Contamination Errors Research Articles

Tuberculosis its Prevalence, Complications and Clinical Aspects among the Population of Northern Part of Bihar

Introduction: It is commonly known as death causing disease of reproductive age group people. It is one of the top five death causing disease. It effects upon every age group people. But dangerous impact of tuberculosis occurs on immunocompetent people. There are a number of complications occur only due to one disease that is tuberculosis. it effects almost all organs and impaired their vital functions. Even if we leave death, even after tuberculosis proved to be most dangerous disease. In this study our main aim to explore the aspects, complications and prevalence of genital tuberculosis. In this study we also explore the ancient technics as well as the modern technics and their methods to ruled out the disease and improvement of treatment from ancient time to modern time. Method: This study was carried out between January 22 to April 23. 342 subjects are selected by inclusion and exclusion method. Subjects are classified in to 3 groups according to their physical appearance clinical symptoms and family history. Further patients are again classified in to negative, positive and doubtful negative patients after conducting routine and special investigations. Results: After all pathological investigation we found that 45 (13.1%) subjects have found positive in which 5.8% were male and 7.2 % were female. Conclusion: Tuberculosis is present in different forms and should be ruled out in early stage to safe from tissue damages. But unfortunately, we haven’t any tools which can detect the disease in its early stage accurately. All the investigation has their own limitations and contamination errors. There are a number of patients in which some can easily identified by their clinical symptoms and related routine examination, some are asymptomatic and identified by advanced diagnostic tools where are some such patient are also found who were strong symptomatic but even not only routine but also advance investigations are fail to detect. In our study we found the root cause of the disease, which are high population density, economically lower standard, poor hygiene life style, compromise food habits, illiteracy, marriage in early stage, multiple marriage, multiple children, non- skilled medical practices are causing and enhancing the incident of tuberculosis.

Classification of COVID19 Patients Using Robust Logistic Regression

Coronavirus disease 2019 (COVID19) has triggered a global pandemic affecting millions of people. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the COVID-19 disease is hypothesized to gain entry into humans via the airway epithelium, where it initiates a host response. The expression levels of genes at the upper airway that interact with the SARS-CoV-2 could be a telltale sign of virus infection. However, gene expression data have been flagged as suspicious of containing different contamination errors via techniques for extracting such information, and clinical diagnosis may contain labelling errors due to the specificity and sensitivity of diagnostic tests. We propose to fit the regularized logistic regression model as a classifier for COVID-19 diagnosis, which simultaneously identifies genes related to the disease and predicts the COVID-19 cases based on the expression values of the selected genes. We apply a robust estimating methods based on the density power divergence to obtain stable results ignoring the effects of contamination or labelling errors in the data and compare its performance with respect to the classical maximum likelihood estimator with different penalties, including the LASSO and the general adaptive LASSO penalties.

Variation in spin contamination and diradical character with distance between a singlet biradical molecule and surface

As diradical molecules are used to perform various unique functions, they are expected to be applied as molecular devices. In addition, theoretical calculations based on density functional theory (DFT) are critical tools in the field of computational material science. In the DFT calculations of a diradical molecule, investigation of the spin contamination error and estimation of the diradical character, which is a feature of diradical molecules, are necessary. However, little is known regarding the variation in the spin contamination error and diradical character with the distance from a surface. These data are essential in the fields of physical chemistry and surface science to enable the study of the effects of surface interactions on strongly correlated electrons. Herein, the variations were clarified by performing approximate spin-projection DFT/plane-wave (AP-DFT/plane-wave) calculations using three reaction model systems: (1) diradical adsorption state → non-diradical molecule, (2) non-diradical adsorption state → diradical molecule, and (3) diradical adsorption state → diradical molecule. Variations in the diradical character were monotonic, whereas the spin contamination error exhibited extreme values and inflections. This was because the interaction with the surface exhibited two opposing effects: (1) the diradical character of the adsorbate increased, which increased the spin contamination error, and (2) the energy difference between the open singlet and high-spin states decreased, which decreased the spin contamination error. When a diradical/non-diradical transformed owing to surface adsorption, the effect of the spin contamination error on the adsorption energy became large. Hence, spin contamination should be analysed when the considered adsorption system features diradical/non-diradical transformations. In addition, the diradical character was affected by a surface even when dispersion forces were the major adsorption stabilisation factor. This indicated that the optimisation of the surface interactions was critical in the immobilisation of diradical molecules.

