Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems.

Rice (Oryza sativa) was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

What does degeneration at the cervicothoracic junction tell us? A kinematic MRI study of 93 individuals.

PURPOSE: Current decision-making in multilevel cervical fusion weighs the potential to protect adjacent levels and reduce reoperation risk by crossing the cervicothoracic junction (C7/T1) against increased operative time and risk of complication. Careful planning is required, and the planned distal and adjacent levels should be assessed for degenerative disc disease (DDD). This study assessed whether DDD at the cervicothoracic junction was associated with DDD, disc height, translational motion, or angular variation in the adjacent superior (C6/C7) or inferior (T1/T2) levels. METHODS: This study retrospectively analyzed 93 cases with kinematic MRI. Cases were randomly selected from a database with inclusion criteria being no prior spine surgery and images having sufficient quality for analysis. DDD was assessed using Pfirrmann classification. Vertebral body bone marrow lesions were assessed using Modic changes. Disc height was measured at the mid-disc in neutral and extension. Translational motion and angular variation were calculated by assessing translational or angular motion segment integrity respectively in flexion and extension. Statistical associations were assessed with scatterplots and Kendall's tau. RESULTS: DDD at C7/T1 was positively associated with DDD at C6/C7 (tau = 0.53, p < 0.01) and T1/T2 (tau = 0.58, p < 0.01), with greater disc height in neutral position at T1/T2 (tau = 0.22, p < 0.01), and with greater disc height in extended position at C7/T1 (tau = 0.17, p = 0.04) and at T1/T2 (tau = 0.21, p < 0.01). DDD at C7/T1 was negatively associated with angular variation at C6/C7 (tau = - 0.23, p < 0.01). No association was appreciated between DDD at C7/T1 and translational motion. CONCLUSION: The association of DDD at the cervicothoracic junction with DDD at the adjacent levels emphasizes the necessity for careful selection of the distal level in multilevel fusion in the distal cervical spine.

Impact of chronic hyperlipidemia on perioperative complications in patients undergoing lumbar fusion: a propensity score matching analysis.

PURPOSE: Lumbar fusion is widely used to treat degenerative and traumatic conditions of the spine, with various perioperative complications. This study compared lumbar fusion complications in patients with and without chronic hyperlipidemia. METHODS: Using the MSpine division of the PearlDiver database, patients with or without chronic hyperlipidemia who underwent lumbar fusions were identified. The appropriate Current Procedural Terminology (CPT) codes identified patients with single- or multi-level lumbar spinal fusion surgeries. International Classification of Diseases (ICD-9 and ICD-10) codes identified patients with chronic hyperlipidemia. The surgical and medical complications were obtained utilizing the appropriate ICD-9, ICD-10, and CPT codes. Propensity score matching analysis was used to control for confounding factors. Chi-square test was applied to compare the incidence of complications among different groups. RESULTS: In single-level fusion group, patients with hyperlipidemia had a higher incidence of wound complications (P < 0.001), surgical site infection (P < 0.001), failed back syndrome (P < 0.001), hardware removal (P < 0.001), deep venous thrombosis/pulmonary embolism (P = 0.031), myocardial infarction (P < 0.001) cerebrovascular accident (P < 0.001), renal failure (P < 0.001), sepsis (P < 0.001), and urinary tract infection/incontinence (P < 0.001). In multi-level fusion group, patients with hyperlipidemia had a higher incidence of nerve root injury (P = 0.034), wound complications (P < 0.001), surgical site infection (P < 0.001), failed back syndrome (P < 0.001), hardware removal (P < 0.001), revision (P = 0.002), myocardial infarction (P < 0.001), renal failure (P < 0.001), and urinary tract infection/incontinence (P < 0.001). CONCLUSION: Following lumbar fusion, patients with chronic hyperlipidemia have an increased risk of perioperative complications, including wound complications, surgical site infection, failed back surgery syndrome, hardware removal, myocardial infarction, renal failure, and urinary tract infection/incontinence.

Onset of mental disorders in patients who developed failed back surgery syndrome.

