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Ultrasound color-flow imaging on a programmable system.

Color-flow imaging is a well-established ultrasound mode and very valuable for visualizing in real time the distribution of blood flow in a specific region of interest. However, it is computationally quite expensive. To meet the large computational need in color-flow imaging, most ultrasound systems have been designed using fixed-function hardware. In this paper, we present a system where all the color-flow processing is supported on a programmable platform. About 95% of the processing modules were programmed in C language. On a single processor, we were able to achieve 7.9 frames/s, when the input data consist of 192 x 512 x 8 (ensemble size) samples for color flow and 384 x 512 for B mode and the output image size is 600 x 420. Additional processors can be added to handle more input data and/or support higher frame rates. Our results demonstrate that a programmable ultrasound system can provide the same functionality for clinical use as conventional ultrasound systems. However, it is more flexible and efficient due to its programmability.

Algorithms↗

Development of a chipscale integrated microelectrode/microelectronic device for brain implantable neuroengineering applications.

An ultralow power analog CMOS chip and a silicon based microelectrode array have been fully integrated to a microminiaturized "neuroport" for brain implantable neuroengineering applications. The CMOS integrated circuit (IC) includes preamplifier and multiplexing circuitry, and a hybrid flip-chip bonding technique was developed to fabricate a functional, encapsulated microminiaturized neuroprobe device. Our neuroport has been evaluated using various methods, including pseudospike detection and local excitation measurement, and showed suitable characteristics for recording neural activities. As a proof-of-concept demonstration, we have measured local field potentials from thalamocortical brain slices of rats, suggesting that the new neuroport can form a prime platform for the development of a microminiaturized neural interface to the brain in a single implantable unit. An alternative power delivery scheme using photovoltaic power converter, and an encapsulation strategy for chronic implantation are also discussed.

Action Potentials↗

Clinical determinants of biomechanics platform measures of balance in aged women.

The cross-sectional associations between clinical variables and biomechanics platform measures of balance (sway) were determined in a random sample of 50 aged single women living in high rise apartment buildings. A history of falling in the previous year was associated with increased areas of sway. Increased body mass was associated with decreased velocity of sway. Poor near, but not far, visual acuity was associated with increased areas of sway. A postural drop of 10 mmHg or more in diastolic pressure was associated with increased velocity of sway. The associations between these variables and the balance measures persisted after adjustment for age and each other to adjust for potential confounding. Slower hand reaction times and poor hearing were associated with increased areas of sway, but these associations were removed after adjustment for age and near visual acuity. There were no associations between any of the balance measures and postural changes in systolic pressure and heart rate. There were no associations between balance measures and base of support. The observed associations, if causal, can aid in development and testing of effective interventions to improve balance and prevent falls in the elderly.

Accidental Falls↗

Parallelization of general-linkage analysis problems.

We describe a parallel implementation of a genetic-linkage analysis program that achieves good speed improvement, even for analyses on a single pedigree and with a single starting recombination fraction vector. Our parallel implementation has been run on three different platforms: an Ethernet network of workstations, a higher-bandwidth asynchronous transfer mode (ATM) network of workstations, and a shared-memory multiprocessor. The same program, written in a shared-memory programming style, is used on all platforms. On the workstation networks, the hardware does not provide shared memory, so the program executes on a distributed shared memory system that implements shared memory in software. These three platforms represent different points on the price/performance scale. Ethernet networks are cheap and omnipresent, ATM networks are an emerging technology that offers higher bandwidth, and shared-memory multiprocessors offer the best performance because communication is implemented entirely by hardware. On 8 processors and for the longer runs, we achieve speedups between 3.5 and 5 on the Ethernet network and between 4.8 and 6 on the ATM network. On the shared-memory multiprocessor, we achieve speedups in the 5.5-6.5 range for all runs.

Algorithms↗

Recommendations from the ASPH/Legacy Scholarship, Training, and Education Program for Tobacco Use Prevention (STEP UP) strategy planning meeting Chicago, May 3, 2005.

