Validation of a deep neural network-based algorithm supporting clinical management of adnexal mass.

Background: Conservative management of adnexal mass is warranted when there is imaging-based and clinical evidence of benign characteristics. Malignancy risk is, however, a concern due to the mortality rate of ovarian cancer. Malignancy occurs in 10-15% of adnexal masses that go to surgery, whereas the rate of malignancy is much lower in masses clinically characterized as benign or indeterminate.

Through the Looking Glass: Unraveling the Stage-Shift of Acute Rejection in Renal Allografts.

Sub-optimal sensitivity and specificity in current allograft monitoring methodologies underscore the need for more accurate and reflexive immunosurveillance to uncover the flux in alloimmunity between allograft health and the onset and progression of rejection. QSant-a urine based multi-analyte diagnostic test-was developed to profile renal transplant health and prognosticate injury, risk of evolution, and resolution of acute rejection. Q-Score-the composite score, across measurements of DNA, protein and metabolic biomarkers in the QSant assay-enables this risk prognostication.

Association between dd-cfDNA levels, de novo donor specific antibodies, and eGFR decline: An analysis of the DART cohort.

Background: Donor-derived cell-free DNA (dd-cfDNA) is a marker of allograft injury in transplant recipients; however, the relationship between dd-cfDNA and other clinical parameters associated with adverse allograft outcomes is not well-characterized.

Methods: We performed a retrospective analysis of kidney transplant recipients from the DART cohort (ClinicalTrials.gov Identifier: NCT02424227) to evaluate the associations between eGFR decline, de novo donor-specific antibodies (dnDSA), and dd-cfDNA.

The transcriptional diversity of 25 Drosophila cell lines.

Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal).

Differential analysis for high density tiling microarray data.

Background: High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association.

RNA maps reveal new RNA classes and a possible function for pervasive transcription.

Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides (nt) and whole-cell RNAs less than 200 nt were investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated.

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments.

Background: High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. Tiling arrays are increasingly used in chromatin immunoprecipitation (IP) experiments (ChIP on chip).

Biological function of unannotated transcription during the early development of Drosophila melanogaster.

Many animal and plant genomes are transcribed much more extensively than current annotations predict. However, the biological function of these unannotated transcribed regions is largely unknown. Approximately 7% and 23% of the detected transcribed nucleotides during D.

Temporal profile of replication of human chromosomes.

Chromosomes in human cancer cells are expected to initiate replication from predictably localized origins, firing reproducibly at discrete times in S phase. Replication products obtained from HeLa cells at different stages of S phase were hybridized to cDNA and genome tiling oligonucleotide microarrays to determine the temporal profile of replication of human chromosomes on a genome-wide scale. About 1,000 genes and chromosomal segments were identified as sites containing efficient origins that fire reproducibly.

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.

Sites of transcription of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes were mapped at 5-base pair resolution in eight cell lines. Unannotated, nonpolyadenylated transcripts comprise the major proportion of the transcriptional output of the human genome. Of all transcribed sequences, 19.

T2 relaxation time measurements in osteoarthritis.

Quantification of changes in T(2) relaxation time, in human cartilage, with progression of osteoarthritis (OA), and evaluation of qualitative correlations with clinical evaluation, histology and polarized light microscopy (PLM). Cartilage-bone plugs were harvested from fresh cadaveric knees (n = 10) and specimens after surgical knee replacement (n = 2) at 12 locations, including lateral and medial sides of tibia, femora and patella. Magnetic resonance imaging was performed at 1.

Osteoarthritis: MR imaging findings in different stages of disease and correlation with clinical findings.

Purpose: To determine whether knee pain, stiffness, and limited function in patients with different stages of osteoarthritis correlate with the degree of disease assessed on magnetic resonance (MR) images and radiographs.

Materials And Methods: Radiographs in 50 patients with varying degrees of osteoarthritis of the knee were assessed by using the the Western Ontario and McMaster University (WOMAC) osteoarthritis index and the Kellgren-Lawrence (KL) scale. MR images were obtained and analyzed by two readers for cartilage lesions, bone marrow edema pattern, and ligamentous and meniscal lesions.

Magnetic resonance imaging of normal and osteoarthritic trabecular bone structure in the human knee.

Objective: To use high-resolution magnetic resonance imaging (MRI) to evaluate the trabecular bone structure in the distal femur and the proximal tibia and its to correlate the findings with different stages of osteoarthritis (OA) of the human knee.

Methods: Axial images of the distal femur and proximal tibia were obtained at 1.5 T in patients without and with mild OA and with severe OA.