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PubMed2005

Structural white matter deficits in high-functioning individuals with autistic spectrum disorder: a voxel-based investigation.

A number of imaging and neuropathological studies have reported structural abnormalities in white matter areas such as the corpus callosum in autism spectrum disorder (ASD). Differences in both global brain volume and the size of specific neural structures have been reported. In order to expand these previously reported findings and to describe more precisely the nature of such structural changes, we performed a voxel-based morphometric whole brain analysis, using a group-specific template, in male adolescents with ASD. Fifteen individuals with normal intelligence and ASD, and a group of 16 controls, matched for age, sex, and IQ, were investigated. High-resolution T1-weighted 3D data sets were acquired and analysed. Local white matter volume deficits were found in the corpus callosum, particularly in the anterior splenium and isthmus, and right hemisphere. White matter volume deficits were also found in the left middle temporal, right middle frontal, and left superior frontal gyri. No significant areas of increased white matter volume were found. Our findings support the hypothesis that reduced white matter volume in the corpus callosum and right hemisphere may play a role in the pathophysiology of ASD.

Adolescent↗
PubMed2003

Peptidomics of the locust corpora allata: identification of novel pyrokinins (-FXPRLamides).

The peptidomes of the corpora allata of Locusta migratoria and Schistocerca gregaria were investigated by both matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and nanoscale liquid chromatography quadrupole time-of-flight tandem mass spectrometry (nanoLC-Q-TOF MSMS). The pyrokinin (-FXPRLamide) family seems to be predominant. In addition to the known pyrokinins, we de novo sequenced four pyrokinins in L. migratoria and five in S. gregaria. In addition, one pyrokinin-like peptide (-PRLamide) was identified in S. gregaria. Besides the -(FX)PRLamides, FLRFamide-1, the allatostatins (A family) and numerous as yet unidentified peptides are also present in the corpora allata.

Amino Acid Sequence↗
PubMed1999

Peptide mobility and peptide mapping in capillary zone electrophoresis. Experimental determination and theoretical simulation.

The electrophoretic mobilities of 58 peptides that varied in size from 2 to 39 amino acids and varied in charge from 0.65 to 7.82 are presented. The measurements were conducted at 22 degrees C using a 10% linear polyacrylamide-coated column and a 50 mM phosphate buffer at pH 2.5. Excellent separation of peptides and highly reliable peptide maps of protein digests are routinely obtained using these experimental conditions. The electrophoretic data were used to test existing theoretical models that correlate electrophoretic mobility with physical parameters. The results indicate that the Offord model that correlates electrophoretic mobility with the charge-to-size parameter q/M2/3 offers the best fit of our reliable experimental data. Furthermore, we also obtained the capillary zone electrophoretic profile of the endoproteinase Lys-C digests of a peptide sequencing standard, melittin, and horse myoglobin under the same experimental conditions as described above. The resulting peptide maps were compared with corresponding theoretical simulation.

Amino Acid Sequence↗
PubMed1988

Computer-aided optimisation of drug enantiomer separation in chiral high-performance liquid chromatography.

The advent of several new column materials for the resolution of chiral compounds in high-performance liquid chromatography has opened up new possibilities for the analysis of drug enantiomers both in the dosage form and in bioanalytical studies. The utility of simplex optimisation, modified simplex and response surface mapping are considered with reference to the antischistosomal drug, oxamniquine, separated on an alpha 1-acid glycoprotein column. The resolution of the enantiomers of three closely related benzodiazepines, temazepam, oxazepam and lorazepam, is attempted on three new column systems: cellulose triacetate, beta-cyclodextrin and the reversed-phase column porous graphitic carbon with beta-cyclodextrin as a mobile phase additive.

Chromatography, High Pressure Liquid↗
PubMed1992

The gene for dominant white color in the pig is closely linked to ALB and PDGRFRA on chromosome 8.

