bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Extra-Hepatic Incidental Findings on Ultrasound Screening for Hepatocellular Carcinoma
Authors: Forrest Allison , Afshari Sam , Franssen Nathan , Ali Naiim 
Published: June 2022

Abstract
Purpose: Abdominal ultrasound is a cost-effective method for screening for hepatocellular carcinoma (HCC) in high-risk individuals. Currently, at many institutions the protocol for obtaining HCC screening ultrasounds includes a traditional examination of the right upper quadrant, including the pancreas and right kidney. There is no consensus on the role of imaging of extra-hepatic structures and there is limited data describing the frequency and clinical significance of incidental findings discovered during HCC screening. The purpose of this retrospective study is to assess the prevalence and significance of extra-hepatic incidental findings during HCC screening ultrasounds.Methods: A single-center retrospective review of all right upper quadrant HCC screening ultrasounds identified 432 HCC screening ultrasounds performed on 294 adults over a 2.5-year period. Findings in all organs evaluated were recorded. Any incidental finding was classified as minor, moderate, or major clinical significance. LI-RADS category and visualization score were also documented. Results: At least one extrahepatic finding was documented in 56.5% of examinations. The most common extra-hepatic findings occurred in the gallbladder (40.3%), most commonly gallstones (25.4%). Four moderate clinically significant incidental findings were recorded (0.9%). Only one of these incidental findings required specific imaging follow up 0.2%). No major clinical significance incidental findings were identified. Conclusions: Potentially clinically significant incidental findings during HCC screenings are rare. Given the low rates of significant incidental findings identified on HCC screening ultrasound, these data support a more limited HCC screening ultrasound protocol.
Morphometric assessment of facial morphology in infants with unilateral cleft lip/palate up to two years of age using 3D stereophotogrammetry
Authors: Jaklová Lenka Kožejová , Kočandrlová Karolina , Dupej Ján , Borský Jiří , Černý Miloš , Velemínská Jana 
Published: June 2022

Abstract
Objectives: To assess modelled facial development of infants with unilateral cleft lip (CL)/cleft lip and palate (UCLP) compared to controls for up to two years.Materials and methods: A total of 201 facial images of children (clefts, controls) were obtained in 4 different age categories (in years; T0: 0.2–0.5; T1: 0.6–1.0; T2: 1.1–1.5; T3: 1.6–2.0); they were evaluated using 3D stereophotogrammetry and geometric morphometrics.Results: In the CL patients, the forehead was significantly retracted (p ≤ 0.001), while the supraorbital and ocular regions were prominent (p ≤ 0.001). The oronasal region appeared convex compared to controls (p ≤ 0.001). The lower lip and chin were non-significantly protruded. In UCLP patients, a significantly retracted forehead and prominent supraorbital region were also apparent (p ≤ 0.001). The most striking deviations were observed in the middle face with a markedly retrusive oronasal region (p ≤ 0.001). The chin was significantly protruded anteriorly (p ≤ 0.01). In both clefts, no progression of deviations was confirmed with increasing age. After the first year, a slight improvement in the morphological features appeared due to the patients' growth potential and surgical method. The shape variability of the clefts and controls overlapped, suggesting comparable modelled facial development.Conclusions: The facial morphology of cleft individuals was comparable to the norm with marked shape deviation in the oronasal region, forehead, and chin, which minimised with increasing age even in complete clefts.Clinical relevance Visualising the facial surface through 3D stereophotogrammetry may improve early childhood surgical planning and postoperative therapy.
Combined effects of temperature and salinity on digestion and respiration metabolism of Pinctada fucata
Authors: Yang Jingru , Fu Zhengyi , Ma Zhenhua , Yu Gang 
Published: June 2022