During this meeting, the participants developed a strategic set of recommendations for ASPH to continue to advance the study of tobacco control in public health through research and education/training programs. The meeting focused on sustaining and further developing tobacco-related research and education/ training programs. All four issues were addressed in depth through valuable discussion and exchange and reflected in the nine areas of focus. Recommendations for advocacy for future funding for SPH in tobacco control included developing collaborative relationships with ASPH partners, organizations, and institutions with complementary objectives (state departments of health, third party payors, etc). Priorities for sustaining and further developing research and education/training programs within SPH included developing a focus on particular research areas (e.g., special populations, economic issues, dissemination and translational issues), building on existing knowledge, and attempting to avoid the effects of "siloing" with collaborative relationships and methods for addressing the sustenance of programs beyond initial funding periods. Methods to maintain vigilance on tobacco control with increasing concerns about other risk factors included fostering an increasing awareness of tobacco-related issues, projects, and programs as well as developing collaborative relationships with organizations and institutions with complementary health-risk related objectives. Other recommendations focused on enhancing SPH leadership in the tobacco control field by developing standards and methodologies and translating research to practice. They included (1) developing standards for consistent tobacco control-related education to public health students, public health professionals, and other students and professionals; (2) developing a standardized method for evaluating tobacco-attributable factors and effects; and (3) conducting effectiveness trials of treatments known to be efficacious. Effectively addressing these perennial issues will enable SPH to enhance its leadership position and contribute greatly to research and education/training in tobacco control. All of these issues were factors in program planning for the second National STEP UP Academic Tobacco Workshop. For instance, reviews of particular research areas might be offered or facilitated as well as methods for developing collaborative partnerships and subsequent efforts. Steps toward the development of tobacco control education core competencies might be developed as well. The second National STEP UP Academic Tobacco Workshop-STEP UP to Sustain Tobacco Control and Prevention through Education and Research--was held on January 30-31, 2006. The topics of discussion ranged from use of secondary data to behavioral economics. More information about the workshop can be found at http://www.asph.org/ document.cfm?page=882. Attention to the recommendations that resulted from the planning meeting will provide a strategic platform from which ASPH and the public health community can continue to address the single greatest cause of preventable disease and death in the world.

Education, Continuing↗

Algorithms and tools for data-driven omics integration to achieve multilayer biological insights: a narrative review.

Systems biology is a holistic approach to biological sciences that combines experimental and computational strategies, aimed at integrating information from different scales of biological processes to unravel pathophysiological mechanisms and behaviours. In this scenario, high-throughput technologies have been playing a major role in providing huge amounts of omics data, whose integration would offer unprecedented possibilities in gaining insights on diseases and identifying potential biomarkers. In the present review, we focus on strategies that have been applied in literature to integrate genomics, transcriptomics, proteomics, and metabolomics in the year range 2018-2024. Integration approaches were divided into three main categories: statistical-based approaches, multivariate methods, and machine learning/artificial intelligence techniques. Among them, statistical approaches (mainly based on correlation) were the ones with a slightly higher prevalence, followed by multivariate approaches, and machine learning techniques. Integrating multiple biological layers has shown great potential in uncovering molecular mechanisms, identifying putative biomarkers, and aid classification, most of the time resulting in better performances when compared to single omics analyses. However, significant challenges remain. The high-throughput nature of omics platforms introduces issues such as variable data quality, missing values, collinearity, and dimensionality. These challenges further increase when combining multiple omics datasets, as the complexity and heterogeneity of the data increase with integration. We report different strategies that have been found in literature to cope with these challenges, but some open issues still remain and should be addressed to disclose the full potential of omics integration.

Algorithms↗

Reagents to measure and manipulate cell functions.

Reagents that are used as part of a discovery platform for the measurement and manipulation of cell functions are at the heart of single and multiplexed high content screening assays. Measurement reagents include physiological indicators, immunoreagents, fluorescent analogs of macromolecules, positional biosensors, and fluorescent protein biosensors. Recent developments in reagents that manipulate specific cell functions including small inhibitory RNAs, caged peptides, proteins, and RNAs, and gene switches complement measurement reagents, especially when both classes of reagents are used in the same living cells. The use measurement and manipulation reagents in multiplexed high content screening assays promises to enable a systems cell biology approach to drug discovery and biomedical research.

