TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation

Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11–3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC.     

Out-of-plane reflection and refraction of light by anisotropic optical antenna metasurfaces with phase discontinuities

Experiments on ultrathin anisotropic arrays of subwavelength optical antennas display out-of-plane refraction. A powerful three-dimensional (3D) extension of the recently demonstrated generalized laws of refraction and reflection shows that the interface imparts a tangential wavevector to the incident light leading to anomalous beams, which in general are noncoplanar with the incident beam. The refracted beam direction can be controlled by varying the angle between the plane of incidence and the antenna array.     

Association of indigo with zeolites for improved color stabilization

The durability of an organic color and its resistance against external chemical agents and exposure to light can be significantly enhanced by hybridizing the natural dye with a mineral. In search for stable natural pigments, the present work focuses on the association of indigo blue with several zeolitic matrices (LTA zeolite, mordenite, MFI zeolite). The manufacturing of the hybrid pigment is tested under varying oxidizing conditions, using Raman and ultraviolet-visible (UV-Vis) spectrometric techniques. Blending indigo with MFI is shown to yield the most stable composite in all of our artificial indigo pigments. In the absence of defects and substituted cations such as aluminum in the framework of the MFI zeolite matrix, we show that matching the pore size with the dimensions of the guest indigo molecule is the key factor. The evidence for the high color stability of indigo@MFI opens a new path for modeling the stability of indigo in various alumino-silicate substrates such as in the historical Maya Blue pigment.     

Survey of disbudding practice on Czech dairy farms

Disbudding is a routine practice in many dairy herds due to the effort to decrease the risk of injuries. Although the disbudding practice is regulated, it can vary among farms. The variation may be caused by many factors, such as herd size or type of breed, but also by farmers' perception of pain caused by disbudding. Hence, the aim of this study was to specify the disbudding practice on dairy farms in the Czech Republic and to assess these practices, including the use of pain mitigation medication, by breed, herd size, and sex of the disbudded calves. We analyzed data from 106 Czech dairy farms, which were collected by a trained interviewer at dairy meetings in 2014–2015. The farmers answered questions regarding the farm's basic characteristics, disbudding practice, and his/her attitude to the pain caused by disbudding. To test the influence of breed, herd size, and sex of disbudded calves on different variables, logistic regression models were used. Disbudding was performed in 92.5% of the surveyed farms; 63.3% of dairy calves were disbudded before 4 wk of age, and Czech Fleckvieh calves were 2.8 times more likely to be disbudded before 4 wk of age than Holstein calves. The hot-iron method was the most used method (69.4%). Calves were 4.5 times more likely to be disbudded by hot iron in herds where both heifers and bulls were disbudded than in herds where only heifers were disbudded. Most (>90%) surveyed farms did not use any pre- or post-procedure medication to mitigate the pain caused by disbudding. The disbudding procedure was performed mainly by farm personnel (94.9%), who were trained by a veterinarian or veterinary technician (46.9%) or by other farm personnel (37.8%) or were not trained (15.3%). Two-thirds of farmers observed behavioral changes in calves after disbudding. Most farmers estimated the pain caused by disbudding to be mild or moderate (20.4 or 45.9%, respectively) and 15.3% of farmers estimated it to be severe. Almost a quarter of interviewed farmers were unable to assess the duration of pain, 39.8% farmers estimated that the pain lasts only several minutes, and 20.4% estimated that the pain lasts up to 6 h. We detected a tendency that farmers of larger herds estimated pain duration to be shorter (odds ratio = 1.2). To improve calves' welfare, training is needed in disbudding practice, focusing on the advantage of pain mitigation.     

Heuristics for the N-product,M-stage,economic lot sizing and scheduling problem with dynamic demand

This paper presents a new composite heuristics approach for solving the N-product, M-stage lot sizing and scheduling problem with dynamic demands and limited production capacity. The first phase of these composite heuristics aims at finding a feasible solution. This solution is such that for each period and for each product, the lot size equals the net demand of the considered period plus the demand of a number of upcoming periods. If capacity does not satisfy all demands of a given period, we try to find earlier periods where we can produce the missing units. The second phase is an improvement procedure which recursively attempts to move back each lot, provided that it is both more economical to do so and capacity feasible. We also provide two variants of this heuristic to handle the case where production capacity can be increased by using overtime. Overtime is a usual practice in real life which, in many cases, allows a reduction of the overall cost. The first variant constructs the initial solution without recourse to overtime and introduces overtime only during the solution improvement phase. The second one considers overtime during both the first and second phases. The performance of the proposed heuristics is numerically assessed and the most efficient ones are identified.     

