Assessing Computational Amino Acid β-Turn Propensities with a Phage-Displayed Combinatorial Library and Directed Evolution

SummaryStructure propensities of amino acids are important determinants in guiding proteins' local and global structure formation. We constructed a phage display library—a hexa-HIS tag upstream of a CXXC (X stands for any of the 20 natural amino acids) motif appending N-terminal to the minor capsid protein pIII of M13KE filamentous phage—and developed a novel directed-evolution procedure to select for amino acid sequences forming increasingly stable β-turns in the disulfide-bridged CXXC motif. The sequences that emerged from the directed-evolution cycles were in good agreement with type II β-turn propensities derived from surveys of known protein structures, in particular, Pro-Gly forming a type II β-turn. The agreement strongly supported the notion that β-turn formation plays an active role in initiating local structure folding in proteins

Archaeobotanical evidence of plant cultivation from the Sanbaopi site in south-western Taiwan during the Late Neolithic and Metal Age

Despite decades of lively debate about Taiwan’s role in the spread of early agriculture, crops and cultivation practices to the Indo-Pacific region, there is little archaeobotanical data from the island. Here we present the first directly dated and systematically analysed macrobotanical records from Taiwan obtained by flotation at the archaeological site Sanbaopi 5 (23°07′03′′N, 120°15′32′′E), representing the Dahu (1400 BCE–100 CE) and Niaosong (100–1400 CE) culture periods. The results suggest that Middle Dahu (900–100 BCE) communities in the study area practiced rainfed crop cultivation with mainly foxtail (Setaria italica) and broomcorn (Panicum miliaceum) millet and rice (Oryza sativa). Pulses (Vigna angularis, Glycine soja/max) were also part of the subsistence of local farmers and used as supplementary food and/or green manure. The archaeobotanical record together with archaeological site data for prehistoric China substantiates evidence that the Dahu culture originates in the Lower Yellow River region and migrated to Taiwan along the East China Sea coast. The emergence of the Dahu culture coincided with the spread of mixed millet-rice farming to the Korean Peninsula and Japan and was possibly related to enhanced economic and political expansion of the Shang and Western Zhou dynasties and the long-term weakening of summer monsoon precipitation. Pigeon pea (Cajanus cajan) and mung bean (V. radiata var. radiata) assemblages from the sixth century CE Niaosong period highlight the influx of goods, crops, knowledge and people from South and Southeast Asia via southern routes in the context of enhanced exchange across the South China Sea region

Interpretable Self-Attention Temporal Reasoning for Driving Behavior Understanding

Performing driving behaviors based on causal reasoning is essential to ensure driving safety. In this work, we investigated how state-of-the-art 3D Convolutional Neural Networks (CNNs) perform on classifying driving behaviors based on causal reasoning. We proposed a perturbation-based visual explanation method to inspect the models' performance visually. By examining the video attention saliency, we found that existing models could not precisely capture the causes (e.g., traffic light) of the specific action (e.g., stopping). Therefore, the Temporal Reasoning Block (TRB) was proposed and introduced to the models. With the TRB models, we achieved the accuracy of $\mathbf{86.3\%}$, which outperform the state-of-the-art 3D CNNs from previous works. The attention saliency also demonstrated that TRB helped models focus on the causes more precisely. With both numerical and visual evaluations, we concluded that our proposed TRB models were able to provide accurate driving behavior prediction by learning the causal reasoning of the behaviors.Comment: Submitted to IEEE ICASSP 2020; Pytorch code will be released soo

Wide Field-of-View, Large-Area Long-wave Infrared Silicon Metalenses

Long-wave infrared (LWIR, 8-12 $\mu m$ wavelengths) is a spectral band of vital importance to thermal imaging. Conventional LWIR optics made from single-crystalline Ge and chalcogenide glasses are bulky and fragile. The challenge is exacerbated for wide field-of-view (FOV) optics, which traditionally mandates multiple cascaded elements that severely add to complexity and cost. Here we designed and experimentally realized a LWIR metalens platform based on bulk Si wafers featuring 140$^\circ$ FOV. The metalenses, which have diameters exceeding 4 cm, were fabricated using a scalable wafer-level process involving photolithography and deep reactive ion etching. Using a metalens-integrated focal plane array, we further demonstrated wide-angle thermal imaging

18F-FDG PET/CT-based gross tumor volume definition for radiotherapy in head and neck Cancer: a correlation study between suitable uptake value threshold and tumor parameters

<p>Abstract</p> <p>Background</p> <p>To define a suitable threshold setting for gross tumor volume (GTV) when using ¹⁸Fluoro-deoxyglucose positron emission tomography and computed tomogram (PET/CT) for radiotherapy planning in head and neck cancer (HNC).</p> <p>Methods</p> <p>Fifteen HNC patients prospectively received PET/CT simulation for their radiation treatment planning. Biological target volume (BTV) was derived from PET/CT-based GTV of the primary tumor. The BTVs were defined as the isodensity volumes when adjusting different percentage of the maximal standardized uptake value (SUVmax), excluding any artifact from surrounding normal tissues. CT-based primary GTV (C-pGTV) that had been previously defined by radiation oncologists was compared with the BTV. Suitable threshold level (sTL) could be determined when BTV value and its morphology using a certain threshold level was observed to be the best fitness of the C-pGTV. Suitable standardized uptake value (sSUV) was calculated as the sTL multiplied by the SUVmax.</p> <p>Results</p> <p>Our result demonstrated no single sTL or sSUV method could achieve an optimized volumetric match with the C-pGTV. The sTL was 13% to 27% (mean, 19%), whereas the sSUV was 1.64 to 3.98 (mean, 2.46). The sTL was inversely correlated with the SUVmax [sTL = -0.1004 Ln (SUVmax) + 0.4464; R²= 0.81]. The sSUV showed a linear correlation with the SUVmax (sSUV = 0.0842 SUVmax + 1.248; R²= 0.89). The sTL was not associated with the value of C-pGTVs.</p> <p>Conclusion</p> <p>In PET/CT-based BTV for HNC, a suitable threshold or SUV level can be established by correlating with SUVmax rather than using a fixed threshold.</p

Towards General-Purpose Text-Instruction-Guided Voice Conversion

This paper introduces a novel voice conversion (VC) model, guided by text instructions such as "articulate slowly with a deep tone" or "speak in a cheerful boyish voice". Unlike traditional methods that rely on reference utterances to determine the attributes of the converted speech, our model adds versatility and specificity to voice conversion. The proposed VC model is a neural codec language model which processes a sequence of discrete codes, resulting in the code sequence of converted speech. It utilizes text instructions as style prompts to modify the prosody and emotional information of the given speech. In contrast to previous approaches, which often rely on employing separate encoders like prosody and content encoders to handle different aspects of the source speech, our model handles various information of speech in an end-to-end manner. Experiments have demonstrated the impressive capabilities of our model in comprehending instructions and delivering reasonable results.Comment: Accepted to ASRU 202