Reproducible Criteria Research Articles

Development and transferability of two multiplexes nSSR in Scots pine (Pinus sylvestris L.)

Single sequence repeat (SSR) multiplexing is a semi high-throughput PCR methodology for the analysis of multiple SSRs. We developed two SSR multiplexes selected from SSR loci previously reported in the pine literature and tested the transferability of both SSR multiplexes in nine other pine species. We tested 234 nuclear SSR loci (nSSRs) previously described in the pine literature and selected ten nSSRs following the simple criteria of interpretability and reproducibility. Selected nuclear loci were divided into two nSSRs multiplex sets and their amplification was optimized for three different multiplex PCR methods based on: (a) a custom PCR protocol, (b) a custom protocol with hotstart taq polymerase, and (c) a commercially available kit for SSR multiplexing. To validate their performance, the level of genetic diversity was assessed in three Scots pine natural populations (Hungary, northern Sweden and southern Sweden). In addition, we also tested the transferability of these multiplexes in nine other pine species. We have developed two nSSRs multiplexes of five loci each that will contribute to reduce the costs of nSSR scoring, while increasing the capacity of nSSR loci analysis. Amplification was successful in all three populations (94 % success) and the level of polymorphism (7.1 alleles/marker) was similar to that previously reported for other Scots pine natural populations. Transferability of both multiplexes was successful for those pine species closely related to Scots pine.

Criteria for biological reproducibility: what does "n" mean?

This Focus tackles the issue of technical versus biological replicates, what constitutes appropriate biological replicates, and appropriate statistical analysis for data with small sample sizes.

Real-time PCR Tests in Dutch Exotic Mosquito Surveys; Implementation of Aedes aegypti and Aedes albopictus Identification Tests, and the Development of Tests for the Identification of Aedes atropalpus and Aedes japonicus japonicus (Diptera: Culicidae).

Since 2009, The Netherlands Food and Consumer Product Safety Authority carries out surveys focusing on, amongst others, the presence of invasive mosquito species (IMS). Special attention is given to exotic container-breeding Aedes species Aedes aegypti (L.), Aedes albopictus (Skuse), Aedes atropalpus (Coquillett), and Aedes japonicus japonicus (Theobald). This study describes the implementation of real-time PCR tests described by Hill etal. (2008) for the identification of Ae. aegypti and Ae. albopictus, and the development of two novel real-time PCR tests for the identification of Ae. atropalpus and Ae. j. japonicus. Initial test showed that optimization of elements of the Ae. aegypti and Ae. albopictus tests was needed. Method validation tests were performed to determine if the implemented and newly developed tests are fit for routine diagnostics. Performance criteria of analytical sensitivity, analytical specificity, selectivity, repeatability, and reproducibility were determined. In addition, experiments were performed to determine the influence of environmental conditions on the usability of DNA extracted from mosquito specimens trapped in BG-Sentinel traps. The real-time PCR tests were demonstrated to be sensitive, specific, repeatable, reproducible, and are less prone to false negative results compared to partial cytochrome c oxidase I gene sequencing owing to the DNA fragmentation caused by environmental influences.

Comparison of three protocols for measuring the maximal respiratory pressures

Introduction To avoid the selection of submaximal efforts during the assessment of maximal inspiratory and expiratory pressures (MIP and MEP), some reproducibility criteria have been suggested. Criteria that stand out are those proposed by the American Thoracic Society (ATS) and European Respiratory Society (ERS) and by the Brazilian Thoracic Association (BTA). However, no studies were found that compared these criteria or assessed the combination of both protocols. Objectives To assess the pressure values selected and the number of maneuvers required to achieve maximum performance using the reproducibility criteria proposed by the ATS/ERS, the BTA and the present study. Materials and method 113 healthy subjects (43.04 ± 16.94 years) from both genders were assessed according to the criteria proposed by the ATS/ERS, BTA and the present study. Descriptive statistics were used for analysis, followed by ANOVA for repeated measures and post hoc LSD or by Friedman test and post hoc Wilcoxon, according to the data distribution. Results The criterion proposed by the present study resulted in a significantly higher number of maneuvers (MIP and MEP – median and 25%-75% interquartile range: 5[5-6], 4[3-5] and 3[3-4] for the present study criterion, BTA and ATS/ERS, respectively; p < 0.01) and higher pressure values (MIP – mean and 95% confidence interval: 103[91.43-103.72], 100[97.19-108.83] and 97.6[94.06-105.95]; MEP: median and 25%-75% interquartile range: 124.2[101.4-165.9], 123.3[95.4-153.8] and 118.4[95.5-152.7]; p < 0.05). Conclusion The proposed criterion resulted in the selection of pressure values closer to the individual’s maximal capacity. This new criterion should be considered in future studies concerning MIP and MEP measurements.

