Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular techniques for the detection of granary weevil (Sitophilus granarius L.) in wheat and flour

The granary weevil (Sitophilus granarius L.) is a stored grain pest that causes major economic losses. It reduces the quantity and quality of the grain by its feeding and excretion. Sequences of S. granarius mitochondrial cytochrome oxidase subunits genes mtCOI and mtCOII were analysed and compared with mtCOI/II sequences available in GenBank. The analysed genes displayed a high level of homology between corresponding subunits. Attempts were undertaken to develop detection methods for contamination by S. granarius in wheat and wheat flour based on the molecular biology techniques: standard and real-time polymerase chain reaction (PCR) with a TaqMan® molecular probe. (TaqMan probes are dual-labelled hydrolysis probes) Specific primers designed based on available sequences for mtCOI and mtCOII genes were applied and optimal reaction conditions established. The specificity of both methods was studied by using a species closely related to S. granarius: S. oryzae and S. zeamais. It is shown that the sensitivity threshold was very high – we were able to detect the equivalent of one beetle per 100 kg of flour when the real-time PCR with TaqMan probe method was applied to model samples. The primer sets used turned out to be species specific, and the technique was rapid, reliable and very sensitive.
Feeding of pregnant sows with mycotoxin-contaminated diets and their non-effect on foetal and maternal hepatic transcription of genes of the insulin-like growth factor system

The insulin-like growth factor (IGF) system regulates foetal and placental growth. It can be influenced by dietary factors, but little is known about the effects of mycotoxin feeding on hepatic levels of the IGF system. The aim was (1) to determine the normal foetal and maternal hepatic transcription of major IGF genes at distinct stages of pregnancy and (2) to find out if the mycotoxins deoxynivalenol (DON) and zearalenone (ZON) affect transcript concentrations. Pregnant sows were fed with naturally contaminated diets from days 35 to 70 (experiment 1), or from days 75 to 110 (experiment 2), or with control diets. Foetal hepatic IGF transcripts were determined at days 70 and 110, maternal transcripts at day 70 by quantitative polymerase chain reaction (qPCR). The highest levels of IGF-I transcripts were found in sows. On the contrary, IGF-II was predominantly expressed in foetuses at day 70. Expression of IGF-IR and IGFBP-3 decreased, whereas that of IGFBP-2 increased towards term. IGF-IIR and IGFBP-1 expression was similar in both foetuses and full-term piglets. IGF-IIR showed reduced levels in the maternal liver. The exposure of pregnant sows to DON- and ZON-contaminated diets significantly reduced the maternal and tended to reduce the weight gain of piglets in experiment 2, but had no effects on hepatic levels of IGF transcripts in both experiments. This suggests that mycotoxin-contaminated diets can induce growth depression in pigs during pregnancy without affecting hepatic transcription of major IGF genes.
Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands‐on collaborative practical sessions for undergraduate students

Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high‐performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These improvements are also benefitting scientific education. Molecular simulations, their underlying theory, and their applications are particularly difficult to grasp for undergraduate students. Having hands‐on experience with the methods contributes to a better understanding and solidification of the concepts taught during the lectures. To this end, we have created a computer practical class, which has been running for the past five years, composed of several sessions where students characterize the conformational landscape of small peptides using molecular dynamics simulations in order to gain insights on their binding to protein receptors. In this report, we detail the ingredients and recipe necessary to establish and carry out this practical, as well as some of the questions posed to the students and their expected results. Further, we cite some examples of the students' written reports, provide statistics, and share their feedbacks on the structure and execution of the sessions. These sessions were implemented alongside a theoretical molecular modelling course but have also been used successfully as a standalone tutorial during specialized workshops. The availability of the material on our web page also facilitates this integration and dissemination and lends strength to the thesis of open‐source science and education. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:160–167, 2016.
Use of glyceroltriheptanoate as marker for processed animal by-products: development and validation of an analytical method

