A comparative analysis exposes an amplification delay distinctive to SARS-CoV-2 Omicron variants of clinical and public health relevance.

ABSTRACTMutations in the SARS-CoV-2 genome may negatively impact a diagnostic test, have no effect, or turn into an opportunity for rapid molecular screening of variants. Using an in-house Emergency Use Authorized RT-qPCR-based COVID-19 diagnostic assay, we combined sequence surveillance of viral variants and computed PCR efficiencies for mismatched templates. We found no significant mismatches for the N, E, and S set of assay primers until the Omicron variant emerged in late November 2021. We found a single mismatch between the Omicron sequence and one of our assay's primers caused a > 4 cycle delay during amplification without impacting overall assay performance.Starting in December 2021, clinical specimens received for COVID-19 diagnostic testing that generated a Cq delay greater than 4 cycles were sequenced and confirmed as Omicron. Clinical samples without a Cq delay were largely confirmed as the Delta variant. The primer-template mismatch was then used as a rapid surrogate marker for Omicron. Primers that correctly identified Omicron were designed and tested, which prepared us for the emergence of future variants with novel mismatches to our diagnostic assay's primers. Our experience demonstrates the importance of monitoring sequences, the need for predicting the impact of mismatches, their value as a surrogate marker, and the relevance of adapting one's molecular diagnostic test for evolving pathogens.

Sex Offender Populations and Clinical Efficacy: A Response to Rosky.

We provide a brief response to a commentary submitted by Rosky in which he questions the rationale and methodological merits of our original study about full-disclosure polygraph outcome differences between juvenile and adult sex offenders. At the heart of Rosky's substantive concerns is the premise that only research tying polygraphy outcomes to actual recidivism is useful or worthwhile. He also questions the overall utility and validity of polygraphy. We acknowledge and challenge these two points. Furthermore, many of the methodological concerns expressed by Rosky represent either a misunderstanding of our research question, study design, and sample, or a disregard for the explicit declarations we made with respect to our study limitations. Overall, it appears Rosky has accused us of not answering well a question we were not trying to ask. Our response addresses the key substantive and methodological concerns extended by Rosky and clarifies the actual aims and scope of our original study. We also argue that a calm, rational, and scientific discussion is the best approach to understanding how to improve clinical methods used in sex offender treatment.

Sexual history disclosure polygraph outcomes: do juvenile and adult sex offenders differ?

Despite the empirical and theoretical chasm between the opponents and proponents of polygraphy, its use is prominent among sex offender agencies in the United States. However, current research on polygraph examination outcomes among juvenile sex offenders, along with potential differences from their adult counterparts, is scarce and outdated. In the present study, we assess the difference between juvenile and adult sex offenders in terms of the propensity for passing a sexual history disclosure polygraph examination. A sample of 324 sex offenders (86 juveniles and 238 adults) who engaged in a sexual history disclosure polygraph examination as part of their treatment in an Intermountain West sex offender treatment agency was used for the analysis. Results from preliminary and logistic regression analyses indicate that juvenile and adult offenders do not significantly differ in the likelihood of passing a sexual history disclosure polygraph examination. Implications and limitations are discussed.

Genetic survey of shallow populations of the Mediterranean red coral [Corallium rubrum (Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation.

Combined action from over-harvesting and recent mass mortality events potentially linked to ongoing climate changes has led to new concerns for the conservation of shallow populations (5-60 m) of Corallium rubrum, an octocorallian that is mainly found in the Mediterranean Sea. The present study was designed to analyse population structure and relationships at different spatial scales (from 10s of meters to 100s of kilometres) with a focus on dispersal pattern. We also performed the first analysis of the distribution of genetic diversity using a comparative approach between regional-clusters and samples. Forty populations dwelling in four distinct regions between 14 and 60 m in depth were genotyped using 10 microsatellites. Our main results indicate (i) a generalized pair-sample differentiation combined with a weak structure between regional-clusters; (ii) the occurrence of isolation by distance at the global scale, but also within two of the three analysed regional-clusters; (iii) a high level of genetic diversity over the surveyed area with a heterogeneous distribution from regional-cluster to sample levels. The evolutionary consequences of these results are discussed and their management implications are provided.

Controlling costs: opportunities for physician-hospital collaborations and ventures.