The updated Cochrane review 2014 on GnRH agonist trigger: repeating the same errors

Cochrane reviews are powerful tools, internationally recognized as the highest standard in evidence-based health care. A Cochrane analysis makes use of precise, reproducible criteria in the selection of studies for review. In the context of a previous Cochrane review (2010) on the subject of gonadotrophin-releasing hormone agonist (GnRHa) trigger, we questioned whether a review should be conducted during the research phase when new concepts are being developed. Recently, an updated Cochrane review was published, reaching the same general conclusion as the first one, i.e., GnRHa triggers lower the chance of pregnancy in fresh autologous IVF and intracytoplasmic injection treatment cycles. We argue that the new review repeats previous errors by compiling data from studies that were not comparable as different luteal phase protocols were used. From the clinical point of view, the luteal support used is the variable which affects the pregnancy rate and not the use of the GnRHa trigger for final oocyte maturation. Therefore, a meaningful comparison between GnRHa and HCG trigger must be confined to outcome measures that are not affected by the luteal support used. We conclude that the updated review falls short of addressing meaningful clinical and fundamental questions in the context of GnRHa trigger.

Appraisal of within- and between-laboratory reproducibility of non-radioisotopic local lymph node assay using flow cytometry, LLNA:BrdU-FCM: Comparison of OECD TG429 performance standard and statistical evaluation

Mouse local lymph node assay (LLNA, OECD TG429) is an alternative test replacing conventional guinea pig tests (OECD TG406) for the skin sensitization test but the use of a radioisotopic agent, 3H-thymidine, deters its active dissemination. New non-radioisotopic LLNA, LLNA:BrdU-FCM employs a non-radioisotopic analog, 5-bromo-2′-deoxyuridine (BrdU) and flow cytometry. For an analogous method, OECD TG429 performance standard (PS) advises that two reference compounds be tested repeatedly and ECt(threshold) values obtained must fall within acceptable ranges to prove within- and between-laboratory reproducibility. However, this criteria is somewhat arbitrary and sample size of ECt is less than 5, raising concerns about insufficient reliability. Here, we explored various statistical methods to evaluate the reproducibility of LLNA:BrdU-FCM with stimulation index (SI), the raw data for ECt calculation, produced from 3 laboratories. Descriptive statistics along with graphical representation of SI was presented. For inferential statistics, parametric and non-parametric methods were applied to test the reproducibility of SI of a concurrent positive control and the robustness of results were investigated. Descriptive statistics and graphical representation of SI alone could illustrate the within- and between-laboratory reproducibility. Inferential statistics employing parametric and nonparametric methods drew similar conclusion. While all labs passed within- and between-laboratory reproducibility criteria given by OECD TG429 PS based on ECt values, statistical evaluation based on SI values showed that only two labs succeeded in achieving within-laboratory reproducibility. For those two labs that satisfied the within-lab reproducibility, between-laboratory reproducibility could be also attained based on inferential as well as descriptive statistics.

