A modular computational framework for medical digital twins.

This paper presents a modular software design for the construction of computational modeling technology that will help implement precision medicine. In analogy to a common industrial strategy used for preventive maintenance of engineered products, medical digital twins are computational models of disease processes calibrated to individual patients using multiple heterogeneous data streams. They have the potential to help improve diagnosis, prognosis, and personalized treatment for a wide range of medical conditions. Their large-scale development relies on both mechanistic and data-driven techniques and requires the integration and ongoing update of multiple component models developed across many different laboratories. Distributed model building and integration requires an open-source modular software platform for the integration and simulation of models that is scalable and supports a decentralized, community-based model building process. This paper presents such a platform, including a case study in an animal model of a respiratory fungal infection.

Three-dimensional geometric morphometric analysis of the skull of Protoceratops andrewsi supports a socio-sexual signalling role for the ceratopsian frill.

Socio-sexual selection is predicted to be an important driver of evolution, influencing speciation, extinction and adaptation. The fossil record provides a means of testing these predictions, but detecting its signature from morphological data alone is difficult. There are, nonetheless, some specific patterns of growth and variation which are expected of traits under socio-sexual selection. The distinctive parietal-squamosal frill of ceratopsian dinosaurs has previously been suggested as a socio-sexual display trait, but evidence for this has been limited. Here, we perform a whole-skull shape analysis of an unprecedentedly large sample of specimens of Protoceratops andrewsi using a high-density landmark-based geometric morphometric approach to test four predictions regarding a potential socio-sexual signalling role for the frill. Three predictions-low integration with the rest of the skull, significantly higher rate of change in size and shape during ontogeny, and higher morphological variance than other skull regions-are supported. One prediction, sexual dimorphism in shape, is not supported, suggesting that sexual differences in P. andrewsi are likely to be small. Together, these findings are consistent with mutual mate choice or selection for signalling quality in more general social interactions, and support the hypothesis that the frill functioned as a socio-sexual signal in ceratopsian dinosaurs.

Placing an upper limit on cryptic marine sulphur cycling.

A quantitative understanding of sources and sinks of fixed nitrogen in low-oxygen waters is required to explain the role of oxygen-minimum zones (OMZs) in controlling the fixed nitrogen inventory of the global ocean. Apparent imbalances in geochemical nitrogen budgets have spurred numerous studies to measure the contributions of heterotrophic and autotrophic N2-producing metabolisms (denitrification and anaerobic ammonia oxidation, respectively). Recently, 'cryptic' sulphur cycling was proposed as a partial solution to the fundamental biogeochemical problem of closing marine fixed-nitrogen budgets in intensely oxygen-deficient regions. The degree to which the cryptic sulphur cycle can fuel a loss of fixed nitrogen in the modern ocean requires the quantification of sulphur recycling in OMZ settings. Here we provide a new constraint for OMZ sulphate reduction based on isotopic profiles of oxygen ((18)O/(16)O) and sulphur ((33)S/(32)S, (34)S/(32)S) in seawater sulphate through oxygenated open-ocean and OMZ-bearing water columns. When coupled with observations and models of sulphate isotope dynamics and data-constrained model estimates of OMZ water-mass residence time, we find that previous estimates for sulphur-driven remineralization and loss of fixed nitrogen from the oceans are near the upper limit for what is possible given in situ sulphate isotope data.

Photosynthetic responses of a dominant C4 grass to an experimental heat wave are mediated by soil moisture.

Extreme heat waves and drought are predicted to increase in frequency and magnitude with climate change. These extreme events often co-occur, making it difficult to separate their direct and indirect effects on important ecophysiological and carbon cycling processes such as photosynthesis. Here, we assessed the independent and interactive effects of experimental heat waves and drought on photosynthesis in Andropogon gerardii, a dominant C4 grass in a native mesic grassland. We experimentally imposed a two-week heat wave at four intensity levels under two contrasting soil moisture regimes: a well-watered control and an extreme drought. There were three main findings from this study. First, the soil moisture regimes had large effects on canopy temperature, leading to extremely high temperatures under drought and low temperatures under well-watered conditions. Second, soil moisture mediated the photosynthetic response to heat; heat reduced photosynthesis under the well-watered control, but not under the extreme drought treatment. Third, the effects of heat on photosynthesis appeared to be driven by a direct thermal effect, not indirectly through other environmental or ecophysiological variables. These results suggest that while photosynthesis in this dominant C4 grass is sensitive to heat stress, this sensitivity can be overwhelmed by extreme drought stress.

