Suppression of MHC class II expression by human class II trans-activator constructs lacking the N-terminal domain

The class II trans-activator (CIITA) is a bi- or multi-functional domain protein which plays a critical role in the expression of MHC class II genes. We report that removal of the N-terminal 151 amino acids, encompassing all of the acidic domain but leaving intact the proline/serine/threonine-rich domain, results in a mutant protein with potent suppressive properties for MHC class II expression. HeLa cells stably or transiently transfected with mutant CIITA constructs showed up to 99% suppression of MHC class II antigen induction by IFN-gamma and marked suppression of HLA-DRA mRNA expression. Transient transfection of a B lymphoma line resulted in up to 89% reduction of constitutive MHC class II expression within 5 days and suppression of HLA-DRA mRNA synthesis.     

The Transmogrifier-2: a 1 million gate rapid-prototyping system

This paper describes the Transmogrifier-2 (TM-2), a second-generation multifield programmable gate array (FPGA) rapid-prototyping system. The largest version of the system will comprise 16 boards that each contain two Altera 10K50 FPGA's, four I-Cube interconnect chips, and up to 8 Mbytes of memory. The inter-FPGA routing architecture of the TM-2 uses a novel interconnect structure, a nonuniform partial crossbar, that provides a constant delay between any two FPGA's in the system. The TM-2 architecture is modular and scalable, meaning that systems of various sizes can be constructed from copies of the same board, while maintaining routability and the constant delay feature. Other features include a system-level programmable clock that allows single-cycle access to off-chip memory, and programmable clock waveforms with edge resolution of 10 ns. The first Transmogrifier-2 boards have been manufactured and are functional. They have recently been used successfully in some simple graphics acceleration applications     

HoxA is a transcriptional regulator for expression of the hup structural genes in free-living Bradyrhizobium japonicum

A chromosomally integrated Bradyrhizobium japonicum hoxA mutant is unable to oxidize hydrogen in free-living conditions. Derepressing conditions that induce hydrogenase activity in free-living, wild-type B. japonicum cells cannot induce expression of the hydrogenase structural genes in the hoxA mutant. The DNA-binding capacity of HoxA at the hup promoter region was studied by means of gel retardation. Both heterotrophically growing cells and cells induced to express hydrogenase activity contain a protein that specifically binds to the hup promoter region. Crude protein extracts isolated from a B. japonicum hoxA mutant do not contain this binding compound. The HoxA protein was overexpressed in E. coli and isolated in the form of a maltose-binding protein (MBP)-HoxA fusion. The MBP-HoxA hybrid protein specifically bound to a 50 bp region of the hupSL promoter known to be important for regulation of hupSL expression.     

Exclusion of BMP6 as a candidate gene for cleidocranial dysplasia

Cleidocranial dysplasia (CCD) is an autosomal dominant, generalized skeletal dysplasia in humans that has been mapped to the short arm of chromosome 6. We report linkage of a CCD mutation to 6p21 in a large family and exclude the bone morphogenetic protein 6 gene (BMP6) as a candidate for the disease by cytogenetic localization and genetic recombination. CCD was linked with a maximal two-point LOD score of 7.22 with marker D6S452 at theta = 0. One relative with a recombination between D6S451 and D6S459 and another individual with a recombination between D6S465 and CCD places the mutation within a 7 cM region between D6S451 and D6S465 at 6p21. A phage P1 genomic clone spanning most of the BMP6 gene hybridized to chromosome 6 in band region p23-p24 using FISH analysis, placing this gene cytogenetically more distal than the region of linkage for CCD. We derived a new polymorphic marker from this same P1 clone and found recombinations between the marker and CCD in this family. The results confirm the map position of CCD on 6p21, further refine the CCD genetic interval by identifying a recombination between D6S451 and D6S459, and exclude BMP6 as a candidate gene.     