Oxygen Reduction Reaction Measurements on Platinum Electrocatalysts Utilizing Rotating Disk Electrode Technique: I. Impact of Impurities, Measurement Protocols and Applied Corrections

The rotating disk electrode (RDE) technique is being extensively used as a screening tool to estimate the activity of novel PEMFC electrocatalysts synthesized in lab-scale (mg) quantities. Discrepancies in measured activity attributable to glassware and electrolyte impurity levels, as well as conditioning, protocols and corrections are prevalent in the literature. The electrochemical response to a broad spectrum of commercially sourced perchloric acid and the effect of acid molarity on impurity levels and solution resistance were also assessed. Our findings reveal that an area specific activity (SA) exceeding 2.0 mA/cm2 (20 mV/s, 25°C, 100 kPa, 0.1 M HClO4) for polished poly-Pt is an indicator of impurity levels that do not impede the accurate measurement of the ORR activity of Pt based catalysts. After exploring various conditioning protocols to approach maximum utilization of the electrochemical area (ECA) and peak ORR activity without introducing catalyst degradation, an investigation of measurement protocols for ECA and ORR activity was conducted. Down-selected protocols were based on the criteria of reproducibility, duration of experiments, impurity effects and magnitude of pseudo-capacitive background correction. Statistical reproducibility of ORR activity for poly-Pt and Pt supported on high surface area carbon was demonstrated.

Biofeedback Therapy After Sphincter-Preservation Surgery for the Treatment of Rectal Cancer.

See Article on Page 138-143 Treatment of rectal cancer has been improved, and the incidence of anal-sphincter-preservation surgery has increased since the popularization of a total mesorectal excision (TME) with pelvic autonomic nerve preservation [1]. Sphincter-preservation surgery with restoration of bowel continuity to avoid a permanent stoma is feasible in 50%-80% of patients. A preserved function after rectal surgery is directly related to better quality of life (QoL), and functional outcome has become an important parameter for defining surgical performance after a low anterior resection (LAR) [1,2]. However, that up to 90% of such patients will subsequently have a change in bowel habit, including fecal incontinence (FI), increased bowel frequency and emptying difficulties, what is called anterior resection syndrome (ARS), is widely accepted [3]. Currently, no specific options for treating ARS or FI exist. Pelvic floor rehabilitation (PFR), including pelvic floor muscle training (PFMT), biofeedback (BF) training, and rectal balloon training has been accepted as a standard technique for the treatment of FI [4]. A systematic review demonstrated that the use of pelvic floor training (PFT) was useful for improving functional outcome after a LAR. Most included studies showed an improvement regarding continence, stool frequency and QoL. However, the available data from studies of limited quality could not be pooled due to heterogeneity of the PFT protocols used and the different FI scoring systems [4]. In studies done in 2012, the Cochrane collaboration found some evidence that BF and ES together enhanced the outcome of treatment compared to ES alone or BF alone [5]. However, they concluded that the role of anal sphincter exercises and BF in the management of FI was not definitive; they used poor methodology and were frequently underpowered. Recently, Visser et al. [4] systematically reviewed the use of PFR after a LAR in 286 patients in five different studies and found that PFT, including BF therapy, was useful for improving functional outcome. Among the studies, only the data of Kim et al. [6] and Pucciani et al. [7] could be pooled and demonstrated improved functional outcome based on anorectal pressures and rectal capacity after the LAR. This was particularly true for patients with FI as the primary symptom [5]. Kim et al. [8] presented a timely paper on this issue in the Annals of Coloproctology. The authors evaluated the efficacy of BF in terms of the change in the defecation pattern and the QoL in patients after rectal-cancer surgery. However, major inherent limitations, such as a very small sample size in both groups, especially the treated patients (biofeedback group), still exist. Regarding the timing of BF for patients with a diverting ileostomy after a LAR, BF is generally introduced after stoma take-down. In this study, the authors introduced BF before stoma closure, and they assessed the response to treatment by using anorectal manometry after stoma closure. These results have led some surgeons to be concerned about whether BF was actually required at relatively early times before stoma takedown after restoration surgery; another concern was wound healing for the neorectum. Regarding physiology if there are no any luminal flow and no bowel peristaltic movement of the neorectum during squeezing (anorectal condition may be different or the real sampling reflex or sensory mechanism could not be tested during stoma), how visual or auditory display or instrument-assisted BF training could be used is not known. Such a situation is not adequate for assessing the objective efficacy of BF therapy for patients with ARS. Potential contributing factors, either treatment or patient related, to and the duration of PFT as a proper treatment for ARS are still under many debate [9]. As the authors' results have shown, BF therapy does not yet seem to be desirable. Still, solid evidence for the routine use of PFR to improve functional outcome after a LAR is lacking. So far, various types of questionnaire surveys have been used in many studies, but standardized and validated evaluation tools are lacking [10]. Nevertheless, this is a meaningful study in establishing the efficacy of BF in the management of FI after sphincter-preservation surgery. In the near future, well-designed studies using uniformly-adopted scoring systems and proper selection of sphincter-preservation-surgery patients based upon reproducible criteria are needed and may be worthwhile.