Abstract
Combined effects of temperature and salinity on the digestion and respiration metabolism of Pinctada fucata was evaluated via response surface methodology and box-benhnken design under laboratory condition. Results indicated that the primary and secondary effects of salinity and temperature had significant effects on amylase (AMS) of P. fucata (P < 0.05)., The digestive enzyme reached the maximum activity when the temperature was 26°C, AMS and trypsin (TRYP) firstly increased, and then decreased with the increasing of temperature. Lipase (LPS) was positively correlated with either salinity or temperature. Salinity had no significant effect on TRYP in the primary effect (P > 0.05), but had significant effect on TRYP in the secondary effect (P < 0.01), which was completely opposite to the effect of temperature on pepsin (PEP) in the primary and secondary effects. The combined effects of salinity and temperature on AMS, TRYP and PEP were significant (P < 0.01), but had no significant effect on LPS (P > 0.05). The primary, secondary and interaction effects of salinity had significant effects on NKA (Na+-K+-ATPase) of P. fucata (P < 0.05), and NKA presented a U-shaped distribution with the increasing of salinity. The quadratic and interactive effects of temperature had a significant effect on AKP (P < 0.05), and AKP showed a U-shaped distribution with the increasing of temperature. lactate dehydrogenase (LDH) activity firstly decreased, and then increased when temperature and salinity changed from 20–30 ℃ and 23‰ to 33‰, respectively. The expression of GPX gene affected by temperature in gill may be delayed compared with that in liver, and its expression is tissue-specific. The appropriate digestion and respiratory metabolism index models were established under the combined temperature and salinity conditions. The optimization results showed that the optimal combination of temperature and salinity was 26.288°C / 28.272‰. The desirability was 0.832. Results from the present study will provide a theoretical reference for shellfish culture affected by environmental interaction and the establishment of related index models.
Androgen deprivation restores ARHGEF2 to promote neuroendocrine differentiation of prostate cancer
Authors: Shang Zhiqun , Chen Xuanrong , Shao Yi , Wei Wanqing , Zhu Shimiao , Li Yang , Chen Yutong , Li Hanlin , Tian Hao , Sun Guijiang , Niu Yuanjie 
Published: June 2022

Abstract
Androgen receptor (AR) plays an important role in the progression of prostate cancer and has been targeted by castration or AR-antagonists. The emergence of castration-resistant prostate cancer (CRPC) after androgen deprivation therapy (ADT) is inevitable. However, it is not entirely clear how ADT fails or how it causes resistance. Through analysis of RNA-seq data, we nominate ARHGEF2 as a pivotal androgen-repressed gene. We show that ARHGEF2 is directly suppressed by androgen/AR. AR occupies the enhancer and communicates with the promoter region of ARHGEF2. Functionally, ARHGEF2 is important for the growth, lethal phenotype and survival of CRPC cells and tumor xenografts. Correspondingly, AR inhibition or AR antagonist treatment can restore ARHGEF2 expression, thereby allowing prostate cancer cells to induce treatment resistance and tolerance. Overall, our findings provide an explanation for the contradictory clinical results that ADT may be caused by the up-regulation of ARHGEF2 and provide a novel target.
Generation of highly-retrievable atom–photon entanglement with a millisecond lifetime via a spatially-multiplexed cavity
Authors: Wang Hai , Wang Minjie , wang Shengzhi , Ma Tengfei , li ya , xie yan , jiao haole , liu hailong , Li Shujing 
Published: June 2022

Abstract
Qubit memory that is entangled with photonic qubit is the building block for quantum repeaters. Realizing ensemble-based repeaters requires qubit simultaneously featuring high retrieval efficiencies and long lifetimes. So far, the longest memory time at 50% retrieval efficiency for entanglement storage reaches ~40 μs. Here, by coupling cold atoms to two spatially-distinctive modes of a polarization-interferometer-based cavity, we achieve cavity-perfectly-enhanced and long-lived atom-photon entanglement. A write-laser beam is applied onto cold atoms, we then create a magnetic-field-insensitive spin-wave qubit that is entangled with the photonic qubit encoded onto two arms of the interferometer. By applying a read beam, the spin-wave qubit is converted to a photonic qubit, whose two modes are resonant with the cavity. Our experimental data shows that zero-delay intrinsic retrieval efficiency is up to 77% and 1/e lifetime 1ms. At 50% efficiency, the storage time reaches 540μs , which is 13.5 times longer than the best reported result.
Complicated nonlinear oscillations caused by maneuvering of a flexible spacecraft equipped with hinged solar arrays
Authors: He Guiqin , Cao Dengqing , Heijden G.H.M. van der 
Published: June 2022

