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PubMed1997

Thrombin generation measured ex vivo following microvascular injury is increased in SLE patients with antiphospholipid-protein antibodies.

Antiphospholipid-protein antibodies (APA) include lupus-type anticoagulant (LA) and antibodies recognizing complexes of anionic phospholipids (e.g. cardiolipin) and proteins (e.g. prothrombin and beta2-glycoprotein I). The presence of APA is associated with an increased risk of both arterial and venous thrombosis. However, the pathogenic mechanism leading to thrombosis in patients with APA remains unclear. We studied 32 patients with systemic lupus erythematosus (SLE) who were divided into two groups depending on the presence (n = 19) or absence (n = 13) of APA. Healthy volunteers (n = 12) matched by age and sex served as controls. In all subjects LA and IgG class anticardiolipin antibodies (ACA) were determined. Thrombin generation was monitored ex vivo measuring fibrinopeptide A (FPA) and prothrombin fragment F1 + 2 (F1 + 2) in blood emerging from a skin microvasculature injury, collected at 30 second intervals. In subjects with antiphospholipid antibodies mean FPA and F1 + 2 concentrations were significantly higher at most blood sampling times than in controls. In some SLE patients with APA the process of thrombin generation was clearly disturbed and very high concentrations of fibrinopeptide A were detected already in the first samples collected. Two minutes after skin incision SLE patients without APA produced slightly more FPA, but not F1 + 2, as compared to healthy subjects. Mathematical model applied to analyze the thrombin generation kinetics revealed that APA patients generated significantly greater amounts of thrombin than healthy controls (p = 0.02 for either marker). In contrast, in the same patients generation of thrombin in recalcified plasma in vitro was delayed pointing to the role of endothelium in the phenomenon studied. In summary, these data show for the first time that in SLE patients with antiphospholipid-protein antibodies thrombin generation after small blood vessel injury is markedly increased. Enhanced thrombin generation might explain thrombotic tendency observed in these patients.

Adult↗
PubMed1997

Inhibition of thrombin generation in plasma by inhibitors of factor Xa.

A series of inhibitors of factor Xa (FXa) were investigated using the thrombin generation assay to evaluate the potency and specificity needed to efficiently block thrombin generation in activated human plasma. By inhibiting FXa the generation of thrombin in plasma is delayed and decreased. Inhibitor concentrations which cause 50 percent inhibition of thrombin generation (IC50) correlate in principle with the Ki values for inhibition of free FXa. Recombinant tick anticoagulant peptide (r-TAP) is able to inhibit thrombin generation with considerably low IC50 values of 49 nM and 37 nM for extrinsic and intrinsic activation, respectively. However, the potent synthetic, low molecular weight inhibitors of FXa (Ki values of about 20 nM) are less effective in inhibiting the generation of thrombin with IC50 values at micromolar concentrations. The overall effect of inhibitors of FXa in the thrombin generation assay was compared to that of thrombin inhibitors. On the basis of similar Ki values for the inhibition of the respective enzyme, synthetic FXa inhibitors are less effective than thrombin inhibitors. In contrast, the highly potent FXa inhibitor r-TAP causes a stronger reduction of the thrombin activity in plasma than the most potent thrombin inhibitor hirudin.

Animals↗
PubMed1976

The cofactors required by C3 nephritic factor to generate a C3 convertase in vitro.

The mechanisms by which a C3 convertase is generated by C3 nephritic factor (NeF) were investigated using purified NeF, C3, C3b, factor B and factor D of the alternative pathway of complement activation. NeF could generate a C3 convertase with C3 and B in the absence of D, and without cleavage of B. At lower concentrations of NeF the addition of D was required to generate a C3 convertase, and B cleavage now occurred. The generation of both the D-independent and D-dependent C3 convertases with NeF was inhibited by preincubation of the C3 source with C3b inactivator (KAF); isolated C3b was more efficient than the C3 preparations used in generating the D-independent C3 convertase with NeF. These experiments indicate that C3b is required for the formation of both convertases, and that the reaction occurring with apparently native C3 is due to trace amounts of C3b. It is concluded that the C3 convertase generated by NeF in the absence of D is C3bB (NeF), and that generated in the presence of D is the feedback convertase C3bBb. The relevance of these experiments to reactions which may occur in vivo is discussed.