Activation of the mitogen-activated protein kinase pathway is involved in and sufficient for megakaryocytic differentiation of CMK cells

Activation of the mitogen-activated protein (MAP) kinase pathway has been associated with both cell proliferation and differentiation. Constitutively activated forms of Mek (MAP kinase/Erk kinase) and Erk (MAP kinase) have been previously shown capable of inducing differentiation or proliferation in nonhematopoietic cells. To specifically examine the role of Erk activation in megakaryocytic growth and development, we activated the MAP kinase pathway by the transfection of constitutively activated Mek or Erk cDNA into a human megakaryoblastic cell line, CMK, by electroporation. The CMK transfectant clones that expressed constitutively activated Mek or Erk showed morphologic changes of differentiation. Transfected cells also showed expression of mature megakaryocytic cell surface markers. The MAP kinase pathway was also activated by treatment of the hematopoietic cells with a cytokine that activates Erk. The treatment of CMK cells with stem cell factor (SCF ) caused MAP kinase activation and induced differentiation by the expression of mature megakaryocytic cell surface markers. The effects of the SCF treatment were inhibited by pretreatment with a specific inhibitor of the MAP kinase pathway, PD98059. In this report, we conclude that activation of the MAP kinase pathway was both necessary and sufficient to induce differentiation in this megakaryoblastic cell line.     

Subspace-based signal analysis using singular value decomposition

A unified approach is presented to the related problems of recovering signal parameters from noisy observations and identifying linear system model parameters from observed input/output signals, both using singular value decomposition (SVD) techniques. Both known and new SVD-based identification methods are classified in a subspace-oriented scheme. The SVD of a matrix constructed from the observed signal data provides the key step in a robust discrimination between desired signals and disturbing signals in terms of signal and noise subspaces. The methods that are presented are distinguished by the way in which the subspaces are determined and how the signal or system model parameters are extracted from these subspaces. Typical examples, such as the direction-of-arrival problem and system identification from input/output measurements, are elaborated upon, and some extensions to time-varying systems are given     

Experimental fetal tracheal ligation reverses the structural and physiological effects of pulmonary hypoplasia in congenital diaphragmatic hernia

Infants with congenital diaphragmatic hernia (DH) and profound pulmonary hypoplasia are currently unsalvageable. The authors previously demonstrated that tracheal ligation (TL) accelerates fetal lung growth and reverses the pulmonary hypoplasia of fetal nephrectomy. The purpose of this study was to determine if the pulmonary hypoplasia of experimental DH could be similarly reversed and, if so, whether the resulting lungs would show better function than those of their DH counterparts. Eighteen fetal lambs were divided into three experimental groups of six animals each. In group 1, DH was created at 90 days' gestation. In group 2, DH was created at 90 days' gestation and TL performed during the same operation. Group 3 consisted of sham-operated controls. These animals were delivered near full-term, and their lungs analyzed by standard morphometric techniques. Ten additional fetal lambs were divided into two experimental groups of five animals each. In group 4, DH was created at 90 days' gestation. In group 5, DH was created at 90 days' gestation and TL performed 20 days later, at 110 days' gestation. These animals were pressure-ventilated via tracheostomy over a 2-hour period in which PaO2, PaCO2, and compliance were measured. Intratracheal pressure (ITP) was measured at the time of delivery in all groups. Upon retrieval, DH animals had abdominal viscera in the chest and small lungs; in contrast, DH/TL animals had the herniated viscera reduced from the chest by enlarged lungs. DH/TL lungs showed markedly increased growth, with significant increases in lung volume:body weight ratio (LV:BW; P = .0001), alveolar surface area (ALV.SA; P = .0001), and alveolar number (ALV#) (P = .0001) when compared with those of the DH or control group. This growth was associated with a normal maturation pattern based on histological appearance, normal airspace fraction, and normal alveolar numerical density. ITP in the DH/TL group was increased when compared with that of DH and control animals (P = .0001). Total lung DNA and protein were both elevated in the DH/TL animals (P = .0001). However, the DNA:protein ratio remained normal, suggesting lung growth had occurred through cell proliferation, not by hypertrophy. When ventilated over a range of settings, DH/TL lungs were more compliant (P = .0001) and achieved higher PaO2s (P < .003) and lower PaCO2s (P = .0001) than their DH counterparts. From these data, the authors conclude: (1) Experimental fetal DH produces hypoplastic lungs that are not capable of adequate gas exchange with conventional ventilation.(ABSTRACT TRUNCATED AT 400 WORDS)     