Accuracy in starphotometry

Abstract. Starphotometry, the night-time counterpart of sunphotometry, has not yet achieved the commonly sought observational error level of 1 %: a spectral optical depth (OD) error level of 0.01. In order to address this issue, we investigate a large variety of systematic (absolute) uncertainty sources. The bright-star catalogue of extraterrestrial references is noted as a major source of errors with an attendant recommendation that its accuracy, particularly its spectral photometric variability, be significantly improved. The small field of view (FOV) employed in starphotometry ensures that it, unlike sun- or moonphotometry, is only weakly dependent on the intrinsic and artificial OD reduction induced by scattering into the FOV by optically thin clouds. A FOV of 45 arcsec (arcseconds) was found to be the best trade-off for minimizing such forward-scattering errors concurrently with flux loss through vignetting. The importance of monitoring the sky background and using interpolation techniques to avoid spikes and to compensate for measurement delay was underscored. A set of 20 channels was identified to mitigate contamination errors associated with stellar and terrestrial atmospheric gas absorptions, as well as aurora and airglow emissions. We also note that observations made with starphotometers similar to our High Arctic instrument should be made at high angular elevations (i.e. at air masses less than 5). We noted the significant effects of snow crystal deposition on the starphotometer optics, how pseudo OD increases associated with this type of contamination could be detected, and how proactive techniques could be employed to avoid their occurrence in the first place. If all of these recommendations are followed, one may aspire to achieve component errors that are well below 0.01: in the process, one may attain a total 0.01 OD target error.

Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment.

Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding.

Organic contamination detection for isotopic analysis of water by laser spectroscopy.

Hydrogen and oxygen stable isotope ratios (δ2 H, δ17 O, and δ18 O values) are commonly used tracers of water. These ratios can be measured by isotope ratio infrared spectroscopy (IRIS). However, IRIS approaches are prone to errors induced by organic compounds present in plant, soil, and natural water samples. A novel approach using 17 O-excess values has shown promise for flagging spectrally contaminated plant samples during IRIS analysis. A systematic assessment of this flagging system is needed to prove it useful. Errors induced by methanol and ethanol water mixtures on measured IRIS and isotope ratio mass spectrometry (IRMS) results were evaluated. For IRIS analyses both liquid- and vapour-mode (via direct vapour equilibration) methods are used. The δ2 H, δ17 O, and δ18 O values were measured and compared with known reference values to determine the errors induced by methanol and ethanol contamination. In addition, the 17 O-excess contamination detection approach was tested. This is a post-processing detection tool for both liquid and vapour IRIS triple-isotope analyses, utilizing calculated 17 O-excess values to flag contaminated samples. Organic contamination induced significant errors in IRIS results, not seen in IRMS results. Methanol caused larger errors than ethanol. Results from vapour-IRIS analyses had larger errors than those from liquid-IRIS analyses. The 17 O-excess approach identified methanol driven error in liquid- and vapour-mode IRIS samples at levels where isotope results became unacceptably erroneous. For ethanol contaminated samples, a mix of erroneous and correct flagging occurred with the 17 O-excess method. Our results indicate that methanol is the more problematic contaminant for data corruption. The 17 O-excess method was therefore useful for data quality control. Organic contamination caused significant errors in IRIS stable isotope results. These errors were larger during vapour analyses than during liquid IRIS analyses, and larger for methanol than ethanol contamination. The 17 O-excess method is highly sensitive for detecting narrowband (methanol) contamination error in vapour and liquid analysis modes in IRIS.