Correlation between Vertical Dimension of Occlusion and Finger Length in Kashmiri Population

Introduction: Measurement of accurate vertical dimension of occlusion (VDO) is of prime importance to the dentist especially a prosthodontist. Though many methods have been proposed in recording VDO in the past but none of them fulfills the criteria of accuracy, reproducibility and ease. This study employs theuse of length of fingers to measure VDO in Kashmiri population. Materials and methods: The study was conducted on 60 dentulous subjects which include 30 males and 30 females in the age range of 18 to 25 years. Measurement of VDO and length of fingers was recorded using a digital vernier caliper. Correlation between VDO and length of fingers was studied using Spearman’s coefficient. Result: Vertical dimension of occlusion was found to be almost the length of index finger in males and little finger in females in Kashmiri population. Conclusion: The study revealed that length of index finger is almost equal to VDO in males and length of little finger is almost equal to VDO in females.

Interpretation and Application of the International Myeloma Working Group (IMWG) Criteria: Proposal for Uniform Assessment and Reporting in Clinical Trials Based on the First Study Independent Response Adjudication Committee (IRAC) Experience

Background: In multiple myeloma (MM), reproducible criteria of disease response and progression are critical to ensuring consistency in trial analysis and reporting.Regulatory Agencies responsible for drug approval often require clinical trials use objective endpoints that are evaluated by Independent Response Adjudication Committees (IRACs). The International Myeloma Working Group (IMWG) has developed objective criteria to define disease evaluability, response, and progression (Durie, Leukemia 2006). However, there are scenarios were IMWG criteria are ambiguous, potentially leading to inconsistency amongst IRAC members or between different IRACs when interpreting response data. To address these practical issues, we developed rules for applying IMWG response criteria to the FIRST trial, the largest study in newly-diagnosed MM (Facon, Blood 2013).Patients and Methods: FIRST is a pivotal phase III trial for previously untreated patients with MM not eligible for ASCT that enrolled 1623 patients; the primary endpoint was progression-free survival (PFS). At 12 in-person meetings between 2010-2013, the IRAC assessed eligibility, evaluability and response status of all patients after each cycle until PD or study discontinuation. These evaluations were used in the trial’s primary analysis. Response was based on central laboratory values and assessed using IMWG criteria. For circumstances where IMWG criteria were ambiguous, rules were developed through unanimous consensus of IRAC members and then applied uniformly throughout the study.Results: Rules addressing identified issues on evaluability, response and progressive disease are shown in tables 1-3. Common situations posing a need for rules concerned to measurability, missing laboratory values, timing of BM exam to assess CR, discrepancies between screening and baseline lab values or measurements in the size of extramedullary plasmacytomasConclusions: These recommendations provide explicit descriptions of response assessment of the FIRST trial, can be used for a more uniform evaluation and reporting in future clinical studies and can assist investigators’ adherence to clinical trial requirements.Table 1Rules for Use of Data for EvaluationIssueRecommendationLight chain (Bence-Jones) myeloma with “non-measurable” serum light chainUse only 24 hour urine M-spike value for response evaluation, except for complete response (CR)IgG, IgA or IgD myeloma with “non-measurable” serum M-spike values and measurable urine M-spikeUse only urine values for response evaluation except for CR or PDDisease with “measurable” values at screening but “non-measurable” at baseline (cycle 1, day 1)All assessments not meeting CR or PD should be “non-evaluable (NE)”Missing data for 2 or more consecutive cyclesConsider “NE” for the specific missing cycle assessmentsM-spike reported as “too small to quantitate” in responding patientAssign value of 0 to allow subsequent calculation of absolute increase to determine PDPlasmacytoma given prior radiation therapy or located only in boneNot used for response assessment, except for potential PDTable 2Rules for Response AssessmentIssueRecommendationAbsence of 2 consecutive negative IFE and simultaneous <5% BMPCsCR not assigned, assess as VGPRExtramedullary plasmacytomas (EMPs)- Visits until first EMP assessmentAssess as NE- Two consecutive missing EMP assessmentsAssess as NE- EMPs not assessed as per protocolAssess as NE (consider a sensitivity analysis (ignoring EMPs))- Patients in serologic VGPR, with ³ 50% decrease in EMP, but still presentAssess as PR, until EMPs have disappearedTable 3Rules for Determining Progressive DiseaseIssueRecommendationIncrease in a previously existing EMP or bone lesion as only source of PDRequest verification of radiologist reports before PD is assignedInitiation of a new antimyeloma therapy before documented PDCensor at the time of last assessment before starting the new therapyPD only based on the BMPCsDetermine reason for BM exam (anemia? bone pain?) before assigning PDRadiation therapy not for pre-planned reasonsAssess as PDPD based on M-protein measurements with no confirmationCensor unless that PD is considered unequivocal by unanimous agreement of IRAC DisclosuresBlade:Janssen: Honoraria, Research Funding; Celgene: Honoraria, Research Funding. Knop:Celgene: Honoraria. Cohen:Celgene: Honoraria. Shah:Onyx Pharmaceuticals: Consultancy, Research Funding; Celgene: Consultancy, Research Funding; Millennium Pharmaceuticals: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Array: Consultancy, Research Funding. Meyer:Celgene: Honoraria.

