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1. Discovery and Extensive Follow-Up of SN 2024ggi, a nearby type IIP supernova in NGC 3621

Author

Chen, Ting-Wan, Yang, Sheng, Srivastav, Shubham, Moriya, Takashi J., Smartt, Stephen J., Rest, Sofia, Rest, Armin, Lin, Hsing Wen, Miao, Hao-Yu, Cheng, Yu-Chi, Aryan, Amar, Cheng, Chia-Yu, Fraser, Morgan, Huang, Li-Ching, Lee, Meng-Han, Lai, Cheng-Han, Liu, Yu Hsuan, K, Aiswarya Sankar., Smith, Ken W., Stevance, Heloise F., Wang, Ze-Ning, Anderson, Joseph P., Angus, Charlotte R., de Boer, Thomas, Chambers, Kenneth, Duan, Hao-Yuan, Erasmus, Nicolas, Gao, Hua, Herman, Joanna, Hou, Wei-Jie, Hsiao, Hsiang-Yao, Huber, Mark E., Lin, Chien-Cheng, Lin, Hung-Chin, Magnier, Eugene A., Man, Ka Kit, Moore, Thomas, Ngeow, Chow-Choong, Nicholl, Matt, Ou, Po-Sheng, Pignata, Giuliano, Shiau, Yu-Chien, Sommer, Julian Silvester, Tonry, John L., Wang, Xiao-Feng, Young, David R., Yeh, You-Ting, and Zhang, Jujia

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

We present the discovery and early observations of the nearby Type II supernova (SN) 2024ggi in NGC 3621 at 6.64 +/- 0.3 Mpc. The SN was caught 5.8 (+1.9 -2.9) hours after its explosion by the ATLAS survey. Early-phase, high-cadence, and multi-band photometric follow-up was performed by the Kinder (Kilonova Finder) project, collecting over 1000 photometric data points within a week. The combined o- and r-band light curves show a rapid rise of 3.3 magnitudes in 13.7 hours, much faster than SN 2023ixf (another recent, nearby, and well-observed SN II). Between 13.8 and 18.8 hours after explosion SN 2024ggi became bluer, with u-g colour dropping from 0.53 to 0.15 mag. The rapid blueward evolution indicates a wind shock breakout (SBO) scenario. No hour-long brightening expected for the SBO from a bare stellar surface was detected during our observations. The classification spectrum, taken 17 hours after the SN explosion, shows flash features of high-ionization species such as Balmer lines, He I, C III, and N III. Detailed light curve modeling reveals critical insights into the properties of the circumstellar material (CSM). Our favoured model has an explosion energy of 2 x 10^51 erg, a mass-loss rate of 10^-3 solar_mass/yr (with an assumed 10 km/s wind), and a confined CSM radius of 6 x 10^14 cm. The corresponding CSM mass is 0.4 solar_mass. Comparisons with SN 2023ixf highlight that SN 2024ggi has a smaller CSM density, resulting in a faster rise and fainter UV flux. The extensive dataset and the involvement of citizen astronomers underscore that a collaborative network is essential for SBO searches, leading to more precise and comprehensive SN characterizations., Comment: 11 pages, 5 figures in manuscript, 6 pages in appendix, submitted to ApJL

Published
2024

2. Transferable Embedding Inversion Attack: Uncovering Privacy Risks in Text Embeddings without Model Queries

Author

Huang, Yu-Hsiang, Tsai, Yuche, Hsiao, Hsiang, Lin, Hong-Yi, and Lin, Shou-De

Subjects
Computer Science - Cryptography and Security, Computer Science - Computation and Language, Computer Science - Machine Learning
Abstract

This study investigates the privacy risks associated with text embeddings, focusing on the scenario where attackers cannot access the original embedding model. Contrary to previous research requiring direct model access, we explore a more realistic threat model by developing a transfer attack method. This approach uses a surrogate model to mimic the victim model's behavior, allowing the attacker to infer sensitive information from text embeddings without direct access. Our experiments across various embedding models and a clinical dataset demonstrate that our transfer attack significantly outperforms traditional methods, revealing the potential privacy vulnerabilities in embedding technologies and emphasizing the need for enhanced security measures., Comment: Accepted at ACL 2024 Main Conference

Published
2024
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4. EDEN Survey: Small Transiting Planet Detection Limits and Constraints on the Occurrence Rates for Late M Dwarfs within 15 pc

Author

Dietrich, Jeremy, Apai, Dániel, Schlecker, Martin, Hardegree-Ullman, Kevin K., Rackham, Benjamin V., Kurtovic, Nicolas, Molaverdikhani, Karan, Gabor, Paul, Henning, Thomas, Chen, Wen-Ping, Mancini, Luigi, Bixel, Alex, Gibbs, Aidan, Boyle, Richard P., Brown-Sevilla, Samantha, Burn, Remo, Delage, Timmy N., Flores-Rivera, Lizxandra, Franceschi, Riccardo, Pichierri, Gabriele, Savvidou, Sofia, Syed, Jonas, Bruni, Ivan, Ip, Wing-Huen, Ngeow, Chow-Choong, Tsai, An-Li, Lin, Chia-Lung, Hou, Wei-Jie, Hsiao, Hsiang-Yao, Lin, Chi-Sheng, Lin, Hung-Chin, and Basant, Ritvik

Subjects
Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Solar and Stellar Astrophysics
Abstract