Spin Contamination Errors in DFT+U/Plane-wave Calculations for LixFeF3 Systems (x = 0–1)

The DFT/plane-wave method is a general first-principles calculation method used for battery materials; nevertheless, the effect of spin contamination errors is yet to be investigated. We calculated...

AVALIAÇÃO DA ESTABILIDADE DE CONTROLES PARA ANÁLISES DE DIAGNÓSTICO IN VITRO EM CONDIÇÕES DE TEMPERATURA REAIS DE TRABALHO LABORATORIAL

A garantia da qualidade é o mecanismo que propicia ao laboratório de análises clínicas apresentar resultados confiáveis adequados e corretamente interpretados. Na rotina de trabalho desses laboratórios, utilizam-se calibradores, que são padrões conhecidos com características quantitativas e/ou qualitativas determinadas, os controles podem ser utilizados para medir alguns parâmetros de qualidade laboratorial. A depender dos fabricantes, existem algumas sugestões de manuseio a ser seguido, para então, obter maior fidedignidade de aferição. O desempenho do calibrador pode ser afetado por erros de reconstituição, de homogeneização, armazenamento incorreto, contaminação da água ou vidraria. Dessa forma, este trabalho avaliou a estabilidade de controles comerciais submetidos a temperaturas diversas encontradas em situações reais de laboratório, como a refrigeração entre 4-8 ºC, exposição sob bancada de trabalho, a temperatura ambiente, e armazenada dentro de um automóvel, em temperaturas de 60-80 ºC, por períodos de 1 a 12 dias. Tanto o tempo quanto a temperatura em que as alíquotas são armazenadas não ocasionaram alterações nesse produto (exceto para a creatinina, apresentou-se instável no 12º dia do estudo), apresentando valores dentro das faixas estimadas, e possivelmente as alíquotas fora das faixas estimadas devem-se a erro sistemático.

Estimation of spin contamination errors in DFT/plane-wave calculations of solid materials using approximate spin projection scheme

Estimation and the importance of spin contamination errors (SCEs) in theoretical calculations related to open-shell molecular systems are well known. However, there is no estimation scheme available for density functional theory (DFT)/plane-wave, a standard first-principles method for solid materials. Therefore, in this study, we established the estimation scheme of SCE in DFT/plane-wave using approximate spin projection, and the new scheme was applied to typical models with stable antiferromagnetic states to illustrate the importance of SCE correction in solid systems.

Pharmaceutical Compounding: a History, Regulatory Overview, and Systematic Review of Compounding Errors.

IntroductionMedications are compounded when a formulation of a medication is needed but not commercially available. Regulatory oversight of compounding is piecemeal and compounding errors have resulted in patient harm. We review compounding in the United States (US), including a history of compounding, a critique of current regulatory oversight, and a systematic review of compounding errors recorded in the literature.MethodsWe gathered reports of compounding errors occurring in the US from 1990 to 2020 from PubMed, Embase, several relevant conference abstracts, and the US Food and Drug Administration “Drug Alerts and Statements” repository. We categorized reports into errors of “contamination,” suprapotency,” and “subpotency.” Errors were also subdivided by whether they resulted in morbidity and mortality. We reported demographic, medication, and outcome data where available.ResultsWe screened 2155 reports and identified 63 errors. Twenty-one of 63 were errors of concentration, harming 36 patients. Twenty-seven of 63 were contamination errors, harming 1119 patients. Fifteen errors did not result in any identified harm.DiscussionCompounding errors are attributed to contamination or concentration. Concentration errors predominantly result from compounding a prescription for a single patient, and disproportionately affect children. Contamination errors largely occur during bulk distribution of compounded medications for parenteral use, and affect more patients. The burden falls on the government, pharmacy industry, and medical providers to reduce the risk of patient harm caused by compounding errors.ConclusionIn the US, drug compounding is important in ensuring access to vital medications, but has the potential to cause patient harm without adequate safeguards.