STUDY DESIGN: Analysis of federal laws, regulations, and commentary relevant to gainsharing and other physician-hospital collaborations. Review of health, legal, and medical literature to identify relevant case studies, primarily from 2000 to the present. OBJECTIVE: To illustrate a number of physician-hospital collaboration and joint venture models to explore opportunities for physicians and hospital partners to enhance revenues and contain costs in the provision of health care. SUMMARY OF BACKGROUND DATA: There are numerous physician-hospital joint ventures throughout the United States and 8 approved gainsharing programs. Few comparisons of gainsharing as compared to other joint venture structures are available to hospitals and physicians. METHODS: A narrative review of health, legal, and business literature, regulations, and commentary to identify physician-hospital collaborations and ventures as well as applicable regulatory authorities. RESULTS: There are numerous joint venture and collaboration models used throughout the country for physician-hospital collaborations with varying degrees of success. Eight approved gainsharing programs have been implemented. CONCLUSIONS: Physician-hospital collaborations, gainsharing, and joint ventures are expanding throughout the country in response to reimbursement pressures and movement of care into the ambulatory setting. These partnerships can be successful where there is sufficient alignment of interests to offset the operational and regulatory complexities that such partnerships present.

Intramuscular hemangioma: recurrence risk related to surgical margins.

The best treatment for intramuscular hemangiomas is unclear in part because the outcome is variable, with recurrence rates ranging from 18% to 61%. This variance is due to deficiencies in previous reports such as an inadequate population size, lack of life table analyses, lack of uniform pathologic criteria, and loose or absent definition of surgical margins. Our goal was to address these deficiencies and support or refute previous results. We identified 110 patients between 1981 and 2005. There were 48 males and 62 females with an average age of 22 years at the time of consult. Kaplan-Meier analysis showed 76% of patients managed initially without excision were surgery-free at 2 years and 66% at 5 years. For patients treated with surgery, 86% and 73% were recurrence free at 2 and 5 years, respectively. There were substantial differences in local recurrence when stratified by margin: 93% of patients were recurrence free at 5 years when the excision was marginal and wide, 65% when intralesional without any gross remaining tumor, and 33% when intralesional with gross remaining tumor. Surgical margins and tumor size were the only identified risk factors for recurrence.

Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to a caesium stress. Influence of potassium supply.

The incorporation and localisation of 133Cs in a plant cellular model and the metabolic response induced were analysed as a function of external K concentration using a multidisciplinary approach. Sucrose-fed photosynthetic Arabidopsis thaliana suspension cells, grown in a K-containing or K-depleted medium, were submitted to a 1 mM Cs stress. Cell growth, strongly diminished in absence of K, was not influenced by Cs. In contrast, the chlorophyll content, affected by a Cs stress superposed to K depletion, did not vary under the sole K depletion. The uptake of Cs was monitored in vivo using 133Cs NMR spectroscopy while the final K and Cs concentrations were determined using atomic absorption spectrometry. Cs absorption rate and final concentration increased in a K-depleted external medium; in vivo NMR revealed that intracellular Cs was distributed in two kinds of compartment. Synchrotron X-ray fluorescence microscopy indicated that one could be the chloroplasts. In parallel, the cellular response to the Cs stress was analysed using proteomic and metabolic profiling. Proteins up- and down-regulated in response to Cs, in presence of K+ or not, were analysed by 2D gel electrophoresis and identified by mass spectrometry. No salient feature was detected excepting the overexpression of antioxidant enzymes, a common response of Arabidopsis cells stressed whether by Cs or by K-depletion. 13C and 31P NMR analysis of acid extracts showed that the metabolome impact of the Cs stress was also a function of the K nutrition. These analyses suggested that sugar metabolism and glycolytic fluxes were affected in a way depending upon the medium content in K+. Metabolic flux measurements using 13C labelling would be an elegant way to pursue on this line. Using our experimental system, a progressively stronger Cs stress might point out other specific responses elicited by Cs.

Differential gene expression in liposarcoma, lipoma, and adipose tissue.

Malignant transformation is thought to be associated with changes in the expression of a number of genes, and this alteration in gene expression is felt to be critical to the development of the malignant phenotype. Sarcomas represent a diverse group of tumors derived from cells of mesenchymal origin. Marked heterogeneity exists in the biological behavior of sarcomas, even within histologic subtypes of sarcomas. In an effort to better understand the biology of liposarcomas, gene expression in normal adipose tissue, lipomas, and liposarcomas was examined using the Affymetrix microarray technology. Differences in gene expression were quantified as the fold change in gene expression among the sample sets. Differences in gene expression among normal adipose tissue, lipomas, and liposarcomas were observed. In addition, genes expressed uniquely in liposarcoma among these and 18 other tissue sample sets were identified. Gene sets were devised that allowed the separation of liposarcomas from other samples, and most normal adipose tissue from most lipomas using the Eisen clustering software "Cluster." We conclude that differences in gene expression can be identified among different tumors derived from the adipocyte series. Such differences in gene expression may help differentiate among subtypes of sarcomas, and may also yield clues to the pathophysiology of this heterogeneous group of tumors.

Gene expression in giant-cell tumors.