PURPOSE: Failed back surgery syndrome (FBSS) is a complex and multifaceted condition associated with significant disability and morbidity. The purpose of this study was to investigate the association between FBSS with new incidences of mental health disorders. METHODS: Our cohort included patients diagnosed with FBSS within 12 months of a posterior fusion, laminectomy, or discectomy, identified using The International Classification of Disease, both Ninth and Tenth Revisions (ICD-9 and ICD-10). In the next step, both non-FBSS and FBSS-diagnosed patients were queried for the diagnosis of first-time occurrence of mental health disorders. The incidence of new mental health disorders was determined within 12-months following FBSS diagnosis. RESULTS: FBSS patients were significantly at greater risk than non-FBSS patients of developing all included mental health pathologies: Depression: OR 1.9, 95% CI 1.8-2.0, p < 0.0001); Anxiety: OR 1.5, 95% CI 1.4-1.6, p < 0.0001; Sleep Disorder: OR 1.9, 95% CI 1.7-2.0, p < 0.0001; Bipolar Disorder: OR 1.7, 95% CI 1.5-2.0 p < 0.0001; PTSD: OR 1.5, 95% CI 1.3-1.8, p < 0.0001; Panic Disorder: OR 1.8, 95% CI 1.5-2.1, p < 0.0001; Suicidal Disorder: OR 1.7 95% CI 1.4-2.0, p < 0.0001, ADHD: OR 1.3, 95% CI 1.0-1.5, p = 0.0367. CONCLUSIONS: In the current study, patients diagnosed with FBSS were at a significantly greater risk of developing mental health pathologies. While other studies have suggested pre-surgical psychological support and treatment, the current results suggest that a post-operative psychologic care may also be warranted. By identifying potential psychosocial unforeseen obstacles that occur in patients diagnosed with FBSS, more precise treatment pathways can be developed leading to improved patient outcomes.

Trends and patterns of cervical degenerative disc disease: an analysis of magnetic resonance imaging of 1300 symptomatic patients.

PURPOSE: To evaluate the trends and patterns of cervical degenerative disc disease in the cervical spine in different age groups of symptomatic patients. METHODS: Overall, 1300 symptomatic patients who had undergone cervical spine MRI from February 2019 to November 2021 were included. Pfirrmann grading was used to evaluate the IVD degeneration. Patients were divided into five groups based on age: group 1 from 20 to 29 years, group 2 from 30 to 39 years, group 3 from 40 to 49 years, group 4 from 50 to 59 years, and group 5 from 60 years and above. The patterns, severity, and the number of degenerated levels in each age group were analysed. RESULTS: The total number of degenerated IVDs (grades IV and V) increased significantly with age, ranging from 76 (4.9%) in group 1 to 677 (43.4%) in group 5. The most common degenerated levels were C2/3 (25% of the total degenerated levels) in group 1, C5/6 (29.0%) in group 2, C5/6 (33.1%) in group 3, C5/6 (31.3%) in group 4, C5/6 (24.8%), in group 5. The number of degenerated IVDs increased significantly with age (P < 0.001). In patients with two or more degenerated levels, contiguous-level disc degeneration was more common than skip lesions. CONCLUSION: This study evaluated the severity and pattern of cervical disc degeneration at each level in different age groups. The severity and number of degenerated levels increased significantly with increased age. Adjacent-level degeneration is more common than skip lesions in patients with more than one-level degeneration.

Comparison of Surgical Outcomes Between Anterior and Posterior Cervical Fusions Stratified by Levels Decompressed.

STUDY DESIGN: Retrospective database study. OBJECTIVE: To compare outcomes between 1-, 2-, 3-, and 4- level anterior cervical discectomy and fusions (ACDF) and posterior cervical fusions (PCF) procedures using a national database. SUMMARY OF BACKGROUND DATA: Surgical outcomes involving 3- or 4-level ACDF and PCF cases are not well-described. As there are situations where both ACDF and PCF can be employed, it is important to compare the risks and benefits of both procedures. MATERIALS AND METHODS: Patients who underwent ACDF or PCF between 2010 and 2020 were identified in PearlDiver using current procedural terminology codes. Surgeries done for infectious, traumatic, or neoplastic etiologies were excluded. 2-year reoperations and 90-day readmissions were queried. Surgical complications and transfusions were compiled using ICD-9/10 billing codes. ACDF and PCF procedures were then matched by age, sex, Charlson Comorbidity Index, and a number of levels fused, and the above outcomes were compared. RESULTS: In all, 31,301 PCFs and 110,526 ACDFs were identified. After matching for age, sex, and Charlson Comorbidity Index, a total of 30,353 ACDF and PCF procedures were compared. Three-level and 4-level PCFs had higher rates of 90-day postoperative surgical complications compared with ACDF (OR=2.4 and 2.87, respectively; P <0.001). In addition, higher rates of 90-day readmissions were noted in 3-level PCF compared with 3-level ACDF (OR=1.24, P <0.001). Ninety-day postoperative transfusions were higher in both 3- and 4-level PCFs (OR=2.44 and 18.27, respectively; P <0.001). Two-year reoperations rates were higher for 3-level PCF procedures than 3-level ACDF (OR=1.22; P =0.01). CONCLUSIONS: Patients who underwent 3-4-level ACDF had lower rates of readmission, blood transfusions, and postoperative complications compared with 3-4-level PCF. This data suggests that in cases of 3-4-level pathology with clinical equipoise regarding approach, ACDF may be associated with less short-term morbidity, however, data on fusion rates and adjacent level disease are needed.