Effect of surface interactions on spin contamination errors of homogeneous spin dimers, chains, and films: model calculations of Au/MgO and Au/BaO systems

It is well known that unrestricted density functional theory (UDFT) calculations include spin contamination errors. While errors in UDFT/plane-wave calculations have not been clarified thus far, some effects of these errors are investigated. Recently, our group estimated spin contamination errors in UDFT/plane-wave calculation results by developing and applying the approximate spin projection (AP) scheme [Chem. Phys. Lett., 701: 103 (2018), Mol. Phys., 117: 2251 (2019), Molecules, 24: 505 (2019), Appl. Phys. Express, 12: 115506 (2019)]. In this study, a systematic theoretical investigation of the surface effects on the spin contamination error was performed. For this purpose, we selected model systems such as Au dimers, chains, and film adsorptions onto MgO and BaO (001) surfaces. The calculation results showed the dependence on the dimensions of the supported materials and lattice constants of the supports. In general, the effects of spin contamination errors are decreased by interaction with the surface. The effects of the errors increased by increasing dimension; i.e. the increasing order of spin contamination errors is film > chain > dimer. In addition, the spin-polarised states are stabilised because of the interaction with the surfaces, and spin contamination errors occur in some cases where the Au–Au distances are small.

Across-vendor standardization of semi-LASER for single-voxel MRS at 3T.

The semi-adiabatic localization by adiabatic selective refocusing (sLASER) sequence provides single-shot full intensity signal with clean localization and minimal chemical shift displacement error and was recommended by the international MRS Consensus Group as the preferred localization sequence at high- and ultra-high fields. Across-vendor standardization of the sLASER sequence at 3 tesla has been challenging due to the B1 requirements of the adiabatic inversion pulses and maximum B1 limitations on some platforms. The aims of this study were to design a short-echo sLASER sequence that can be executed within a B1 limit of 15 μT by taking advantage of gradient-modulated RF pulses, to implement it on three major platforms and to evaluate the between-vendor reproducibility of its perfomance with phantoms and in vivo. In addition, voxel-based first and second order B0 shimming and voxel-based B1 adjustments of RF pulses were implemented on all platforms. Amongst the gradient-modulated pulses considered (GOIA, FOCI and BASSI), GOIA-WURST was identified as the optimal refocusing pulse that provides good voxel selection within a maximum B1 of 15 μT based on localization efficiency, contamination error and ripple artifacts of the inversion profile. An sLASER sequence (30 ms echo time) that incorporates VAPOR water suppression and 3D outer volume suppression was implemented with identical parameters (RF pulse type and duration, spoiler gradients and inter-pulse delays) on GE, Philips and Siemens and generated identical spectra on the GE 'Braino' phantom between vendors. High-quality spectra were consistently obtained in multiple regions (cerebellar white matter, hippocampus, pons, posterior cingulate cortex and putamen) in the human brain across vendors (5 subjects scanned per vendor per region; mean signal-to-noise ratio > 33; mean water linewidth between 6.5 Hz to 11.4 Hz). The harmonized sLASER protocol is expected to produce high reproducibility of MRS across sites thereby allowing large multi-site studies with clinical cohorts.

Spin contamination errors on spin-polarized density functional theory/plane-wave calculations for crystals of one-dimensional materials

An estimation scheme is established for the spin contamination error (SCE) in spin-polarized density functional theory calculations with the plane-wave basis for crystals of one-dimensional materials. The size consistency of the scheme was confirmed via H-chain models, and the accuracy was confirmed by the comparison with the reported experimental values. The scheme was applied to real systems, specifically, tribromo-trioxotriangulene and [Ni(cyclohexanediamine)2Br]Br2 crystals. It clarified the SCEs on the energies of calculated models (0.049–3.093 eV). The presented scheme will enable the appropriate investigation and design of functional materials of nano (molecular) wire, superconductors, catalysts, quantum computing, and so on.