Antiviral RNA silencing suppression activity of Tomato spotted wilt virus NSs protein.

In addition to regulating gene expression, RNA silencing is an essential antiviral defense system in plants. Triggered by double-stranded RNA, silencing results in degradation or translational repression of target transcripts. Viruses are inducers and targets of RNA silencing. To condition susceptibility, most plant viruses encode silencing suppressors that interfere with this process, such as the Tomato spotted wilt virus (TSWV) NSs protein. The mechanism by which NSs suppresses RNA silencing and its role in viral infection and movement remain to be determined. We cloned NSs from the Hawaii isolate of TSWV and using two independent assays show for the first time that this protein restored pathogenicity and supported the formation of local infection foci by suppressor-deficient Turnip mosaic virus and Turnip crinkle virus. Demonstrating the suppression of RNA silencing directed against heterologous viruses establishes the foundation to determine the means used by NSs to block this antiviral process.

[Sleeve gastrectomy as a revision procedure for failed gastric banding]. / Schlauchmagenbildung als Revisionseingriff nach Magenbandversagen.

The number of bariatric surgical procedures is still increasing in Germany and also worldwide. According to the German quality assurance study of surgical treatment of obesity, the laparoscopic adjustable gastric banding (LAGB) was the most common bariatric operation with a total of 678 cases between 2004 and 2006 in Germany. In the meantime a high rate of LAGB treatment failures has been reported, so that a high rate of revisional bariatric operations is required. But still the question is open which bariatric procedure can be recommended. The aim of this study is to report the results and follow-up of conversion of failed LAGB to laparoscopic sleeve gastrectomy (LSG). Between 8/2008 and 4/2012 39 patients (31♀/8♂) with a mean age of 43.7 ± 7.8 (26-61) years and a BMI of 47.1 ± 9.1 (30.4 to 67.4) kg/m² had revisional surgery for converting a failed LAGB to LSG. The indications for conversion were dysphagia (38.5 %), weight regain (33.3 %), band slippage (17.9 %), band erosion (5.1 %), band defect (2.6 %) as well as band sepsis (2.6 %). 19 procedures were performed as a one-stage operation and 20 procedures as a two-stage operation. The average operating time was 129 ± 49 (50-312) min. The complication rate was 7.7 %. There were one proximal leak, one gastric sleeve stenosis and one pronounced wound infection. The percent excess weight loss was 23 %, 39 %, 51 %, 52 %, 60 % and 46 % after 1, 3, 6, 12, 24 and 36 months follow- up, respectively. Converting a failed LAGB into a LSG is a revision procedure with low complication rate and promising results, which can be performed as a two-stage as well as a one-stage procedure.

Building digital twins of the human immune system: toward a roadmap.

Digital twins, customized simulation models pioneered in industry, are beginning to be deployed in medicine and healthcare, with some major successes, for instance in cardiovascular diagnostics and in insulin pump control. Personalized computational models are also assisting in applications ranging from drug development to treatment optimization. More advanced medical digital twins will be essential to making precision medicine a reality. Because the immune system plays an important role in such a wide range of diseases and health conditions, from fighting pathogens to autoimmune disorders, digital twins of the immune system will have an especially high impact. However, their development presents major challenges, stemming from the inherent complexity of the immune system and the difficulty of measuring many aspects of a patient's immune state in vivo. This perspective outlines a roadmap for meeting these challenges and building a prototype of an immune digital twin. It is structured as a four-stage process that proceeds from a specification of a concrete use case to model constructions, personalization, and continued improvement.

Media and technology usage and attitudes in emergency department patients.