Abstract
We present a general methodology for the nonlinear dynamical modeling of a three-axis stabilized spacecraft equipped with flexible solar arrays. The large-span multi-panel solar arrays are modeled as flexible thin plates that are connected to the rigid central body of the spacecraft by means of nonlinear flexible hinges. We construct a low-dimensional yet accurate dynamical model by using a Galerkin expansion in terms of global modes of the system that we compute first by using the Rayleigh-Ritz method. The hinged connections between the rigid and flexible parts of the system are imposed by means of Lagrange multipliers. We use the model to study the spacecraft response triggered by various maneuvering scenarios. We in particular focus on the coupling between vibrations of the flexible components and the rigid motion of the spacecraft induced by hinge nonlinearities during these orbital and attitude maneuvering operations. In all cases considered we find that four global modes are sufficient to accurately compute the system’s response. We also observe other complicated nonlinear dynamical phenomena such as hysteresis and superharmonic resonance that may be of concern in spacecraft design. Our modeling approach can straightforwardly be applied to other multibody systems.
ADAR1 promotes miR-3144-3p editing to simultaneously induce oncogenic MSI2 and suppress tumor suppressor SLC38A4 in liver cancer
Authors: Kim Hyung Seok , Na Min Jeong , Son Keun hong , Yang Hee Doo , Kim Sang Yean , Shin Eunbi , Ha Jin Woong , Jeon Soyoung , Kang Keunsoo , Moon Kiho , Park Won Sang , Nam Suk Woo 
Published: June 2022

Abstract
Background: Aberrant adenosine-to-inosine (A-to-I) RNA editing, catalyzed by adenosine deaminase acting on double-stranded RNA (ADAR), is implicated in various cancers, but the mechanisms by which microRNA (miRNA) editing contributes to cancer development are currently largely unknown.Method: Our multi-step hepatocellular carcinogenesis transcriptome data analyses, together with publicly available data, indicated that ADAR1 is the most dysregulated gene among the RNA editing enzyme families in hepatocellular carcinoma (HCC). Targeted inactivation of ADAR1 inhibits in vitro tumorigenesis of HCC cells. Integrative computational analyses of RNA editing hotspots and the editing frequency of miRNAs suggested miR-3144-3p a potential mRNA edited by ADAR1 in hepatocellular carcinogenesis.Result: Through direct sequencing of ADAR1-knocked-down or -overexpressing cells, we demonstrated that ADAR1 promoted A-to-I editing of the canonical miR-3144-3p to change position 3 adenosine in the seed region to guanine (ED_miR-3144-3p(3_A<G)) in HCC cells. We then demonstrated that Musashi RNA-binding protein 2 (MSI2) is a specific target of miR-3144-3p, and that MSI2 overexpression is due to ADAR1-dependent over-editing of the canonical miR-3144-3p in HCC cells. Notably miR-3144-3p treatments showed similar to in vitro anti-tumor activities of ADAR1-specifc siRNA in HCC. In addition, target prediction analyses and validation experiments identified solute carrier family 38 member 4 (SLC38A4) as specific target gene for ED_miR-3144-3p(3_A<G). We also demonstrated that ectopic expressions of both ADAR1 and ED_miR-3144-3p(3_A<G) mimics enhanced mitotic activities and that ADAR1 suppressed SLC38A4 in HCC cells. Treatments with mouse-specific ADAR1-, MSI2-siRNA or SLC38A4-expressing plasmids suppressed tumor incidence and growth in a spontaneous mouse HCC model. Conclusions: Our findings suggest that aberrant regulation of ADAR1 augments oncogenic MSI2 via overediting the canonical miR-3144-3p, and the resultant ED_miR-3144-3p(3_A<G) simultaneously suppresses tumor suppressor SLC38A4, thereby contributing to hepatocellular carcinogenesis.
The effect and tolerability of second-line chemotherapy are associated with disease control of nivolumab chemotherapy in patients with gastric cancer
Authors: Matsuoka Hiroshi , Mizuno Tomohiro , Sakai Minami , Suzuki Kazumitsu , Serizawa Michiko , Nakauchi Masaya , Tanaka Tsuyoshi , Shibasaki Susumu , Hayashi Takahiro , Suda Koichi 
Published: June 2022