Association of Hyperlipidemia With Perioperative Complications in Posterior Cervical Spine Fusion: A Comparative Retrospective Study.

STUDY DESIGN: A retrospective database study. OBJECTIVES: The purpose of the current study was to investigate the impact of hyperlipidemia (HLD) on the incidence of perioperative complications associated with posterior cervical spine fusion (PCF). BACKGROUND: HLD is a very common disease that leads to atherosclerosis. Therefore, it can cause fatal diseases as well as lifestyle-related diseases. The possible impact of HLD on outcomes after PCF has not yet been investigated. METHODS: Patients with cervical degeneration underwent initial PCF from 2010 through the third quarter of 2020 using the MSpine subset of the PearlDiver Patient Record Database. The incidence of perioperative complications was queried using relevant ICD-9, 10, and CPT codes. χ 2 analysis was performed in age-, sex-, and Charlson Comorbidity Index (CCI)-matched populations to compare between non-HLD and HLD patients in each single-level and multilevel PCF. RESULTS: Through propensity score matching, 1600 patients each in the HLD and non-HLD groups were analyzed in the single-level PCF, 6855 patients were analyzed in the multilevel PCF were analyzed. The comorbidity of HLD significantly decreased the incidence of respiratory failure in single-level PCF (OR=0.58, P <0.01). In the multilevel PCF, the presence of HLD increased the incidence of cervicalgia (OR=1.26, P =0.030). On the contrary, the incident of spinal cord injury (OR=0.72, P <0.01), dysphagia (OR=0.81, P =0.023), respiratory failure (OR=0.85, P =0.030), pneumonia (OR=0.70, P =0.045), neurological bladder (OR=0.84, P =0.041), and urinary tract infection (OR=0.85, P =0.021) in the HLD group were significantly lower than those in non-HLD group. CONCLUSIONS: In the current study, the presence of HLD significantly increased the incidence of postoperative cervicalgia in multilevel PCF. On the other hand, the incidence of some complications was significantly decreased with HLD. Further studies are needed taking into account other factors such as the treatment of HLD, its efficacy, and intraoperative events. LEVEL OF EVIDENCE: Level III.

The Effect of Hyperlipidemia as a Risk Factor on Postoperative Complications in Patients Undergoing Anterior Cervical Discectomy and Fusion.

STUDY DESIGN: Retrospective cohort study. OBJECTIVE: To analyze the effect of hyperlipidemia (HLD) on postoperative complications in patients who underwent anterior cervical discectomy and fusion (ACDF). SUMMARY OF BACKGROUND DATA: ACDF represents the standard procedure performed for focal anterior nerve root or spinal cord compression with low complication rates. HLD is well known as a risk factor for major complications after vascular and transplant surgery, and orthopedic surgery. To date, there have been no studies on HLD as a risk factor for cervical spine surgery. PATIENTS AND METHODS: Patients who underwent ACDF from 2010 through quarter 3 of 2020 were enrolled using the MSpine subset of the PearlDiver Patient Record Database. The patients were divided into single-level ACDF and multilevel ACDF groups. In addition, each group was divided into subgroups according to the presence or absence of HLD. The incidence of surgical and medical complications was queried using relevant International Classification of Disease and Current Procedural Terminology codes. Charlson Comorbidity Index was used as a broad measure of comorbidity. χ 2 analysis, with populations matched for age, sex, and Charlson Comorbidity Index, was performed. RESULTS: A total of 24,936 patients who underwent single-level ACDF and 26,921 patients who underwent multilevel ACDF were included. In the multilevel ACDF group, wound complications were significantly higher in the patients with HLD. Among medical complications, myocardial infarction, renal failure, and urinary tract infection/urinary incontinence were significantly higher in the patients with HLD in both groups. Revision surgery and readmission were significantly higher in the patients with HLD who underwent multilevel ACDF. CONCLUSIONS: In patients who underwent ACDF, several surgical and medical complications were found to be higher in patients with HLD than in patients without HLD. Preoperative serum lipid concentration levels and management of HLD should be considered during preoperative planning to prevent postoperative complications in patients undergoing ACDF.