White is a widespread coat color among domestic pig breeds and is controlled by an autosomal dominant gene I. The segregation of this gene was analyzed in a reference pedigree for gene mapping developed by crossing the European wild pig and a Large White domestic breed. The gene for dominant white color was shown to be closely linked to the genes for albumin (ALB) and platelet-derived growth factor receptor alpha (PDGFRA) on chromosome 8. An unexpected phenotype with patches of colored and white coat was observed among the F1 and F2 animals. The segregation data indicated that the phenotype was controlled by a third allele, denoted patch (Ip), most likely transmitted by one of the Large White founder animals. It is shown that the ALB, PDGFRA, I linkage group shares homologies with parts of mouse chromosome 5, human chromosome 4, and horse linkage group II, all of which contain dominant genes for white or white spotting. Candidate genes for the dominant white and patch mutations in the pig are proposed on the basis on these linkage homologies and the recent molecular definition of the dominant white spotting (W) and patch (Ph) mutations in the mouse.

Albumins↗
PubMed2006

Effects of familiarity on mothers' talk about nouns and verbs.

Modifications mothers make when talking to young English-speaking children between the ages of 1;8 and 3;0 (average age = 2;4) about words perceived to be familiar versus unfamiliar were investigated. Nineteen mothers and their children participated in two toy play tasks; one designed to elicit talk about familiar and unfamiliar animals and the other designed to elicit talk about familiar and unfamiliar actions. It was found that mothers' talk involving unfamiliar words differed from talk involving familiar words in a number of ways. Some modifications served to highlight the unfamiliar word which could assist in segmenting the unfamiliar word and mapping it to its referent. Compared to familiar nouns and verbs, unfamiliar nouns and verbs were produced more frequently in highly salient utterance positions and were paired more consistently with a clear nonverbal referent. Familiar nouns but, not verbs, were produced in longer utterances than unfamiliar nouns which could support the child's elaboration of the lexical representation of the familiar word.

Adult↗
PubMedDate not supplied

Trypsin-based monolithic bioreactor coupled on-line with LC/MS/MS system for protein digestion and variant identification in standard solutions and serum samples.

The applicability of a trypsin-based monolithic bioreactor coupled on-line with LC/MS/MS for rapid proteolytic digestion and protein identification is here described. Dilute samples are passed through the bioreactor for generation of proteolytic fragments in less than 10 min. After digestion and peptide separation, electrospray ionization tandem mass spectrometry is used to generate a peptide map and to identify proteolytic peptides by correlating their fragmentation spectra with amino acid sequences from a protein database. By digesting picomoles of proteins sufficient data from ESI and MS/MS were obtained to unambiguously identify proteins alone and in serum samples. This approach was also extended to locate mutation sites in beta-lactoglobulin A and B variants.

Amino Acid Sequence↗
PubMed2006

Protein separation and characterization by np-RP-HPLC followed by intact MALDI-TOF mass spectrometry and peptide mass mapping analyses.

Because of their complexity, the separation of intact proteins from complex mixtures is an important step to comparative proteomics and the identification and characterization of the proteins by mass spectrometry (MS). In the study reported, we evaluated the use of nonporous-reversed-phase (np-RP)-HPLC for intact protein separation prior to MS analyses. The separation system was characterized and compared to 1D-SDS-PAGE electrophoresis in terms of resolution and sensitivity. We demonstrate that np-RP-HPLC protein separation is highly reproducible and provides intact protein fractions which can be directly analyzed by MALDI-TOF-MS for intact molecular weight determination. An in-well digestion protocol was developed, allowing for rapid protein identification by peptide mass fingerprinting (PMF) and resulted in comparable or improved peptide recovery compared with in-gel digestion. The np-RP sensitivity of detection by UV absorbance at 214 nm for intact proteins was at the low ng level and the sensitivity of peptide analysis by MALDI-TOF-MS was in the 10-50 fmol level. A membrane protein fraction was characterized to demonstrate application of this methodology. Among the identified proteins, multiple forms of vimentin were observed. Overall, we demonstrate that np-RP-HPLC followed by MALDI-TOF-MS allows for rapid, sensitive, and reproducible protein fractionation and very specific protein characterization by integration of PMF analysis with MS intact molecular weight information.