Earth-sized exoplanets that transit nearby, late spectral type red dwarfs will be prime targets for atmospheric characterization in the coming decade. Such systems, however, are difficult to find via wide-field transit surveys like Kepler or TESS. Consequently, the presence of such transiting planets is unexplored and the occurrence rates of short-period Earth-sized planets around late M dwarfs remain poorly constrained. Here, we present the deepest photometric monitoring campaign of 22 nearby late M dwarf stars, using data from over 500 nights on seven 1-2 meter class telescopes. Our survey includes all known single quiescent northern late M dwarfs within 15 pc. We use transit-injection-and-recovery tests to quantify the completeness of our survey, successfully identify most ($>80\%$) transiting short-period (0.5-1 d) super-Earths ($R > 1.9 R_\oplus$), and are sensitive ($\sim50\%$) to transiting Earth-sized planets ($1.0-1.2 R_\oplus$). Our high sensitivity to transits with a near-zero false positive rate demonstrates an efficient survey strategy. Our survey does not yield a transiting planet detection, yet it provides the most sensitive upper limits on transiting planets orbiting our target stars. Finally, we explore multiple hypotheses about the occurrence rates of short-period planets (from Earth-sized planets to giant planets) around late M dwarfs. We show, for example, that giant planets at short periods ($<1$ day) are uncommon around our target stars. Our dataset provides some insight into occurrence rates of short-period planets around TRAPPIST-1-like stars, and our results can help test planetary formation and system evolution models, as well as guide future observations of nearby late M dwarfs., Comment: 27 pages, 11 figures

Published
2023
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6. Comprehensive Cohort Analysis of Mutational Spectrum in Early Onset Breast Cancer Patients.

Author

Midha, Mohit K, Huang, Yu-Feng, Yang, Hsiao-Hsiang, Fan, Tan-Chi, Chang, Nai-Chuan, Chen, Tzu-Han, Wang, Yu-Tai, Kuo, Wen-Hung, Chang, King-Jen, Shen, Chen-Yang, Yu, Alice L, Chiu, Kuo-Ping, and Chen, Chien-Jen

Subjects
early onset breast cancer, germline mutations, missense mutations, nonsynonymous mutations, somatic mutations, Oncology and Carcinogenesis
Abstract

Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel the underlying mechanisms of EOBC etiopathogenesis. Sequence data generated by whole-exome sequencing (WES) and whole-genome sequencing (WGS) from white blood cell (WBC)-tumor pairs were analyzed to identify somatic missense mutations, copy number variations (CNVs) and germline missense mutations. Similar to regular breast cancer, the key somatic mutation-susceptibility genes of EOBC include TP53 (40% prevalence), PIK3CA (37%), GATA3 (17%) and KMT2C (17%), which are frequently reported in breast cancer; however, the structural protein-coding genes MUC17 (19%), FLG (16%) and NEBL (11%) show a significantly higher prevalence in EOBC. Furthermore, the top 2 genes harboring EOBC germline mutations, MUC16 (19%) and KRT18 (19%), encode structural proteins. Compared to conventional breast cancer, an unexpectedly higher number of EOBC susceptibility genes encode structural proteins. We suspect that mutations in structural proteins may increase physical permeability to environmental hormones and carcinogens and cause breast cancer to occur at a young age.

Published
2020

7. Physical properties of near-Earth asteroids with a low delta-${\it v}$: Survey of target candidates for the Hayabusa2 mission

Author

Hasegawa, Sunao, Kuroda, Daisuke, Kitazato, Kohei, Kasuga, Toshihiro, Sekiguchi, Tomohiko, Takato, Naruhisa, Aoki, Kentaro, Arai, Akira, Choi, Young-Jun, Fuse, Tetsuharu, Hanayama, Hidekazu, Hattori, Takashi, Hsiao, Hsiang-Yao, Kashikawa, Nobunari, Kawai, Nobuyuki, Kawakami, Kyoko, Kinoshita, Daisuke, Larson, Steve, Lin, Chi-Sheng, Miyasaka, Seidai, Miura, Naoya, Nagayama, Shogo, Nagumo, Yu, Nishihara, Setsuko, Ohba, Yohei, Ohta, Kouji, Ohyama, Youichi, Okumura, Shin-Ichiro, Sarugaku, Yuki, Shimizu, Yasuhiro, Takagi, Yuhei, Takahashi, Jun, Toda, Hiroyuki, Urakawa, Seitaro, Usui, Fumihiko, Watanabe, Makoto, Weissman, Paul, Yanagisawa, Kenshi, Yang, Hongu, Yoshida, Michitoshi, Yoshikawa, Makoto, Ishiguro, Masateru, and Abe, Masanao

Subjects
Astrophysics - Earth and Planetary Astrophysics
Abstract

Sample return from the near-Earth asteroid known as 25143 Itokawa was conducted as part of the Hayabusa mission, with a large number of scientific findings being derived from the returned samples. Following the Hayabusa mission, Hayabusa2 was planned, targeting sample return from a primitive asteroid. The primary target body of Hayabusa2 was asteroid 162173 Ryugu; however, it was also necessary to gather physical information for backup target selection. Therefore, we examined five asteroids spectroscopically, 43 asteroids spectrophotometrically, and 41 asteroids through periodic analysis. Hence, the physical properties of 74 near-Earth asteroids were obtained, which helped the Hayabusa2 backup target search and, also, furthered understanding of the physical properties of individual asteroids and their origins., Comment: 31 pages, 2 figures, and 4 tables, accepted for publication in PASJ

Published
2018
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8. Art-like wealth : the foundation of Paiwan hierarchy

Author

Hsiao, Hsiang-Wei

Subjects
301
Abstract

In examining the Paiwan, an indigenous group in Taiwan, this thesis illustrates how wealth affects social hierarchy amongst people in house societies. Paiwan wealth is examined through the idea of abduction of agency, as suggested by Gell (1998), to reveal how people associate with past interactions in perceiving both present and future social relations. Investigating the notion of Paiwan wealth provides a means by which Lévi-Strauss' idea of the 'house society' is reconsidered. In possessing wealth, as Lévi-Strauss (1982:194) emphasises, the house is "a corporate body holding an estate made up of both material and immaterial wealth" for organising social groups. In addition to providing an argument for how people are grouped in and by the house itself, this thesis focuses on the processes that form the house as an agent in itself. Moreover, studying Paiwan wealth gives further insights into how features of Dumontian hierarchy (Dumont 1980) and precedence (Fox 1994, 2004) can co-exist in terms of employing multiple values to achieve supreme value of owning wealth. In mapping out the aim of this thesis, discussion begins from how the fieldwork process leads to certain empirical elucidation. By re-examining pervious research about the Paiwan, the significance of processes of interactions from past to present is explored. The social interaction not only enables the position of a house to be established and further gives Christian churches hierarchical position to be a house in the society. By participating in social interaction, Paiwan wealth shows its quality of index in Gell's (1998) argument of art. The association between hierarchy, house and wealth is, therefore, can be exemplified by looking into the Paiwan marriage. Under these circumstances, the study of Paiwan society offers a channel to encompass different perspectives of anthropology to approach indigenous context.

