We demonstrate an end-to-end question answering system that integrates BERT with the open-source Anserini information retrieval toolkit. In contrast to most question answering and reading comprehension models today, which operate over small amounts of input text, our system integrates best practices from IR with a BERT-based reader to identify answers from a large corpus of Wikipedia articles in an end-to-end fashion. We report large improvements over previous results on a standard benchmark test collection, showing that fine-tuning pretrained BERT with SQuAD is sufficient to achieve high accuracy in identifying answer spans.

Background B-box (BBX) proteins are important factors involving in the regulation of plant growth and development, and have been identified in many plant species. However, the characteristics and transcription patterns of BBX genes in wild peanut are limited. Results In the present study, we identified and characterized 24 BBX genes in a wild peanut Arachis duranensis. The AdBBX members distributed on 9 of the 10 chromosomes and chromosome 3 contained the most AdBBX members, with 6 AdBBXs. 16 AdBBX proteins had two distinct BBX domains, 11 members contained one CCT domain, and 7 genes had both BBX and CCT domains. Protein structure analysis revealed that AdBBX were classified into five clades: I (3 genes), II (4 genes), III (4 genes), IV (9 genes) and V (4 genes), on the basis of the diversity of conserved BBX and CCT domains. Moreover, 15 distinct motifs were found in these 24 AdBBX proteins and motif 1 and 5 existed in all the AdBBX proteins. Duplication analysis revealed that 4 interchromosomal duplicated gene pairs were obtained and all of them belonged to group IV. In addition, 95 kinds of cis-acting elements were found in the promoter regions of AdBBXs and 53 types were predicted to have putative functions. The numbers and types of cis-acting elements varied in these AdBBX promoters, as a result, AdBBX genes exhibited distinct expression levels in different tissues. The transcription investigation combined with synteny analysis suggested AdBBX8 might be the key factor involving in flowering time regulation in Arachis duranensis. Conclusion Overall, this study provides a genome-wide identification of BBX genes in a wild peanut Arachis duranensis. Characteristic and transcription pattern analysis revealed their critical roles in plant growth and development. Our study will provide essential information for further functional characteristic investigation of AdBBX genes.

The medial preoptic area (mPOA) differs between males and females in nearly all species examined to date, including humans. Here, using fiber photometry recordings of Ca2+ transients in freely behaving mice, we show ramping activities in the mPOA that precede and correlate with sexually dimorphic display of male-typical mounting and female-typical pup retrieval. Strikingly, optogenetic stimulation of the mPOA elicits similar display of mounting and pup retrieval in both males and females. Furthermore, by means of recording, ablation, optogenetic activation, and inhibition, we show mPOA neurons expressing estrogen receptor alpha (Esr1) are essential for the sexually biased display of these behaviors. Together, these results underscore the shared layout of the brain that can mediate sex-specific behaviors in both male and female mice and provide an important functional frame to decode neural mechanisms governing sexually dimorphic behaviors in the future.

Purpose: To evaluate the feasibility and accuracy of magnetic resonance imaging (MRI)-based treatment planning using pseudo CTs generated through atlas registration. Methods: A pseudo CT, providing electron density information for dose calculation, was generated by deforming atlas CT images previously acquired on other patients. The authors tested 4 schemes of synthesizing a pseudo CT from single or multiple deformed atlas images: use of a single arbitrarily selected atlas, arithmetic mean process using 6 atlases, and pattern recognition with Gaussian process (PRGP) using 6 or 12 atlases. The required deformation for atlas CT images was derived from a nonlinear registration of conjugated atlas MR images to that of the patient of interest. The contrasts of atlas MR images were adjusted by histogram matching to reduce the effect of different sets of acquisition parameters. For comparison, the authors also tested a simple scheme assigning the Hounsfield unit of water to the entire patient volume. All pseudo CT generating schemes were applied to 14 patients with common pediatric brain tumors. The image similarity of real patient-specific CT and pseudo CTs constructed by different schemes was compared. Differences in computation times were also calculated. The real CT in the treatment planning system was replaced with the pseudo CT, and the dose distribution was recalculated to determine the difference. Results: The atlas approach generally performed better than assigning a bulk CT number to the entire patient volume. Comparing atlas-based schemes, those using multiple atlases outperformed the single atlas scheme. For multiple atlas schemes, the pseudo CTs were similar to the real CTs (correlation coefficient, 0.787-0.819). The calculated dose distribution was in close agreement with the original dose. Nearly the entire patient volume (98.3%-98.7%) satisfied the criteria of chi-evaluation (<2% maximum dose and 2 mm range). The dose to 95% of the volume and the percentage of volume receiving at least 95% of the prescription dose in the planning target volume differed from the original values by less than 2% of the prescription dose (root-mean-square, RMS < 1%). The PRGP scheme did not perform better than the arithmetic mean process with the same number of atlases. Increasing the number of atlases from 6 to 12 often resulted in improvements, but statistical significance was not always found. Conclusions: MRI-based treatment planning with pseudo CTs generated through atlas registration is feasible for pediatric brain tumor patients. The doses calculated from pseudo CTs agreed well with those from real CTs, showing dosimetric accuracy within 2% for the PTV when multiple atlases were used. The arithmetic mean process may be a reasonable choice over PRGP for the synthesis scheme considering performance and computational costs.

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