Animals↗
PubMed2004

Relative timing of isolated potentials during postinfarction ventricular tachycardia and sinus rhythm.

BACKGROUND: In postinfarction patients, isolated potentials separated by an isoelectric segment from the ventricular electrogram indicate areas of block. Isolated potentials can be recorded during both sinus rhythm and ventricular tachycardia (VT). In an attempt to differentiate bystander pathways from critical sites within a reentry circuit, we compared the relative timing of isolated potentials during VT and sinus rhythm. METHODS: In 19 patients (mean age 68 +/- 6 years) with postinfarction VT who were referred for VT ablation, mapping was performed in the presence and absence of VT. Forty-three sites at which there was concealed entrainment during 35 VT's (mean cycle length 469 +/- 74 ms) displayed an isolated potential separated from the main portion of the ventricular electrogram by an isoelectric segment of >/=30 msec in the presence and absence of VT. The interval between the ventricular electrogram and the isolated potential was measured during VT and baseline rhythm, and the absolute difference (DeltaIPI) was calculated. The DeltaIPI was significantly greater at effective ablation sites (119 +/- 69 ms) than at ineffective ablation sites (30 +/- 28 ms, p < 0.001). The positive predictive value of a DeltaIPI > 85 ms for an effective ablation site was 100%. CONCLUSION: At sites of concealed entrainment, an absolute difference >85 ms between the isolated potential intervals during sinus rhythm and VT is highly specific for a critical area of the VT reentry circuit in post-infarction patients.

Action Potentials↗
PubMed1988

An enhancer-like element present in the promoter of a T-DNA gene from the Ti plasmid of Agrobacterium tumefaciens.

The promoter of the 780 gene of T-right [Thomashow, M., Nutter, R., Montoya, A., Gordon, M. & Nester, E. (1980) Cell 19, 729-739] from Agrobacterium tumefaciens Ti plasmid (pTi15955) was shown to contain an upstream cis-acting element (activator) having enhancer-like properties. To characterize the properties of this promoter element, it was placed in both polarities, upstream and downstream of a Delta-37 deletion mutant of the 780 gene. The Delta-37 deletion contains the entire 780 gene with the 5' flanking sequences deleted upstream of TATA to -37. The effect of the activator on in vivo transcriptional activity was assessed by S1 nuclease mapping utilizing a homologous reference gene as an internal standard. Transcript levels from sunflower crown gall tumors were between 127% and 90% of the wild-type 780 gene depending on the polarity of the activator element when placed directly upstream to the 780 gene Delta-37 promoter. Repositioning the activator element 613 base pairs further upstream increased transcription by 2-fold regardless of polarity. However, the activator element did not promote transcription when placed in either polarity approximately 200 base pairs downstream of the poly(A) addition site. Upstream promoter fragments (TATA-distal) from the octopine synthase (ocs) and agropine synthase (ags) genes were also tested for activation of the Delta-37 construction. The ocs sequences activated transcription of the Delta-37 deletion to 14% of wild-type levels when placed upstream in the B (reverse) orientation. All other constructions with the ocs and ags sequences showed no enhancement of promoter activity.

Journal Article↗
PubMed1990

Distinct antibody specificities to a 64-kD islet cell antigen in type 1 diabetes as revealed by trypsin treatment.