Malignant transformation is thought to be associated with changes in the expression of a number of genes, and this alteration in gene expression is considered critical to the development of the malignant phenotype. In this study, gene expression in 8 samples of giant-cell tumor (GCT) of bone, as well as in bone at the site of osteoarthritis and in a variety of normal tissues, was determined at Gene Logic Inc (Gaithersburg, Md) with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 genes/expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic GeneExpress Software System. Differences in gene expression between GCTs and bone were observed. In addition, genes expressed uniquely in GCTs among these and 519 samples from 20 other tissue types were identified. Some of the genes that were found to be overexpressed in GCTs, such as tartrate-resistant acid phosphatase and the lysosomal H + -transporting ATPase, are also expressed by osteoclasts. Osteoprotegrin ligand (OPGL) was also selectively overexpressed in GCTs. The genes found to be overexpressed in GCTs appear to reflect the genetic profile of osteoclast-lineage cells and also the genetic profile of an osteoclastogenic environment. The genes identified in this study may play a role in the pathogenesis of GCTs, confirm the likely importance of OPGL in GCT pathogenesis, and may indicate other possible targets to which antitumor therapy could be directed.

Cell death after cartilage impact occurs around matrix cracks.

The damage from rapid high energy impacts to cartilage may contribute to the development of osteoarthritis (OA). Understanding how and when cells are damaged during and after the impact may provide insight into how these lesions progress. Mature bovine articular cartilage on the intact patella was impacted with a flat impacter to 53 MPa in 250 ms. Cell viability was determined by culturing the cartilage with nitroblue tetrazolium for 18 h or for 4 days in medium containing 5% serum before labeling (5-day sample) and compared to adjacent, non-impacted tissue as viable cells per area. There was a decrease in viable cell density only in specimens with macroscopic cracks and the loss was localized primarily near matrix cracks, which were in the upper 25% of the tissue. This was confirmed using confocal microscopy with a fluorescent live/dead assay, using 5'-chloromethylfluorescein diacetate and propidium iodide. Cell viability in the impacted regions distant from visible cracks was no different than the non-impacted control. At 5 days, viable cell density decreased in the surface layer in both the control and impacted tissue, but there was no additional impact-related change. In summary, cell death after the impaction of cartilage on bone occurred around impact induced cracks, but not in impacted areas without cracks. If true in vivo, early stabilization of the damaged area may prevent late sequelae that lead to OA.

Diagnostic value of open and needle biopsies in tumors of the sacrum.

STUDY DESIGN: A retrospective study with statistical analysis of 25 percutaneous needle biopsies and 54 open biopsies performed on 60 patients with tumors located in the sacrococcygeal region. OBJECTIVES: To analyze the diagnostic value of open and needle biopsies in tumors of the sacrum as well as to determine factors leading to a false or equivocal result. SUMMARY OF BACKGROUND DATA: Although percutaneous needle biopsies of the spine are valuable for thoracolumbar levels, the benefit in the sacrococcygeal region, specifically, has not previously been shown. This region is unique because of anatomic and oncologic factors. METHODS: Medical charts, imaging studies, and operative and pathologic records of patients with tumors diagnosed between 1965 and 1996 in the sacrococcygeal region reviewed were analyzed. Accuracy and effective accuracy of each procedure were then calculated. RESULTS: There were 54 primary lesions (17 benign, 37 malignant) and 6 metastatic tumors. The accuracy and effective accuracy of open biopsies was 87% and 81% but in percutaneous needle biopsies was only 44% and 12%, respectively. An unclear diagnosis resulted in the need for another biopsy in 12 of 21 primary percutaneous needle biopsies but only in 2 of 39 open biopsies (P < 0.0001, chi2). The average number of biopsies required to obtain a definitive diagnosis was significantly less if an open biopsy were performed first instead of a percutaneous needle biopsy, 1.1 versus 1.8, respectively (P = 0.0004, two-sample t test). There was a significant delay in treatment if the initial biopsy was a percutaneous needle biopsy compared with an open biopsy, mean 46 versus 4 days, respectively (P = 0.004, two-sample t test). CONCLUSION: We conclude that for sacral tumors, open biopsies have a higher effective accuracy, whereas needle biopsies are associated with a longer delay in treatment.

Proximal femoral replacement.

Reconstruction of the proximal femur after extensive bone loss is clinically challenging. Options for reconstruction depend on the classification and extent of the proximal femoral defect. Although reconstitution of the native proximal femoral bone stock are the traditional goals of most revision techniques for the proximal femur, these techniques lose their effectiveness after numerous revisions due to the severe loss of a sufficient amount of structural bone needed to reconstruct the femur and abductor attachment. Consequently, the proximal femoral bone becomes fragile with extensive bone loss despite bone grafting. Techniques that use allograft-prosthetic composite and femoral megaprosthesis can successfully restore a patient's ambulatory ability despite the absence of significant portions of the proximal femur.