Difference limens for formant patterns of vowel sounds

Studies of thresholds for discrimination of formant frequency variation in synthetic vowel sounds have been predominantly limited to variations in a single formant. Here, differences limens (DLs) are presented for multiformant variations expressed in measures of delta F and as distances in the auditory-perceptual space (APS) proposed by J. D. Miller [J. Acoust. Soc. Am. 85, 2114-2134 (1989)]. DLs for four subjects were estimated along 102 synthetic vowel continua representing five patterns of formant variation [(1) single variation in F1; (2) single variation in F2; (3) parallel simultaneous variation in F1 and F2; (4) opposing simultaneous variation in F1 and F2; and parallel simultaneous variation in F1, F2, and F3] and 17 within- or between-category vowel sounds. Minimal uncertainty methodology was employed utilizing an adaptive up-down procedure with a cued, two-interval forced-choice (2IFC) task. The results of this experiment reflect smaller DLs for both single- and multiple-formant changes than have been found in the past and also suggest that discrimination of parallel multiformant variation is significantly better than opposing multiformant or single-formant variation.     

Nanocell logic gates for molecular computing

Molecular electronics seeks to build electrical devices to implement computation - logic and memory - using individual or small collections of molecules. These devices have the potential to reduce device size and fabrication costs, by several orders of magnitude, relative to conventional CMOS. However, the construction of a practical molecular computer will require the molecular switches and their related interconnect technologies to behave as large-scale diverse logic, with input/output wires scaled to molecular dimensions. It is unclear whether it is necessary or even. possible to control the precise regular placement and interconnection of these diminutive molecular systems. This paper describes genetic algorithm-based simulations of molecular device structures in a nanocell where placement and connectivity of the internal molecular switches are not specifically directed and the internal topology is generally disordered. With some simplifying assumptions, these results show that it is possible to use easily fabricated nanocells as logic devices by setting the internal molecular switch states after the topological molecular assembly is complete. Simulated logic devices include an inverter, a NAND gate, an XOR gate and a 1-bit adder. Issues of defect and fault tolerance are addressed.     

The Generic Bilinear Calibration-Estimation Problem

We identify a very general, recurring pattern in a number of well known problems in biological and machine vision. Many problems are of a peculiar double-sided nature: One attempts to estimate certain properties of the environment using a certain type of equipment and simultaneously one attempts to calibrate the same equipment on the structure of the environment. At first sight this appears the kind of the chicken and the egg problem that might well prove to be insoluble. However, due to basic constraints that universally apply (e.g., the world is only three-dimensional), a solution—up to a certain class of ambiguity transformations—often exists. The more complicated the problem is, the less important the remaining ambiguity will be, at least in a relative sense. Many well known problems are special in that they can be cast in bilinear form, sometimes after transformation or the introduction of dummy variables. Instances include photometric stereo, photometric estimations (e.g., of lightness), local (differential) image operators, a variety of photogrammetric problems, etc. It turns out that many of these problems—and together these make up a large fraction of the generic problems in machine vision today—can be cast in a simple universal framework. This framework enables one to handle arbitrarily large (that is, not minimal, consistent configurations), noisy (thus inconsistent) date sets automatically. The level at which prior information (either of a deterministic or a statistical nature) is used (assumptions such as constant albedo, rigidity, uniform distributions, etc.) is clearly separated as an additional, typically nonlinear, stage.