Published
2019

9. Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females.

Author

Huang, Yu-Feng, Chen, Yen-Ju, Fan, Tan-Chi, Chang, Nai-Chuan, Chen, Yi-Jie, Midha, Mohit K, Chen, Tzu-Han, Yang, Hsiao-Hsiang, Wang, Yu-Tai, Yu, Alice L, and Chiu, Kuo-Ping

Subjects
Humans, Breast Neoplasms, DNA, Bacterial, Prognosis, Case-Control Studies, Age of Onset, Adult, Female, Biomarkers, Cell-Free Nucleic Acids, Cell-free circulating DNA, Microbial cfDNA, Microbial cfDNA reads per million quality PE reads, DNA, Bacterial, Genetics, Medical Biochemistry and Metabolomics, Oncology and Carcinogenesis, Genetics & Heredity
Abstract

BACKGROUND:Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases. Those mapped concordantly to unique microbial species were assembled into contigs, which were subsequently aligned to the same databases. Microbial species uniquely aligned were identified and compared across all individuals on MCRPM (Microbial CfDNA Reads Per Million quality PE reads) basis. RESULTS:The predominant microbial cfDNAs in all plasma samples examined are originated from bacteria and these bacteria were limited to only a few genera. Among those, Acinetobacter johnsonii XBB1 and low levels of Mycobacterium spp. were commonly found in all healthy females, but also present in an EOBC patient. Compared to those in healthy counterparts, bacterial species in EOBC patients are more diverse and more likely to present at high levels. Among these three EOBC patients tested, a patient who has record high titer (2,724 MCRPM) of Pseudomonas mendocina together with 8.82 MCRPM of Pannonibacter phragmitetus has passed away; another patient infected by multiple Sphingomonas species remains alive; while the third patient who has similar microbial species (Acinetobacter johnsonii XBB1) commonly seen in normal controls is having a normal life. CONCLUSIONS:Our preliminary data on the profiles of microbial cfDNA sequences suggested that it may have some prognostic value in cancer patients. Validation in larger number of patients is warranted.

Published
2018

10. RZ Leonis Minoris Bridging between ER Ursae Majoris-Type Dwarf Nova and Novalike System

Author

Kato, Taichi, Ishioka, Ryoko, Isogai, Keisuke, Kimura, Mariko, Imada, Akira, Miller, Ian, Masumoto, Kazunari, Nishino, Hirochika, Kojiguchi, Naoto, Kawabata, Miho, Sakai, Daisuke, Sugiura, Yuki, Furukawa, Hisami, Yamamura, Kenta, Kobayashi, Hiroshi, Matsumoto, Katsura, Wang, Shiang-Yu, Chou, Yi, Ngeow, Chow-Choong, Chen, Wen-Ping, Panwar, Neelam, Lin, Chi-Sheng, Hsiao, Hsiang-Yao, Guo, Jhen-Kuei, Lin, Chien-Cheng, Omarov, Chingis, Kusakin, Anatoly, Krugov, Maxim, Starkey, Donn R., Pavlenko, Elena P., Antonyuk, Kirill A., Sosnjvskij, Aleksei A., Antonyuk, Oksana I., Pit, Nikolai V., Baklanov, Alex V., Babina, Julia V., Itoh, Hiroshi, Padovan, Stefano, Akazawa, Hidehiko, Kafka, Stella, de Miguel, Enrique, Pickard, Roger D., Kiyota, Seiichiro, Shugarov, Sergey Yu., Chochol, Drahomir, Krushevska, Viktoriia, Sekeras, Matej, Pikalova, Olga, Sabo, Richard, Dubovsky, Pavol A., Kudzej, Igor, Ulowetz, Joseph, Dvorak, Shawn, Stone, Geoff, Tordai, Tamas, Dubois, Franky, Logie, Ludwig, Rau, Steve, Vanaverbeke, Siegfried, Vanmunster, Tonny, Oksanen, Arto, Maeda, Yutaka, Kasai, Kiyoshi, Katysheva, Natalia, Morelle, Etienne, Neustroev, Vitaly V., and Sjoberg, George

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We observed RZ LMi, which is renowned for the extremely (~19d) short supercycle and is a member of a small, unusual class of cataclysmic variables called ER UMa-type dwarf novae, in 2013 and 2016. In 2016, the supercycles of this object substantially lengthened in comparison to the previous measurements to 35, 32, 60d for three consecutive superoutbursts. We consider that the object virtually experienced a transition to the novalike state (permanent superhumper). This observed behavior extremely well reproduced the prediction of the thermal-tidal instability model. We detected a precursor in the 2016 superoutburst and detected growing (stage A) superhumps with a mean period of 0.0602(1)d in 2016 and in 2013. Combined with the period of superhumps immediately after the superoutburst, the mass ratio is not as small as in WZ Sge-type dwarf novae, having orbital periods similar to RZ LMi. By using least absolute shrinkage and selection operator (Lasso) two-dimensional power spectra, we detected possible negative superhumps with a period of 0.05710(1)d. We estimated the orbital period of 0.05792d, which suggests a mass ratio of 0.105(5). This relatively large mass ratio is even above ordinary SU UMa-type dwarf novae, and it is also possible that the exceptionally high mass-transfer rate in RZ LMi may be a result of a stripped core evolved secondary which are evolving toward an AM CVn-type object., Comment: 14 pages, 14 figures, accepted for publication in PASJ; includes Supplementary_draft_aph.pdf with somewhat degraded figures