Introduction: Digital health technologies are increasingly being used in emergency medicine, many of which utilize smartphones and computers. Patient willingness to use these modalities is an important factor in successful implementation. Therefore, this study aimed to assess emergency department (ED) patients' use of and attitudes towards technology. Methods: This was a pooled sub-analysis of ED patients (≥18 years old) that were enrolled in two studies evaluating the ED patient experience in response to novel technological interventions. Participants completed the Media and Technology Usage and Attitudes Scale (MTUAS) that assessed computer and smartphone ownership; frequency of use of phone calls, texting, email, and smartphones; and anxiety and dependence attitudes on these technologies. Results: One hundred and forty-four participants completed the survey. Mean age was 47.2 years (SD 17.94); 61.8% were female; and 61.1% were white. There was high usage of smartphones (93.1%) and computers (74.3%). Participants most frequently used phone calling and texting and least commonly used email. Participants had a positive attitude (mean 3.9/5, SD 0.68) towards the use of these technologies. Discussion: ED patients reported high ownership of smartphones and computers, had a positive attitude towards their use, and had varying frequency with which they used different technologies. Future studies can use this information to inform the development of digital health interventions that utilize technologies that patients find most acceptable.

Cytokeratin No. 9, an epidermal type I keratin characteristic of a special program of keratinocyte differentiation displaying body site specificity.

Plantar epidermis of the bovine heel pad as well as human plantar and palmar epidermis contain large amounts of an acidic (type I) keratin polypeptide (No. 9) of Mr 64,000 which so far has not been found in epidermis of other sites of the body. We present evidence for the keratinous nature of this protein, including its ability to form cytokeratin complexes and intermediate-sized filaments in vitro. We have isolated RNA from plantar epidermis of both species and show, using translation in vitro, that these polypeptides are genuine products of distinct mRNAs. Using immunofluorescence microscopy with specific antibodies against this protein, we demonstrate its location in most cells of suprabasal layers of plantar epidermis as well as in sparse keratinocytes which occur, individually or in small clusters, in upper layers of epidermis of other body locations. We conclude that cytokeratin No. 9 is characteristic of a special program of keratinocyte differentiation which during morphogenesis is expressed in most epidermal keratinocytes of soles and palms but only in a few keratinocytes at other body sites. This example of cell type-specific expression of a member of a multigene family in relation to a body site-related program of tissue differentiation raises important biological questions concerning the regulation of keratinocyte differentiation and morphogenesis as well as the function of such topological heterogeneity within a given type of tissue.

Variation among biomes in temporal dynamics of aboveground primary production.

Interannual variability in aboveground net primary production (ANPP) was assessed with long-term (mean = 12 years) data from 11 Long Term Ecological Research sites across North America. The greatest interannual variability in ANPP occurred in grasslands and old fields, with forests the least variable. At a continental scale, ANPP was strongly correlated with annual precipitation. However, interannual variability in ANPP was not related to variability in precipitation. Instead, maximum variability in ANPP occurred in biomes where high potential growth rates of herbaceous vegetation were combined with moderate variability in precipitation. In the most dynamic biomes, ANPP responded more strongly to wet than to dry years. Recognition of the fourfold range in ANPP dynamics across biomes and of the factors that constrain this variability is critical for detecting the biotic impacts of global change phenomena.

A pilot study of high-dose short duration daptomycin for the treatment of patients with complicated skin and skin structure infections caused by gram-positive bacteria.

BACKGROUND: Methicillin-susceptible and -resistant (MRSA) Staphylococcus aureus are significant causes of complicated skin and skin structure infections (cSSSI). The bactericidal antibiotic daptomycin is approved for gram-positive cSSSI at 4 mg/kg/day for 7-14 days, but the optimal dose level and duration of therapy have not been firmly established. This pilot study evaluated the efficacy and safety of daptomycin at 10 mg/kg every 24 h for 4 days [high-dose short duration (HDSD) regimen] vs. standard of care therapy with vancomycin or semi-synthetic penicillin for the treatment of cSSSI. METHODS: This was a semi-single blind, randomised, multicentre, comparative trial. The primary efficacy end-point was the clinical response 7-14 days posttherapy. RESULTS: One hundred patients were randomised; 48 in each arm were treated. The treatment groups were well balanced with respect to demographics, comorbidities and the type of infection (75% because of MRSA). Overall, clinical success rates were 75.0% (36/48) for daptomycin and 87.5% (42/48) for comparator (95% confidence interval for the difference: -27.9, 2.9). The median duration of comparator therapy was 8 days. Two comparator patients and no daptomycin patients experienced treatment-related serious adverse events requiring hospitalisation. CONCLUSION: We found that the HDSD regimen had a safety profile similar to that seen in previous studies. Although the differences were not statistically significant, clinical success rates for comparator were higher than for daptomycin. In post hoc analyses HDSD daptomycin performed better in some subgroups (e.g. outpatients) than in others (e.g. certain MRSA infections). These observations require confirmation in larger trials.