69. IMPROVED IVF SUCCESS OF COMBINED PGT-M AND PGT-A APPLICATIONS

Introduction Preimplantation Genetic Testing (PGT) has been performed since 1989 and utilized in the diagnosis of all genetic conditions at preimplantation stage ( 1 ). In the previous years, only a disorder could be diagnosed with the use of multiplex nested PCR in PGT applications. Increased use of trophectoderm biopsy and vitrification together with Whole Genome Amplification (WGA) technology enabled the detection of single gene disorders together with 24 chromosome screening. This approach allowed us to select healthy and chromosomally euploid embryos. Even though single gene disorder carrier patients are mostly young and fertile, they still have high risk of spontaneous miscarriage. In the recent years, it has been reported that when the embryos are screened for aneuploidy (PGT-A) in addition to single gene disorder testing (PGT-M), pregnancy rates can be increased from 45% to 68% and spontaneous miscarriage rates decreased from 15% to 5%. 34 single gene disorder patients, whose embryos were found to be healthy in terms of single gene disorder, were included in this study and these embryos were further screened for aneuploidy using Next Generation Sequencing (NGS) technology ( 2 ). Materials & Method On the 5th and 6th days of embryonic development, WGA was performed using SurePlex DNA Amplification System (Illumina, USA) and DOPlify (PerkinElmer Health Sciences - Australia). Following multiplex nested PCR on WGA samples, fragment analysis for haplotyping and sequence analysis for mutation detection were performed. Embryos found to be suitable for transfer regarding the single gene disorder have further been screened for aneuploidy using NGS technology with VeriSeq PGS Kit (Illumina, USA). Results This study was conducted for single gene disoder and 24 chromosome screening in 44 patients with an average age of 34. 280 embryos derived from these patients were included in PGT-M. Among 153 embryos that were found to be suitable for transfer after PGT-M, PGT-A was performed on 121 embryos upon patients' requests and 49% of these embryos were euploid. Embryo transfer could not be performed in 12 patients due to the absence of euploid embryos. According to the data we acquired, 64% pregnancy was achieved in the rest of the patients. Conclusion While pregnancy ratio can be improved with this approach, Allele drop out (ADO) and contamination errors are still major limitation which can lead to misdiagnosis of embryos. ADO ratio was demonstrated to be 25% in PGT for blastomere cells, whereas this ratio drops down to 5% when 5-7 cells obtained by trophectoderm biopsy are tested. Thus trophectoderm cells are more appropriate for PGT-M applications combined with PGT-A. Since stable and homogenous amplification of the entire genome is a crucial step, optimised WGA technologies will be a key factor in these applications.

Locally Most Powerful Test for the Random Coefficient Autoregressive Model

In this article, we study the problem of testing the constancy of the coefficient in a class of stationary first-order random coefficient autoregressive (RCAR(1)) model. We construct a new test statistic based on the locally most powerful-type (LMP) test. Under the null hypothesis, we derive the limiting distribution of the proposed test statistic. In the simulation, we compare the power between LMP test and empirical likelihood (EL) test and find that the accuracy of using LMP is 6.7%, 28.8%, and 26.1% higher than that of EL test under normal, student’s t, and symmetric contamination errors, respectively. A real life data is given to illustrate the practical effectiveness of our test.

Extent of Spin Contamination Errors in DFT/Plane-wave Calculation of Surfaces: A Case of Au Atom Aggregation on a MgO Surface.