A recently published European Regulation requires that the artificial marker, glycerol triheptanoate (GTH), be added to processed animal by-product (ABPs) prohibited from entering the food chain. The objective of this new requirement is to allow full traceability and ensure that these materials are disposed of in a proper way. Here, we report the development and single-laboratory validation of an analytical method for the determination of GTH in meat and bone meal plus animal fat. The method comprises three steps: (1) extraction of GTH from the samples with petroleum ether when analysing meat and bone meal or dissolving the sample in n-hexane when analysing fat; (2) clean-up of the extract using commercially available SPE cartridges; (3) determination of GTH by GC/MS or GC with flame ionisation detection (FID). The results of the validation study demonstrated that the relative standard for intermediate precision varied between 2.5 and 8.2%, depending on GTH concentration and the detector utilised. In all cases, the relative recovery rate was above 96%. The limit of quantification was 16 mg kg−1 (GTH/fat content of the sample) with MS as detector and 20 mg kg−1 with FID. Moreover, the method has been successfully applied in a second laboratory, indicating its transferability. Considering the minimum GTH concentration in ABPs of 250 mg kg−1, the method is considered suitable for the intended purpose and can be utilised by EU Member States laboratories for official control and monitoring.
Comparison of a fluoroquinolone surface plasmon resonance biosensor screening assay with established methods

The performance of a previously developed immunochemical biosensor screening method for fluoroquinolone (FQ) antibiotics in poultry muscle, fish and egg was compared with established methods. Blank sample material of the target matrices was individually spiked with the FQs at half maximum residue levels. Homogeneity of the test materials was confirmed by liquid chromatography–mass spectrometry (LC–MS/MS). Identical sets of spiked samples as well as incurred samples from a previous feeding experiment were sent to three independent laboratories and analysed by LC–MS/MS, a microbiological assay and the new biosensor assay. The new method correctly identified all contaminated samples and demonstrated advantages in sensitivity and analysis time compared to the microbiological screening assay.
Systematic Review of Magnetic Resonance Imaging Characteristics That Affect Treatment Decision Making and Predict Clinical Outcome in Patients With Cervical Spondylotic Myelopathy

Study Design. Systematic review. Objective. To determine whether there are magnetic resonance imaging (MRI) characteristics in patients with cervical spondylotic myelopathy that affect treatment decisions or predict postsurgical outcomes or adverse events. Summary of Background Data. Although the role of MRI in confirming the clinical diagnosis of cervical spondylotic myelopathy and directing surgical management is well established, its potential value as a prognostic tool is largely unknown. Methods. A systematic search was conducted using PubMed and the Cochrane Collaboration Library for articles published between January 1, 1956, and November 20, 2012. The overall body of evidence with respect to each clinical question was determined on the basis of precepts outlined by the Grading of Recommendation Assessment, Development and Evaluation Working Group and recommendations made by the Agency for Healthcare Research and Quality. Results. The initial search yielded 268 citations. Twenty publications met all inclusion criteria and were included in the review. Three of these assessed MRI predictors of clinical deterioration in the case of conservative treatment and 17 evaluated MRI anatomic or cord characteristics that could predict surgical outcome or adverse events. There is low evidence suggesting that a high signal intensity (SI) grade on T2WI is not associated with patient deterioration during conservative treatment. High SI grade on T2WI, along with compression ratio and canal diameter, was not an important predictor of outcome. There is low evidence identifying number of high SI segments on T2WI, low SI segments on T1WI, combined T1/T2 SI, and SI ratio as important negative predictors of surgical outcome. Conclusion. On the basis of this review and on low-quality evidence, we have identified 3 important negative predictors of surgical outcome: number of high SI segments on T2WI, combined T1/T2 signal change, and SI ratio. Evidence-Based Clinical Recommendations. Recommendation 1. We suggest that when clinically feasible, surgeons rely on MRI to confirm the diagnosis of CSM and rely on clinical history and examination to determine progression and severity of disease. Overall Strength of Evidence. Low Strength of Recommendation. Weak Recommendation 2. T2 signal may be a useful prognostic indicator when used in combination with low SI change on T1WI, or as a ratio comparing compressed with noncompressed segments, or as a ratio of T2 compared with T1WI. We suggest that if surgeons use MRI signal intensity to estimate the risk of a poor outcome after surgery, they use high SI change on T2WI in combination with other signal intensity parameters, and not in isolation. Overall Strength of Evidence: Low Strength of Recommendation: Weak
Application of FTIR and Raman microspectroscopy to the study of food/packaging interactions

