Multimodal machine learning models identify chemotherapy drugs with prospective clinical efficacy in dogs with relapsed B-cell lymphoma.

Dogs with B-cell lymphoma typically respond well to first-line CHOP-based chemotherapy, but there is no standard of care for relapsed patients. To help veterinary oncologists select effective drugs for dogs with lymphoid malignancies such as B-cell lymphoma, we have developed multimodal machine learning models that integrate data from multiple tumor profiling modalities and predict the likelihood of a positive clinical response for 10 commonly used chemotherapy drugs. Here we report on clinical outcomes that occurred after oncologists received a prediction report generated by our models. Remarkably, we found that dogs that received drugs predicted to be effective by the models experienced better clinical outcomes by every metric we analyzed (overall response rate, complete response rate, duration of complete response, patient survival times) relative to other dogs in the study and relative to historical controls.

Serial assessment of somatic and cardiovascular development in patients with single ventricle undergoing Fontan procedure.

BACKGROUND: The palliation of patients with single ventricle (SV) undergoing Fontan procedure led to improved long-term survival but is still limited due to cardiovascular complications. The aim of this study was to describe the somatic and cardiovascular development of Fontan patients until adolescence and to identify determining factors. METHODS: We retrospectively assessed somatic growth, vascular growth of pulmonary arteries, and cardiac growth of the SV and systemic semilunar valve from 0 to 16 years of age using transthoracic echocardiography. The Doppler inflow pattern of the atrioventricular valve was quantified by E-, A-wave and E/A ratio. All data were converted to z-scores and analyzed using linear mixed effect models to identify associations with age at Fontan procedure, gender, and ventricular morphology. RESULTS: 134 patients undergoing Fontan procedure at a median age of 2.4 (IQR 2.12 to 2.8) years were analyzed. A catch-up of somatic growth after Fontan procedure until school age was found, with lower body height and weight z-scores in male patients and patients with systemic right ventricles. An early time of Fontan procedure was favorable for somatic growth, but not for vascular growth. Cardiac development indicated a decrease of SV end-diastolic diameter z-score until adolescence. Despite a trend towards normalization, E-wave and E/A ratio z-scores were diminished over the entire period. CONCLUSIONS: There is a catch-up growth of somatic, vascular and cardiac parameters after Fontan procedure, which in our cohort depends on the time of Fontan procedure, ventricular morphology, and gender. Beside other factors, diastolic function of the SV remains altered.

Dynamics of DNA replication in a eukaryotic cell.

Each genomic locus in a eukaryotic cell has a distinct average time of replication during S phase that depends on the spatial and temporal pattern of replication initiation events. Replication timing can affect genomic integrity because late replication is associated with an increased mutation rate. For most eukaryotes, the features of the genome that specify the location and timing of initiation events are unknown. To investigate these features for the fission yeast, Schizosaccharomyces pombe, we developed an integrative model to analyze large single-molecule and global genomic datasets. The model provides an accurate description of the complex dynamics of S. pombe DNA replication at high resolution. We present evidence that there are many more potential initiation sites in the S. pombe genome than previously identified and that the distribution of these sites is primarily determined by two factors: the sequence preferences of the origin recognition complex (ORC), and the interference of transcription with the assembly or stability of prereplication complexes (pre-RCs). We suggest that in addition to directly interfering with initiation, transcription has driven the evolution of the binding properties of ORC in S. pombe and other eukaryotic species to target pre-RC assembly to regions of the genome that are less likely to be transcribed.

Long-term operation of a novel electrically-enhanced biomass concentrator reactor for wastewater treatment.