Biological Products↗
PubMed1998

Atherogenic lipoproteins support assembly of the prothrombinase complex and thrombin generation: modulation by oxidation and vitamin E.

The importance of lipoproteins in the etiology of atherosclerosis is well established. Evidence is now accumulating to implicate thrombin in the pathogenesis of atherosclerosis. We have investigated whether atherogenic lipoproteins can support thrombin generation. In the absence of platelets or endothelial cells, both very low-density lipoprotein (VLDL) and oxidized low-density lipoprotein (LDL) support assembly of the prothrombinase complex and generation of thrombin. Thrombin generation (per microgram of apolipoprotein) supported by VLDL was 19.4-fold greater than that supported by high-density lipoprotein (HDL), P < .00001, and 11.7-fold greater than that supported by LDL, P < .00001. Oxidation of LDL increased lipoprotein-supported thrombin generation 12-fold compared to unmodified LDL, P < .0001. We have shown that the phenomenon of lipoprotein-supported thrombin generation is mediated predominantly by specific phospholipids and is enhanced by oxidation of these phospholipids. The addition of vitamin E (alpha-tocopherol) markedly reduced the increase in thrombin generation observed after oxidation of LDL (822 +/- 57 v 138 +/- 47 nmol/L; P < .0001). These effects suggest that lipoproteins are important in the production of thrombin and that vitamin E may confer protection from the detrimental effects of lipoprotein oxidation by limiting thrombin formation. These results suggest that atherogenic lipoproteins are linked to the development of atherosclerosis in part by their capacity to support thrombin generation.

Adult↗
PubMed1998

Ageing and generational conflicts: a reply to Sarah Irwin.

In response to Sarah Irwin, the article develops a conflict model of inter-generational exchanges and treats generation as a neglected dimension of social stratification theory and research. Against Irwin's focus on individual attitudes from survey data towards intra-familial co-operation between generations, the article draws on public policy on dependency, legislation on retirement, superannuation and pensions, and stereotypes of the elderly to study inter-generational inequalities. Employing Pierre Bourdieu's distinction between cultural and economic capital, it considers the formation of generations around political events, shared culture and strategic advantage. Generational conflict is structurally organized around the tensions between early retirement, age-related competency, legislation on ageism, and youth unemployment. Given rapid and radical changes to the labour market, generational cohesion is an important dimension therefore of strategies of social closure.

Aged↗
PubMedDate not supplied

Computer-generated correspondence for patients attending an open-access chest pain clinic.

AIM: To determine whether general practitioners (GPs) prefer structured computer-generated or standard dictated outpatient clinic letters. DESIGN: Questionnaire survey of all GPs referring patients to an open-access chest pain clinic at a district general hospital in London. The GPs were asked to compare three twinned examples of structured computer-generated and unstructured dictated letters. RESULTS: Of 93 respondents (response rate 77.5%), 75 (80.6%) preferred the computer-generated letter and 16 (17.2%) preferred the dictated letter (p < 0.0005). The preferred features of the computer-generated letter were its clear presentation, subheadings, and concise information. The computer-generated letter scored significantly higher than the dictated letter: for clarity, mean 8.2 vs 6.5 (p < 0.0005); content, mean 8.5 vs 6.9 (p < 0.0005); and readability, mean 8.2 vs 6.8 (p < 0.0005). The GPs in the survey considered a mean delay of 3.4 days to be acceptable for receiving the letter from the chest pain clinic. CONCLUSION: GPs prefer structured computer-generated letters to unstructured dictated letters for patients referred to an open-access chest pain clinic. Computer-generated correspondence allows rapid feedback of information to the referring GP, one of the key requirements of open-access clinics.

Ambulatory Care Facilities↗
PubMed1998

Trauma and identity through two generations of the Holocaust.