Type 1 diabetes is associated with antibodies that immunoprecipitate a 64-kD islet cell membrane protein from detergent extracts of pancreatic islets. In this study we have determined whether mild trypsin treatment of islet membranes can release fragments of the antigen that bind antibodies in the serum of Type 1 diabetic patients. Partial tryptic proteolysis of [35S]methionine-labeled 64-kD antigen immunoprecipitated from detergent extracts of rat islets resulted in the formation of 50-, 40-, and 37-kD fragments. Similar sized fragments were recovered when sera from diabetic patients were employed to immunoprecipitate polypeptides solubilized by mild trypsin treatment of a particulate fraction of radiolabeled rat islets. Of 27 diabetic patients, 22 possessed antibodies to the 50-kD polypeptide and 21 to the 40- and 37-kD polypeptides. A positive association was found between 64k antibodies and antibodies to the 50-kD fragment but not between 64k antibodies and antibodies to the 40- or 37-kD fragments. Some 64k antibody negative patients possessed antibodies that efficiently immunoprecipitated the latter fragments. Serum from 25 of 27 (93%) diabetic patients immunoprecipitated at least one of the three tryptic polypeptides. One of 20 nondiabetic controls immunoprecipitated a 50-kD polypeptide and all controls were negative for antibodies to 40- and 37-kD fragments. Thus, Type 1 diabetes is associated with the presence of at least two antibody reactivities to distinct determinants of the 64-kD antigen, and some patients may possess antibodies to a cryptic epitope on the detergent-solubilized molecule. These data suggest that the detection of antibodies (present in 93% of patients) to epitopes on tryptic polypeptides of the 64-kD antigen may be of even greater diagnostic value for the onset of Type 1 diabetes than analyses of antibodies reactive with the intact 64-kD antigen.

Adolescent↗
PubMed2026

NoisyFlow: differentially private optimal transport using neural networks for secure biomedical data sharing across multiple institutions.

MOTIVATION: Biomedical models improve when trained on data pooled across institutions, but sensitive patient records (e.g. genomics, clinical data, and medical images) are difficult to share due to privacy constraints. Moreover, data collected at different sites often have shifted distributions because of covariate differences (including batch effects), so privacy-preserving sharing alone cannot simply resolve cross-site mismatch. Methods that protect individuals while explicitly aligning distributions are needed to enable reliable multi-institutional analyses. RESULTS: We present NoisyFlow, a three-stage differentially private framework for cross-institutional harmonization under distribution shift. In stage I, each site learns a differentially private flow-based generator of its local labeled distribution. In stage II, it learns a neural optimal transport map to a shared reference distribution. In stage III, a central server composes the released models to generate reference-aligned pseudo-data for downstream analysis without accessing raw records. Across four biomedical settings spanning single-cell genomics, histopathology, neurogenomics, and wearable sensing, NoisyFlow reduces distribution shift while preserving downstream utility under formal differential privacy guarantees. AVAILABILITY AND IMPLEMENTATION: The implementation of NoisyFlow is available at https://github.com/gersteinlab/NoisyFlow.

Information Dissemination↗
PubMed1999

The Eukaryotic Promoter Database (EPD): recent developments.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Recent efforts have focused on exhaustive cross-referencing to the EMBL nucleotide sequence database, and on the improvement of the WWW-based user interfaces and data retrieval mechanisms. EPD can be accessed at http://www.epd.isb-sib.ch

Algorithms↗
PubMedDate not supplied

Use of jackknife resampling techniques to estimate the confidence intervals of fMRI parameters.

PURPOSE: The objective of this study was to determine the reliability and the confidence intervals of task-activated functional MRI (fMRI) parameters using a computer-intensive resampling technique. The jackknife, a commonly used method for resampling mathematical data, was used to calculate the confidence interval of fMRI parameters for a simple bilateral finger-tapping paradigm. METHOD: Four healthy test subjects (three men, one woman) were used to test the correlation coefficient and variability in the data. Each subject performed 4.5 cycles, each cycle having 20 s of bilateral finger tapping alternating with rest periods of equal time, producing 90 images. One additional scan of 10 cycles (200 images) was used to test the stability of the method itself. One thousand jackknifed resampled data sets of 85 elements each (from 90 original points) were generated, and the correlation coefficient was determined using an idealized "on/off" box-car reference waveform. RESULTS: Activation maps were generated that had the same confidence intervals at each pixel. These maps were more localized with less extraneous activated pixels than the maps generated with a fixed correlation coefficient threshold. There was no significant difference in the distribution of correlation coefficients between the 85, 90, and 95 element, jackknifed data sets; similar robustness was seen, as well. CONCLUSION: The jackknife resampling technique for data analysis produced reliable distributions and statistical parameters. The jackknife estimates were shown to be stable, even from a small initial sample size. This method may be used in lieu of test-retest analysis.