Gene Expression Profiling of IgM Monoclonal Gammopathy of Undetermined Significance (IgM-MGUS)

The 2nd IWWM tried to define reproducible criteria for the diagnosis of IgM-MGUS and Waldenstrom’s Macroglobulinemia. IgM-MGUS was defined as asymptomatic condition characterized by serum IgM monoclonal protein (MC) without morphologic evidence of bone marrow (BM) lymphoplasmacytic infiltration. The proposal of the guidelines was to classify as MGUS also patients with equivocal evidence of BM infiltration, such as those presenting clonal B-cells by multiparameter flow cytometry (MFC) in the absence of morphologic evidence of BM infiltration, as well as those with equivocal BM infiltrates not confirmed by immunophenotypic studies.PatientsThe diagnosis of IgM-MGUS was made in 11 patients (6 males, 5 females) according to the consensus panel criteria. The median age at diagnosis was 73 (range, 60-77). Ten patients had K light chains. The median erythrocyte sedimentation rate was 11. The MC level at diagnosis ranged from 0.1 to 1.2 g/dL (median 0.4). Only one patient had MC value > 1.0 g/dL. The median IgM value was 697 mg/dL (range 116-1790). Five of 11 IgM-MGUS patients showed a small clonal B-cell population (light-chain-isotype-positive B-cells) detected by MFC without histologic evidence of BM infiltration. Therefore, patients were divided in 2 groups: group 1 (n=5) showing a clonal B-cell population, and group 2 (n=6) with polyclonal B-cells at MFC.Methods and resultsWe isolated BM CD19+ cells in the 11 IgM-MGUS patients using Miltenyi Microbeads and performed microarray with Affymetrix-HG-U133 Plus 2.0 array. Gene set enrichment analysis (GSEA) was performed and different sets of genes were defined based on REACTOME pathways, KEGG pathways and GO Biological Process Terms. Interestingly, 17 top-ranking gene sets including differently expressed genes, reached a nominal p-value lower than 0.001; 2 gene sets were upregulated (while 15 gene sets were downregulated in monoclonal vs. polyclonal IgM-MGUS (table 1).No genes resulted significantly differentially expressed between group 1 and group 2 using a classic SAM test for microarrays and correcting for multiple testing with a false discovery rate (FDR) threshold of 5%. Similarly, IgM and MC were not differentially expressed between the two groups, although IgM showed a nominal p-value of 0.09 (t-test).However, when using linear regression to explain each gene expression data as a function of both IgM and MC, UBTF, TRIM5, FLJ35816, RDH10 genes were selected based on a FDR equal to 5%, applied to the F-statistic p-value. In particular, the model fitting UBTF had a p-value of 9.461e-07 and an adjusted R-squared of 0.9786; table 2 displays the coefficients of the model and the related p-values, showing a positive co-regulation of UBTF with MC.ConclusionsIn conclusion, microarray of IgM-MGUS gives insights into gene expression differences in IgM-MGUS. Notably, UBTF is a transcription factor which plays a crucial role in the transcription of rRNA in ERK-pathway, suggesting a possible role of ERK-pathway in IgM-MGUS. Additional gene expression measurements are ongoing in a larger cohort of IgM-MGUS patients.Table 1Upregulated gene sets in monoclonal vs. polyclonal IgM-MGUSGENE SET NAMEREACTOME_XENOBIOTICSREGULATION_OF_CHROMOSOME_ORGANIZATION_AND_BIOGENESISDownregulated gene sets in monoclonal vs. polyclonal IgM-MGUSTable 2Linear regression results of both IgM and MC on UBTF expressionGENE SET NAMEREACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSISREACTOME_P38MAPK_EVENTSREACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLEREACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASEKEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISMCHROMATIN_ASSEMBLY_OR_DISASSEMBLYESTABLISHMENT_AND_OR_MAINTENANCE_OF_CHROMATIN_ARCHITECTUREPROTEIN_DNA_COMPLEX_ASSEMBLYRESPONSE_TO_DNA_DAMAGE_STIMULUSCHROMATIN_ASSEMBLYCHROMOSOME_ORGANIZATION_AND_BIOGENESISDOUBLE_STRAND_BREAK_REPAIRCHROMATIN_REMODELINGCENTROSOME_ORGANIZATION_AND_BIOGENESISMICROTUBULE_ORGANIZING_CENTER_ORGANIZATION_AND_BIOGENESISTable 3Coefficientp-valueIntercept7.07388016.47e-12IgM-0.00215933.78e-07MC1.19250550.000501IgM:MC0.00105770.000152 DisclosuresNo relevant conflicts of interest to declare.