In summary, these four second generation women were/are in search of an equilibrium which includes integrating approach-avoidance feelings about their upbringing. They have struggled in various ways, through their own personal styles, with issues of enmeshment with their parents' ordeals, and this has helped to shape their identities. The approach-avoidance dilemma around the suffering of their parents involves finding a way to separate from, yet to include in the meaning of their lives, the suffering of their parents. In these women, empathy preserves the "good" aspect of the parent and in the end allows for separateness to be achieved. An evolution of their approach to the Holocaust occurs throughout their lives and is enhanced by their having children. Creativity and knowledge play an important role in the expression of tormented feelings in both second and third generations. The issues grappled with by the second generation reverberate in their children. This is a group of resolute, serious people who believe in the preciousness of life. They are also thoughtful, empathic youngsters, aware of social and political inequities. These third-generation members feel somewhat burdened by the legacy of the Holocaust, inasmuch as they feel obligated to stand up for Jewish identity and be successful in their own lives. Placing the suffering in a larger group context helps the second generation confront the suffering of their parents. This diminishes individual liability so that the suffering does not have to be taken on personally. The cause goes beyond the self and the family. When, as in Sylvia's case, this outlook is not achieved, the struggle against family enmeshment continues. Seeing the suffering in a group context creates a different set of responsibilities, that of allegiance and closeness to the group. It promotes a need to find meaning in the suffering, a need to cope with the sense of identification with group loss. This urge for empathy is accompanied by its opposite, a wish to dissociate, and the need consequently to negotiate boundaries. The struggle for integration of various feelings becomes a part of their identity in both generations. This paper points to the possibility that, as the Holocaust becomes part of a story, a myth, it becomes a guide (albeit perhaps of a demanding one) by which to live life rather than simply a recall of death. The work of memory has been completed, at times embellished. It also includes, however, a continuous wake up call to vulnerability, a sense of burden, a "chronic" sense of the seriousness and preciousness of life. This paper therefore reflects the fact that suffering can be channeled into identity formation, integrated into an articulation of the meaning of life and a philosophy of life. As the third generation's identity becomes intimately intertwined with its origins, a feeling of continuity is developed which provides a sense of affirmation of the group and of the self. It does, however, also include an awareness of the suffering of that group and in the world at large.

Adolescent↗
PubMed2026

Deep generative models in biological sequence and structure analysis and design.

Deep generative models have transformed biological sequence modeling from predictive analysis toward increasingly controllable design. Early biological applications of Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs) established latent representation learning and sequence synthesis, while recent advances in transformer-based language models, discrete diffusion, flow-matching, and multimodal generative frameworks have substantially expanded the scope of biological design. This review examines generative models for DNA, RNA, and protein sequence design, emphasizing how different model classes represent biological constraints, operate over discrete and continuous spaces, and integrate sequence, structure, and function. We compare VAEs, GANs, autoregressive and masked language models, diffusion models, and flow-based approaches across genomics, transcriptomics, and proteomics, with particular attention to controllability, long-range dependency modeling, structural grounding, generalization, and experimental utility. We further examine evaluation strategies, out-of-distribution generalization, and closed-loop design-build-test-learn workflows that connect in silico generation with empirical validation. We distinguish fundamental modality-dependent constraints including sequence discreteness, context length, structural coupling, and physical or thermodynamic requirements from architecture-dependent advantages that reflect the current state of the field. Current studies suggest that long-context models are particularly useful for genome-scale representation and sequence modeling, whereas structure-aware diffusion, flow-based, and inverse-folding approaches provide better frameworks for geometry-constrained RNA and protein design. This perspective provides a critical framework for understanding the present capabilities, limitations, and convergence of generative approaches toward reliable and experimentally grounded biological design.

Biological sequence analysis↗
PubMed2026

Generative artificial intelligence for enzyme design and biocatalysis.

Sparked by innovations in generative artificial intelligence (AI), the field of protein design has undergone a paradigm shift with an explosion of new models for optimizing existing enzymes or creating them from scratch. After more than one decade of low success rates for computationally designed enzymes, generative AI models are now frequently used for designing proficient enzymes. Here, we provide a comprehensive overview and classification of generative AI models for enzyme design, highlighting models with experimental validation relevant to real-world settings and outlining their respective limitations. We argue that generative AI models now have the maturity to create and optimize enzymes for industrial applications. Wider adoption of generative AI models with experimental feedback loops can speed up the development of biocatalysts and serve as a community assessment to inform the next generation of models.

Biocatalysis↗
PubMed2006

The costs, air quality, and human health effects of meeting peak electricity demand with installed backup generators.