UV radiation induces genome-mediated, site-specific cleavage in viral proteins

Much research has been dedicated to understanding the molecular basis of UV damage to biomolecules, yet many questions remain regarding the specific pathways involved. Here we describe a genome-mediated mechanism that causes site-specific virus protein cleavage upon UV irradiation. Bacteriophage MS2 was disinfected with 254 nm UV, and protein damage was characterized with ESI- and MALDI-based FT-ICR, Orbitrap, and TOF mass spectroscopy. Top-down mass spectrometry of the products identified the backbone cleavage site as Cys46-Ser47 in the virus capsid protein, a location of viral genome-protein interaction. The presence of viral RNA was essential to inducing backbone cleavage. The similar bacteriophage GA did not exhibit site-specific protein cleavage. Based on the major protein fragments identified by accurate mass analysis, a cleavage mechanism is proposed by radical formation. The mechanism involves initial oxidation of the Cys46 side chain followed by hydrogen atom abstraction from Ser47 C(α). Computational protein QM/MM studies confirmed the initial steps of the radical mechanism. Collectively, this study describes a rare incidence of genome-induced protein cleavage without the addition of sensitizers.     

Polysaccharides from Sesamum indicum meal: Isolation and structural features

Defatted Sesamum indicum seed cake was extracted, following two separate sequences, and the effects of extraction medium on yield and composition of the extracts were compared. Polysaccharides extracted sequentially with dilute acid and alkali represented 250 mg/g of defatted meal. The isolated polymers contained arabinan, rhamnogalacturonan I (RG I) and arabinogalactan proteins. Polysaccharides extracted during chlorite treatment and with dilute alkali had a higher proportion of rhamnose, suggesting a more branched variety of polymer. Three extracts, which were further characterized by size exclusion chromatography, gave two overlapping peaks. Structural characterisation of hemicellulosic polysaccharides, isolated with KOH, using specific enzyme hydrolysis, ion exchange chromatography (HPAEC) and matrix assisted laser desorption ionisation-time-of-flight (MALDI-TOF) mass spectroscopy, showed that sesame meal xyloglucan (XG) contained XXXG, XXFG and XXLG, and XLLG (named according to Fry et al., 1993) as the major building sub-units in the ratio of 1:0.9:0.3. Hydrolysis with endo-β-(1 → 4)-d-xylanase and analysis of the xylan derived oligosaccharides showed the presence of monomeric xylose (40%), xylobiose (46%) and acidic xylan oligosaccharides containing 4-O-methyl-d-glucuronic acid residues (14%).     

Migration of additives from polymers into food simulants: numerical solution of a mathematical model taking into account food and polymer interactions

The principle of a computing program describing precisely the migration of additives from a polymer into a food simulant is presented. As six parameters are used to fit the simulant sorption and additive extraction kinetics, the parameters have been determined by independent experiments. Owing to the complicated coupling between the liquid and additive diffusion processes, migration kinetics cannot be obtained by a mathematical resolution of kinetic equations, but they must be calculated by numerical analysis. The method is applied to a UV absorber in polypropylene migrating into glyceryl tripelargonate, a pure triglyceride, of which behaviour and average molecular weight are similar to official fatty food simulants. Properly designed experiments validate the model used to fit the migration kinetics. The possibility of erasing any parameters is also discussed.     

Combining fuzzy querying of imprecise data and predictive microbiology using category-based reasoning for prediction of the possible microbial spoilage in foods: application to Listeria monocytogenes

Various predictive models of microbial behavior have been created and extensive data collection has been done by numerous private or public laboratories. However, significant differences between predicted and observed values in foods have been observed and need to be stressed, understood and explained as much as possible. In this paper, we present a software tool (currently at the level of a prototype) able: (i) to store in a database all relevant information expressed on one hand as qualitative or quantitative data and on the other hand as precise or imprecise data; (ii) to retrieve the more relevant information from the database using queries where criteria may be expressed as fuzzy values in order to enhance the flexibility of the search: (iii) to compute, in addition to the nearest data, an estimation of searched values using statistical models. The architecture of this software tool is structured as a category-based reasoning system. Example queries about Listeria monocytogenes (L. monocytogenes) illustrate the functionalities of this tool.