiments.
Hydrogen isotope analysis in W-tiles using fs-LIBS
Authors: Mittelmann Steffen , Touchet Kévin , Mao Xianglei , Park Minok , Brezinsek Sebastijan , Pretzler Georg , Zorba Vassilia 
Published: February 2023

AbstractLaser-Induced Breakdown Spectroscopy (LIBS) is a promising technology for in-situ analysis of Plasma-Facing Components in magnetic confinement fusion facilities. It is of major interest to monitor the hydrogen isotope retention i.e. tritium and deuterium over many operation hours to guarantee safety and availability of the future reactor. In our studies we use ultraviolet femtosecond laser pulses to analyze tungsten (W) tiles that were exposed to a deuterium plasma in the linear plasma device PSI-2, which mimics conditions at the first wall. A high-resolution spectrometer is used to detect the Balmer-$$\alpha$$
α
transition of the surface from implanted hydrogen isotopes (H and D). We use Calibration Free CF-LIBS to quantify the amount of deuterium stored in W. This proof-of-principle study shows the applicability of femtosecond lasers for the detection of low deuterium concentration as present in first wall material of prevailing fusion experiments.
Detection of oral squamous cell carcinoma in clinical photographs using a vision transformer
Authors: Flügge Tabea , Gaudin Robert , Sabatakakis Antonis , Tröltzsch Daniel , Heiland Max , van Nistelrooij Niels , Vinayahalingam Shankeeth 
Published: February 2023

AbstractOral squamous cell carcinoma (OSCC) is amongst the most common malignancies, with an estimated incidence of 377,000 and 177,000 deaths worldwide. The interval between the onset of symptoms and the start of adequate treatment is directly related to tumor stage and 5-year-survival rates of patients. Early detection is therefore crucial for efficient cancer therapy. This study aims to detect OSCC on clinical photographs (CP) automatically. 1406 CP(s) were manually annotated and labeled as a reference. A deep-learning approach based on Swin-Transformer was trained and validated on 1265 CP(s). Subsequently, the trained algorithm was applied to a test set consisting of 141 CP(s). The classification accuracy and the area-under-the-curve (AUC) were calculated. The proposed method achieved a classification accuracy of 0.986 and an AUC of 0.99 for classifying OSCC on clinical photographs. Deep learning-based assistance of clinicians may raise the rate of early detection of oral cancer and hence the survival rate and quality of life of patients.
Novel application of sodium manganese oxide in removing acidic gases in ambient conditions
Authors: Gupta Nishesh Kumar , Achary Srungarpu N. , Viltres Herlys , Bae Jiyeol , Kim Kwang Soo 
Published: February 2023

AbstractIn this study, we have demonstrated the application of sodium manganese oxide for the chemisorption of toxic acidic gases at room temperature. The fabricated alkali ceramic has Na0.4MnO2, Na2Mn3O7, and NaxMnO2 phases with a surface area of 2.6 m2 g–1. Na-Mn oxide was studied for oxidation of H2S, SO2, and NO2 gases in the concentration range of 100–500 ppm. The material exhibited a high uptake capacity of 7.13, 0.75, and 0.53 mmol g–1 for H2S, SO2, and NO2 in wet conditions, respectively. The material was reusable when regenerated simply by soaking the spent oxide in a NaOH-H2O2 solution. While the H2S chemisorption process was accompanied by sulfide, sulfur, and sulfate formation, the SO2 chemisorption process yielded only sulfate ions. The NO2 chemisorption process was accomplished by its conversion to nitrite and nitrate ions. Thus, the present work is one of the first reports on alkali ceramic utilization for room-temperature mineralization of acidic gases.
Deep consistency-preserving hash auto-encoders for neuroimage cross-modal retrieval
Authors: Wang Xinyu , Zeng Xianhua 
Published: February 2023

AbstractCross-modal hashing is an efficient method to embed high-dimensional heterogeneous modal feature descriptors into a consistency-preserving Hamming space with low-dimensional. Most existing cross-modal hashing methods have been able to bridge the heterogeneous modality gap, but there are still two challenges resulting in limited retrieval accuracy: (1) ignoring the continuous similarity of samples on manifold; (2) lack of discriminability of hash codes with the same semantics. To cope with these problems, we propose a Deep Consistency-Preserving Hash Auto-encoders model, called DCPHA, based on the multi-manifold property of the feature distribution. Specifically, DCPHA consists of a pair of asymmetric auto-encoders and two semantics-preserving attention branches working in the encoding and decoding stages, respectively. When the number of input medical image modalities is greater than 2, the encoder is a multiple pseudo-Siamese network designed to extract specific modality features of different medical image modalities. In addition, we define the continuous similarity of heterogeneous and homogeneous samples on Riemann manifold from the perspective of multiple sub-manifolds, respectively, and the two constraints, i.e., multi-semantic consistency and multi-manifold similarity-preserving, are embedded in the learning of hash codes to obtain high-quality hash codes with consistency-preserving. The extensive experiments show that the proposed DCPHA has the most stable and state-of-the-art performance. We make code and models publicly available: https://github.com/Socrates023/DCPHA.
The PROTECTOR strategy employs dCas orthologs to sterically shield off-target sites from CRISPR/Cas activity
Authors: Sapozhnikov Daniel M. , Szyf Moshe 
Published: February 2023

AbstractOff-target mutagenesis of CRISPR/Cas systems must be solved to facilitate safe gene therapy. Here, we report a novel approach, termed "PROTECTOR", to shield known off-target sites by directing the binding of an orthologous nuclease-dead Cas protein to the off-target site to sterically interfere with Cas activity. We show that this method reduces off-target mutation rates of two well-studied guide RNAs without compromising on-target activity and that it can be used in combination with high-fidelity Cas enzymes to further reduce off-target editing. This expands the suite of off-target mitigation strategies and offers an ability to protect off-target sites even when their sequences are fully identical to target sites.