Membrane biological reactors (MBRs) are a key technology in wastewater treatment nowadays. However, due to their high construction cost and energetic requirements, alternatives based on the same principle of biomass retention have been designed and operated. Amongst these, biomass concentrator reactors (BCRs), using a coarser filter medium instead of a membrane, have shown to be able to remove a wide range of contaminants from wastewater and groundwater. A new BCR-derived technology enhanced with an electric field, called the electrically-enhanced biomass concentrator reactor (E2BCR), was designed and tested for urban wastewater treatment at different organic loads for a period of 180 days. The electrically-enhanced reactor showed better chemical oxygen demand (COD) removal performances than a non-enhanced control reactor (92.4% and 83.6% respectively) thanks also to electrocoagulation effects, and a lower fouling tendency, and proved to be more energy efficient in comparison with the control reactor in terms of energy consumption per mass of COD removed.

Effects of process operating conditions on the autotrophic denitrification of nitrate-contaminated groundwater using bioelectrochemical systems.

Nitrates have been detected in groundwater worldwide, and their presence can lead to serious groundwater use limitations, especially because of potential health problems. Amongst different options for their removal, bioelectrochemical systems (BESs) have achieved promising results; in particular, attention has raised on BES-driven autotrophic denitrification processes. In this work, the performance of a microbial electrolysis cell (MEC) for groundwater autotrophic denitrification, is assessed in different conditions of nitrate load, hydraulic retention time (HRT) and process configuration. The system obtained almost complete nitrate removal under all conditions, while nitrite accumulation was recorded at nitrate loads higher than 100mgNO3-L-1. The MEC system achieved, in different tests, a maximum nitrate removal rate of 62.15±3.04gNO3--Nm-3d-1, while the highest TN removal rate observed was 35.37±1.18gTNm-3d-1. Characteristic of this process is a particularly low (in comparison with other reported works) energy consumption: 3.17·10-3±2.26·10-3kWh/gNO3-N removed and 7.52·10-2±3.58·10-2kWhm-3 treated. The anolyte configuration in closed loop allowed the process to use less clean water, while guaranteeing identical performances as in other conventional configurations.

Does transcription-associated DNA damage limit lifespan?

Small mammals undergo an aging process similar to that of larger mammals, but aging occurs at a dramatically faster rate. This phenomenon is often assumed to be the result of damage caused by reactive oxygen species generated in mitochondria. An alternative explanation for the phenomenon is suggested here. The rate of RNA synthesis is dramatically elevated in small mammals and correlates quantitatively with the rate of aging among different mammalian species. The rate of RNA synthesis is reduced by caloric restriction and inhibition of TOR pathway signaling, two perturbations that increase lifespan in multiple metazoan species. From bacteria to man, the transcription of a gene has been found to increase the rate at which it is damaged, and a number of lines of evidence suggest that DNA damage is sufficient to induce multiple symptoms associated with normal aging. Thus, the correlations frequently found between the rate of RNA synthesis and the rate of aging could potentially reflect an important role for transcription-associated DNA damage in the aging process.

Coordination of DNA damage tolerance mechanisms with cell cycle progression in fission yeast.

DNA damage tolerance (DDT) mechanisms allow cells to synthesize a new DNA strand when the template is damaged. Many mutations resulting from DNA damage in eukaryotes are generated during DDT when cells use the mutagenic translesion polymerases, Rev1 and Polζ, rather than mechanisms with higher fidelity. The coordination among DDT mechanisms is not well understood. We used live-cell imaging to study the function of DDT mechanisms throughout the cell cycle of the fission yeast Schizosaccharomyces pombe. We report that checkpoint-dependent mitotic delay provides a cellular mechanism to ensure the completion of high fidelity DDT, largely by homology-directed repair (HDR). DDT by mutagenic polymerases is suppressed during the checkpoint delay by a mechanism dependent on Rad51 recombinase. When cells pass the G2/M checkpoint and can no longer delay mitosis, they completely lose the capacity for HDR and simultaneously exhibit a requirement for Rev1 and Polζ. Thus, DDT is coordinated with the checkpoint response so that the activity of mutagenic polymerases is confined to a vulnerable period of the cell cycle when checkpoint delay and HDR are not possible.