Evaluating Changes to the Modified K-Line Using Kinematic MRIs.

STUDY DESIGN: Retrospective cross-sectional review of a large database. OBJECTIVE: Little is known regarding extension K-lines for treatment of cervical myelopathy. Therefore, this study seeks to examine differences between K-lines drawn in neutral and extension. SUMMARY OF BACKGROUND DATA: The modified K-line is a radiological tool used in surgical planning of the cervical spine. As posterior cervical decompression and fusion often results in patients being fused in a more lordotic position than the preoperative neutral radiograph, a K-line measured in the extension position may offer better utility for these patients. MATERIALS AND METHODS: Total of 97 patients were selected with T2-weighted, upright cervical magnetic resonance imaging taken in neutral and extension. For each patient, the K-line was drawn at the mid-sagittal position for both neutral and extension. The distance from the most posterior portion of each disk (between C2 and C7) to the K-line was measured in neutral and extension and the difference was calculated. Paired t test was used to assess significant differences. RESULTS: Across all levels between C2 and C7 there was an increase in the distance between the dorsal aspect of the disk and K-line when comparing neutral and extension radiographs. The average change in difference (extension minus neutral) at each cervical spinal level was 0.9 mm (C2-C3), 2.5 mm (C3-C4), 2.6 mm (C4-C5), 2.0 mm (C5-C6), and 0.9 mm (C6-C7). A paired t test showed that the K-line increase from neutral to extension was statistically significant across all disk levels ( P <0.001). CONCLUSION: When positioned in extension, patients experience a significant increase in distance from the dorsal aspect of a disk to the K-line compared to when positioned in neutral, especially between C3 and C6. This is clinically relevant for surgeons considering a posterior cervical decompression and fusion in patients with a negative modified K-line on preoperative magnetic resonance imaging, as these patients may have enough cervical cord drift back when fused in an extended position, maximizing likelihood of improving postoperative DSM functional outcomes.

Use of graft materials and biologics in spine deformity surgery: a state-of-the-art review.

PURPOSE: The aim of the current review is to summarize the current evidence on graft materials used in fusion procedures for spinal deformity corrections. METHODS: PubMed, Embase, and Cochrane Library were searched for relevant published observational studies and clinical trials using osteobiologics and biomaterials in spinal deformity surgery. RESULTS: The use of autograft in deformity correction surgeries has been reported in a limited number of studies, with the harvest sites including iliac crest, ribs, and local bone. Various allografts and biologics have been used in the treatment of spinal deformities including idiopathic and degenerative scoliosis, either as stand alone or in combination with autograft. Limited number of studies reported no differences in fusion rates or outcomes. Use of rh-BMP2 in anterior, posterior or front/back approaches showed higher fusion rates than other graft materials in patients with spinal deformities. Due to the limited number of quality studies included in the review, as well as alternative factors, such as costs, availability, and surgeon expertise/preference, no definitive conclusion or recommendations can be made as to the ideal graft choice in spinal deformity surgery. CONCLUSIONS: Most commonly used grafts included autograft, allograft and rh-BMP2, with new biologics and biomaterials constantly emerging in the market. Limited number of high-quality comparative studies and heterogeneity in study design prevented direct comparisons that can lead to meaningful recommendations. Further studies are needed to prove superiority of any single graft material and/or biologic that is also cost-effective and safe.

Postoperative Complication Rates After One-Level Cervical Spine Surgery in Patients with Parkinson Disease: A Database Study.

OBJECTIVE: Parkinson disease (PD) is a risk factor for worse surgical outcomes. The degree to which PD affects outcomes in cervical spine surgery is not well understood. Therefore, we characterize rates of postoperative complications among patients with PD who undergo cervical spine surgery. METHODS: Using the PearlDiver database, we identified patients who underwent 1-level anterior cervical discectomy and fusion (ACDF), posterior cervical fusion (PCF), or discectomy/decompression with concomitant PD between 2011 and 2019. Patients with PD who underwent surgery and had 1 year follow-up were included. Complications 30, 60, and 90 days after surgery were identified and aggregated into body systems (e.g., respiratory and gastrointestinal). Comparison controls without concomitant PD who received cervical spine (C-spine) surgery were matched for age, sex, and comorbidities. RESULTS: A total of 259,443 ACDFs, 30,929 PCFs, and 29,563 decompressions were identified. Of these procedures, 1117 were performed on patients with PD (0.35%). The highest 90-day complications rates in patients with PD were pulmonary and gastrointestinal related (6.05%) in those who received ACDF, neuro related (8.51%) in those who received PCF, and genitourinary related (8.76%) in those who received a decompression. Compared with patients without PD, postoperative complications rates were similar and not significantly different. CONCLUSIONS: Patients with PD who receive ACDF have higher rates of pulmonary (6.05%), neurologic (5.24%), and psychiatric (3.23%) complications at 90 days. The differences did not reach statistical significance. This finding suggests that patients with PD do not experience higher rates of acute postoperative complications when undergoing 1-level cervical spine surgery.

