RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.

BACKGROUND: As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources. RESULTS: We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs. CONCLUSIONS: RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.

Unearthing old rice germplasm, illuminating a new way to improvement.

Rice germplasm collections contain vast reserves of genetic diversity but remain understudied. This Commentary highlights the effectiveness of mining genetic resources from germplasm as a means to overcome current yield constraints, using clustered-spikelet rice as an example.

SpeedFlower: a comprehensive speed breeding protocol for indica and japonica rice.

To increase rice yields and feed billions of people, it is essential to enhance genetic gains. However, the development of new varieties is hindered by longer generation times and seasonal constraints. To address these limitations, a speed breeding facility has been established and a robust speed breeding protocol, SpeedFlower is developed that allows growing 4-5 generations of indica and/or japonica rice in a year. Our findings reveal that a high red-to-blue (2R > 1B) spectrum ratio, followed by green, yellow and far-red (FR) light, along with a 24-h long day (LD) photoperiod for the initial 15 days of the vegetative phase, facilitated early flowering. This is further enhanced by 10-h short day (SD) photoperiod in the later stage and day and night temperatures of 32/30 °C, along with 65% humidity facilitated early flowering ranging from 52 to 60 days at high light intensity (800 µmol m-2 s-1). Additionally, the use of prematurely harvested seeds and gibberellic acid treatment reduced the maturity duration by 50%. Further, SpeedFlower was validated on a diverse subset of 198 rice accessions from 3K RGP panel encompassing all 12 distinct groups of Oryza sativa L. classes. Our results confirmed that using SpeedFlower one generation can be achieved within 58-71 days resulting in 5.1-6.3 generations per year across the 12 sub-groups. This breakthrough enables us to enhance genetic gain, which could feed half of the world's population dependent on rice.

Deep learning generated lower extremity radiographic measurements are adequate for quick assessment of knee angular alignment and leg length determination.

PURPOSE: Angular and longitudinal deformities of leg alignment create excessive stresses across joints, leading to pain and impaired function. Multiple measurements are used to assess these deformities on anteroposterior (AP) full-length radiographs. An artificial intelligence (AI) software automatically locates anatomical landmarks on AP full-length radiographs and performs 13 measurements to assess knee angular alignment and leg length. The primary aim of this study was to evaluate the agreements in LLD and knee alignment measurements between an AI software and two board-certified radiologists in patients without metal implants. The secondary aim was to assess time savings achieved by AI. METHODS: The measurements assessed in the study were hip-knee-angle (HKA), anatomical-tibiofemoral angle (aTFA), anatomical-mechanical-axis angle (AMA), joint-line-convergence angle (JLCA), mechanical-lateral-proximal-femur-angle (mLPFA), mechanical-lateral-distal-femur-angle (mLDFA), mechanical-medial-proximal-tibia-angle (mMPTA), mechanical-lateral-distal-tibia- angle (mLDTA), femur length, tibia length, full leg length, leg length discrepancy (LLD), and mechanical axis deviation (MAD). These measurements were performed by two radiologists and the AI software on 164 legs. Intraclass-correlation-coefficients (ICC) and Bland-Altman analyses were used to assess the AI's performance. RESULTS: The AI software set incorrect landmarks for 11/164 legs. Excluding these cases, ICCs between the software and radiologists were excellent for 12/13 variables (11/13 with outliers included), and the AI software met performance targets for 11/13 variables (9/13 with outliers included). The mean reading time for the AI algorithm and two readers, respectively, was 38.3, 435.0, and 625.0 s. CONCLUSION: This study demonstrated that, with few exceptions, this AI-based software reliably generated measurements for most variables in the study and provided substantial time savings.

Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome.

Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.

Development of a phenotyping protocol for combined drought and salinity stress at seedling stage in rice.