Bone marrow- or vessel wall-derived osteoprotegerin is sufficient to reduce atherosclerotic lesion size and vascular calcification.

OBJECTIVE: Osteoprotegerin (OPG) is a decoy receptor for the osteoclast differentiation factor receptor activator of NF-κB ligand. OPG regulates bone homeostasis, and its inactivation in mice results in severe osteoporosis. OPG deficiency in apolipoprotein E (ApoE)(-/-) mice results in increased atherosclerotic lesion size and calcification. Furthermore, receptor activator of NF-κB ligand enhances macrophage-dependent smooth muscle cell calcification in vitro. Here, we hypothesized that reconstitution of ApoE(-/-)OPG(-/-) mice with ApoE(-/-)OPG(+/+) bone marrow (BM) would be sufficient to rescue lesion progression and vascular calcification. Conversely, reconstitution of ApoE(-/-)OPG(+/+) mice with ApoE(-/-)OPG(-/-) BM may accelerate lesion progression and vascular calcification. APPROACH AND RESULTS: ApoE(-/-)OPG(-/-) mice transplanted with ApoE(-/-)OPG(+/+) BM developed smaller atherosclerotic lesions and deposited less calcium in the innominate artery than that of ApoE(-/-)OPG(-/-) mice transplanted with ApoE(-/-)OPG(-/-) BM. There were no differences in lesion size and calcification in ApoE(-/-)OPG(+/+) mice transplanted with BM from ApoE(-/-)OPG(-/-) or ApoE(-/-)OPG(+/+) mice. The large lesions observed in the ApoE(-/-)OPG(-/-) mice transplanted with OPG(-/-) BM were rich in chondrocyte-like cells, collagen, and proteoglycans. Importantly, the ApoE(-/-)OPG(-/-) mice transplanted with OPG(+/+) BM remained osteoporotic, and the ApoE(-/-)OPG(+/+) mice did not show signs of bone loss regardless of the type of BM received. In coculture experiments, macrophages and mesenchymal stem cells derived from ApoE(-/-)OPG(-/-) BM induced more vascular smooth muscle cell calcification than cells derived from ApoE(-/-)OPG(+/+) mice. CONCLUSIONS: These results indicate that OPG derived either from the BM or from the vessel wall is sufficient to slow down lesion progression and vascular calcification independent of bone turnover.

Postreplication gaps at UV lesions are signals for checkpoint activation.

Exposure of eukaryotic cells to UV light induces a checkpoint response that delays cell-cycle progression after cells enter S phase. It has been hypothesized that this checkpoint response provides time for repair by signaling the presence of structures generated when the replication fork encounters UV-induced DNA damage. To gain insight into the nature of the signaling structures, we used time-lapse microscopy to determine the effects of deficiencies in translesion DNA polymerases on the checkpoint response of the fission yeast Schizosaccharomyces pombe. We found that disruption of the genes encoding translesion DNA polymerases Polkappa and Poleta significantly prolonged the checkpoint response, indicating that the substrates of these enzymes are signals for checkpoint activation. Surprisingly, we found no evidence that the translesion polymerases Rev1 and Polzeta repair structures that are recognized by the checkpoint despite their role in maintaining viability after UV irradiation. Quantitative flow cytometry revealed that cells lacking translesion polymerases replicate UV-damaged DNA at the same rate at WT cells, indicating that the enhanced checkpoint response of cells lacking Polkappa and Poleta is not the result of stalled replication forks. These observations support a model in which postreplication DNA gaps with unrepaired UV lesions in the template strand act both as substrates for translesion polymerases and as signals for checkpoint activation.

Shedding light on the DNA damage checkpoint.