Existing generators installed for backup during blackouts could be operated during periods of peak electricity demand, increasing grid reliability and supporting electricity delivery. Many generators, however, have non-negligible air emissions and may potentially damage air quality and harm human health. To evaluate using these generators, we compare the levelized private and social (health) costs of diesel internal combustion engines (ICE) with and without diesel particulate filters (DPF), natural gas ICEs, and microturbines to a new peaking plant in New York, NY. To estimate the social cost, first we calculate the upper range emissions for each generator option from producing 36,000 megawatt-hours (MWh) of electricity over 3 days. We then convert the emissions into ambient concentrations with a 3-D chemical transport model, PMCAMx, and Gaussian dispersion plumes. Using a Monte Carlo approach to incorporate the uncertainties, we calculate the health endpoints using concentration-response functions and multiply the response by its economic value. While uncontrolled diesel ICEs would harm air quality and health, a generator with a DPF has a social cost, comparable to natural gas options. We conclude on a full cost basis that backup generators, including controlled diesel ICEs, are a cost-effective method of meeting peak demand.

Air Pollution↗
PubMed2026

PepGen: conditional generation of peptides for MHC binding.

MOTIVATION: Peptide-MHC II binding drives adaptive immunity, yet discovery of novel binder peptides remains challenging due to open binding grooves of MHC-II that accommodate variable-length peptides. While discriminative models perform well, they are unfeasible for generation via enumeration due to vast peptide space (2013&#x2248;8&#xd7;1016 for peptides of length 13 amino acids). Generative AI approaches could accelerate binder design to enable vaccines targeted to particular MHC-II alleles or optimize other peptide chemical properties. RESULTS: We introduce PepGen, the first protein language model for MHC II peptide generation building on Generalized Language Modeling. PepGen conditions on alleles, arbitrary partial peptides including putative TCR-interacting motifs, and continuous binding affinity. Across multiple benchmarks including infilling and de novo generation, PepGen outperformed frequency sampling, Gibbs clustering, and autoregressive baselines. Adjusted log-probabilities enable good classification performance. Experimental validation confirmed that the SARS-CoV-2 peptide TEGALNTPKDHIGTR binding the HLA-DQA101:03-DQB106:03 allele can be redesigned to bind the HLA-DQA101:02-DQB105:02 allele. PepGen generated three putative TCR-motif-preserving binders gaining up to 70% of original MFI. Overall, PepGen provides scalable, motif-constrained MHC II peptide redesign and de novo generation, validated through thorough benchmarks and functional assays. AVAILABILITY AND IMPLEMENTATION: Code and Data are available at https://github.com/DaniTheOrange/PepGen.

Peptides↗
PubMed2005

Efficacy and safety of second-generation antidepressants in the treatment of major depressive disorder.

BACKGROUND: Reviews have compared the efficacy and tolerability of newer second-generation antidepressants with those of placebo or older treatments, but comparative evidence for use of second-generation antidepressants to treat major depressive disorder has not been evaluated. PURPOSE: To systematically evaluate comparative data on the efficacy, effectiveness, and tolerability of commonly prescribed second-generation antidepressants (selective serotonin reuptake inhibitors, bupropion, duloxetine, mirtazapine, and venlafaxine) in the treatment of major depressive disorder. DATA SOURCES: MEDLINE, EMBASE, and PsychLit; the Cochrane Library; and the International Pharmaceutical Abstracts were searched from January 1980 through February 2005 for reviews; randomized, controlled trials; meta-analyses; and observational studies. STUDY SELECTION: The authors reviewed 46 head-to-head randomized, controlled trials comparing one second-generation antidepressant with another. Twenty-four observational studies and placebo-controlled trials were also included for assessment of safety and tolerability. DATA EXTRACTION: Two researchers independently reviewed titles and abstracts. Trained reviewers abstracted data from each study and assigned an initial quality rating. A second reviewer verified the data extraction and quality rating. DATA SYNTHESIS: According to fair to good evidence, the second-generation antidepressants that were compared had only minimal differences in efficacy, and 88% of comparative efficacy studies reported no statistically significant difference in any outcome measure at the end of the study. One effectiveness trial rated good and 2 effectiveness trials rated fair reported no statistically significant differences in primary outcome measures for compared drugs. Meta-analyses showed a modest but statistically significant additional treatment effect for sertraline and venlafaxine compared with fluoxetine. About 96% of comparative trials were sponsored by or had at least 1 author affiliated with a pharmaceutical company; the remaining trials did not report funding sources. Adverse event profiles differed among drugs; however, the degree and quality of adverse event assessment varied and only 13% of trials used a standardized scale to assess adverse events. LIMITATIONS: Quantitative analyses could not be done for many drug comparisons because the quantity and quality of the evidence were inadequate. Most published evidence was from trials sponsored by pharmaceutical companies, and publication bias may have occurred. CONCLUSIONS: Overall, second-generation antidepressants probably do not differ substantially for treatment of major depressive disorder. Choosing the agent that is most appropriate for a given patient is difficult.