Animals↗

Surface-enhanced Raman scattering for cancer diagnostics: detection of the BCL2 gene.

A method of detection for cancer genes, such as B-cell lymphoma 2 gene, has been developed using surface-enhanced Raman scattering-active substrates. This method uses Raman active dye-labeled DNA gene probes and metallic nanostructures as surface-enhanced Raman scattering-active platforms. A self-assembled monolayer system composed of mercapto hexane-labeled, single-strand DNA (SH-(CH2)6-ssDNA/ 6-mercapto-1-hexanol) is formed on a silver surface. The Raman-active dye-labeled gene is hybridized with its complementary probe, which is immobilized on the silver surface. The surface-enhanced Raman gene probes in this study can be used to detect DNA targets via hybridization to complementary DNA probes. The probes do not involve the use of radioactive labels and have great potential to provide both sensitivity and selectivity. The utility of this approach is investigated.

DNA Probes↗

Static versus dynamic prosthetic weight bearing in elderly trans-tibial amputees.

The purpose of this study was to compare prosthetic weight-bearing tolerance in the standing position to the dynamic vertical ground reaction forces (VGRF) experienced during walking in elderly dysvascular trans-tibial amputees. Ten unilateral trans-tibial amputees attending an amputee clinic (mean age = 67 +/- 6.5 years) were selected as subjects. Selection criteria were the level of amputation, age, medical fitness to participate and informed consent. Each participant completed five trials of standing (static) weight bearing measurement followed by 10 walking (dynamic) trials on a 10m level walkway, five trials for each limb, Static weight bearing (SWB) was measured using standard bathroom scales. Dynamic weight bearing (DWB) was measured during gait using a Kistler multichannel force platform. T-tests for dependent means indicated that the forces borne in prosthetic single limb stance (mean = 0.97 +/- 0.03 times body weight (BW)) were significantly lower than the forces borne by the prosthetic limb during the first peak (weight acceptance) VGRF (mean = 1.08 +/- 0.08 BW; t = -4.999; p = 0.001) and significantly higher than the midstance VGRF (mean = 0.82 +/- 0.07 BW; t = 5.401; p < 0.001). However, there was no significant difference between SWB and the second peak (push-off) VGRF generated by the prosthetic limb during walking (mean = 0.96 +/- 0.03 BW). It was concluded that clinical gait training may utilise SWB as a guide to an amputees' prosthetic weight bearing tolerance and requirements during walking.

Aged↗

High-efficiency multiplex capillary electrophoresis single strand conformation polymorphism (multi-CE-SSCP) mutation screening of SCN5A: a rapid genetic approach to cardiac arrhythmia.

Mutations in the SCN5A gene coding for the alpha-subunit of the cardiac Na(+) ion channel cause long QT syndrome, Brugada syndrome, idiopathic ventricular fibrillation, sick sinus node syndrome, progressive conduction disease, dilated cardiomyopathy and atrial standstill. These diseases exhibit variable expressivity, and identification of gene carriers is clinically important, particularly in sudden infant and adult death syndromes. The SCN5A gene comprises 28 exons distributed over 100 kbp of genomic sequence at chromosome 3p21. Disease-causing mutations are private and scattered over the DNA sequence, making it difficult to screen for specific mutations. We developed a multiplex capillary-electrophoresis single-strand conformation polymorphism (Multi-CE-SSCP) mutation screening protocol on the ABI 3100 platform and applied it to 10 previously slab-gel SSCP identified mutations and SNPs and used it to identify one novel deletion. The method is highly efficient, with a turnover of 23 patients per 24 h and a false positive rate of 0.5% of the analyzed amplicons. Each variant has a particular elution pattern, and all 20 carriers of the H558R polymorphism out of 57 persons were correctly identified. We suggest that the method could become part of routine work-up of patients with suspicious syncope and of members of families with sudden unexplained death.

Amino Acid Substitution↗

ATG deserts define a novel core promoter subclass.