Biogas purification with biomass ash.

The aim of the study was to investigate the option to purify biogas from small-scale biogas plants by entrapping CO2 and H2S with regionally available biomass ash. Connected to the existing biogas plant Neustift (Tyrol) wood ash placed in a 1 m3 container was used as a trap for CO2 and H2S in the biogas. With the process conditions chosen, for a period of a few hours CO2 was trapped resulting in pure methane. The removal of H2S was much longer-lasting (up to 34 d). The cumulative H2S uptake by the biomass ash ranged from 0.56 to 1.25 kg H2S per ton of ash. The pH of the ash and the leachability of Lead and Barium were reduced by the flushing with biogas, however toxicity towards plants was increased thus reducing the potential of ash use in agriculture. It can be concluded that biomass ash may be used for removal of hydrogen sulphide from biogas in small and medium biogas plants. The economic evaluation, however, indicated that the application of this system is limited by transport distances for the ash and its potential use afterwards.

LC-MS/MS method for quantification of baclofen in hair: A useful tool to assess compliance in alcohol dependent patients?

To evaluate adherence to treatment, we developed and validated a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for baclofen quantification in hair.Twenty mg was washed twice with dichloromethane, incubated in phosphate buffer (pH 5) for 10 minutes at 95°C, then extracted by liquid-liquid extraction in alkaline condition. Baclofen-d4 was used as the internal standard. This method was applied to assess compliance in4 treated alcohol-dependent patients (3 dead and one living). Blood quantification of baclofen and ethanol were performed in the 4 cases. Hair ethylglucuronide (ethanol metabolite, EtG) measurement (2x3 cm) was associated in 1 patient. Baclofen quantification in hair was validated over the range 10-5000 pg/mg. The accuracy was within 96.0%-110.9% and the precision was less than 9.3%. Baclofen segmental (3x2cm) hair concentrations found in the living patient were 4420, 4260, and 4380 pg/mg, reflecting a regular exposure over the last 6 months and suggesting patient compliance. However, the high EtG level found in this patient in the analyzed segments (225 pg/mg and 215 pg/mg) showed excessive alcohol consumption during the same period, suggesting therapeutic failure. In the 3 deceased patients, the non-segmental analysis of hair showed baclofen concentrations of 15, 545, and 2475 pg/mg. The low concentrations in the 2 first cases are compatible either with a poor compliance or to a beginning of a treatment. This is the first measurement of baclofen in hair of alcohol dependent patients. It could be used as a monitoring biomarker to assess patient's compliance.

Evidence that the V kappa III gene usage is nonstochastic in both adult and newborn peripheral B cells and that peripheral CD5+ adult B cells are oligoclonal.