DNA damage checkpoint genes are required to restrain cell cycle progression during DNA repair and to maintain chromosome stability. Checkpoint mutants are highly sensitive to killing by UV light, so the responses mediated by these genes are likely to be essential for survival during exposure to solar radiation. Yet it is still unclear exactly how checkpoint responses coordinate the cell cycle with DNA repair in the presence of UV lesions. At high doses, the UV response shares features with the ionizing radiation response, such as G1/S and G2/M checkpoints. At lower doses, only a postreplication checkpoint is evident. In this perspective we attempt to reconcile these observations and address their physiological meaning, with an emphasis on insights gained from direct cell-cycle measurements and recent studies in yeast.

UV irradiation induces a postreplication DNA damage checkpoint.

Eukaryotic cells irradiated with high doses of UV exhibit cell-cycle responses referred to as G(1)/S, intraS, and G(2)/M checkpoints. After a moderate UV dose that approximates sunlight exposure and is lethal to fission yeast checkpoint mutants, we found unexpectedly that these cell-cycle responses do not occur. Instead, cells at all stages of the cell cycle carry lesions into S phase and delay cell-cycle progression for hours after the completion of bulk DNA synthesis. Both DNA replication and the checkpoint kinase, Chk1, are required to generate this cell-cycle response. UV-irradiation of Deltachk1 cells causes chromosome damage and loss of viability only after cells have replicated irradiated DNA and entered mitosis. These data suggest that an important physiological role of the cell-cycle response to UV is to provide time for postreplication repair.

Liquid crystal alignment on carbonaceous surfaces with orientational order.

We used near-edge x-ray absorption fine structure (NEXAFS) spectroscopy to link the orientational bond order at three carbonaceous surfaces-rubbed polyimide, ion beam-irradiated polyimide, and ion beam-irradiated diamondlike carbon films-with the direction of liquid crystal (LC) alignment on these surfaces. We show that, in general, LC alignment can be created on any carbonaceous substrate by inducing orientational order at its surface. Our results form the scientific basis for LC alignment layers consisting of amorphous carbon films in which orientational order near the surface is induced by a directional low-energy ion beam.

Atomic-beam alignment of inorganic materials for liquid-crystal displays.

The technique used to align liquid crystals-rubbing the surface of a substrate on which a liquid crystal is subsequently deposited-has been perfected by the multibillion-dollar liquid-crystal display industry. However, it is widely recognized that a non-contact alignment technique would be highly desirable for future generations of large, high-resolution liquid-crystal displays. A number of alternative alignment techniques have been reported, but none of these have so far been implemented in large-scale manufacturing. Here, we report a non-contact alignment process, which uses low-energy ion beams impinging at a glancing angle on amorphous inorganic films, such as diamond-like carbon. Using this approach, we have produced both laptop and desktop displays in pilot-line manufacturing, and found that displays of higher quality and reliability could be made at a lower cost than the rubbing technique. The mechanism of alignment is explained by adopting a random network model of atomic arrangement in the inorganic films. Order is induced by exposure to an ion beam because unfavourably oriented rings of atoms are selectively destroyed. The planes of the remaining rings are predominantly parallel to the direction of the ion beam.

Dialkylaminoalkylnaphthalenes as novel opioid-like analgesics.

The study of dialkylaminoalkylnaphthalenes as novel opioid-like analgesics is reported. In particular, the synthesis of (1R,2R/1S,2S)-1-ethyl-1-[2-(6-hydroxynaphthyl)]-1-hydrox-2-m ethyl-2-dimethylaminoethane and its structural analogue (1R,2R/1S,2S)-1-ethyl-1-[2-(6-fluoronaphthyl)]-1-hydroxy-2-methyl- 2-dimethylaminoethane and the configurational analysis by X-ray and 1H NMR spectroscopy are described. Pharmacological profiles are discussed on the basis of the experimental results of analgesia tests (hot plate and writhing test) and rota-rod test, which was performed to distinguish analgesia from drug-induced motor changes. The compounds showed dose-dependent antinociception, with less potency than morphine. Motor coordination appeared to be less involved.