The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro. Here, we define a novel core promoter feature that supports regulated transcription through selective transcription start site (TSS) usage. We demonstrate that TSS selection is actively regulated and context dependent. Basal and activated transcriptions initiate from largely nonoverlapping TSS regions. Transcripts derived from multiple TSS encode a single protein, due to the absence of any ATG triplets within approximately 430 bp upstream of the major transcription start site. Thus, the PD1 core promoter is embedded within an "ATG desert". Remarkably, extending this analysis genome-wide, we find that ATG deserts define a novel promoter subclass. They occur nonrandomly, are significantly associated with non-TATAA promoters that use multiple TSS, independent of the presence of CpG islands (CGI). We speculate that ATG deserts may provide a core promoter platform upon which complex upstream regulatory signals can be integrated, targeting multiple TSS whose products encode a single protein.

Animals↗

High throughput genotyping technologies for pharmacogenomics.

Genetic differences between individuals play a role in determining susceptibility to diseases as well as in drug response. The challenge today is first to discover the range of genetic variability in the human population and then to define the particular gene variants, or alleles, that contribute to clinically important outcomes. Consequently, high throughput, automated methods are being developed that allow rapid scoring of microsatellite alleles and single nucleotide polymorphisms (SNPs). Many detection technologies are being used to accomplish this goal, including electrophoresis, standard fluorescence, fluorescence polarization, fluorescence resonance energy transfer, and mass spectrometry. SNP alleles may be distinguished by any one of several methods, including single nucleotide primer extension, allele-specific hybridization, allele-specific primer extension, oligonucleotide ligation assay, and invasive signal amplification. Newer methods require less sample manipulation, increase sensitivity, allow more flexibility, and decrease reagent costs. Recent developments show promise for continuing these trends by combining amplification and detection steps and providing flexible, miniaturized platforms for genotyping.

Automation↗

OligoSeq: Rapid nanopore-sequencing of single-stranded oligonucleotides.

Nanopore-based DNA sequencing technology has achieved remarkable success in sequencing increasingly long DNA strands (e.g., over a million nucleotides long) for genomics research and biotechnology applications. However, the same level of progress has not been achieved for DNA oligonucleotides (usually &#x2264; 300 nucleotides long). Oligonucleotides play a crucial role in genome engineering efforts through oligo library generation and in DNA data storage, where they are used to encode computer information, such as binary (digital) data in DNA libraries. To enable these applications, accurate sequencing of oligonucleotides in a way that allows to assess for sequence variability, quality and length is essential. But sequencing solutions for oligonucleotides - particularly DNA primers for PCR, oligo DNA libraries used for mutagenesis or cDNA libraries used in gene expression analysis - remain inadequate. To address this gap, OligoSeq is presented as an innovative approach that integrates two complementary techniques: AmpliSeq (based on PCR) and RevSeq (based on reverse complementation with sequence-specific or random primers) to facilitate sequencing of single-stranded oligonucleotides using reference sequence anchor matches of more than &#x2265; 90% identity spanning from about 70% to 10% with AmpliSeq or RevSeq with random nonamers, respectively, and resolving the final reference sequence based on the most likely candidate from basecall frequencies, regardless of length and double-stranding method. OligoSeq can be integrated with nanopore sequencing technology pipelines and can be used as a reference for other sequencing platforms requiring double-stranded adapters, offering a practical and scalable alternative for standard quality control in single-stranded oligonucleotide synthesis. The use of nanopore technology, compatible with the double-stranding methods showcased, is shown to be the most cost-effective method for resolving original DNA sequences of different length and quality, and to assess its sequence variability, compared to other methods such as Illumina, PacBio or HPLC/MS.

Sequence Analysis, DNA↗

Microgenomics: Identification of new expression profiles via small and single-cell sample analyses.