There is evidence that in certain situations the expressed antibody repertoire is dominated by small subsets of V gene segments. They include fetal, CD5+, and autoantibody-forming B cells as well as low grade B cell malignancies. For instance, inside the V kappa III family of approximately 10 members, only 3 (humkv325, 328, and Vg) are used recurrently for autoantibody production. However, the significance of this recurrence is difficult to interpret without a clear vision of the actual repertoire in normal subjects. To address this, we have sequenced and compared two sets of rearranged V kappa III genes generated by cDNA PCR amplification from a normal newborn, a normal adult, and from CD5+ B cells of the same adult donor. The results show that: (a) only four V kappa III gene segments are used by neonatal and total adult B cells (humkv325, humkv328, Vg, and kv305), humkv325 being overexpressed in both repertoires; (b) there is no significant difference in terms of V kappa III gene usage between the adult and newborn repertoires; (c) regarding the junction regions, there is a favored use of the most 5' JK gene segments (Jk1-Jk2); approximately 20% of the newborn and adult junction sequences was characterized by one or two additional codons, most probably resulting from a nontemplate addition of nucleotides; (d) adult clones, in contrast to most newborn clones, show sequence divergences from prototype sequences with patterns which suggest antigen-driven diversity; (e) regarding the adult CD5+ B cell library, it is most probable that the 78 clones analyzed derived from no more than nine different VK-JK rearrangements. Humkv325 is used by at least six of them, and most of the expressed V genes were in exact or very near germline configuration. Collectively these results suggest that the expressed antibody V kappa III repertoire in the adult represents only a fraction of the potential genetic information and that it resembles the preimmune repertoire of the neonate. The data, which also suggest that the adult peripheral blood CD5+ B cell population may be dominated by a small number of B cell clones, are discussed with regards to the V kappa III usage in pathological situations.

A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.

We have found that a novel basic helix-loop-helix (bHLH) protein is expressed almost exclusively in the epidermal attachments sites for the somatic muscles of Drosophila melanogaster. A Drosophila cDNA library was screened with radioactively labeled E12 protein, which can dimerize with many HLH proteins. One clone that emerged from this screen encoded a previously unknown protein of 360 amino acids, named delilah, that contains both basic and HLH domains, similar to a group of cellular transcription factors implicated in cell type determination. Delilah protein formed heterodimers with E12 that bind to the muscle creatine kinase promoter. In situ hybridization with the delilah cDNA localized the expression of the gene to a subset of cells in the epidermis which form a distinct pattern involving both the segmental boundaries and intrasegmental clusters. This pattern was coincident with the known sites of attachment of the somatic muscles to tendon cells in the epidermis. delilah expression persists in snail mutant embryos which lack mesoderm, indicating that expression of the gene was not induced by attachment of the underlying muscles. The similarity of this gene to other bHLH genes suggests that it plays an important role in the differentiation of epidermal cells into muscle attachment sites.

The response of c-jun/AP-1 to chronic hypoxia is hypoxia-inducible factor 1 alpha dependent.

Hypoxia (low-oxygen tension) is an important physiological stress that influences responses to a wide range of pathologies, including stroke, infarction, and tumorigenesis. Prolonged or chronic hypoxia stimulates expression of the stress-inducible transcription factor gene c-jun and transient activation of protein kinase and phosphatase activities that regulate c-Jun/AP-1 activity. Here we describe evidence obtained by using wild-type and HIF-1 alpha nullizygous mouse embryonic fibroblasts (mEFs) that the induction of c-jun mRNA expression and c-Jun phosphorylation by prolonged hypoxia are completely dependent on the presence of the oxygen-regulated transcription factor hypoxia-inducible factor 1 alpha (HIF-1 alpha). In contrast, transient hypoxia induced c-jun expression in both types of mEFs, showing that the early or rapid induction of this gene is independent of HIF-1 alpha. These findings indicate that the c-jun gene has a biphasic response to hypoxia consisting of inductions that depend on the degree or duration of exposure. To more completely define the relationship between prolonged hypoxia and c-Jun phosphorylation, we used mEFs from mice containing inactivating mutations of critical phosphorylation sites in the c-Jun N-terminal region (serines 63 and 73 or threonines 91 and 93). Exposure of these mEFs to prolonged hypoxia demonstrated an absolute requirement for N-terminal sites for HIF-1 alpha-dependent phosphorylation of c-Jun. Taken together, these findings suggest that c-Jun/AP-1 and HIF-1 cooperate to regulate gene expression in pathophysiological microenvironments.

Epidermal growth factor modifies cell cycle control in A431 human squamous carcinoma cells damaged by ionizing radiation.