This study assesses the suitability of Fourier transform infrared spectrometer (FTIR) and Raman spectroscopy for potential use as analytical tools to determine the diffusivity of a migrant in a plastic packaging material, one of the key points in safety assessment of food-contact materials. Despite its relative low sensitivity, FTIR-based analysis supplied data for the material on desorption of an additive (Uvitex OB) and sorption of a food constituent (olive oil) in a non-destructive and ‘in situ’ mode. These data allowed the determination of the diffusivity of Uvitex OB (8.0 ± 2.5 · 10−14 m2 s−1) and olive oil (6.9 ± 3.4 · 10−14 m2 s−1) in Linear Low Density Polyethylene (LLDPE). Raman cartography innovatively supplied the profile of additive concentration in the z-direction (thickness) of the food-contact material and confirmed that mass transfer in the system roughly followed a Fickean behaviour.
Hyperthermia MRI temperature measurement: Evaluation of measurement stabilisation strategies for extremity and breast tumours

Purpose: MR thermometry using the proton resonance frequency shift (PRFS) method has been used to measure temperature changes during clinical hyperthermia treatment. However, frequency drift of the MRI system can add large errors to the measured temperature change. These drifts can be measured and corrected using oil references placed around the treatment region. In this study, the number and position of four or more oil references were investigated to obtain a practical approach to correct frequency drift during PRFS thermometry in phantoms and in vivo. Materials and methods: Experiments were performed in a 140 MHz four antenna mini-annular phased array (MAPA) heat applicator (for treatment of extremity tumours) and an applicator for heating of the breast, with symmetric and asymmetric positioning of the oil references, respectively. Temperature change PRFS images were obtained during an hour or more of measurement with no application of heat. Afterwards, errors in calculating temperature change due to system drift were quantified with and without various oil reference correction arrangements. Results: Results showed good temperature correction in phantoms and in a human leg, with average errors of 0.28°C and 0.94°C respectively. There was further improvement in the leg when using eight or more oil references, reducing the average error to 0.44°C, while the phantoms showed no significant improvement. Conclusions: These results indicate that oil reference correction performs well in vivo, and that eight references can improve the correction by up to 0.5°C compared to four references.
High-intensity focused ablation (HIFU) of single benign thyroid nodule rarely alters underlying thyroid function

Abstract Background: High intensity focused ultrasound (HIFU) is a promising ablation technique for benign thyroid nodules. However, its effect on underlying thyroid function remains unknown. We aimed to evaluate the 6 months changes in serum thyroid stimulating hormone (TSH) and free thyroxine (FT4) after HIFU treatment. Methods: Eighty-three consecutive patients who underwent single HIFU ablation for symptomatic benign thyroid nodule were analysed. Eligible patients had serum TSH and FT4 checked before treatment (baseline), 1 week, 3 and 6 months following HIFU treatment. Primary endpoints were hypothyroidism (FT4 < 12 pmol/L) and hyperthyroidism (FT4 > 23 pmol/L) in the 6 months following treatment. To express extent of nodule ablation relative to the total gland volume, an ablation volume ratio was calculated by [(Ablated nodule volume/total thyroid volume)/(total thyroid volume)] × 100. Results: Relative to baseline, 1-week serum TSH significantly dropped (from 1.16 to 0.76 mIU/L, p < 0.001) while 1-week serum FT4 significantly rose (from 16.0 to 17.8 pmol/L, p < 0.001). However, 3- and 6-months TSH and FT4 did not changed significantly from baseline (p > 0.05). No patients developed hyperthyroidism while one (1.4%) developed hypothyroidism (FT4 = 11 pmol/L) at 3 months and 6 months. Interestingly, this patient had a previous lobectomy and an ablation volume ratio of 64.00%. Conclusions: Hypothyroidism following single HIFU ablation occurred rarely (1.4%) and resulted in little clinical relevance. Given that only one patient developed hypothyroidism following single HIFU ablation, it remains unclear how patients with different amount of parenchyma and relative extent of ablation may affect subsequent thyroid function.
Quantification of 1-(13) C-L-methionine in rat serum with hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry and its application in pharmacokinetic study.