Introduction: The case of combined drought and salinity stress is increasingly becoming a constraint to rice production, especially in coastal areas and river deltas where low rainfall not only reduces soil moisture levels but also reduces the flow of river water, resulting in intrusion of saline sea-water. A standardized screening method is needed in order to systematically evaluate rice cultivars under combined drought+salinity at the same time because sequential stress of salinity followed by drought or vice-versa is not similar to simultaneous stress effects. Therefore, we aimed to develop a screening protocol for combined drought+salinity stress applied to soil-grown plants at seedling stage. Methods: The study system used 30-L soil-filled boxes, which allowed a comparison of plant growth under control conditions, individual drought and salinity stress, as well as combined drought+salinity. A set of salinity tolerant and drought tolerant cultivars were tested, together with several popular but salinity and drought-susceptible varieties that are grown in regions prone to combined drought+salinity. A range of treatments were tested including different timings of the drought and salinity application, and different severities of stress, in order to determine the most effective that resulted in visible distinction among cultivars. The challenges related to determining a protocol with repeatable seedling stage stress treatment effects while achieving a uniform plant stand are described here. Results: The optimized protocol simultaneously applied both stresses by planting into saline soil at 75% of field capacity which was then allowed to undergo progressive drydown. Meanwhile, physiological characterization revealed that chlorophyll fluorescence at seedling stage correlated well with grain yield when drought stress was applied to vegetative stage only. Discussion: The drought+salinity protocol developed here can be used for screening rice breeding populations as part of a pipeline to develop new rice varieties with improved adaptation to combined stresses.

Natural variation of OsML1, a mitochondrial transcription termination factor, contributes to mesocotyl length variation in rice.

Mesocotyl length (ML) is a crucial factor in determining the establishment and yield of rice planted through dry direct seeding, a practice that is increasingly popular in rice production worldwide. ML is determined by the endogenous and external environments, and inherits as a complex trait. To date, only a few genes have been cloned, and the mechanisms underlying mesocotyl elongation remain largely unknown. Here, through a genome-wide association study using sequenced germplasm, we reveal that natural allelic variations in a mitochondrial transcription termination factor, OsML1, predominantly determined the natural variation of ML in rice. Natural variants in the coding regions of OsML1 resulted in five major haplotypes with a clear differentiation between subspecies and subpopulations in cultivated rice. The much-reduced genetic diversity of cultivated rice compared to the common wild rice suggested that OsML1 underwent selection during domestication. Transgenic experiments and molecular analysis demonstrated that OsML1 contributes to ML by influencing cell elongation primarily determined by H2 O2 homeostasis. Overexpression of OsML1 promoted mesocotyl elongation and thus improved the emergence rate under deep direct seeding. Taken together, our results suggested that OsML1 is a key positive regulator of ML, and is useful in developing varieties for deep direct seeding by conventional and transgenic approaches.

Duration of Symptoms Does Not Significantly Influence Short-term Outcomes for Patients Undergoing Periacetabular Osteotomy.

Factors influencing the clinical outcomes after periacetabular osteotomy (PAO) have not been well explored. This study evaluated the influence of symptom duration in developmental dysplasia of the hip on short-term patient-reported outcomes after PAO. A retrospective review of prospectively collected data identified PAOs performed on 139 patients. Sixty-five patients were then stratified into two groups based on preoperative symptom duration: 2 years or less (n=22) vs more than 2 years (n=43). We compared the results of hip-specific patient-reported outcome surveys collected preoperatively and postoperatively. When comparing the two groups, we found no significant differences in clinical outcome scores except for the UCLA Activity Scale. The shorter duration group achieved improvement 6 months postoperatively on the visual analog scale average pain score (from 4.5 to 2.167; P=.0017), International Hip Outcome Tool-12 (from 42.95 to 59.19; P=.0176), and Harris Hip Score (from 53.88 to 69.88; P=.049). The longer duration group also achieved postoperative improvement across multiple surveys. Nevertheless, a multivariate analysis controlling for age, sex, and body mass index and found that symptom duration did not independently affect the change in clinical outcomes. Although PAO leads to improvements in functional status and pain, preoperative symptom duration does not significantly affect these clinical outcomes. [Orthopedics. 2023;46(6):365-372.].

Lost genome segments associate with trait diversity during rice domestication.