Published
2016
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11. Identification of subtypes of anticancer peptides based on sequential features and physicochemical properties

Author

Kai-Yao Huang, Yi-Jhan Tseng, Hui-Ju Kao, Chia-Hung Chen, Hsiao-Hsiang Yang, and Shun-Long Weng

Subjects
Medicine, Science
Abstract

Abstract Anticancer peptides (ACPs) are a kind of bioactive peptides which could be used as a novel type of anticancer drug that has several advantages over chemistry-based drug, including high specificity, strong tumor penetration capacity, and low toxicity to normal cells. As the number of experimentally verified bioactive peptides has increased significantly, various of in silico approaches are imperative for investigating the characteristics of ACPs. However, the lack of methods for investigating the differences in physicochemical properties of ACPs. In this study, we compared the N- and C-terminal amino acid composition for each peptide, there are three major subtypes of ACPs that are defined based on the distribution of positively charged residues. For the first time, we were motivated to develop a two-step machine learning model for identification of the subtypes of ACPs, which classify the input data into the corresponding group before applying the classifier. Further, to improve the predictive power, the hybrid feature sets were considered for prediction. Evaluation by five-fold cross-validation showed that the two-step model trained with sequence-based features and physicochemical properties was most effective in discriminating between ACPs and non-ACPs. The two-step model trained with the hybrid features performed well, with a sensitivity of 86.75%, a specificity of 85.75%, an accuracy of 86.08%, and a Matthews Correlation Coefficient value of 0.703. Furthermore, the model also consistently provides the effective performance in independent testing set, with sensitivity of 77.6%, specificity of 94.74%, accuracy of 88.99% and the MCC value reached 0.75. Finally, the two-step model has been implemented as a web-based tool, namely iDACP, which is now freely available at http://mer.hc.mmh.org.tw/iDACP/ .

Published
2021
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12. VI-Band Follow-Up Observations of Ultra-Long-Period Cepheid Candidates in M31

Author

Ngeow, Chow-Choong, Lee, Chien-Hsiu, Yang, Michael Ting-Chang, Lin, Chi-Sheng, Hsiao, Hsiang-Yao, Cheng, Yu-Chi, Lin, Zhong-Yi, Lin, I-Ling, Kanbur, Shashi M., and Ip, Wing-Huen

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

The ultra-long period Cepheids (ULPCs) are classical Cepheids with pulsation periods exceeding $\approx 80$ days. The intrinsic brightness of ULPCs are ~1 to ~3 mag brighter than their shorter period counterparts. This makes them attractive in future distance scale work to derive distances beyond the limit set by the shorter period Cepheids. We have initiated a program to search for ULPCs in M31, using the single-band data taken from the Palomar Transient Factory, and identified eight possible candidates. In this work, we presented the VI-band follow-up observations of these eight candidates. Based on our VI-band light curves of these candidates and their locations in the color-magnitude diagram and the Period-Wesenheit diagram, we verify two candidates as being truly ULPCs. The six other candidates are most likely other kinds of long-period variables. With the two confirmed M31 ULPCs, we tested the applicability of ULPCs in distance scale work by deriving the distance modulus of M31. It was found to be $\mu_{M31,ULPC}=24.30\pm0.76$ mag. The large error in the derived distance modulus, together with the large intrinsic dispersion of the Period-Wesenheit (PW) relation and the small number of ULPCs in a given host galaxy, means that the question of the suitability of ULPCs as standard candles is still open. Further work is needed to enlarge the sample of calibrating ULPCs and reduce the intrinsic dispersion of the PW relation before re-considering ULPCs as suitable distance indicators., Comment: 13 pages, with 14 Figures and 4 Tables (one online table). AJ accepted

Published
2015
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13. Risk of Death and Cardiovascular Events in Asian Patients With Atrial Fibrillation and Chronic Obstructive Pulmonary Disease: A Report From the Prospective APHRS Registry

Author

Bucci, Tommaso, primary, Romiti, Giulio Francesco, additional, Shantsila, Alena, additional, Teo, Wee‐Siong, additional, Park, Hyung‐Wook, additional, Shimizu, Wataru, additional, Corica, Bernadette, additional, Proietti, Marco, additional, Tse, Hung‐Fat, additional, Chao, Tze‐Fan, additional, Frost, Frederick, additional, Lip, Gregory Y. H., additional, David, Chun‐Wah Siu, additional, Yodogawa, Kenji, additional, Tsutsui, Hiroyuki, additional, Mukai, Yasushi, additional, Tomita, Hirofumi, additional, Horiuchi, Daisuke, additional, Hagii, Joji, additional, Aonuma, Kazutaka, additional, Okumura, Yasuo, additional, Goya, Masahiko, additional, Hirao, Kenzo, additional, Hagiwara, Nobuhisa, additional, Suzuki, Atsushi, additional, Yamane, Teiichi, additional, Ikeda, Takanori, additional, Yuzawa, Hitomi, additional, Satomi, Kazuhiro, additional, Yazaki, Yoshinao, additional, Fukuda, Keiichi, additional, Kobayashi, Yoshinori, additional, Morita, Norishige, additional, Murohara, Toyoaki, additional, Watanabe, Eiichi, additional, Harada, Masahide, additional, Sakagami, Satoru, additional, Saeki, Takahiro, additional, Kusano, Kengo, additional, Miyamoto, Koji, additional, Miyazaki, Shinsuke, additional, Tada, Hiroshi, additional, Inoue, Koichi, additional, Tanaka, Nobuaki, additional, Koretsune, Yukihiro, additional, Abe, Haruhiko, additional, Kihara, Yasuki, additional, Nakano, Yukiko, additional, Shimizu, Akihiko, additional, Yoshiga, Yasuhiro, additional, Sakamoto, Tomohiro, additional, Okumura, Ken, additional, Takahashi, Naohiko, additional, Shinohara, Tetsuji, additional, Soejima, Kyoko, additional, Takagi, Masahiko, additional, Kawamura, Mitsuharu, additional, Munetsugu, Yumi, additional, Kim, Sung‐Hwan, additional, Shim, Jae‐Min, additional, Uhm, Jae Sun, additional, Im, Sung Il, additional, Par, Hyoung‐Seob, additional, Kim, Jun Hyung, additional, On, Young Keun, additional, Oh, Il‐Young, additional, Shin, Seung Yong, additional, Ko, Jum Suk, additional, Park, Jun Beom, additional, Wong, Kelvin Cheok‐Keng, additional, Lim, Toon‐Wei, additional, Foo, David, additional, Chen, Shih‐Ann, additional, Lin, YennJiang, additional, Chung, Fa‐Po, additional, Hu, Yu‐Feng, additional, Chang, Shil‐Lin, additional, Tuan, Ta‐Chuan, additional, Liao, Jo‐Nan, additional, Li, Cheng‐Hung, additional, Huang, Jin‐Long, additional, Hsieh, Yu‐Cheng, additional, Wu, Tsu‐Juey, additional, Liao, Ying‐Chieh, additional, Chiang, Cheng‐Hung, additional, Hsiao, Hsiang‐Chiang, additional, Yeh, Tung‐Chen, additional, Lin, Wei‐Siang, additional, Lin, Wen‐Yu, additional, Kuo, Jen‐Yuan, additional, Hong, Chong‐Lie, additional, Wu, Yih‐Je, additional, Li, Ying‐Siang, additional, Tsai, Jui‐Peng, additional, Sung, Kuo‐Tzu, additional, and Chang, Sheng‐Hsiung, additional

