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Recent advances in atomic resolution three-dimensional holography
No full textThree-dimensional (3D) local atomic structure around specific functional atom plays a crucial role in functional materials, but it has not been able to be analyzed by a standard structure analysis method of x-ray diffraction (XRD) because this kind of small amount of atom has no translational symmetry. Recently several atomic-resolution holography methods have been developed, which can directly display the 3D atomic structure around this kind of specific atoms with no translational symmetry. These are the ‘photoelectron holography’, ‘x-ray fluorescence holography’, and ‘CTR holography’. Their accuracy improved dramatically by the development of new analysis codes and sensitive analyzers and detectors. A new technique of direct 3D atomic structure analysis method ‘stereography of atomic arrangement’ has also been developed. These techniques received renewed attention recently, and a project ‘3D Active-Site Science’ of JSPS Grant-in-Aid for Scientific Research on Innovative Areas has been pursued for 5 years. This article reviews principles and some results of atomic-resolution holography methods.review articl
Beyond heat waves: Unlocking epigenetic heat stress memory in Arabidopsis
Get PDFPlants remember their exposure to environmental changes and respond more effectively the next time they encounter a similar change by flexibly altering gene expression. Epigenetic mechanisms play a crucial role in establishing such memory of environmental changes and fine-tuning gene expression. With the recent advancements in biochemistry and sequencing technologies, it has become possible to characterize the dynamics of epigenetic changes on scales ranging from short term (minutes) to long term (generations). Here, our main focus is on describing the current understanding of the temporal regulation of histone modifications and chromatin changes during exposure to short-term recurring high temperatures and reevaluating them in the context of natural environments. Investigations of the dynamics of histone modifications and chromatin structural changes in Arabidopsis after repeated exposure to heat at short intervals have revealed the detailed molecular mechanisms of short-term heat stress memory, which include histone modification enzymes, chromatin remodelers, and key transcription factors. In addition, we summarize the spatial regulation of heat responses. Based on the natural temperature patterns during summer, we discuss how plants cope with recurring heat stress occurring at various time intervals by utilizing 2 distinct types of heat stress memory mechanisms. We also explore future research directions to provide a more precise understanding of the epigenetic regulation of heat stress memory.journal articl
Monolingual Paraphrase Detection Corpus for Low Resource Pashto Language at Sentence Level
No full textParaphrase detection is a task to identify if two sentences are semantically similar or not. It plays an important role in maintaining the integrity of written work such as plagiarism detection and text reuse detection. Formerly, researchers focused on developing large corpora for English. However, no research has been conducted on sentence-level paraphrase detection in low-resource Pashto language. To bridge this gap, we introduce the first fully manually annotated Pashto sentential paraphrase detection corpus collected from authentic cases in journalism covering 10 different domains, including Sports, Health, Environment, and more. Our proposed corpus contains 6,727 sentences, encompassing 3,687 paraphrased and 3,040 non-paraphrased. Experimental findings reveal that our proposed corpus is sufficient to train XLM-RoBERTa to accurately detect paraphrased sentence pairs in Pashto with an F1 score of 84%. To compare our corpus with those in other languages, we also applied our fine-tuned model to the Indonesian and English paraphrase datasets in a zero-shot manner, achieving F1 scores of 82% and 78%, respectively. This result indicates that the quality of our corpus is not less than commonly used datasets. It‘s a pioneering contribution to the field. We will publicize a subset of 1,800 instances from our corpus, free from any licensing issues.conference pape
N-terminal truncation of PhaCBP-M-CPF4 and its effect on PHA production
No full textBackground
Among the polyhydroxyalkanoate (PHA), poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] [P(3HB-co-3HHx)] is reported to closely resemble polypropylene and low-density polyethylene. Studies have shown that PHA synthase (PhaC) from mangrove soil (PhaCBP-M-CPF4) is an efficient PhaC for P(3HB-co-3HHx) production and N-termini of PhaCs influence its substrate specificity, dimerization, granule morphology, and molecular weights of PHA produced. This study aims to further improve PhaCBP-M-CPF4 through N-terminal truncation.
Results
The N-terminal truncated mutants of PhaCBP-M-CPF4 were constructed based on the information of the predicted secondary and tertiary structures using PSIPRED server and AlphaFold2 program, respectively. The N-terminal truncated PhaCBP-M-CPF4 mutants were evaluated in C. necator mutant PHB$22124 based on the cell dry weight, PHA content, 3HHx molar composition, molecular weights, and granule morphology of the PHA granules. The results showed that most transformants harbouring the N-terminal truncated PhaCBP-M-CPF4 showed a reduction in PHA content and cell dry weight except for PhaCBP-M-CPF4 G8. PhaCBP-M-CPF4 G8 and A27 showed an improved weight-average molecular weight (Mw) of PHA produced due to lower expression of the truncated PhaCBP-M-CPF4. Transformants harbouring PhaCBP-M-CPF4 G8, A27, and T74 showed a reduction in the number of granules. PhaCBP-M-CPF4 G8 produced higher Mw PHA in mostly single larger PHA granules with comparable production as the full-length PhaCBP-M-CPF4.