BACKGROUND: DNA mutations of diverse types provide the raw material required for phenotypic variation and evolution. In the case of crop species, previous research aimed to elucidate the changing patterns of repetitive sequences, single-nucleotide polymorphisms (SNPs), and small InDels during domestication to explain morphological evolution and adaptation to different environments. Additionally, structural variations (SVs) encompassing larger stretches of DNA are more likely to alter gene expression levels leading to phenotypic variation affecting plant phenotypes and stress resistance. Previous studies on SVs in rice were hampered by reliance on short-read sequencing limiting the quantity and quality of SV identification, while SV data are currently only available for cultivated rice, with wild rice largely uncharacterized. Here, we generated two genome assemblies for O. rufipogon using long-read sequencing and provide insights on the evolutionary pattern and effect of SVs on morphological traits during rice domestication. RESULTS: In this study, we identified 318,589 SVs in cultivated and wild rice populations through a comprehensive analysis of 13 high-quality rice genomes and found that wild rice genomes contain 49% of unique SVs and an average of 1.76% of genes were lost during rice domestication. These SVs were further genotyped for 649 rice accessions, their evolutionary pattern during rice domestication and potential association with the diversity of important agronomic traits were examined. Genome-wide association studies between these SVs and nine agronomic traits identified 413 candidate causal variants, which together affect 361 genes. An 824-bp deletion in japonica rice, which encodes a serine carboxypeptidase family protein, is shown to be associated with grain length. CONCLUSIONS: We provide relatively accurate and complete SV datasets for cultivated and wild rice accessions, especially in TE-rich regions, by comparing long-read sequencing data for 13 representative varieties. The integrated rice SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in rice.

Unraveling the genetics underlying micronutrient signatures of diversity panel present in brown rice through genome-ionome linkages.

Rice (Oryza sativa) is an important staple crop to address the Hidden Hunger problem not only in Asia but also in Africa where rice is fast becoming an important source of calories. The brown rice (whole grain with bran) is known to be more nutritious due to elevated mineral composition. The genetics underlying brown rice ionome (sum total of such mineral composition) remains largely unexplored. Hence, we conducted a comprehensive study to dissect the genetic architecture of the brown rice ionome. We used genome-wide association studies, gene set analysis, and targeted association analysis for 12 micronutrients in the brown rice grains. A diverse panel of 300 resequenced indica accessions, with more than 1.02 million single nucleotide polymorphisms, was used. We identified 109 candidate genes with 5-20% phenotypic variation explained for the 12 micronutrients and identified epistatic interactions with multiple micronutrients. Pooling all candidate genes per micronutrient exhibited phenotypic variation explained values ranging from 11% to almost 40%. The key donor lines with larger concentrations for most of the micronutrients possessed superior alleles, which were absent in the breeding lines. Through gene regulatory networks we identified enriched functional pathways for central regulators that were detected as key candidate genes through genome-wide association studies. This study provided important insights on the ionome variations in rice, on the genetic basis of the genome-ionome relationships and on the molecular mechanisms underlying micronutrient signatures.

CRISPR-mediated promoter editing of a cis-regulatory element of OsNAS2 increases Zn uptake/translocation and plant yield in rice.

Developing nutritious rice with a higher yield is one approach to alleviating the problem of micronutrient deficiency in developing countries, especially human malnutrition involving zinc and iron (Fe) deficiency, and achieving better adoption. The transport of micronutrients such as Fe and Zn is mainly regulated via the nicotianamine synthase (OsNAS) gene family, whereas yield is a complex trait that involves multiple loci. Genome editing via CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9, focusing on the OsNAS2 promoter, particularly the deletion of the cis-regulatory element ARR1AT at position -933, was conducted for an enhanced accumulation of Zn in the grain and per plant. The results showed that our promoter editing increased Zn concentration per plant. Evidence also showed that an improved spikelet number per main panicle led to increased grain per plant. The traits were inherited in "transgene-free" and homozygous plant progenies. Further investigation needs to be conducted to validate trait performance under field conditions and elucidate the cause of the spikelet increase.

Artificial intelligence-generated hip radiological measurements are fast and adequate for reliable assessment of hip dysplasia : an external validation study.

