Combined Transfer Learning and Test-Time Augmentation Improves Convolutional Neural Network-Based Semantic Segmentation of Prostate Cancer from Multi-Parametric MR Images.

Purpose: Multiparametric MRI (mp-MRI) is a widely used tool for diagnosing and staging prostate cancer. The purpose of this study was to evaluate whether transfer learning, unsupervised pre-training and test-time augmentation significantly improved the performance of a convolutional neural network (CNN) for pixel-by-pixel prediction of cancer vs. non-cancer using mp-MRI datasets.

Immune response gene polymorphisms in renal transplant recipients.

Background: T-cell activation and regulation are under genetic control and vary between individuals. However, the influence of functional immune response gene polymorphisms on transplant outcomes remains controversial.

Methods: A case-control design compared 100 white renal transplant recipients with or without acute graft rejection during the first year posttransplant and 50 normal controls.

A two-component signal transduction system with a PAS domain-containing sensor is required for virulence of Mycobacterium tuberculosis in mice.

Mycobacterium tuberculosis, the causative organism of tuberculosis, encounters oxidative stress during phagocytosis by the macrophage and following macrophage activation during an acquired immune response, and also from internally generated sources of radical oxygen intermediates through intermediary metabolism. We have identified the SenX3 protein, a sensor in 1 of the 11 complete pairs of two-component signal transduction systems in M. tuberculosis, as a possible orthologue of the Mak2p protein from the fission yeast Schizosaccharomyces pombe that is known to sense peroxide stress.

Expression of QK/QR/RRRAA or DERAA motifs at the third hypervariable region of HLA-DRB1 and disease severity in rheumatoid arthritis.

Objective: To examine the relationship between disease severity in patients with confirmed rheumatoid arthritis (RA) and the carriage of alleles expressing the high risk epitope (HRE) QK/QR/RRRAA or the low risk epitope (LRE) DERAA at positions 70-74 of the third hypervariable region of HLA-DRB1.

Methods: A case-control design to compare allele carriage rates in 204 Caucasian subjects with severe RA and mild RA and healthy controls. Patients had a mean disease duration of 12-18 years and severity of RA was defined using clinical and therapeutic criteria.

Identification of four novel dinucleotide repeat polymorphisms in the IL-2 and IL-2beta receptor genes.

Two polymorphic regions have been described within the IL-2 and IL-2 receptor beta genes comprising 15 and 8 alleles, respectively. Whether these polymorphisms have biologic importance is unknown, although they have been variably identified in associated with certain chronic disease states. We report here the detection of four new alleles designated IL-2 A* (122 bp), IL-2R-2 (169 bp), IL-2R 0 (165 bp), and IL-2R 9 (147 bp) in patients with rheumatoid arthritis and normal controls from the Pacific Northwest.

Association between dinucleotide repeat in non-coding region of interferon-gamma gene and susceptibility to, and severity of, rheumatoid arthritis.

Background: Rheumatoid arthritis ranges from a mild, non-deforming arthropathy with little long-term disability to severe, incapacitating, deforming arthritis which may be refractory to conventional disease-modifying agents. Epidemiological studies show an important genetic influence in rheumatoid arthritis, and MHC region genes and cytokine genes within and outside this region have been considered as candidates. We did a case-control study to test whether polymorphisms in the interferon-gamma gene are associated with severity of rheumatoid arthritis.

Identification of four novel dinucleotide repeat polymorphisms in the TNF-alpha and TNF-beta genes.

Five polymorphic regions (a to e) have been recognized within the TNF gene region. These polymorphisms appear to be of biological importance as individual alleles have been associated with higher production of TNF and/or an increased risk of rheumatoid arthritis or diabetes mellitus. We report here the detection of four new alleles designated a14 (122 bp), b8 (131 bp), b9 (132 bp), and d0 (122 bp) in patients with rheumatoid arthritis and normal controls from the Pacific Northwest.

A novel DR beta 1*03 allele identified by polymerase chain reaction-restriction fragment length polymorphism.

This report describes a new MHC class II allele, HLA-DR beta 1*0306, discovered in a 31-year-old Norwegian male. The allele typed serologically as DRw52 (DR3) and amplified in PCR using DR52-associated group primers. This product could not be identified using established restriction digests, however.

Successful paternity of twins following bone marrow transplantation with busulfan, melphalan and cyclophosphamide conditioning.

A 33-year-old man who had received previous chemotherapy with cytarabine, daunorubicin and mitoxantrone followed by an autologous marrow transplant after conditioning with busulfan, melphalan and cyclophosphamide, fathered sex-mismatched fraternal twins approximately 6 years post-transplant. HLA and DNA analyses showed the probability of paternity to be in excess of 99% for each twin. To our knowledge this represents the first documented case of paternity following conditioning with this combination of marrow ablative agents and the first report of twin paternity following autologous marrow transplantation.

Hemophilia B carrier determination based on family-specific mutation detection by DNA single-strand conformation analysis.

Single-strand conformation (SSC) analysis can distinguish normal from variant DNA fragments containing single point mutations by conformation-induced electrophoretic mobility shifts in non-denaturing polyacrylamide gels. We studied 25 hemophilia B kindreds by using SSC analysis after polymerase chain reaction (PCR) amplification of the eight factor IX exons and their intron boundaries. Variant SSC fragments were unambiguously identified in 24 kindreds, and direct DNA sequencing of variant PCR fragments identified 20 different hemophilia B mutations.

