Comparison of a combined quantum mechanics/interatomic potential function approach with its periodic quantum-mechanical limit: Proton siting and ammonia adsorption in zeolite chabazite

Published versio

An in vitro alveolar macrophage assay for predicting the short-term inhalation toxicity of nanomaterials

Additional file 1: Table S1. Comparison of significant in vitro LOAECs (significant as compared to the negative benchmark material corundum) to NOAECs and LOAECs recorded in rat STISs. Table S2. Bioactivity of four types of CeO2 NMs in rat STISs as compared to cellular effects recorded in the in vitro NR8383 AM assay

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays

Background DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR) in this yeast species, as compared to S. cerevisiae. Results By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer). To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT) or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts. Conclusion The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes involved in translation, ribosome biogenesis, and organelle biosynthesis, indicating that the regulatory events triggered by DTT treatment only partially overlap with the reactions to overexpression of HAC1. The high reproducibility of the results achieved with two different oligo sets is a good indication for their robustness, and underlines the importance of less stringent selection of regulated features, in order to avoid a large number of false negative results

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays

Background DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR) in this yeast species, as compared to S. cerevisiae. Results By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer). To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT) or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts. Conclusion The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes involved in translation, ribosome biogenesis, and organelle biosynthesis, indicating that the regulatory events triggered by DTT treatment only partially overlap with the reactions to overexpression of HAC1. The high reproducibility of the results achieved with two different oligo sets is a good indication for their robustness, and underlines the importance of less stringent selection of regulated features, in order to avoid a large number of false negative results

Limitations of Dutch Growth Research Foundation Commercial Software Weight Velocity for Age Standard Deviation Score

BACKGROUND The commercial software for hospitals, Weight Velocity for Age Standard Deviation Score (SDSWVA), claims to document the growth and development of children, although published details are unavailable. The statistics-derived parameter SDSWVA includes the weight velocity at age t, WV(t) (weight gained between t and (t-1.23) years, divided by 1.23), and 3 standard weight velocity curves at average age AA, defined as AA=t-1.23/2 years. SDSWVA denotes the number of standard deviations that WV(t) deviates from the 0 SD weight velocity at AA. WV(t) yielded erroneous outcomes when applied to weights of a seriously underweight boy with an allergy to cows' milk who showed strong weight growth after being fed on food free of cows' milk. The SDSWVA software tacitly suggests that it is more accurate than WV(t). CASE REPORT The case of this boy was previously described in this Journal. Using SDSWVA(t,AA) software, his weight growth was analyzed by his third pediatrician, beginning at age 1.5 years. The diagnosis of the mother with Pediatric Condition Falsification was confirmed, adding 6 months to foster care, which totalled 8.5 months. Testing of the SDSWVA software on the boy's weight curve yielded results that were complex, nontransparent, and as erroneous as WV(t), explaining the misdiagnosis by the third pediatrician. CONCLUSIONS SDSWVA software should not be used for children under 3 years and during variable weight behavior. Erroneous performance, unpublished details, and an error identified in their new but untested software make the Dutch Growth Research Foundation unlikely to meet the 2020 European Union regulations for in vitro medical devices

Fabrication of nanostructure via self-assembly of nanowires within the AAO template

The novel nanostructures are fabricated by the spatial chemical modification of nanowires within the anodic aluminum oxide (AAO) template. To make the nanowires better dispersion in the aqueous solution, the copper is first deposited to fill the dendrite structure at the bottom of template. During the process of self-assembly, the dithiol compound was used as the connector between the nanowires and nanoparticles by a self-assembly method. The nanostructures of the nano cigars and structure which is containing particles junction are characterized by transmission electron microscopy (TEM). These kinds of novel nanostructure will be the building blocks for nanoelectronic and nanophotonic devices

Fine material in grain

Fine material in grain: an overview / Richard Stroshine -- Factors that affect the costs of fines in the corn export market / Lowell D. Hill, Mack Leath -- Effects of fine material on mold growth in grain / David B. Sauer, Richard A. Meronuck, John Tuite -- Effects of fine material on insect infestation: a review / Paul W. Flinn, William H. McGaughey, Wendell E. Burkholder -- Reducing or controlling damage to grain from handling: a review / Charles R. Martin, George H. Foster -- Evaluating grain for potential production of fine material - breakage susceptibility testing / Steven R. Eckhoff -- Genotypic differences in breakage susceptibility of corn and soybeans -- M. R. Paulsen, L. L. Darrah, R. L. Stroshin

lentiglobin gene therapy for transfusion dependent β thalassemia outcomes from the phase 1 2 northstar and phase 3 northstar 2 studies