AIMS: Hip dysplasia (HD) leads to premature osteoarthritis. Timely detection and correction of HD has been shown to improve pain, functional status, and hip longevity. Several time-consuming radiological measurements are currently used to confirm HD. An artificial intelligence (AI) software named HIPPO automatically locates anatomical landmarks on anteroposterior pelvis radiographs and performs the needed measurements. The primary aim of this study was to assess the reliability of this tool as compared to multi-reader evaluation in clinically proven cases of adult HD. The secondary aims were to assess the time savings achieved and evaluate inter-reader assessment. METHODS: A consecutive preoperative sample of 130 HD patients (256 hips) was used. This cohort included 82.3% females (n = 107) and 17.7% males (n = 23) with median patient age of 28.6 years (interquartile range (IQR) 22.5 to 37.2). Three trained readers' measurements were compared to AI outputs of lateral centre-edge angle (LCEA), caput-collum-diaphyseal (CCD) angle, pelvic obliquity, Tönnis angle, Sharp's angle, and femoral head coverage. Intraclass correlation coefficients (ICC) and Bland-Altman analyses were obtained. RESULTS: Among 256 hips with AI outputs, all six hip AI measurements were successfully obtained. The AI-reader correlations were generally good (ICC 0.60 to 0.74) to excellent (ICC > 0.75). There was lower agreement for CCD angle measurement. Most widely used measurements for HD diagnosis (LCEA and Tönnis angle) demonstrated good to excellent inter-method reliability (ICC 0.71 to 0.86 and 0.82 to 0.90, respectively). The median reading time for the three readers and AI was 212 (IQR 197 to 230), 131 (IQR 126 to 147), 734 (IQR 690 to 786), and 41 (IQR 38 to 44) seconds, respectively. CONCLUSION: This study showed that AI-based software demonstrated reliable radiological assessment of patients with HD with significant interpretation-related time savings.Cite this article: Bone Jt Open 2022;3(11):877-884.

Does surgery change pelvic tilt? : an investigation in patients with osteoarthritis of the hip, dysplasia, and femoroacetabular impingement.

AIMS: Pelvic tilt is believed to affect the symptomology of osteoarthritis (OA) of the hip by alterations in joint movement, dysplasia of the hip by modification of acetabular cover, and femoroacetabular impingement by influencing the impingement-free range of motion. While the apparent role of pelvic tilt in hip pathology has been reported, the exact effects of many forms of treatment on pelvic tilt are unknown. The primary aim of this study was to investigate the effects of surgery on pelvic tilt in these three groups of patients. METHODS: The demographic, radiological, and outcome data for all patients operated on by the senior author between October 2016 and January 2020 were identified from a prospective registry, and all those who underwent surgery with a primary diagnosis of OA, dysplasia, or femoroacetabular impingement were considered for inclusion. Pelvic tilt was assessed on anteroposterior (AP) standing radiographs using the pre- and postoperative pubic symphysis to sacroiliac joint (PS-SI) distance, and the outcomes were assessed with the Hip Outcome Score (HOS), International Hip Outcome Tool (iHOT-12), and Harris Hip Score (HHS). RESULTS: The linear regression model revealed a significant negative predictive association between the standing pre- and postoperative PS-SI distances for all three groups of patients (all p < 0.001). There was a significant improvement in all three outcome measures between the pre- and postoperative values (p < 0.05). CONCLUSION: There is a statistically significant decrease in pelvic tilt after surgery in patients with OA of the hip, dysplasia, and femoroacetabular impingement. These results confirm that surgery significantly alters the pelvic orientation. Pelvic tilt significantly decreased after total hip arthroplasty, periacetabular osteotomy, and arthroscopy/surgical hip dislocation. The impact of surgery on pelvic tilt should be considered within the therapeutic plan in order to optimize pelvic orientation in these patients.Cite this article: Bone Joint J 2022;104-B(9):1025-1031.

Know your way around acute unenhanced CT during global iodinated contrast crisis: a refresher to ED radiologists.