A rapid, selective and sensitive hydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass spectrometry (MS/MS) method was developed to determine 1-(13) C-l-methionine in rat serum. Proteins in serum were precipitated using acetonitrile and the supernatant was separated after centrifugation. 1-(13) C-l-phenylalnine was used as the internal standard. HILIC-tandem mass spectrometry analysis was performed on a hydrophilic interaction silica column (TSK-GEL AMIDE-80) using a linear gradient elution system, acetonitrile-5 mm ammonium acetate containing 0.1% formic acid and multiple reaction monitoring mode for 1-(13) C-l-methionine and 1-(13) C-l-phenylalnine. The assay was validated with a linear range between 10 and 150 ng mL(-1) (r ≥ 0.99) and a lower limit of quantification of 10 ng mL(-1) , calculated with weighted (1/x(2) ) least squares linear regression. The RSD of intra-day precision was smaller than 3.6% and the inter-day RSD less than 6.5%, while the average recovery was 100.48% with an RSD of accuracy within 2.9%, determined from quality control samples. The HILIC-MS/MS method was fully validated and successfully applied to the in vivo pharmacokinetic study of stable-isotope 1-(13) C-l-methionine in rats.
Interferon‐α for chronic hepatitis C: An analysis of pretreatment clinical predictors of response

To identify predictors of short‐term and sustained ALT normalization after interferon treatment in adult patients with chronic hepatitis C, we performed a metanalysis of individual patients' data, with construction and cross‐validation of a prediction rule, in 361 patients from two randomized trials. In one trial, 116 subjects with transfusion‐related chronic hepatitis C were treated with lymphoblastoid interferon (5 MU/m2 three times a week for 2 mo, then 3 MU/m2 three times a week for 4 or 10 mo). In the other study, 245 patients with community‐acquired chronic hepatitis C received recombinant interferon‐α2b (10 MU three times a week for 2 mo, then 5 MU three times a week for 4 mo; then random allocation of subjects with normal aminotransferase levels to stop or continue interferon for a further 6 mo). Overall, 164 subjects (45%; 95% confidence interval, 40% to 50%) had short‐term responses; 61 (18%; 95% confidence interval, 14% to 22%) maintained sustained responses. Sixty patients (17%; 95% confidence interval, 13% to 21%) withdrew from treatment because of side effects or subjective intolerance. Logistic regression analysis showed that short‐term and sustained response were independently predicted by lobular structure on pretreatment liver biopsy (p < 0.0001) and by short disease duration, defined as the time elapsed since transfusion in posttransfusion cases or since the first observation of abnormal aminotransferase levels in cryptogenic disease (p < 0.01). Rules to predict short‐term and sustained response to interferon were derived from these items, showing a discriminatory ability of 0.73 and 0.70. We conclude that, in patients with C hepatitis, presence of cirrhosis and long disease duration predict low likelihood of response to interferon. Although the predictive rule based on these items is not sufficiently accurate for decision‐making in individual patients, it can definitely assist when applied to groups of patients for planning or interpreting therapeutic studies. The addition of virological features such as quantitation of viremia and hepatitis C virus genotypes may improve the ability to predict treatment outcomes. (HEPATOLOGY 1994;19:820–828.)
Spinal Osteotomy: Correcting Sagittal Balance in Tuberculous Spondylitis