Systematic review of cadaveric studies on anatomic posterior cruciate ligament reconstruction: the landmarks in anatomic posterior cruciate ligament reconstruction.

Recently, several new techniques for anatomic posterior cruciate ligament reconstruction (PCLR) have emerged and are believed to restore the normal anatomy of the posterior cruciate ligament more accurately. Despite the latest trend, the optimal methods for anatomic PCLR remain controversial. The purpose of this research is to review surgical techniques for PCLR in cadaver studies and suggest consistent and reproducible technical criteria. For the review of the literature, MEDLINE and EMBASE were screened for articles on anatomic PCLR. Only basic science studies on PCLR performed on human cadavers and written in English were included. Seventeen studies were included in this systematic review. Only the tunnel positions, graft types, and surgical techniques were reported in the majority of the studies. There were many variations of the reported tunnel positions, graft types, and surgical techniques among the studies. In most studies, surgical techniques for consistent and reproducible anatomic PCLR were not explained clearly. Therefore, high level medical research should be encouraged in order to establish standard surgical techniques for anatomic PCLR.

Malignant odontogenic tumors: an update on selected tumors.

This is an update on selected odontogenic malignancies. The article deals with aspects of recognized odontogenic carcinomas, odontogenic sarcoma and a yet unrecognized entity, sclerosing odontogenic carcinoma. Odontogenic malignancies are exceedingly rare, complicating a thorough understanding of the biologic behavior, reproducible standardized diagnostic criteria, appropriate classification and clinical management. Without the knowledge of the tumor's biologic behavior, adequate clinical management is difficult and patient outcomes uncertain. The histopathologic features are emphasized as well as the more recent biomarker findings. These recent advances may facilitate further understanding of this group of malignancies and provide useful stratification to guide patient management.