The aggregation of Au atoms onto a Au dimer (Au2) on a MgO (001) surface was calculated by restricted (spin-un-polarized) and unrestricted (spin-polarized) density functional theory calculations with a plane-wave basis and the approximate spin projection (AP) method. The unrestricted calculations included spin contamination errors of 0.0–0.1 eV, and the errors were removed using the AP method. The potential energy curves for the aggregation reaction estimated by the restricted and unrestricted calculations were different owing to the estimation of the open-shell structure by the unrestricted calculations. These results show the importance of the open-shell structure and correction of the spin contamination error for the calculation of small-cluster-aggregations and molecule dimerization on surfaces.

On approximate projection models

ABSTRACTApproximate projection (AP) schemes are widely used in computational studies of diradicals and transition metal systems to remove spin contamination in unrestricted density functional theory and Hartree–Fock results. Spin contamination results from an inability of single-reference descriptions to correctly model orbital degeneracies. Spin projection methods, including AP, avoid more expensive approaches using multi-reference wave functions to rectify the spin contamination error. Efficient derivations of the AP derivatives have allowed the computation of improved geometries and properties. In this work, we establish a connection between AP and formulations developed using Löwdin's projection operator to obtain an understanding of where the method will work and highlight situations in which caution should be exercised.

Effect of spin contamination error on surface catalytic reaction: NO reduction by core-shell catalysts

ABSTRACTThe effects of spin contamination errors on the activation barriers of catalytic NO reduction by TiO2/Ag and ZrO2/Cu core-shell catalyst models were investigated using an approximate spin projection method and an unrestricted density functional theory calculation with the plane-wave basis set. The estimated barrier of the TiO2/Ag system increased (0.03 eV), whereas that of the ZrO2/Cu system decreased (0.04 eV) after the correction of the spin contamination error. This difference in the estimated barriers of the two systems can be attributed to the difference in their surface structures. The error obtained for the TiO2/Ag system was larger than that obtained for the gas phase, i.e. the spin contamination error was induced by the molecule/surface interaction. Moreover, the error correction also changed the rate-determining step of ZrO2/Cu. These results demonstrate the importance of the correction of spin contamination errors for the detailed investigation of catalytic reactions.

Estimation of spin contamination error in dissociative adsorption of Au2 onto MgO(0 0 1) surface: First application of approximate spin projection (AP) method to plane wave basis

Spin contamination error in the total energy of the Au2/MgO system was estimated using the density functional theory/plane-wave scheme and approximate spin projection methods. This is the first investigation in which the errors in chemical phenomena on a periodic surface are estimated. The spin contamination error of the system was 0.06 eV. This value is smaller than that of the dissociation of Au2 in the gas phase (0.10 eV). This is because of the destabilization of the singlet spin state due to the weakening of the Au-Au interaction caused by the Au-MgO interaction.

Dynamic Resource Allocation for Virtualized Wireless Networks in Massive-MIMO-Aided and Fronthaul-Limited C-RAN

This paper considers the uplink dynamic resource allocation in a cloud radio access network (C-RAN) serving users belonging to different service providers (called slices) to form virtualized wireless networks (VWN). In particular, the C-RAN supports a pool of base-station (BS) baseband units (BBUs), which are connected to BS radio remote heads (RRHs) equipped with massive massive multiple input multiple output (MIMO), via fronthaul links with limited capacity. Assuming that each user can be assigned to a single RRH–BBU pair, we formulate a resource allocation problem aiming to maximize the total system rate, constrained on the minimum rates required by the slices and the maximum number of antennas and power allocated to each user. The effects of pilot contamination error on the VWN performance are investigated and pilot duration is considered as a new optimization variable in resource allocation. This problem is inherently nonconvex, NP-hard and, thus, computationally inefficient. By applying the successive convex approximation and complementary geometric programming approach, we propose a two-step iterative algorithm: one to adjust the RRH, BBU, and fronthaul parameters, and the other for power and antenna allocation to users. Simulation results illustrate the performance of the developed algorithm for VWNs in a massive-MIMO-aided and fronthaul-limited C-RAN, and demonstrate the effects of imperfect channel state information estimation due to pilot contamination error, and the optimal pilot duration.