Structure and solid-state chemistry of anhydrous and hydrated crystal forms of the trimethoprim-sulfamethoxypyridazine 1:1 molecular complex.

The crystal structure of the equimolar trimethoprim (TMP) and sulfamethoxypyridazine (SMPD) complex in the anhydrous form (TMP. SMPD) and that of the species with 1.5 molecules of water of crystallization (TMP.SMPD.W) are reported in this article. X-ray powder diffraction patterns (both computer generated and experimental) and thermal analytical data from differential scanning calorimetry (DSC) and thermogravimetry useful for the characterization of TMP.SMPD and TMP.SMPD.W are provided. The stability of TMP.SMPD.W, which retains its crystallographic order under 0% relative humidity (RH) conditions at room temperature (22 degrees C) and 20 mmHg, is accounted for in terms of crystal structure and hydrogen bonding. Transformation of TMP.SMPD to the hydrate complex by exposure to approximately 100% RH, suspension in water, and wet granulation, and dehydration of TMP.SMPD.W by thermal treatment and by desiccation with methanol were investigated and tentatively interpreted in terms of crystal properties. Interactions in the physical mixture of TMP and SMPD by grinding, compression, heating, and contact with water were also studied. Water-mediated formation of TMP.SMPD.W by wetting and metastable eutectic melting-mediated formation of TMP.SMPD by heating was demonstrated. Mechanical activation by milling makes the physical mixture prone to solid-state transformation into dimorphic anhydrous cocrystals by supply of thermal energy during a DSC scan.

Low-voltage organic transistors on plastic comprising high-dielectric constant gate insulators

The gate bias dependence of the field-effect mobility in pentacene-based insulated gate field-effect transistors (IGFETs) was interpreted on the basis of the interaction of charge carriers with localized trap levels in the band gap. This understanding was used to design and fabricate IGFETs with mobility of more than 0.3 square centimeter per volt per second and current modulation of 10(5), with the use of amorphous metal oxide gate insulators. These values were obtained at operating voltage ranges as low as 5 volts, which are much smaller than previously reported results. An all-room-temperature fabrication process sequence was used, which enabled the demonstration of high-performance organic IGFETs on transparent plastic substrates, at low operating voltages for organic devices.

Endoarticular loose bodies and calcifications of the disk of the temporomandibular joint: morphological features and chemical composition.

We studied articular disks and endoarticular loose bodies taken from patients suffering from different types of temporomandibular joint (TMJ) pathology. The scanning electron microscopy (SEM) analysis of the disks and the endoarticular loose bodies was followed by a chemical-compositional analysis using an energy dispersive spectrometer (EDS) and by characterization of the crystalline phases by X-ray powder diffraction (XRD). The articular disks were composed of a central radiopaque area lacking any evident structural features, surrounded by compact bundles of collagen fibers. EDS and XRD analyses showed that endodiscal radio-opaque areas were hydroxyapatite. By SEM, we observed a fibrous network only in circumscribed areas of the endoarticular loose bodies. The chemical-compositional analysis showed that the loose bodies were composed of calcite (CaCO3). The results of this investigation, along with the clinical history of the patients, allow us to formulate some hypotheses regarding the etiopathogenesis of these structural anomalies. The endodiscal calcifications could be the result of a chronic inflammatory process that produces displastic alterations of the articular disk. Moreover, an acute inflammatory process with modifications in the mechanisms of the synovial fluid turnover seems to be the event that leads to the formation of endoarticular loose bodies.

Demographic evolution and production structure in Naples according to the information of the latest censuses.

Changes in the industrial structure of Naples, Italy, between 1971 and 1981 are examined using census data. The first part analyzes demographic shifts in the city's population. "In the closing years of that period a decline in population growth was observed and, over its last decade, there was also a change in its structure in that there was an increase in the labour force due to the huge number of young people who entered the labour market."