Due to a contrast shortage crisis resulting from the decreased supply of iodinated contrast agents, the American College of Radiology (ACR) has issued a guidance statement followed by memoranda from various hospitals to preserve and prioritize the limited supply of contrast. The vast majority of iodinated contrast is used by CT, with a minority used by vascular and intervention radiology, fluoroscopy, and other services. A direct consequence is a paradigm shift to large volume unenhanced CT scans being utilized for acute and post traumatic patients in EDs, an uncharted territory for most radiologists and trainees. This article provides radiological diagnostic guidance and a pictorial example through systematic review of common unenhanced CT findings in the acute setting.

Image quality improvement and motion degradation reduction in shoulder MR imaging: comparison of BLADE and rectilinear techniques at 3-Tesla scanning.

OBJECTIVE: MR imaging of joints, particularly shoulder, requires a high degree of spatial resolution to ascertain anatomy and pathology. Unfortunately, motion artifacts can reduce the clinical quality of the examinations. BLADE sequence reduces motion degradation improving overall diagnostic imaging quality. The objective was to compare standard, rectilinear k-space coverage turbo spin echo (TSE), and BLADE sequences. MATERIAL AND METHODS: Over a 4-month period, fifty-seven consecutive patients (22 males, 35 females; mean age: 48.5 years, range: 23-64 years) were scanned using traditional intermediate-weighted spin echo and BLADE sequences. Qualitative evaluation was performed by three musculoskeletal fellowship trained radiologists, each with more than 5 years of experience. Image sequences were evaluated using a Likert scale for each of the following five categories: motion degradation, ghosting/phase misregistration artifacts, star/radial encoding artifacts, fat suppression quality, and overall diagnostic quality. Additionally, image sequences were evaluated for signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) using manually drawn regions of interest (ROI) analysis. RESULTS: Ghosting and phase artifacts were lower within BLADE sequence while streak artifacts were higher (p < 0.001). Image fat suppression, tendon and labral appearances, and the overall SNR and CNR were comparable on both sequences (p > 0.05). CONCLUSION: Addition of BLADE reduces motion degradation and improves overall diagnostic imaging quality. Application of BLADE in patient scans suspected of motion artifacts can reduce the frequency of repeat imaging in patients with claustrophobia or those where motion is a concern. By reducing overall imaging time and call backs, it could reduce the cost burden to patients and healthcare system.

Functional outcomes are preserved in adult acetabular dysplasia with radiographic evidence of lumbosacral spine anomalies: an investigation in hip-spine syndrome.

PURPOSE: Acetabular dysplasia (AD) is a debilitating condition which results in impaired hip function, leading to hip-spine syndrome with anomalies identifiable on plain radiographs. However, no study to date has investigated the association between radiographic spine anomalies and functional outcomes in AD. We hypothesize that AD patients with radiographic evidence of lumbar spine anomalies are associated with decreased function in comparison to those without such radiographic findings. PATIENTS AND METHODS: One hundred thirty-five hips underwent a full four-view hip radiograph series, and two observers analyzed hip and spine variables using standard radiographs and obtained Castellvi grade, assessment of spondylolisthesis, and L4-S1 interpedicular distance. A comprehensive hip questionnaire was administered which included Harris Hip Score (HHS) and Hip Disability and Osteoarthritis Outcome Score (HOOS) to assess patient function. Correlations between HHS and HOOS and radiographic spinal measurements were calculated, and p-values were corrected for multiple comparison using the Holm's method. RESULTS: Out of 135 patients, 119 were female (88.1%) and 16 were male (11.9%). Average age of presentation was 34.2 years, and average BMI was 26. There was no statistically significant correlation between Castellvi grade, presence of spondylolisthesis, or L4-S1 interpedicular distance and the patient-reported outcome measures HHS or HOOS. Conversely, a significant correlation was observed between Femoro-Epiphyseal Acetabular Roof (FEAR) index and HOOS of the contralateral hip (correlation coefficient = 0.38, adjusted p = 0.03) and Tönnis angle of AD severity and HHS of the contralateral hip (correlation coefficient = - 0.33, adjusted p = 0.04). CONCLUSION: Severity of spinal anomalies measured by Castellvi grade and spondylolisthesis in patients with AD was not associated with decreased patient function in the ipsilateral diseased hip. To our knowledge, this is the first study to date to report the relationship between radiographically identifiable lumbosacral abnormalities and hip function in AD.