Published
2024
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17. Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

Author

Yu-Feng Huang, Yen-Ju Chen, Tan-Chi Fan, Nai-Chuan Chang, Yi-Jie Chen, Mohit K. Midha, Tzu-Han Chen, Hsiao-Hsiang Yang, Yu-Tai Wang, Alice L. Yu, and Kuo-Ping Chiu

Subjects
Cell-free circulating DNA (cfDNA), Microbial cfDNA reads per million quality PE reads (MCRPM), Microbial cfDNA, Internal medicine, RC31-1245, Genetics, QH426-470
Abstract

Abstract Background Cell-free circulating DNA (cfDNA) is becoming a useful biopsy for noninvasive diagnosis of diseases. Microbial sequences in plasma cfDNA may provide important information to improve prognosis and treatment. We have developed a stringent method to identify microbial species via microbial cfDNA in the blood plasma of early-onset breast cancer (EOBC) patients and healthy females. Empirically, microbe-originated sequence reads were identified by mapping non-human PE reads in cfDNA libraries to microbial databases. Those mapped concordantly to unique microbial species were assembled into contigs, which were subsequently aligned to the same databases. Microbial species uniquely aligned were identified and compared across all individuals on MCRPM (Microbial CfDNA Reads Per Million quality PE reads) basis. Results The predominant microbial cfDNAs in all plasma samples examined are originated from bacteria and these bacteria were limited to only a few genera. Among those, Acinetobacter johnsonii XBB1 and low levels of Mycobacterium spp. were commonly found in all healthy females, but also present in an EOBC patient. Compared to those in healthy counterparts, bacterial species in EOBC patients are more diverse and more likely to present at high levels. Among these three EOBC patients tested, a patient who has record high titer (2,724 MCRPM) of Pseudomonas mendocina together with 8.82 MCRPM of Pannonibacter phragmitetus has passed away; another patient infected by multiple Sphingomonas species remains alive; while the third patient who has similar microbial species (Acinetobacter johnsonii XBB1) commonly seen in normal controls is having a normal life. Conclusions Our preliminary data on the profiles of microbial cfDNA sequences suggested that it may have some prognostic value in cancer patients. Validation in larger number of patients is warranted.

Published
2018
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22. The efficacy and safety of cupping as complementary and alternative therapy for metabolic syndrome: A systematic review and meta-analysis

Author

Wu, Li-Kung, primary, Chen, Yi-Chen, additional, Hung, Chung-Shan, additional, Yen, Chih-Yu, additional, Chang Chien, Chen-Ying, additional, Ciou, Jian-Ruei, additional, Torng, Hsiao-Hsiang, additional, Chang, Yi-Chin, additional, Hua, Shiuan, additional, Lu, Peng-Nien, additional, Liu, Yuan-Yuan, additional, Lai, Chun-Yu, additional, Kung, Yen-Lun, additional, Huang, Huei-Kai, additional, Chen, Zhong-Kui, additional, and Ho, Tsung-Jung, additional

Published
2023
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23. EDEN Survey: Small Transiting Planet Detection Limits and Constraints on the Occurrence Rates of Planets around Late-M Dwarfs within 15 pc

Author

Dietrich, Jeremy, primary, Apai, Dániel, additional, Schlecker, Martin, additional, Hardegree-Ullman, Kevin K., additional, Rackham, Benjamin V., additional, Kurtovic, Nicolas, additional, Molaverdikhani, Karan, additional, Gabor, Paul, additional, Henning, Thomas, additional, Chen, Wen-Ping, additional, Mancini, Luigi, additional, Bixel, Alex, additional, Gibbs, Aidan, additional, Boyle, Richard P., additional, Brown-Sevilla, Samantha, additional, Burn, Remo, additional, Delage, Timmy N., additional, Flores-Rivera, Lizxandra, additional, Franceschi, Riccardo, additional, Pichierri, Gabriele, additional, Savvidou, Sofia, additional, Syed, Jonas, additional, Bruni, Ivan, additional, Ip, Wing-Huen, additional, Ngeow, Chow-Choong, additional, Tsai, An-Li, additional, Lin, Chia-Lung, additional, Hou, Wei-Jie, additional, Hsiao, Hsiang-Yao, additional, Lin, Chi-Sheng, additional, Lin, Hung-Chin, additional, and Basant, Ritvik, additional