Results of treatment for metastatic osteosarcoma with neoadjuvant chemotherapy and surgery.

The purpose of the current study was to define the survival outcome variables for the 85 patients with Stage IIB osteosarcoma treated with neoadjuvant chemotherapy at the authors' institution from 1982 to 1997. A minimum 4-year followup or death was a requisite for inclusion. Forty-three patients were relapse-free survivors and 14 had no evidence of disease at followup for an overall survival of 67%. Twenty-nine patients had thoracotomy and nine have no evidence of disease with a minimum 4-year followup from last thoracotomy. The mean time to metastasis after diagnosis for patients presenting with Stage IIB disease was 12.8 months. There was no difference in the survival for any of the three chemotherapy protocols, used during the 15 years included in this analysis. There was a significant relation between length of time to relapse and survival. For each additional year without relapse, there is an 18% increase in chance of survival. In patients who were treated with thoracotomy, the number of metastatic nodules was a significant predictor of survival; specifically, each nodule increased the risk of death by 43%. A favorable outcome in this cohort of patients is related to the length of time between initiation of therapy and diagnosis of metastasis, and the number of metastatic foci.

Pathologic fracture in osteosarcoma : prognostic importance and treatment implications.

BACKGROUND: The presence of a pathologic fracture in an osteosarcoma has been considered a poor prognostic factor and an indication for immediate amputation. The purpose of the present study was to determine, in the current era of neoadjuvant chemotherapy, whether a pathologic fracture in an osteosarcoma has prognostic importance and whether limb salvage can be safely performed in such patients without compromising clinical outcome. METHODS: In a cooperative effort of the Musculoskeletal Tumor Society, members from eight institutions provided retrospective data on fifty-two patients with osteosarcoma who had a pathologic fracture and on fifty-five patients with osteosarcoma who had not had a pathologic fracture and had been followed for at least two years or until disease recurrence, metastasis, or death. The two groups were matched for patient age and tumor location. Outcomes examined were survival and local recurrence. A subgroup analysis was performed to assess differences in outcome within the group with the pathologic fracture. RESULTS: The five-year estimated survival rates were 55% for the group with a pathologic fracture and 77% for the group without a fracture (p = 0.02). The rate of survival without a local recurrence at five years was 75% for the group with a fracture and 96% for the group without a fracture (p = 0.007). In the group with a fracture, seven (23%) of the thirty patients managed with limb salvage and four (18%) of the twenty-two managed with an amputation had a local recurrence (p = 0.75). Eleven (37%) of the thirty patients with a fracture who were managed with limb salvage and ten (45%) of the twenty-two patients with a fracture who were managed with an amputation died of the disease (p = 0.50). Five patients underwent open reduction and internal fixation followed by limb-salvage surgery. Two of them had a local recurrence and died at an average of eight months postoperatively. The remaining three patients were alive at an average of 6.1 years postoperatively. Local disease control and the survival of these patients were not significantly different from those for the thirty-three patients who were treated with nonoperative immobilization of the fracture followed by limb-salvage surgery. CONCLUSIONS: Patients with osteosarcoma who present with a pathologic fracture or sustain one during preoperative chemotherapy have an increased risk of local recurrence and a decreased rate of survival compared with patients who have not sustained a pathologic fracture. The performance of a limb-salvage procedure in carefully selected patients with a pathologic fracture does not significantly increase the risk of local recurrence or death. Factors predictive of improved outcome, such as the response to chemotherapy and union of the fracture, should be taken into account when limb salvage is being considered.

Regulation of protein degradation and protease expression by mannose in maize root tips. Pi sequestration by mannose may hinder the study of its signaling properties.

The effects of mannose (Man) and glucose (Glc) on central metabolism, proteolysis, and expression of the root starvation-induced protease (RSIP; F. James, R. Brouquisse, C. Suire, A. Pradet, P. Raymond [1996] Biochem J 320: 283-292) were investigated in maize (Zea mays L. cv DEA) root tips. Changes in metabolite concentrations (sugars, ester-phosphates, adenine nucleotides, and amino acids) were monitored using in vivo and in vitro (13)C- and (31)P-NMR spectroscopy, in parallel with the changes in respiration rates, protein contents, proteolytic activities, and RSIP amounts. The inhibition of proteolysis, the decrease in proteolytic activities, and the repression of RSIP expression triggered by Man, at concentrations usually used to study sugar signaling (2 and 10 mM), were found to be related to a drop of energy metabolism, primarily due to a Man-induced Pi sequestration. However, when supplied at low concentration (2 mM) and with the adequate phosphate concentration (30 mM), energy metabolism was restored and Man repressed proteolysis similarly to Glc, when provided at the same concentration. These results indicate that Man should be used with caution as a Glc analog to study signalization by sugars in plants because possible signaling effects may be hindered by Pi sequestration.