Antidepressive Agents, Second-Generation↗
PubMed1996

Time-resolved observations of shock waves and cavitation bubbles generated by femtosecond laser pulses in corneal tissue and water.

BACKGROUND AND OBJECTIVE: Photodisruption in ocular media with high power pulsed lasers working at non-absorbing frequencies have become a well established surgical tool since the late seventies. Shock waves and cavitation bubbles generated by the optical breakdown may strongly influence the surgical effect of photodisruptive lasers. We have investigated the shock wave and cavitation bubble effects of femtosecond laser pulses generated during photodisruption in corneal tissue and water. The results are compared to those obtained with longer laser pulses. STUDY DESIGN/MATERIALS AND METHODS: Laser pulses with 150 fs duration at approximately 620 nm wavelength have been focused into corneal tissue and water to create optical breakdown. Time-resolved flash photography has been used to investigate the dynamics of the generated shock waves and cavitation bubbles. RESULTS: A rapid decay of the shock waves is observed in both materials with similar temporal characteristics and with a spatial range considerably smaller than that of shock waves induced by picosecond (or nanosecond) optical breakdown. Cavitation bubbles are observed to develop more rapidly and to reach smaller maximum diameter than those generated by longer pulses. In corneal tissue, single intrastromal cavitation bubbles generated by femtosecond pulses disappear within a few tens of seconds, notably faster than cavitation bubbles generated by picosecond pulses. CONCLUSIONS: The reduced shock wave and cavitation bubble effects of the femtosecond laser result in more localized tissue damage. Therefore, a more confined surgical effect should be expected from a femtosecond laser than that from picosecond (or nanosecond) lasers. This indicates a potential benefit from the applications of femtosecond laser technology to intraocular microsurgery.

Absorption↗
PubMed1997

Reactive oxygen species generation by human spermatozoa is induced by exogenous NADPH and inhibited by the flavoprotein inhibitors diphenylene iodonium and quinacrine.

Human spermatozoa possess a specialized capacity to generate reactive oxygen species (ROS) that is thought to be of significance in the redox regulation of sperm capacitation (De Lamirande and Gagnon, 1993; Aitken et al., 1995). However, the mechanisms by which ROS are generated by these cells are not understood. In this study we have examined the possible significance of NADPH as a substrate for ROS production by human spermatozoa. Addition of NADPH to viable populations of motile spermatozoa induced a sudden dose-dependent increase in the rate of superoxide generation via mechanisms that could not be disrupted by inhibitors of the mitochondrial electron transport chain (antimycin A, rotenone, carbonyl cyanide m-chlorophenylhydrazone [CCCP], and sodium azide), diaphorase (dicoumarol) xanthine oxidase (allopurinol), or lactic acid dehydrogenase (sodium oxamate). However, NADPH-induced ROS generation could be stimulated by permeabilization and was negatively correlated with sperm function. Both NADH and NADPH were active electron donors in this system, while NAD+ and NADP+ exhibited little activity. Stereo-specificity was evident in the response in that only the beta-isomer of NADPH supported superoxide production. The involvement of a flavoprotein in the electron transfer process was indicated by the high sensitivity of the oxidase to inhibition by diphenylene iodonium and quinacrine. These results indicate that NAD(P)H can serve as an electron donor for superoxide generation by human spermatozoa and present a simple strategy for the production of motile populations of free radical generating cells with which to study the significance of these molecules in the control of normal and pathological sperm function.

Acridines↗
PubMed1998

Generation of the vesicular stomatitis virus nucleoprotein cytotoxic T lymphocyte epitope requires proteasome-dependent and -independent proteolytic activities.