Does Preoperative Activity Level Affect Postoperative Outcomes Following Total Hip Arthroplasty?

BACKGROUND: Many patients electing to undergo total hip arthroplasty (THA) value continuing active lifestyles when considering treatment options. Addressing these concerns requires evaluating the effect of preoperative activity level on patient-reported outcomes and improvement following THA. METHODS: Three hundred thirty-five patients (368 hips) who underwent THA with a minimum 6-month (mean 533 ± 271 days) follow-up completed preoperative and postoperative University of California, Los Angeles (UCLA) activity score along with various patient-reported measures of function, pain, and mental state. Preoperative UCLA score divided patients into inactive, mild, and active groups. Analysis of covariance controlling for age, sex, body mass index, surgical approach, implant, bilateral cases, conversions, and follow-up time evaluated differences among groups for postoperative outcomes with subsequent Tukey-Kramer pairwise comparisons. RESULTS: Mildly active patients (73:139 male:female) had better postoperative outcomes than inactive patients (40:70 male:female) for UCLA score, EuroQol Visual Analog Scale (EQVAS), Hip Outcome Score (HOS), 12-item Short-Form (SF-12) Physical, and Visual Analog Pain Scale (average/now/worst) (P values <0.001/<0.001/<0.001/<0.001/0.003/<0.001/<0.001). Active patients (32:14 male:female) had better postoperative outcomes than inactive patients for UCLA score, EQVAS, HOS, SF-12 Physical, and Visual Analog Pain Scale Worst (P values <0.001/0.024/0.001/0.001/0.017). No postoperative outcome differences existed between active and mild patients. Inactive patients displayed greater outcome improvements than mildly active patients for UCLA score, Harris Hip Score, and International Hip Outcome Tool (P values <0.001/<0.001/0.013) and active patients for UCLA score, EQVAS, HOS, International Hip Outcome Tool, and SF-12 Physical (P values <0.001/0.008/0.013/0.022/0.004). CONCLUSIONS: Inactive patients achieve greater measure improvements following THA. Active patients achieve better absolute outcomes than inactive patients; however, increasing activity levels do not incrementally improve patient-reported outcome measures. Patients similarly improve pain and mental health regardless of activity level.

Genome-wide selection and introgression of Chinese rice varieties during breeding.

China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China (400) and other regions in Asia (670). Among the six major rice groups (aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroups developed during different phases of rice breeding. The genomic segments underlying the differences between these subgroups span 36.32 Mb. The Chinese japonica rice varieties fall into the temperate japonica group, consisting of two subgroups based on their geographical distribution. The genomic segments underlying the differences between these subgroups span 27.69 Mb. These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width. Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups. These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.

Deep Learning-Based Abdominal Muscle Segmentation on CT Images of Surgical Patient Populations.

Computed tomography (CT) is commonly used for the characterization and tracking of abdominal muscle mass in surgical patients for both pre-surgical outcome predictions and post-surgical monitoring of response to therapy. In order to accurately track changes of abdominal muscle mass, radiologists must manually segment CT slices of patients, a time-consuming task with potential for variability. In this work, we combined a fully convolutional neural network (CNN) with high levels of preprocessing to improve segmentation quality. We utilized a CNN based approach to remove patients' arms and fat from each slice and then applied a series of registrations with a diverse set of abdominal muscle segmentations to identify a best fit mask. Using this best fit mask, we were able to remove many parts of the abdominal cavity, such as the liver, kidneys, and intestines. This preprocessing was able to achieve a mean Dice similarity coefficient (DSC) of 0.53 on our validation set and 0.50 on our test set by only using traditional computer vision techniques and no artificial intelligence. The preprocessed images were then fed into a similar CNN previously presented in a hybrid computer vision-artificial intelligence approach and was able to achieve a mean DSC of 0.94 on testing data. The preprocessing and deep learning-based method is able to accurately segment and quantify abdominal muscle mass on CT images.