Published
2023
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25. Primitive Neuroectodermal Tumor Presenting with Elevating Carcinoembryonic Antigen

Author

Hsiao-Hsiang Cheng and Chuang-Chi Liaw

Subjects
PNET, CEA, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Primitive neuroectodermal tumor (PNET) is a rare disease and mostly diagnosed in children and young adults. This tumor is presumed to be of neuroectodermal origin, probably developing from migrating embryonic cells of the neural crest. Carcinoembryonic antigen is a glycoprotein and frequently elevated in patients with a variety of epithelial malignancies. We report hereby a 59-year old male patient with pelvic PNET, and the initial presentation was merelyelevating serum CEA of unknown origin. This case might help to support the theory that PNET may have a potential for epithelial or neuroendocrine differentiation.

Published
2014
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26. Pre-treatment high body mass index is associated with poor survival in Asian premenopausal women with localized breast cancer

Author

Wen-Chi Shen, Shin-Cheh Chen, Hsiao-Hsiang Cheng, Yung-Chang Lin, and Yi-Ting Huang

Subjects
Oncology, Subset Analysis, medicine.medical_specialty, obesity, Multivariate analysis, business.industry, Estrogen receptor, body mass index, Overweight, medicine.disease, Obesity, Breast cancer, breast cancer, Internal medicine, Cohort, medicine, medicine.symptom, business, prognostic factor, Body mass index, Research Paper
Abstract

Background: Obesity is associated with poor prognosis in breast cancer patients. This study aimed to evaluate the effect of obesity measured by body mass index (BMI) on survival of Taiwanese breast cancer patients in a single institution. Methods: We observed 5000 patients who were diagnosed with stage I-III breast cancer between 1990 and 2005. Information on BMI at diagnosis, and clinical follow-up for disease recurrence and death, up to 20 years post-diagnosis were available. BMI (in kg/m2) categories included normal weight (BMI

Published
2021

36. Loss of the p12 subunit of DNA polymerase delta leads to a defect in HR and sensitization to PARP inhibitors

Author

Xiaoxiao Wang, Sufang Zhang, Hsiao Hsiang Chao, Zhongtao Zhang, Marietta Y.W.T. Lee, and Ernest Y.C. Lee

Subjects
Mitomycin, viruses, Poly ADP ribose polymerase, Poly(ADP-ribose) Polymerase Inhibitors, Biology, Biochemistry, DNA polymerase delta, Article, Olaparib, Gene Knockout Techniques, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Cell Line, Tumor, Humans, DNA Breaks, Double-Stranded, Homologous Recombination, Rucaparib, Molecular Biology, Polymerase, DNA Polymerase III, 030304 developmental biology, 0303 health sciences, Cell Biology, Molecular biology, Protein Subunits, chemistry, Cell culture, 030220 oncology & carcinogenesis, PARP inhibitor, biology.protein, Cisplatin, Homologous recombination, HeLa Cells
Abstract

Human DNA polymerase δ is normally present in unstressed, non-dividing cells as a heterotetramer (Pol δ4). Its smallest subunit, p12, is transiently degraded in response to UV damage, as well as during the entry into S-phase, resulting in the conversion of Pol δ4 to a trimer (Pol δ3). In order to further understand the specific cellular roles of these two forms of Pol δ, the gene (POLD4) encoding p12 was disrupted by CRISPR/Cas9 to produce p12 knockout (p12KO) cells. Thus, Pol δ4 is absent in p12KO cells, leaving Pol δ3 as the sole source of Pol δ activity. GFP reporter assays revealed that the p12KO cells exhibited a defect in homologous recombination (HR) repair, indicating that Pol δ4, but not Pol δ3, is required for HR. Expression of Flag-tagged p12 in p12KO cells to restore Pol δ4 alleviated the HR defect. These results establish a specific requirement for Pol δ4 in HR repair. This leads to the prediction that p12KO cells should be more sensitive to chemotherapeutic agents, and should exhibit synthetic lethal killing by PARP inhibitors. These predictions were confirmed by clonogenic cell survival assays of p12KO cells treated with cisplatin and mitomycin C, and with the PARP inhibitors Olaparib, Talazoparib, Rucaparib, and Niraparib. The sensitivity to PARP inhibitors in H1299-p12KO cells was alleviated by expression of Flag-p12. These findings have clinical significance, as the expression levels of p12 could be a predictive biomarker of tumor response to PARP inhibitors. In addition, small cell lung cancers (SCLC) are known to exhibit a defect in p12 expression. Analysis of several SCLC cell lines showed that they exhibit hypersensitivity to PARP inhibitors, providing evidence that loss of p12 expression could represent a novel molecular basis for HR deficiency.

Published
2019
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41. S,S-dimethyl dithiocarbonate: a convenient reagent for the synthesis of symmetrical and unsymmetrical ureas

Author

Leung, Man-kit, Lai, Jun-Liang, Lau, King-Hang, Yu, Hsiao-hua, and Hsiao, Hsiang-Ju

Subjects
Carbonates -- Research, Urea -- Research, Amines -- Research, Carbamates -- Research, Biological sciences, Chemistry
Abstract

The selectivity of S,S-dimethyl dithiocarbonate (DMDTC) to amines is exploited in the preparation of symmetrical and unsymmetrical ureas. Bisaniline is produced straight from 4-aminobenzylamine and DMDTC with no further protection and deprotection manipulations. A 7:3 mixture of bis(3-hydroxypropyl)urea and cyclic urethane is obtained upon heating DMDTC and 3-aminopropanol. In addition, cyclic ureas or carbamates are yielded from the dilute solution reactions of aliphatic amine, which incorporates a hydroxy or amino group at the beta or gamma position.