The Incidence of Double Crush Syndrome in Surgically Treated Patients.

STUDY DESIGN: Retrospective Cohort Study. OBJECTIVES: Cervical radiculopathy and peripheral entrapment neuropathies often have overlapping symptoms that are difficult to distinguish on physical examination. Small-scale studies have attempted to report the incidence of this phenomenon, often called double crush syndrome (DCS), with varying results. The present study aims to determine the incidence of concomitant cervical radiculopathy and peripheral nerve compression and to determine if the DCS hypothesis, which states that compression of a nerve at one site leaves it more susceptible to compression at another, is valid. METHODS: The PearlDiver database was queried from 2010 to 2020. The incidence of peripheral neuropathy in cervical radiculopathy was assessed. Propensity score matching was used to determine if patients with cervical radiculopathy were more likely to have peripheral nerve compression compared to controls, and vice versa, to test the DCS hypothesis. RESULTS: The database contains records of 90,772 632 patients. The incidence of carpal tunnel syndrome (CTS) or peripheral ulnar nerve compression (PUnC) in cervical radiculopathy was 9.98% and 3.15%, respectively. The incidence of both carpal tunnel syndrome and PUnC in cervical radiculopathy was 1.84%. Patients with cervical radiculopathy were more likely than matched controls to have both CTS (P < .001) and PUnC (P < .001). Patients with CTS (P < .001) and with PUnC (P < .001) were more likely to have cervical radiculopathy than the control cohort. CONCLUSIONS: The incidence of DCS is reported. Patients with cervical radiculopathy are more likely than matched controls to have peripheral nerve compression, and vice versa, in support of the DCS hypothesis.

Secondary Fracture Rate After Vertebral Osteoporotic Compression Fracture Is Decreased by Anti-Osteoporotic Medication but Not Increased by Cement Augmentation.

BACKGROUND: Painful vertebral osteoporotic compression fractures (OCFs) are often treated with cement augmentation, although controversies exist as to whether or not this increases the secondary fracture risk. Prevention of secondary fracture includes treatment of underlying osteoporosis. The purposes of this study were to determine (1) whether cement augmentation increases the rate of secondary fracture compared with nonoperative management, (2) whether anti-osteoporotic medications reduce the rate of secondary fracture, and (3) the rate of osteoporosis treatment with medications following vertebral OCF. METHODS: The PearlDiver database was queried for all patients with a diagnosis of OCF from 2015 to 2019. Patients were excluded if they were <50 years old, had a diagnosis of spinal neoplasm or infection, or underwent lumbar fusion in the perioperative period. Secondary fracture risk was assessed using univariate and multivariate logistic regression analysis, with kyphoplasty, vertebroplasty, anti-osteoporotic medications, age, gender, and Elixhauser Comorbidity Index as variables. RESULTS: A total of 36,145 patients were diagnosed with an OCF during the study period. Of those, 25,904 (71.7%) underwent nonoperative management and 10,241 (28.3%) underwent cement augmentation, including 1,556 who underwent vertebroplasty and 8,833 who underwent kyphoplasty. Patients who underwent nonoperative management had a secondary fracture rate of 21.8% following the initial OCF, compared with 14.5% in the vertebroplasty cohort and 18.5% in the kyphoplasty cohort, which was not a significant difference on multivariate analysis. In the entire cohort, 2,833 (7.8%) received anti-osteoporotic medications and 33,312 (92.2%) did not. The rate of secondary fracture was 10.1% in patients who received medications and 21.9% in those who did not, which was a significant difference on multivariate analysis (odds ratio = 1.23, p < 0.001). CONCLUSIONS: Cement augmentation did not alter the rate of secondary fracture, whereas anti-osteoporotic medications significantly decreased the risk of subsequent OCF by 19%. Only 7.8% of patients received a prescription for an anti-osteoporotic medication following the initial OCF. LEVEL OF EVIDENCE: Therapeutic Level III . See Instructions for Authors for a complete description of levels of evidence.

Genome-wide association mapping of date palm fruit traits.

Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species.

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.

Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.