Epidermal growth factor (EGF) has been shown to radiosensitize A431 and other human squamous carcinoma cells with high numbers of surface EGF receptors. In this study of the mechanistic basis of EGF-induced radiosensitization, both EGF and ionizing radiation caused G1 phase arrests in cycling A431 cells, but only radiation caused a G2-M arrest. However, EGF enhanced the magnitude of this G2-M arrest, suggesting an interaction of signaling pathways involved in cellular responses to EGF and radiation damage. EGF and radiation also uniquely perturbed cyclin A and B1 mRNA levels during the time of maximum radiation-induced G2-M arrest. The effects of EGF on G2-M events probably originated in cells in G1. It is possible that aberrant EGF signal transduction in human squamous carcinoma cells may be exploited as a novel strategy for radiotherapy.

Opposing effects of hypoxia on expression of the angiogenic inhibitor thrombospondin 1 and the angiogenic inducer vascular endothelial growth factor.

Tumor angiogenesis, the development of new blood vessels during malignant progression, is a regulated process that has both genetic and physiological controls. Physiologically, angiogenesis is stimulated by decreases in tissue oxygenation (i.e., hypoxia). We investigated the effect of hypoxia on the expression of two angiogenic factors reported to be genetically regulated by the p53 tumor suppressor gene: (a) the angiogenic inhibitor thrombospondin 1 (TSP-1); and (b) the angiogenic inducer vascular endothelial growth factor (VEGF). Analysis of rodent cells that differ in their p53 genotype (p53+/+ or p53-/-) indicated that in vitro exposure to hypoxia simultaneously suppressed TSP-1 and induced VEGF expression, regardless of the p53 genotype. On transformation of these cells with E1A and oncogenic H-ras, the basal level of TSP-1 expression was strongly diminished, whereas that of VEGF could still be induced by hypoxia. Consistent with these in vitro findings, sections of tumors derived from the transformed p53+/+ and p53-/- cells showed that VEGF protein overlapped with regions of hypoxia, whereas TSP-1 protein was below the limits of detection in tumor tissue. Using a panel of normal/immortalized and transformed human cells, it was found that the ability of hypoxia to inhibit TSP-1 expression depends on the cell type and/or the degree of transformation. In contrast, VEGF expression was induced by hypoxia in all of the human cell types examined. Together, these findings suggest that hypoxic and oncogenic signals could interact in the tumor microenvironment to inhibit TSP-1 and induce VEGF expression, promoting the switch to the angiogenic phenotype.

The novel tubulin-binding drug BTO-956 inhibits R3230AC mammary carcinoma growth and angiogenesis in Fischer 344 rats.

BTO-956 [methyl-3,5-diiodo-4-(4'-methoxyphenoxy)benzoate], a novel tubulin-binding drug and thyroid hormone analogue, was originally found to inhibit human carcinoma cell proliferation in vitro and to have potent growth delay activity in human breast and ovarian carcinoma xenografts in nude mice. Here we report that BTO-956 given to Fischer 344 rats also inhibits corneal angiogenesis and the growth and neovascularization of the R3230Ac rat mammary carcinoma tumor implanted in skin-fold window chambers. Hydron pellets containing recombinant human basic fibroblast growth factor (50 ng) and Sucralfate (20 microg) were implanted into surgically created corneal micropockets (day 0). BTO-956 was administrated by oral gavage (500 mg/kg, twice a day for 6 days) on days 1-6 (controls received vehicle alone). On day 7, rats received retrograde infusions of India ink via the thoracic aorta to visualize the corneal vasculature. Digitized images of slide-mounted corneas from control and treated animals were taken with a microscope. For the tumor growth and angiogenesis study, small pieces of R3230Ac tumor from a donor rat were implanted into surgically prepared window chambers (day 0). BTO-956 was given during days 5-11, and images of the tumors and their vasculature were recorded on day 12. No body weight loss was observed in either study. BTO-956 significantly inhibited corneal angiogenesis (by 50-80%), as assessed by measurements of limbal circumference displaying neovascularization, vessel length, vascularized area, and vascular area density. In the window chamber assay, tumors from treated animals were >50% smaller than tumors in control animals. In addition, vascular length densities in peripheral tumor zones were 30% less in treated compared with control animals. Together, these findings demonstrate that BTO-956 can inhibit angiogenesis induced by a growth factor in the rat cornea and in the peripheral area of implanted tumors, where tumor angiogenesis is most active.