Published
1996

42. Comprehensive Cohort Analysis of Mutational Spectrum in Early Onset Breast Cancer Patients

Author

Yu-Feng Huang, Nai-Chuan Chang, Mohit K. Midha, Alice L. Yu, Chen-Yang Shen, Kuo Ping Chiu, King-Jen Chang, Tan-Chi Fan, Yu-Tai Wang, Chien-Jen Chen, Tzu-Han Chen, Hsiao-Hsiang Yang, and Wen-Hung Kuo

Subjects
0301 basic medicine, Oncology, Cancer Research, medicine.medical_specialty, Oncology and Carcinogenesis, early onset breast cancer, lcsh:RC254-282, Article, Germline, early onset breast cancer (EOBC), 03 medical and health sciences, missense mutations, nonsynonymous mutations, 0302 clinical medicine, Breast cancer, Germline mutation, Clinical Research, Internal medicine, Breast Cancer, Genetics, 2.1 Biological and endogenous factors, Medicine, Missense mutation, Copy-number variation, Aetiology, Cancer, business.industry, Prevention, Mortality rate, Human Genome, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, medicine.disease, 030104 developmental biology, 030220 oncology & carcinogenesis, Cohort, somatic mutations, germline mutations, business, Biotechnology, Cohort study
Abstract

Early onset breast cancer (EOBC), diagnosed at age ~40 or younger, is associated with a poorer prognosis and higher mortality rate compared to breast cancer diagnosed at age 50 or older. EOBC poses a serious threat to public health and requires in-depth investigation. We studied a cohort comprising 90 Taiwanese female patients, aiming to unravel the underlying mechanisms of EOBC etiopathogenesis. Sequence data generated by whole-exome sequencing (WES) and whole-genome sequencing (WGS) from white blood cell (WBC)&ndash, tumor pairs were analyzed to identify somatic missense mutations, copy number variations (CNVs) and germline missense mutations. Similar to regular breast cancer, the key somatic mutation-susceptibility genes of EOBC include TP53 (40% prevalence), PIK3CA (37%), GATA3 (17%) and KMT2C (17%), which are frequently reported in breast cancer, however, the structural protein-coding genes MUC17 (19%), FLG (16%) and NEBL (11%) show a significantly higher prevalence in EOBC. Furthermore, the top 2 genes harboring EOBC germline mutations, MUC16 (19%) and KRT18 (19%), encode structural proteins. Compared to conventional breast cancer, an unexpectedly higher number of EOBC susceptibility genes encode structural proteins. We suspect that mutations in structural proteins may increase physical permeability to environmental hormones and carcinogens and cause breast cancer to occur at a young age.

Published
2020
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43. TCTAP A-060 Safety and Efficacy of Bioresorbable Scaffolds in Daily Practice: Experience from a Single Center in Taiwan

Author

Yang, Tse-Husan, primary, Liu, En-Shao, additional, Mar, Guang-Yuan, additional, Cheng, Chin-Chang, additional, Hung, Cheng Chung, additional, Chiang, Cheng-Hung, additional, Kuo, Feng Yu, additional, Yeh, Tung-Chen, additional, Hsiao, Hsiang-Chiang, additional, Lee, Tao-Yu, additional, Liang, Hsin-Li, additional, Huang, Wei-Chun, additional, and Liu, Chun-Peng, additional

Published
2019
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45. Design of microarray probes for virus identification and detection of emerging viruses at the genus level

Author

Ho Mei-Shang, Lin Yi-Ling, Hsiao Hsiang-Yun, Chen Chun-Houh, Lee Te-Tsui, Chou Cheng-Chung, Yang Pan-Chyr, and Peck Konan

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Most virus detection methods are geared towards the detection of specific single viruses or just a few known targets, and lack the capability to uncover the novel viruses that cause emerging viral infections. To address this issue, we developed a computational method that identifies the conserved viral sequences at the genus level for all viral genomes available in GenBank, and established a virus probe library. The virus probes are used not only to identify known viruses but also for discerning the genera of emerging or uncharacterized ones. Results Using the microarray approach, the identity of the virus in a test sample is determined by the signals of both genus and species-specific probes. The genera of emerging and uncharacterized viruses are determined based on hybridization of the viral sequences to the conserved probes for the existing viral genera. A detection and classification procedure to determine the identity of a virus directly from detection signals results in the rapid identification of the virus. Conclusion We have demonstrated the validity and feasibility of the above strategy with a small number of viral samples. The probe design algorithm can be applied to any publicly available viral sequence database. The strategy of using separate genus and species probe sets enables the use of a straightforward virus identity calculation directly based on the hybridization signals. Our virus identification strategy has great potential in the diagnosis of viral infections. The virus genus and specific probe database and the associated summary tables are available at http://genestamp.sinica.edu.tw/virus/index.htm.

Published
2006
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46. Physical properties of near-Earth asteroids with a low delta-${\it v}$: Survey of target candidates for the Hayabusa2 mission

Author

Choi, Young-Jun, Hsiao, Hsiang-Yao, Larson, Steve, Lin, Chi-Sheng, Miura, Naoya, Nagumo, Yu, Weissman, Paul, Yang, Hongu, Hasegawa, Sunao, Kuroda, Daisuke, Kitazato, Kohei, Kasuga, Toshihiro, Sekiguchi, Tomohiko, Takato, Naruhisa, Aoki, Kentaro, Arai, Akira, Fuse, Tetsuharu, Hanayama, Hidekazu, Hattori, Takashi, Kashikawa, Nobunari, Kawai, Nobuyuki, Kawakami, Kyoko, Kinoshita, Daisuke, Miyasaka, Seidai, Nagayama, Shogo, Nishihara, Setsuko, Ohba, Yohei, Ohta, Kouji, Ohyama, Youichi, Okumura, Shin-ichiro, Sarugaku, Yuki, Shimizu, Yasuhiro, Takagi, Yuhei, Takahashi, Jun, Toda, Hiroyuki, Urakawa, Seitaro, Usui, Fumihiko, Watanabe, Makoto, Yanagisawa, Kenshi, Yoshida, Michitoshi, Yoshikawa, Makoto, Ishiguro, Masateru, and Abe, Masanao