Abstract
Background: Immune-related adverse events (irAEs) are associated with the efficacy of nivolumab. However, whether the tolerability of second-line chemotherapy is associated with the efficacy of nivolumab monotherapy (third-line chemotherapy) remains unclear. Our study aimed to investigate whether the results of second-line treatment were associated with the efficacy of nivolumab in patients with gastric cancer.Methods: This was a retrospective cohort study. We enrolled Japanese patients aged ≥ 20 years with gastric cancer who were treated with nivolumab as a third-line chemotherapy at Fujita Health University Hospital from October 2017 to September 2021.Patients with the evaluations of complete response, partial response, and stable disease after third-line chemotherapy were included in the disease control (DC) group, while others were included in the progressive disease (PD) group.Results: A total of 126 patients were enrolled. The population of patients aged over 65 years in the DC group was significantly higher than that in the PD group (p = 0.017). The neutrophil-lymphocyte ratio in the PD group was higher than that in the DC group (p = 0.081). The number of patients continuing second-line chemotherapy for >7 months was significantly higher in the DC than in the PD group (p = 0.021). Age over 65 years (odds ratio [ OR ] =2.67, p = 0.040), duration of second-line chemotherapy over 7 months (OR = 3.10, p = 0.031), and the occurrence of irAEs (OR = 3.60, p = 0.006) were detected as the factors associated with disease control after nivolumab chemotherapy.Conclusions: The effect and the tolerability of second-line chemotherapy, and age over 65 years are the factors of DC after nivolumab chemotherapy. The control of tumour inflammatory status might be important for improvements in treatment outcomes.
MiR-130a Regulates FUNDC1-Mediated Mitophagy by Targeting GJA1 in Myocardial Ischemia/Reperfusion Injury
Authors: Yan Yan , Tian Liu-yang , Jia Qian , Han Yang , Chen Hui-ning , Cui Sai-jia , Yao Yong-Ming , Zhao Xiao-jing 
Published: June 2022

Abstract
To understand the complex pathogenesis in myocardial ischemia/reperfusion (I/R) injury (IRI) is the urgent problem solved in clinical trials. Increasing evidences have suggested that miRNAs are involved in the occurrence and development of heart diseases by regulating the mitochondria-related genes expression. Mitochondria have been acknowledged as the key triggers of cardiac I/R injury. However, the potential impact of miR-130a on mitochondria remains unclear in myocardial IRI. Exploring the regulatory mechanism of miR-130a on mitochondria may provide a new target for IRI therapy. In the present study, we found that miR-130a was significantly increased in the acute myocardial infarction (AMI) patients and myocardial I/R rats. Over-expression of miR-130a resulted in mitochondrial dysfunction, evidenced by decreases in mitochondrial ATP production rate as well as mitochondrial membrane potential (MMP), and increase in reactive oxygen species (ROS) production. However, suppression of miR-130a could protect mitochondrial damage, showing elevation of mitochondrial ATP production rate and MMP, and reduction of ROS production. We further explored the effect of miR-130a on mitochondrial quality control (MQC) system by determining mitochondrial-protein-specific proteases, and mitochondrial morphology was analyzed by fluorescence imaging and electron microscopy, respectively. It was noted that miR-130a could obviously suppress mitochondrial fusion and FUNDC1-mediated mitophagy to accelerate myocardial IRI. Moreover, we investigated the potential miR-130a targetd mitochondria-related genes to understand the regulatory mechanism of miR-130a in the setting of myocardial IRI. It was revealed that miR-130a evidently targeted GJA1, and GJA1 rescued IRI through protecting MMP and activating mitophagy. In addition, knockdown of miR-130a significantly activated FUNDC1-mediated mitophagy, while knockdown of GJA1 reversed the relevant response. Collectively, our findings suggest that miR-130a regulates FUNDC1-mediated mitophagy by targeting GJA1 in myocardial IRI.
Characterization of Extracellular Free Water Pathologies in Schizophrenia Using Multi-Site Diffusion MRI Harmonization
Authors: Cetin-Karayumak Suheyla , Lyall Amanda , Biase Maria Di , Seitz-Holland Johanna , Zhang Fan , Kelly Sinead , Elad Doron , Pearlson Godfrey , Tamminga Carol , Sweeney John , Clementz Brett , Schretlen David , Stegmayer Katharina , Walther Sebastian , Lee Jungsun , Crow Timothy , James Anthony , Voineskos Aristotle , Buchanan Robert , Szeszko Philip , Malhotra Anil , Keshavan Matcheri , Shenton Martha , Rathi Yogesh , Pasternak Ofer , Kubicki Marek 
Published: June 2022