Introduction Transfusion-dependent β-thalassemia (TDT) is a severe genetic disease characterized by anemia, iron overload and serious comorbidities for which gene therapy may be an effective treatment option. LentiGlobin gene therapy contains autologous CD34+ hematopoietic stem cells (HSCs) transduced ex vivo with the BB305 lentiviral vector (LVV) encoding β-globin with a T87Q substitution. Objective Evaluate the efficacy and safety of LentiGlobin in patients with TDT in the phase 1/2 Northstar (HGB-204; NCT01745120) and phase 3 Northstar-2 (HGB-207; NCT02906202) studies. Methods Patients with TDT (≥100 mL/kg/yr of red blood cells [RBCs] or ≥8 RBC transfusions/yr) received G-CSF and plerixafor for mobilization and HSCs were transduced with the BB305 LVV. Patients underwent single agent busulfan myeloablative conditioning, were infused with transduced cells, and were followed for engraftment, safety, and efficacy. Statistics are presented as median (min – max). Results As of March 7, 2018, 18 patients (12 – 35 yrs) were treated in Northstar (follow-up 32.1 [23.1 – 41.9] months) and as of May 15, 2018, 11 patients (12 – 24 yrs) were treated in Northstar-2 (follow-up 8.5 [0.3 – 16.2] months). Patients received a median cell dose of 8.0 (5.0 – 19.4) CD34+ cells × 106/kg in both studies. The median time to neutrophil and platelet engraftment in both studies was 19 (14 – 30) days and 44 (19 – 191) days, respectively; 1 patient in Northstar-2 (0.3 months follow-up) had not engrafted at time of analysis. Of 6 patients with platelet engraftment ≥ Day 60, 4 had non-serious bleeding events prior to engraftment. All 6 had intact spleens and 3/6 received G-CSF between Days 0 – 21. Both factors appeared associated with time to platelet engraftment. In Northstar, 8/10 patients with non-β0/β0 genotypes and 2/8 patients with β0/β0 genotypes achieved transfusion independence (TI; weighted average hemoglobin [Hb] ≥ 9 g/dL without RBC transfusions for ≥ 12 months). Median Hb during TI was 10.0 (9.3 – 13.1) g/dL. In Northstar-2, 7/8 patients with non-β0/β0 genotypes and ≥ 6 months follow-up stopped RBC transfusions with Hb of 11.1 – 13.3 g/dL at last visit; the first patient treated achieved TI. Non-hematologic grade ≥ 3 adverse events post-infusion in ≥ 5/29 (15%) patients were stomatitis, febrile neutropenia, and pharyngeal inflammation. Veno-occlusive liver disease attributed to busulfan occurred in 4/29 patients (Table 1). There was no transplant-related mortality, vector-mediated replication competent lentivirus, or clonal dominance. Conclusion In Northstar, 80% of patients with non-β0/β0 genotypes achieved TI and early Northstar-2 data suggest that patients can achieve near-normal Hb without transfusions. The safety profile of LentiGlobin is consistent with myeloablative busulfan conditioning. Longer time to platelet engraftment was observed in few patients, but no graft failure or deaths were reported

Limitations of Weight Velocity Analysis by Commercial Computer Program Growth Analyser Viewer Edition

Commercial software package “Growth Analyser Viewer Edition” (“GAVE”) aims to document, monitor and analyze growth and development in children and adolescents. Although its clinical and scientific use is widespread, there are no published studies that describe the method and its validation. We were informed that GAVE calculates the weight velocity (kg/year) at age t from the weight difference between t and 448 days earlier or at birth, divided by the time difference. We recently discussed a case of false child abuse diagnosis (Pediatric Condition Falsification), resulting in the separation of the child from its parents, in which GAVE played a negative contributing role. To prevent such inappropriate diagnoses, we analyzed GAVE from a schematic representation of the measured clinical weight curve, with precisely defined weight velocities. In conclusion, the 448 days included for weight velocity predictions by GAVE caused the erroneous outcomes. Until the necessary changes to the software are implemented and validated, we advise against the use of GAVE in infants younger than 1.5 years, if multiple weight changes occur within 448 days, and following a long-lasting weight velocity change. Our analysis suggests to discard all medical software packages that lack public description and proof of validation

Limitations of Weight Velocity Analysis by Commercial Computer Program Growth Analyser Viewer Edition

Commercial software package “Growth Analyser Viewer Edition” (“GAVE”) aims to document, monitor and analyze growth and development in children and adolescents. Although its clinical and scientific use is widespread, there are no published studies that describe the method and its validation. We were informed that GAVE calculates the weight velocity (kg/year) at age t from the weight difference between t and 448 days earlier or at birth, divided by the time difference. We recently discussed a case of false child abuse diagnosis (Pediatric Condition Falsification), resulting in the separation of the child from its parents, in which GAVE played a negative contributing role. To prevent such inappropriate diagnoses, we analyzed GAVE from a schematic representation of the measured clinical weight curve, with precisely defined weight velocities. In conclusion, the 448 days included for weight velocity predictions by GAVE caused the erroneous outcomes. Until the necessary changes to the software are implemented and validated, we advise against the use of GAVE in infants younger than 1.5 years, if multiple weight changes occur within 448 days, and following a long-lasting weight velocity change. Our analysis suggests to discard all medical software packages that lack public description and proof of validation