Conclusion
This research showed that N-terminal truncation had effects on PHA accumulation, substrate specificity, Mw, and granule morphology. This study also showed that N-terminal truncation of the amino acids that did not adopt any secondary structure can be an alternative to improve PhaCs for the production of PHA with higher Mw in mostly single larger granules.journal articl
Investigation of the Interaction between Poly(trimethylene carbonate) and Various Hydroxyl Groups
Get PDFThe interaction of poly(trimethylene carbonate) (PTMC) with hydroxyl group compounds was investigated as a model for polymer blending with polysaccharides. While 1-butanol, 2-butanol, ethylene glycol, and 1,2-cyclohexanediol showed almost no detectable interaction with PTMC in both solution states with the 1H NMR and solid states with the FT-IR, glucose and cellobiose suggested a slight change in the spectral pattern in FT-IR analysis. The thermal properties of the blended samples of PTMC and these hydroxyl groups were also investigated. Although the blends of PTMC with 1-butanol and 2-butanol did not influence thermal degradation behaviors due to their low boiling points, the PTMC blend with a higher number of hydroxyl groups, especially glucose and cellobiose, tended to increase thermal resistance and glass transition temperature, hence showing the existence of an interaction through hydrogen bonding.journal articl
Explainable deep-learning-based ischemia detection using hybrid O-15 H2O perfusion positron emission tomography and computed tomography imaging with clinical data
No full textBackground We developed an explainable deep-learning (DL)-based classifier to identify flow-limiting coronary artery disease (CAD) by O-15 H2O perfusion positron emission tomography computed tomography (PET/CT) and coronary CT angiography (CTA) imaging. The classifier uses polar map images with numerical data and visualizes data findings. Methods A DLmodel was implemented and evaluated on 138 individuals, consisting of a combined image—and data-based classifier considering 35 clinical, CTA, and PET variables. Data from invasive coronary angiography were used as reference. Performance was evaluated with clinical classification using accuracy (ACC), area under the receiver operating characteristic curve (AUC), F1 score (F1S), sensitivity (SEN), specificity (SPE), precision (PRE), net benefit, and Cohen's Kappa. Statistical testing was conducted using McNemar's test. Results The DL model had a median ACC = 0.8478, AUC = 0.8481, F1S = 0.8293, SEN = 0.8500, SPE = 0.8846, and PRE = 0.8500. Improved detection of true-positive and false-negative cases, increased net benefit in thresholds up to 34%, and comparable Cohen's kappa was seen, reaching similar performance to clinical reading. Statistical testing revealed no significant differences between DL model and clinical reading. Conclusions The combined DL model is a feasible and an effective method in detection of CAD, allowing to highlight important data findings individually in interpretable manner.journal articl
The influence of perspective on VR job interview training
No full textThird-person perspectives in virtual reality (VR) based public speaking training enable trainees to objectively observe themselves through self-avatars, potentially enhancing their public speaking skills. Taking a job interview as a case study, this study investigates the influence of perspective on the training effects in VR public speaking training and explores the relationship between training effects and the sense of embodiment (SoE) and presence, as these concepts are central to virtual experiences. In the experiment, VR job interview training was conducted under three conditions: a first-person perspective (1PP), a typical third-person perspective from behind the avatar (Back), and a third-person perspective from the front of the avatar (Front). The results indicate that participants trained in the Front condition received higher evaluations from others in terms of verbal communication skills and the overall impression of the interview compared to those trained in the other conditions, highlighting the advantages of training while observing a self-avatar. Furthermore, it was confirmed that training effects correlated with the subcomponents of SoE and presence, suggesting that these trends may vary depending on perspective.journal articl
ダイキボ ゲンゴ モデル ニ ヨル ヒント セイセイ シュホウ ノ プログラミング エンシュウ エ ノ ドウニュウ
Get PDF近年，プログラミング初学者に対する学習の支援を目的として大規模言語モデル(LLM)を用いた研究が盛んに行われている． LLMのプログラミング学習への適用において，モデルの出力をそのまま用いると課題の答えが提示されてしまうことがあり，学生が自力で学べないという問題がある． そのため，これまでに直接答えを提示せずに品質の高いヒントを生成して提示する手法の提案が行われている． この手法では，GPT-4モデルを用いて生成したヒントをGPT-3.5モデルを用いて検証を行った上で提示が行われている． 本研究ではこの手法の拡張を行い，著者らが所属する大学院大学で行われているプログラミング演習の授業に導入し，その効果を測る． 学生視点での評価を行った結果，特にプログラミング経験が浅い初級者にとって提案手法は有用であることが示唆された．conference pape
Prefix Alignment for Training Simultaneous Machine Translation
No full textSimultaneous translation is a task that starts translation even before the speaker has finished speaking. This study focuses on prefix-to-prefix translation and proposes a method to align prefixes in a bilingual sentence pair iteratively to train a machine translation model to work with prefix-to-prefix. In the experiments, the proposed method demonstrated higher BLEU than those of the baseline methods in low latency ranges on the IWSLT simultaneous translation benchmark. However, the proposed method degraded the performance in high latency ranges in the English-to-Japanese experiments; thus, we analyzed it in length ratios and prefix boundary prediction accuracies. The obtained results suggested that the degraded performance was due to the large word order difference between English and Japanese.journal articl