Adolescent↗
PubMed2004

Amorphous silicon, flat-panel, x-ray detector: reliability of digital image fusion regarding angle and distance measurements in long-leg radiography.

RATIONALE AND OBJECTIVES: To evaluate composed long-leg images acquired with a large-area, flat-panel x-ray detector with regard to angle and distance measurements. METHODS: Radiographs of a long-leg phantom were acquired at 13 different angle settings with a 43-cm x 43-cm digital x-ray detector based on cesium iodide (CsI) and amorphous silicon (a-Si) technology. Three overlapping single images of the phantom were reconstructed at a workstation using a generalized correlation method. Four blinded observers were instructed to determine the angle of the axis of the long-legs as well as the length of "femur" and "tibia" on soft-copy displays. For that, the angle and distance measurement software integrated in the workstation was used. The images were analyzed with and without prior manual fine tuning of the primary composition result according to a mapped scale. Standard of reference was angle and distance determination at the phantom. RESULTS: On average, the difference between the observers' angle measurements and the standard of reference was 0.4 degrees for both images with and without prior manual correction. Regarding distance measurements, the average discrepancies to the standard were 0.2 cm (femur) and 0.1 cm (tibia) when analyzing images that had undergone manual fine tuning and 0.5 cm and 0.7 cm, respectively, for images without manual correction. CONCLUSIONS: The evaluated image fusion algorithm in conjunction with a 43-cm x 43-cm flat-panel detector is feasible regarding angle and distance measurements on long-leg images. In the case of inaccurate primary composition, results can be corrected easily by manual fine tuning.

Algorithms↗
PubMed2005

Examining the architecture of cellular computing through a comparative study with a computer.

The computer and the cell both use information embedded in simple coding, the binary software code and the quadruple genomic code, respectively, to support system operations. A comparative examination of their system architecture as well as their information storage and utilization schemes is performed. On top of the code, both systems display a modular, multi-layered architecture, which, in the case of a computer, arises from human engineering efforts through a combination of hardware implementation and software abstraction. Using the computer as a reference system, a simplistic mapping of the architectural components between the two is easily detected. This comparison also reveals that a cell abolishes the software-hardware barrier through genomic encoding for the constituents of the biochemical network, a cell's "hardware" equivalent to the computer central processing unit (CPU). The information loading (gene expression) process acts as a major determinant of the encoded constituent's abundance, which, in turn, often determines the "bandwidth" of a biochemical pathway. Cellular processes are implemented in biochemical pathways in parallel manners. In a computer, on the other hand, the software provides only instructions and data for the CPU. A process represents just sequentially ordered actions by the CPU and only virtual parallelism can be implemented through CPU time-sharing. Whereas process management in a computer may simply mean job scheduling, coordinating pathway bandwidth through the gene expression machinery represents a major process management scheme in a cell. In summary, a cell can be viewed as a super-parallel computer, which computes through controlled hardware composition. While we have, at best, a very fragmented understanding of cellular operation, we have a thorough understanding of the computer throughout the engineering process. The potential utilization of this knowledge to the benefit of systems biology is discussed.

Cell Physiological Phenomena↗
PubMed2025

A complete diploid human genome benchmark for personalized genomics.

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental duplications, and satellite repeats, including 39,144 protein-coding genes across both haplotypes. To facilitate application of the benchmark, we developed tools for measuring the accuracy of sequencing reads, phased variant call sets, and genome assemblies against a diploid reference. Genome-wide analyses show that state-of-the-art de novo assembly methods resolve 2-7% more sequence and outperform variant calling accuracy by an order of magnitude, yielding just one error per 100 kb across 99.9% of the benchmark regions. Adoption of genome-based benchmarking is expected to accelerate the development of cost-effective methods for complete genome sequencing, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.

Journal Article↗