Subjects
Physics, Earth and Planetary Astrophysics (astro-ph.EP), Near-Earth object, 010504 meteorology & atmospheric sciences, FOS: Physical sciences, Astronomy and Astrophysics, minor planets, asteroids: general, 01 natural sciences, Methods observational, Astrobiology, Delta-v (physics), techniques: photometric, Space and Planetary Science, Asteroid, 0103 physical sciences, methods: observational, 010303 astronomy & astrophysics, techniques: spectroscopic, Astrophysics - Earth and Planetary Astrophysics, 0105 earth and related environmental sciences
Abstract

著者人数: 43名, Accepted: 2018-10-02, 資料番号: SA1180347000

Published
2018
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47. dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation

Author

Yen-Chen Liao, Wei-Chieh Ching, Kai-Yao Huang, Hsiao-Hsiang Yang, Min-Gang Su, Yu-Ju Chen, Cheng-Tsung Lu, Yi-Ju Chen, and Tzong-Yi Lee

Subjects
Cell signaling, Regulator, Protein Data Bank (RCSB PDB), Computational biology, Biology, Nitric Oxide, Mice, Protein Interaction Mapping, Genetics, Animals, Humans, Database Issue, Disease, Amino Acids, Databases, Protein, Gene, chemistry.chemical_classification, Internet, Proteins, Rats, Amino acid, Metabolic pathway, Biochemistry, chemistry, Phosphorylation, Signal transduction, Protein Processing, Post-Translational, Metabolic Networks and Pathways, Signal Transduction
Abstract

Given the increasing number of proteins reported to be regulated by S-nitrosylation (SNO), it is considered to act, in a manner analogous to phosphorylation, as a pleiotropic regulator that elicits dual effects to regulate diverse pathophysiological processes by altering protein function, stability, and conformation change in various cancers and human disorders. Due to its importance in regulating protein functions and cell signaling, dbSNO (http://dbSNO.mbc.nctu.edu.tw) is extended as a resource for exploring structural environment of SNO substrate sites and regulatory networks of S-nitrosylated proteins. An increasing interest in the structural environment of PTM substrate sites motivated us to map all manually curated SNO peptides (4165 SNO sites within 2277 proteins) to PDB protein entries by sequence identity, which provides the information of spatial amino acid composition, solvent-accessible surface area, spatially neighboring amino acids, and side chain orientation for 298 substrate cysteine residues. Additionally, the annotations of protein molecular functions, biological processes, functional domains and human diseases are integrated to explore the functional and disease associations for S-nitrosoproteome. In this update, users are allowed to search a group of interested proteins/genes and the system reconstructs the SNO regulatory network based on the information of metabolic pathways and protein-protein interactions. Most importantly, an endogenous yet pathophysiological S-nitrosoproteomic dataset from colorectal cancer patients was adopted to demonstrate that dbSNO could discover potential SNO proteins involving in the regulation of NO signaling for cancer pathways.

Published
2014
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48. Physical properties of near-Earth asteroids with a low delta-v: Survey of target candidates for the Hayabusa2 mission

Author

Hasegawa, Sunao, primary, Kuroda, Daisuke, additional, Kitazato, Kohei, additional, Kasuga, Toshihiro, additional, Sekiguchi, Tomohiko, additional, Takato, Naruhisa, additional, Aoki, Kentaro, additional, Arai, Akira, additional, Choi, Young-Jun, additional, Fuse, Tetsuharu, additional, Hanayama, Hidekazu, additional, Hattori, Takashi, additional, Hsiao, Hsiang-Yao, additional, Kashikawa, Nobunari, additional, Kawai, Nobuyuki, additional, Kawakami, Kyoko, additional, Kinoshita, Daisuke, additional, Larson, Steve, additional, Lin, Chi-Sheng, additional, Miyasaka, Seidai, additional, Miura, Naoya, additional, Nagayama, Shogo, additional, Nagumo, Yu, additional, Nishihara, Setsuko, additional, Ohba, Yohei, additional, Ohta, Kouji, additional, Ohyama, Youichi, additional, Okumura, Shin-ichiro, additional, Sarugaku, Yuki, additional, Shimizu, Yasuhiro, additional, Takagi, Yuhei, additional, Takahashi, Jun, additional, Toda, Hiroyuki, additional, Urakawa, Seitaro, additional, Usui, Fumihiko, additional, Watanabe, Makoto, additional, Weissman, Paul, additional, Yanagisawa, Kenshi, additional, Yang, Hongu, additional, Yoshida, Michitoshi, additional, Yoshikawa, Makoto, additional, Ishiguro, Masateru, additional, and Abe, Masanao, additional

Published
2018
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50. A study on the critical success factors for corporations embarking on knowledge community-based e-learning

Author

Ruey-Shun Chen and Chin-Hsiao Hsiang

Subjects
Information Systems and Management, Knowledge management, business.industry, Knowledge value chain, Competitive advantage, Computer Science Applications, Theoretical Computer Science, Empirical research, Artificial Intelligence, Control and Systems Engineering, Critical success factor, Organizational learning, Personal knowledge management, Business, Knowledge community, Knowledge transfer, Software
Abstract

Corporations have felt the pressure for fast-paced innovations and knowledge transfer as major driving forces in raising their sustainable competitive advantage and organizational total productivity. Thus, the development of the knowledge community through e-learning is an important strategy in implementing knowledge management policy. This paper illustrates an empirical study with which to conduct qualitative research of learning organization. From the case company’s real progress and practical experience, some core principles were extracted from four managerial aspects, such as: strategy, technology, process, and personnel. These aspects were analyzed in order to understand the value chain framework and the major concerns of knowledge community development. Further, the main benefits are addressed and certain critical factors are proposed and shown in this paper to ensure the success of corporations embarking on knowledge community-based e-learning.

Published
2007
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