The proteasome is involved in the generation of most of the MHC class I antigenic epitopes. However, it is not known if the proteasome generates the exact cytotoxic T lymphocyte (CTL) epitope or only epitope precursors which require further modification by additional proteases. Digestion of the extended vesicular stomatitis virus nucleoprotein epitope 52-59 (RGYVYQGL) by the 20S proteasome in vitro shows that the proteasome is capable of generating the correct C terminus but not the exact N terminus of the CTL epitope. This finding suggests that proteolytic activity in addition to the proteasome is required for generation of the CTL epitope. By using the proteasome inhibitor lactacystin we were able to confirm this finding in vivo. Lactacystin prevented the processing of N- and C-terminally extended epitopes, whereas the processing of only N-terminally extended epitopes was unaffected. Thus, the proteasome is necessary and sufficient for the generation of the exact C terminus of this CTL epitope, whereas the exact N terminus seems to be generated by a different protease.

Acetylcysteine↗
PubMed2000

In situ generation and screening of a dynamic combinatorial carbohydrate library against concanavalin A.

Dynamic combinatorial chemistry (DCC) is a recently introduced approach that is based on the generation of combinatorial libraries by reversible interconversion of the library constituents. In this study, the implementation of such libraries on carbohydrate-lectin interactions was examined. The dynamic carbohydrate libraries were generated from a small set (four or six compounds) of initial carbohydrate dimers through mild disulfide interchange, and selection was performed under two conditions defining either adaptive or pre-equilibrated libraries. Upon initiation, libraries were formed that contained comparable amounts of 10 or 21 individual dimeric species, dynamically interchanging during the scrambling process. They were probed with respect to binding to the plant lectin concanavalin A, either present during library generation or added after equilibration. The libraries could be generated easily both in the presence and absence of the receptor, and a bis-mannose structure was preferentially bound and selected from the mixture. Scrambling of the library in the presence of the receptor resulted in slightly higher yields than when the receptor was added after scrambling, indicating that the receptor to some extent acts as a thermodynamic trap during library generation. The present results illustrate the extention of the DCC approach to carbohydrate recognition groups, the generation of isoenergetic dynamic libraries, and the implementation of either adaptive or pre-equilibrated procedures.

Carbohydrate Conformation↗
PubMed2000

Defining sameness: historical, biological, and generative homology.

Current debate concerning homology arises from three different research interests-phylogenetics, character evolution, and generative pathways. Phylogenetic homology focuses on descent of the character from a common ancestor. Biological homology addresses character evolution and diversification. Exceptions to the general case complicate these two approaches: historically and biologically homologous characters may be produced by different generative pathways, and minutely similar characters produced by the same generative pathways may have a sporadic phylogenetic distribution. We suggest that for studies of comparative developmental biology, new descriptive terms are needed to distinguish similar structures that result from the same generative pathways from those that result from different generative pathways. The terms syngeny, meaning "same genesis", and allogeny, meaning "different genesis", allow the acknowledgement of sameness at the generative level and can be used in combination with the terminology of historical homology and biological homology to describe any given character.

Animals↗
PubMed2004

Expanded RED products and loci containing CAG/CTG repeats on chromosome 17 (ERDA1) and chromosome 18 (CTG18.1) in trans-generational pairs with bipolar affective disorder.

The purpose of the present study was to further test if expanded CAG repeats detected by the repeat expansion detection (RED) method in bipolar affective disorder (BPAD) are correlated with ERDA1 (17q21.3) and/or CTG18.1 (18q21.1) loci expansions, and changes of phenotype severity in successive generations (anticipation). The sample was designed to analyze ERDA1 and CTG18.1 expansions in trans-generational pairs of affected individuals (parent-offspring pairs: G1 and G2). Clinical and genetic information was available on 95 two-generations pairs. We found in our sample no one patient carrying an expanded allele at the CTG18.1 locus. This observation is true for all individuals in G1 and G2. Using the conditional logistic regression, no statistical difference was observed between the two generations for ERDA1 alleles (chi(2) = 0.2, P = 0.65). These data do not support the correlation between expanded RED products (RED fragments >120) and expanded alleles at ERDA1 in trans-generational pairs with BPAD. We were not able to detect any correlation for CTG18.1. Earlier age at onset in offspring generation was also not associated with expanded RED products explained by expanded ERDA1 alleles.

Adult↗