Brain dysgenesis and congenital intracerebral calcification associated with 3-hydroxyisobutyric aciduria.

Monozygotic male twins born to nonconsanguineous parents had dysmorphic facial features, microcephaly, migrational brain disorder, and congenital intracerebral calcification. They excreted excessive amounts of 3-hydroxyisobutyric acid, a metabolite of valine, and had evidence of impaired oxidative metabolism and metabolic acidosis. The level of 3-hydroxyisobutyrate in stored samples of midtrimester amniotic fluid was found to be high.

Hemophilia A carrier detection by restriction fragment length polymorphism analysis and discriminant analysis based on ELISA of factor VIII and vWf.

We performed carrier determination on female subjects from 32 hemophilia A kindreds with a combination of restriction fragment length polymorphism analysis and discriminant analysis of factor VIII antigen and von Willebrand factor antigen analyzed by enzyme-linked immunosorbent assay. Subjects included 25 obligate carriers, 30 at-risk female subjects from 19 kindreds each with two or more male subjects, with hemophilia and 28 at-risk female subjects from 13 kindreds each with a single sporadic case. Deoxyribonucleic acid (DNA) analysis with factor VIII intragenic probes clarified the carrier status of 15 female subjects, and extragenic probes classified an additional 14.

Diagnosis of Duchenne and Becker muscular dystrophies by polymerase chain reaction. A multicenter study.

OBJECTIVE--To assess the efficiency, reliability, and ease of use of DNA diagnosis for Duchenne and Becker muscular dystrophies (DMD/BMD) using the polymerase chain reaction (PCR). DESIGN--DNA from the patients was screened for deletion mutations using multiplex PCR, and the results were compared with those obtained by Southern blot analysis. The PCR multiplex reaction detects nine specific "hot-spot" exons in the dystrophin gene while the Southern analysis detects 66 specific dystrophin gene restriction fragments.

Identification of factor IX mutations in haemophilia B: application of polymerase chain reaction and single strand conformation analysis.

The molecular characterization of two haemophilia B defects, Calgary 1 and Calgary 2, was carried out using polymerase chain reaction (PCR) amplification and direct dideoxy sequencing. It had been previously shown that the Calgary 1 mutation affects the 5' TaqI restriction site of exon VIII, whereas Calgary 2 involves the loss of the 3' TaqI site of exon VIII of the factor IX gene. Sequencing data has now revealed that each of these alterations involves a C-to-T transition within a CpG dinucleotide.

Tentative assignment of gene for oto-palato-digital syndrome to distal Xq (Xq26-q28).

Detailed physical mapping of oto-palato-digital (OPD) syndrome gene on the X-chromosome was attempted on a family of 3 generations with 2 affected men. Although the result remains statistically non-significant, it indicates that the OPD-I gene might be located on the distal Xq.

Severe combined immune deficiency presenting with cyclic hematopoiesis.

At age 2 months a male infant presented with a cyclic clinical syndrome every 14-21 days that included pharyngeal aphthous ulcers, high fever, lymphadenopathy, pallor, and malaise. Serial blood studies indicated cycling of all blood cell elements, compatible with a diagnosis of cyclic hematopoiesis (CH). He also manifested a progressively severe immune deficiency, not described before in human CH.

Genetic stability of the D1Z2 region: implications for DNA genotyping and paternity testing.

The aim of the present study was to examine a single locus variable number tandem repeat for the purpose of DNA genotyping ("fingerprinting"). DNAs of 175 individuals from five ethnic groups (Black, Chinese, Japanese, Caucasian, and Melanesian) were analyzed. Restriction fragment length polymorphic analysis of random individuals revealed individual specific DNA patterns in all but one group.

Kinetochore analysis of micronuclei allows insights into the actions of colcemid and mitomycin C.

We have induced micronuclei in two strains of diploid human fibroblasts with a known aneugen, colcemid, and a known clastogen, mitomycin C. Using immunofluorescence to detect the presence of kinetochores in micronuclei, we were able to demonstrate a 26.8-fold increase in fluorescence-positive micronuclei (aneuploidy) in colcemid-treated cells.

Pallister-Killian syndrome: additional manifestations of cleft palate and sacral appendage.

We report a case of Pallister-Killian syndrome in a 28 week gestation infant. In addition to the characteristic phenotype, this patient had a cleft palate, diaphragmatic hernia, sacral appendage, and imperforate anus. The lymphocyte karyotype showed 96% 46,XX/4% 47,XX+i (12p) and the fibroblast karyotype 47,XX,+marker (presumed i(12p].

A familial interstitial deletion of the long arm of chromosome 21.

A mother and daughter with an interstitial deletion of the chromosome segment 21q11 to 21q21.3 have similar minor dysmorphism and mild mental retardation. These two patients are compared to others in the literature with deletion of the same region of chromosome 21.

Ethnic-specific allelic variation within the D1Z2 locus.

DNAs from 122 individuals representing 5 ethnic groups (Black, Chinese, Japanese, Caucasian and Melanesian) were analyzed for restriction fragment length polymorphisms (RFLPs) with a hypervariable repeated sequence located uniquely on chromosome 1 (hMF No.1; is a component of the D1Z2 locus). When human genomic DNA is digested with a variety of enzymes (TaqI, EcoRI, SinI, PstI, HaeIII) the hMF No.