BACKGROUND: Since the sequencing of the human genome has been finished, microgenomics has been booming, employing highly sophisticated, high-throughput platforms. But these mainly chip-based methods can only generate biologically relevant data if the samples investigated consist of homogeneous cell populations, in which no unwanted cells of different specificity and/or developmental stage obscure the results. METHODS: Different sampling methods have been routinely applied to overcome the problem presented by heterogeneous samples, e.g., global surveys, cell cultures, and microdissection. Various methods of laser-assisted microdissection, employing either positive or negative selection of tissue areas or even single cells, are available. RESULTS: These laser-assisted microdissection methods allow for fast and precise procurement of extremely small samples. Through subsequent application of recently developed methods of linear mRNA amplification in a pool of isolated total RNA, it has now become possible to perform complex high-throughput RNA expression profiling by microdissecting and processing even single-cell samples. CONCLUSIONS: Studies using the tools and methods of microgenomics have shed light on how those new approaches will eventually aid in the development of a new generation of diagnostics, e.g., leading to new patient-specific drugs tailored to the requirements assessed by assaying only a few biopsy cells.

Cell Separation↗

An HPLC/mass spectrometry platform for the development of multimodality contrast agents and targeted therapeutics: prostate-specific membrane antigen small molecule derivatives.

The production of disease-targeted agents requires the covalent conjugation of a targeting molecule with a contrast agent or therapeutic, followed by purification of the product to homogeneity. Typical targeting molecules, such as small molecules and peptides, often have high charge-to-mass ratios and/or hydrophobicity. Contrast agents and therapeutics themselves are also diverse, and include lanthanide chelates for MRI, (99m)Tc chelates for SPECT, (90)Y chelates for radiotherapy, (18)F derivatives for PET, and heptamethine indocyanines for near-infrared fluorescent optical imaging. We have constructed a general-purpose HPLC/mass spectrometry platform capable of purifying virtually any targeted agent for any modality. The analytical sub-system is composed of a single dual-head pump that directs mobile phase to either a hot cell for the purification of radioactive agents or to an ES-TOF MS for the purification of nonradioactive agents. Nonradioactive agents are also monitored during purification by ELSD, absorbance and fluorescence. The preparative sub-system is composed of columns and procedures that permit rapid scaling from the analytical system. To demonstrate the platform's utility, we describe the preparation of five small molecule derivatives specific for prostate-specific membrane antigen (PSMA): a gadolinium derivative for MRI, indium, rhenium and technetium derivatives for SPECT, and an yttrium derivative for radiotherapy. All five compounds are derived from a highly anionic targeting ligand engineered to have a single nucleophile for N-hydroxysuccinimide-based conjugation. We also describe optimized column/mobile phase combinations and mass spectrometry settings for each class of agent, and discuss strategies for purifying molecules with extreme charge and/or hydrophobicity. Taken together, our study should expedite the development of disease-targeted, multimodality diagnostic and therapeutic agents.

Antigens, Surface↗

A Programmable Nanovaccine Platform Based on M13 Bacteriophage for Personalized Cancer Vaccine and Therapy.

Nanovaccines co-assemble antigens and adjuvants to elicit robust immune responses but often require complex synthesis and post-modification procedures. Here, a programmable nanovaccine platform based on the M13 bacteriophage is developed for the scalable production of vaccines and single-step modular engineering of adjuvanticity, length, and antigen density. By reprogramming the sequence and size of the noncoding phage genome, the Toll-like receptor 9 activation and the length of the phage are precisely controlled. With a novel molecular engineering approach, the antigen density is tuned from 13.6% to 70.3%. A systematic modulation reveals an optimal adjuvanticity at a constant antigen density for maximum anti-tumor CD8+ T cell response, and vice versa, using the model antigen SIINFEKL. The M13 phage-based nanovaccine induces durable memory immunity lasting over a year. In addition, a 24-fold increase in neoantigen-specific CD8+ T cell frequency is achieved when increasing both the adjuvanticity and antigen density. Furthermore, when combined with anti-PD-1 therapy, the M13 phage-based personalized vaccine eradicates established MC-38 tumors in 75% of treated animals and they develop 100% resistance against tumor invasion when challenged 5 months after treatment. These findings establish M13 phage as a powerful and versatile nanovaccine platform with transformative potential for personalized cancer immunotherapy.

Cancer Vaccines↗

Leftist sexual politics and homosexuality: a historical overview.