G.P.133: Ankle muscle weakness but not balance trouble account for walking disability in patients with myotonic dystrophy type 1

Myotonic dystrophy type 1 (DM1) is an autosomal dominant disease for which treatments are being developed. There is a need to define reliable and reproducible criteria to evaluate neuromuscular function in order to assess their effects. The main aim of our study consists of a follow-up of the natural history of DM1 patients over 3years. Here, baseline values for the 6-min walk distance (6MWD), the lower limb muscle strength and balance measured by the movement rate of the centre of foot pressure on a force plateform are compared between patients and age- and sex-matched healthy controls. DM1 patients and healthy controls (10 females and 7 males between 26 and 49years old in each group) of similar mean height and weight were compared. The 6MWD in percentage of predicted value was significantly reduced in DM1 patients by about 50% (Mann Whitney, p p p p p p

Launching the Theoretical Crystallography Open Database

As computational chemistry methods enjoy unprecedented growth, computer power increases and price/performance ratio drops, a large number of crystal structures can today be refined and their properties computed using modern theoretical approaches, such as DFT, post-HF, QM/MM, MCMM methods. Availability of several open source codes for computational and quantum chemistry and open-access crystallographic databases enables large scale computations of material structures and properties. We thus increasingly feel that an open collection of theoretically computed chemical structures would be a valuable resource for the scientific community. To address this need, we have launched a Theoretical Crystallography Open Database (TCOD, http://www.crystallography.net/tcod/). The TCOD sets a goal to collect a comprehensive set of computed crystal structures that would be made available under an Open Data license and invites all scientists to deposit their published results or pre-publication data. Accompanied with a large set of experimental structures in the COD database [1], the TCOD opens immediate possibilities for experimental and theoretical data cross-validation. To ensure high quality of deposited data, TCOD offers ontologies in a form of CIF [2] dictionaries that describe parameters of computed chemical and crystal structures, and an automated pipeline that checks each submitted structure against a set of community-specified criteria for convergence, computation quality and reproducibility. The scope of TCOD and validation tools make TCOD a high-quality, comprehensive theoretical structure database, useful in a broad range of disciplines. First-principle calculations are also of huge interest to simulate physical properties, either prospectively or for materials that do not grow as sufficiently large crystals. The property results can now be tested against the Material Properties Open Database [3] (http://www.materialproperties.org/) to ameliorate the used models.

An experimental analysis of the onset of buckling in sheet metal forming

In this study a test method is presented in which buckling phenomena can be investigated at a fundamental level. A rectangular sheet sample is fixed in a specially designed mounting device which transfers tensile forces in the longitudinal direction as well as compressive forces in the perpendicular direction. The mechanical principle used ensures a steady ratio of the corresponding strains. Onset and growth of the wrinkle can be monitored by special measuring equipment. The aim of the experimental and theoretical investigations described in this paper was to check the operational characteristics and capabilities of the equipment and to deduce a reproducible criterion for the formation of wrinkles.

Modeling Stroke in Mice: Permanent Coagulation of the Distal Middle Cerebral Artery

Stroke is the third most common cause of death and a main cause of acquired adult disability in developed countries. Only very limited therapeutical options are available for a small proportion of stroke patients in the acute phase. Current research is intensively searching for novel therapeutic strategies and is increasingly focusing on the sub-acute and chronic phase after stroke because more patients might be eligible for therapeutic interventions in a prolonged time window. These delayed mechanisms include important pathophysiological pathways such as post-stroke inflammation, angiogenesis, neuronal plasticity and regeneration. In order to analyze these mechanisms and to subsequently evaluate novel drug targets, experimental stroke models with clinical relevance, low mortality and high reproducibility are sought after. Moreover, mice are the smallest mammals in which a focal stroke lesion can be induced and for which a broad spectrum of transgenic models are available. Therefore, we describe here the mouse model of transcranial, permanent coagulation of the middle cerebral artery via electrocoagulation distal of the lenticulostriatal arteries, the so-called “coagulation model”. The resulting infarct in this model is located mainly in the cortex; the relative infarct volume in relation to brain size corresponds to the majority of human strokes. Moreover, the model fulfills the above-mentioned criteria of reproducibility and low mortality. In this video we demonstrate the surgical methods of stroke induction in the “coagulation model” and report histological and functional analysis tools.