Study Design Retrospective case analysis. Objective Tuberculosis spondylitis is a cause of sagittal imbalance and neurologic impairment. In this study, the result of decompression and closing wedge osteotomy with instrumented fusion performed in patients with tuberculous spondylitis were analyzed retrospectively. Summary of Background Data Twelve patients with angular kyphotic deformity underwent decompression and closing wedge osteotomy with instrumented fusion between 2000 and 2004. Clinical and radiologic assessment was based on pain, functional and neurologic status, and radiologic measurements. Methods There were 7 men and 5 women with median age of 52 years (range, 24 to 76 y). The average follow-up period was 62 months (range, 48 to 70 mo). The radiologic involvement included the angle of kyphosis on the anteroposterior and lateral radiographs. The preoperative and postoperative clinical assessments were performed by the using Oswestry Disability Index. All patients were asked to rate their preoperative and postoperative pain measurement using a pain visual analog scale. Results Visual analog scale scores improved from 5.8 in average (range, 4 to 8) to 2.2 in average (range, 1 to 4) and in the mean and Oswestry Disability Index from 54.2 (46 to 60) preoperatively to 15.2 (8 to 22) at the latest follow-up. Four patients presented neurologic findings. Three patients had improvement in their neurologic status, 1 patient did not improve and remained as American Spinal Injury Association (ASIA) grade C. Kyphotic deformity of the patients has improved from 51.1 to 23.2 degrees postoperatively. One of them has to be revised and instrumentation was extended to upper levels. Fusion was achieved at the last follow-up. Conclusions Despite developing pseudarthrosis secondary to implant failure in 1 case, we recommend debridement, closing wedge osteotomy, and posterior instrumented fusion to correct sagittal balance in tuberculous spondylitis.
Clinical Outcome of Nonoperative Treatment for Lumbar Spinal Stenosis, and Predictive Factors Relating to Prognosis, in a 5-Year Minimum Follow-up

Study Design A prospective long-term follow-up study of nonoperative treatment for lumbar spinal stenosis (LSS) and multivariable analysis of the prognosis. Objectives To clarify the outcomes of nonoperative treatment for LSS over a long-term follow-up, and to extrapolate factors relating to the prognosis of treatment. Summary of Background Data The indicators of treatment for LSS remain controversial, and few reports have evaluated the prognosis of its nonoperative treatment, or extrapolated the factors that aid prognosis. Methods One hundred twenty patients who received inpatient nonoperative treatment were followed up for 5 years or longer. Patients' nerve involvement and myelographic findings were classified, and the disturbance level of activities of daily living (ADL) at final follow-up was graded. The association between patients' age and sex, classification of nerve involvement and myelographic findings, recovery rate by initial nonoperative treatment, presence or absence of degenerative spondylolisthesis/scoliosis, and disturbance level of ADL were evaluated statistically to extrapolate prognostic factors. Results In all, 52.5% of patients showed no hindrance to ADL at follow-up. Patients who were classified as radicular type, or responded well to initial nonoperative treatment, exhibited statistically better results than did other patients. In contrast, accompanying degenerative scoliosis tended to be related to a poorer prognosis. Conclusion The current study demonstrated the long-term follow-up outcome of nonoperative treatment for LSS. Important factors relating to the prognosis were demonstrated. These factors could aid the decision-making process for treatment of LSS patients.
Sensitive, selective and rapid determination of bupropion and its major active metabolite, hydroxybupropion, in human plasma by LC-MS/MS: application to a bioequivalence study in healthy Indian subjects.

A sensitive, selective and rapid liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed for the simultaneous determination of bupropion (BUP) and its major active metabolite hydroxybupropion (HBUP) in human plasma. Separation of both the analytes and venlafaxine as internal standard (IS) from 50 μL human plasma was carried out by solid-phase extraction. The chromatographic separation of the analytes was achieved on a Zorbax Eclipse XDB C(18) (150 × 4.6 mm, 5 µm) analytical column using isocratic mobile phase consisting of 20 mm ammonium acetate-methanol (10:90, v/v), with a resolution factor of 3.5. The method was validated over a wide dynamic concentration range of 0.1-350 ng/mL for BUP and 0.1-600 ng/mL for HBUP. The matrix effect was assessed by post-column infusion and the mean process efficiency was 96.08 and 94.40% for BUP and HBUP, respectively. The method was successfully applied to a bioequivalence study of 150 mg BUP (test and reference) extended release tablet formulation in 12 healthy Indian male subjects under fed conditions.