Abstract
Studies applying Free Water Imaging have consistently reported significant global increases in extracellular FW in populations of individuals with early psychosis. However, these published studies focused on homogenous clinical participant groups (e.g., only first episode or chronic), thereby limiting our understanding of the time course of free water (FW) elevations across illness stages. Moreover, the relationship between FW and duration of illness has yet to be directly tested. Leveraging our multi-site diffusion magnetic resonance imaging(dMRI) harmonization approach, we analyzed dMRI scans collected by 12 international sites from 441 healthy controls and 434 individuals diagnosed with schizophrenia-spectrum disorders who represent different illness stages and ages (15–58 years). We characterized the pattern of age-related FW changes by assessing whole brain white matter in individuals with schizophrenia and healthy controls. Quadratic and non-parametric curves were used to model between-group FW differences in averaged whole brain white matter. In individuals with schizophrenia, whole brain FW was higher than in controls across all ages, with the greatest FW values observed from 15 to 23 years of age (effect size range= [0.70-0.87]). Following this peak, FW exhibited a monotonic decrease until reaching a minima at the age of 39 years. After 39 years of age, an attenuated monotonic increase in FW was observed, but with markedly lower effect sizes when compared to younger patients (effect size range = [0.32-0.43]). Importantly, FW was found to be negatively associated with duration of illness in schizophrenia (p=0.006), independent of the effects of age. In summary, our study finds in a large, age-diverse sample that participants with schizophrenia with a shorter duration of illness showed higher FW values compared to participants with more prolonged illness. Our findings indicate that FW might be a reliable imaging marker of acute, extracellular processes which appear to occur predominantly in the early stages of schizophrenia.
Re_Trans: Combined Retrieval and transformer model for Source Code Summarization
Authors: Zhang Chunyan , Zhou Qinglei , Qiao Meng , Tang Ke , Xu Lianqiu , Liu Fudong 
Published: June 2022

Abstract
Source code summarization (SCS) refers to the natural language description on what a source code is performing. It can help developers understand programs and maintain software efficiently. Retrieval methods (RM) generate SCS reorganize terms selected from source code or use SCS of similar code snippets. Generative methods (GM) generate SCS via attentional encoder-decoder architecture. However, a GM can generate SCS for any code, but sometime the accuracy is still far from expectation (due to the lack of numerous high-quality training set). A RM is considered with a higher accuracy, but usually fail to generate SCS for a source code in the absence of a similar candidate in the database. In order to effectively combine the advantages of RM and GM, we propose a new method Re_Trans. For a given code, we first utilize RM to get the most similar code w.r.t sematic and its SCS (S_RM). Then, we input the given code and similar code into the trained discriminator. If the discriminator outputs 1, we take S_RM as the result, otherwise, we utilize the GM, transformer, to generate the given code’ SCS. Particularly, we use AST-augmented and code sequence-augmented information to make the source code semantic extraction more fully. Furthermore, we build a new SCS retrieval library through the public dataset. We evaluate our method on a data set of 2.1 million Java code-comment pairs, and experimental results show improvement over the state-of-the-art (SOTA) benchmarks, which demonstrates the effectiveness and efficiency of our method.
Efficacy of two lines of pupa defence in highly specialised Darwin wasp parasitoids associated with spider hosts (Hymenoptera, Ichneumonidae)
Authors: Korenko Stanislav , Sýkora Jakub , Kostro-Ambroziak Agata , Pekár Stano 
Published: June 2022

Abstract
Insects in the pupal stage are vulnerable to various predators because the pupa is immobile. The pupae of parasitoid Darwin wasps associated with spider hosts have evolved two lines of defence against predators, namely a cocoon spun by the parasitoid larva and a web provided by the spider host. The web is derived from a normal or modified spider web built by the spider under manipulation by the penultimate instar of the parasitoid wasp. In laboratory experiments, we tested the efficacy of these two defensive lines using six potential predators with two different types of mouthparts coming from three foraging guilds. The cocoon significantly reduced predation. Scavengers with chewing mouthparts, e.g., cockroaches and crickets, attacked and consumed pupae within both sparse and strong cocoon walls. Scavengers with piercing mouthparts were able to attack pupae in cocoons with a sparse wall, but not with a strong wall. Collectors and true predators showed no interest in cocoons. The presence of a web increased pupa protection up to 80% when the web was on the ground and up to 95% when the web was in the air. Only scavengers with chewing mouthparts were able to reach and consume the pupae sheltered by the web. We provide the first evidence of how the two lines of defence contribute to parasitoid defence during the pupal stage.