For almost a full century now, the revolutionary prospect of socialism has fuelled opening forays first of the homosexual emancipation and later of the gay liberation movements, both in Europe and in North America. It inspired Edward Carpenter and Magnus Hirschfeld at the turn of the century; André Gide and Richard Linsert in the post-World War I years; Harry Hay and Jim Kepner in the post-World War II era; and the British and American Gay Liberation Front, the Italian Fuori!, the French FHAR, the German "Rotzschwule," and the Dutch Red Faggots following the Stonewall rebellion. While the official socialist parties of Northwestern Europe may have made only limited contributions to homosexual emancipation, they certainly have a better record than conservative and Christian parties and even the liberals, who have consistently, if contradictorily, underlined the freedom of private life. Even so, parties across the entire political spectrum have gradually come to endorse at least some of the movement's goals. As it has advanced, the gay movement has changed as well, and it now finds itself pulled in divergent directions. Gay leftists who still subscribe to the ideals expressed in Marxist and utopian socialist writings now find themselves at demonstrations shoulder-to-shoulder with members of ACT UP and Queer Nation, to say nothing of gay conservatives and gay Christians. The successes achieved by the contemporary gay movement despite or precisely because of its diversity support Foucault's argument that "there is no single locus of great Refusal, no soul of revolt, source of all rebellions, or pure law of the revolutionary. Instead there is a plurality of resistances, each of them a special case...." At the close of the twentieth century, the welfare state has reached its apogee in Northwestern Europe. As blue-collar workers historically committed to class struggle have become relatively well-to-do and minoritarian, socialist parties have increasingly lost their traditional base of support and been forced into the defensive. Depending only on the socialists would mean relying on an ineffectual partner, for nowhere are they in a stable position of power. Long before the collapse of "really existing socialism" in Eastern Europe and the former Soviet Union, gay and lesbian movements began developing their own autonomous politics independent of parties. They moved in this direction in part because the coalition with leftism so frequently led to disappointment, particularly when gays and lesbians working within socialist parties were called upon to subordinate or abandon their own goals in favor of party platforms. In other cases the gay-left coalition failed to yield results because a single-minded reliance on one party placed limits on lobbying other parties and entering compromises. We have reached a time when inherited ideologies are no longer capable of laying claim to the undivided loyalty of the gay movement, if indeed they ever were. As it has developed autonomous theories and practices, the gay movement's choice of coalition partners has increasingly come to be based on pragmatism and success in advancing the gay agenda. Indeed, the roles of the gay movement and political parties have undergone a notable switch in recent years, with parties currying the support of the gay movement rather than vice versa. This signals a shift from the desire for politics to a politics of desire, going far beyond traditional socialist ideologies.

Europe↗

Synchronization of motor units in human soleus muscle during standing postural tasks.

During standing posture, the soleus muscles acts to control sway in the anteroposterior (AP) direction. The soleus muscles bilaterally share a common function during standing tasks. We sought to determine whether common descending inputs, as evidenced by the synchronization of bilateral motor unit pairs, were employed as a strategy to control this common function. Single motor units were recorded from the soleus muscles in subjects who stood on adjacent force platforms for 5 min with their eyes open or closed. While standing with the eyes open, only 4/39 bilateral motor unit pairs showed significant synchronization. Similarly, only 3/36 motor unit pairs were significantly synchronized during the eyes closed task. The low incidence of synchronization was observed despite a high correlation in the amount of sway in the AP direction between legs in both the eyes open and eyes closed tasks (rho = 0.80 and rho = 0.83, respectively). When the extent of synchronization was assessed between pairs of motor units within the same leg with the eyes open, 10/12 pairs were synchronized. Furthermore, when pairs of soleus motor units were recorded both bilaterally and unilaterally during voluntary isometric ankle plantarflexion, only 4/30 bilateral pairs showed significant synchronization, whereas 19/24 unilateral pairs had significant synchronization. In this study, there was little evidence of the existence of synchronization between bilateral soleus motor unit pairs in either postural tasks or voluntary isometric contractions. In cases in which bilateral synchronization was observed, it was considerably weaker than the synchronization of motor units within a single soleus muscle. The results of this study reveal that it is rather uncommon for bilateral soleus motoneurons to receive common descending synaptic inputs, whereas two motoneurons within a single soleus muscle do.

Action Potentials↗