Modeling Stroke in Mice: Permanent Coagulation of the Distal Middle Cerebral Artery

Stroke is the third most common cause of death and a main cause of acquired adult disability in developed countries. Only very limited therapeutical options are available for a small proportion of stroke patients in the acute phase. Current research is intensively searching for novel therapeutic strategies and is increasingly focusing on the sub-acute and chronic phase after stroke because more patients might be eligible for therapeutic interventions in a prolonged time window. These delayed mechanisms include important pathophysiological pathways such as post-stroke inflammation, angiogenesis, neuronal plasticity and regeneration. In order to analyze these mechanisms and to subsequently evaluate novel drug targets, experimental stroke models with clinical relevance, low mortality and high reproducibility are sought after. Moreover, mice are the smallest mammals in which a focal stroke lesion can be induced and for which a broad spectrum of transgenic models are available. Therefore, we describe here the mouse model of transcranial, permanent coagulation of the middle cerebral artery via electrocoagulation distal of the lenticulostriatal arteries, the so-called “coagulation model”. The resulting infarct in this model is located mainly in the cortex; the relative infarct volume in relation to brain size corresponds to the majority of human strokes. Moreover, the model fulfills the above-mentioned criteria of reproducibility and low mortality. In this video we demonstrate the surgical methods of stroke induction in the “coagulation model” and report histological and functional analysis tools.

Spirometric standards and patient characteristics: an exploratory study of factors affecting fulfillment in routine clinical practice.

Spirometry is an apparently simple test, yet the recommended criteria for acceptability and reproducibility can be difficult to fulfill. This study aimed (1) to prospectively assess the number of tests that meet the American Thoracic Society/European Respiratory Society (ATS/ERS) 2005 acceptability and repeatability criteria in the routine practice of an experienced technician at a referral hospital's lung function laboratory, (2) to identify the most common errors, and (3) to explore patient characteristics possibly associated with failure to meet standards. We prospectively evaluated 257 consecutive spirometries supervised by the same technician, who gave priority to achieving a minimum of 3 correct maneuvers within a maximum of 8 attempts. We recorded FVC, FEV1, expiratory time (TE), back-extrapolated volume (VE), end-of-test volume (VEOT), number of maneuvers with and without errors, and errors (VE > 0.15 L or 5% of FVC, TE < 6 s, and VEOT ≥ 0.025 L for ≥ 1 s). Two-hundred and fifteen spirometries (83.7%, 95% CI 78.6-87.7%) met the ATS/ERS 2005 criteria. Acceptability criteria were met in 73.9% (95% CI 71.2-76.3%) of the maneuvers and repeatability criteria in 90.7% (95% CI 86.5-93.6%). A mean ± SD of 3.3 ± 1.4 per subject was acceptable, and a mean ± SD of 4.5 ± 1.9 was obtained. TE and VEOT errors were the most common. Nearly 15% of the subjects failed to fulfill all the ATS/ERS 2005 criteria for spirometry performed even though they were coached by a qualified and regularly trained technician in a hospital lung function laboratory. The fact that the ATS/ERS 2005 criteria cannot be met by all patients in optimal technical conditions should be further considered and explored.

Analysis of tissue surrounding thyroid nodules by ultrasound digital images.

Since US is not easily reproducible, the digital image analysis (IA) has been proposed so that the image evaluation is not subjective. In fact, IA meets the criteria of objectivity, accurateness, and reproducibility by a matrix of pixels whose value is displayed in a gray level. This study aims at evaluating via IA the tissue surrounding a thyroid nodule (backyard tissue, BT) from goitres with benign (b-BT) and malignant (m-BT) lesions. Sixty-nine US images of thyroid nodules surrounded by adequate thyroid tissue was classified as normoechoic and homogeneous were enrolled as study group. Forty-three US images from normal thyroid (NT) glands were included as controls. Digital images of 800 × 652 pixels were acquired at a resolution of eight bits with a 256 gray levels depth. By one-way ANOVA, the 43 NT glands were not statistically different (P = 0.91). Mean gray level of normal glands was significantly higher than b-BT (P = 0.026), and m-BT (P = 0.0001), while no difference was found between b-BT and m-BT (P = 0.321). NT tissue boundary external to the nodule was found at 6.0 ± 0.5 mm in cancers and 4.0 ± 0.5 mm in benignancies (P = 0.001). These data should indicate that the tissue surrounding a thyroid nodule may be damaged even when assessed as normal by US. This is of interest to investigate the extranodular effects of thyroid tumors.