Recommendations for handling bitumen prior to FTIR spectroscopy

The application of chemical analysis on bituminous materials has increased drastically over the past decades. One of the most common spectroscopic methods used in the field of research is Attenuated Total Reflection (ATR) Fourier Transform Infrared (FTIR) spectroscopy. Since ATR-FTIR is a surface sensitive method, sample or specimen handling of a complex material like bitumen prior to its analysis needs to be considered, especially for people new to the field or analysis technique. This study looks at the impact of heating time and temperature as well as storage time and conditions on the oxidation of the bituminous specimen. Four binders from the same crude oil source but different specification classes (unmodified and styrene–butadiene–styrene polymer modified) and two binders from different crude oil sources were investigated. The results show that heating small quantities of bitumen at 180 °C for up to 30 min has little impact on the formation of oxidized species, when proper thermal monitoring is conducted. Special cases where oxidation does occur are reported in detail. Furthermore, strong oxidation is induced by day light, when bitumen is stored behind glass with no UV radiation present, which can reach short-term ageing level within 1 h. Thus, heating bitumen at 180 °C for 5–10 min followed by storage in the dark, climatized room and measured within one hour after preparation is recommended. These results should act as recommendation for future specimen handling prior to FTIR spectroscopic analysis to ensure unbiased and comparable measurements.

Biopsy bacterial signature can predict patient tissue malignancy

Considerable recent research has indicated the presence of bacteria in a variety of human tumours and matched normal tissue. Rather than focusing on further identification of bacteria within tumour samples, we reversed the hypothesis to query if establishing the bacterial profile of a tissue biopsy could reveal its histology / malignancy status. The aim of the present study was therefore to differentiate between malignant and non-malignant fresh breast biopsy specimens, collected specifically for this purpose, based on bacterial sequence data alone. Fresh tissue biopsies were obtained from breast cancer patients and subjected to 16S rRNA gene sequencing. Progressive microbiological and bioinformatic contamination control practices were imparted at all points of specimen handling and bioinformatic manipulation. Differences in breast tumour and matched normal tissues were probed using a variety of statistical and machine-learning-based strategies. Breast tumour and matched normal tissue microbiome profiles proved sufficiently different to indicate that a classification strategy using bacterial biomarkers could be effective. Leave-one-out cross-validation of the predictive model confirmed the ability to identify malignant breast tissue from its bacterial signature with 84.78% accuracy, with a corresponding area under the receiver operating characteristic curve of 0.888. This study provides proof-of-concept data, from fit-for-purpose study material, on the potential to use the bacterial signature of tissue biopsies to identify their malignancy status.

SARS-CoV-2 laboratory diagnostic methods: a systematic review

Background The new SARS-CoV-2 is a single-stranded RNA β-coronavirus, and it is comprising by structural proteins (N), (S), (E) and (M). Timely and accurate detection is necessary for spread control of SARS-CoV-2 infection, avoiding inaccurate outcomes. Therefore, in this systematic review, it is purpose to evaluate a set of laboratory diagnostic techniques and methods, analyse their specificity, sensitivity, contributing to improve detection rates and reduce false negative and false positive diagnostic results. Methods In this review, we used literature available on the indexed search database ‘PubMed’, concerning the following keywords: ‘SARS-CoV-2’, ‘Specimen handling’, ‘Cell Culture Technique’, ‘Viral Antigen’, ‘Immunoassay’, ‘NAAT’ according to Medical Subject Headings Mesh and applying the Prisma Diagram methodology. Results DD-PCR and CRISPER had more promising results, but they are unconventional and expensive NAAT methods, the usage of the target RdRp/He gene has exhibited very encouraging results improving sensitivity and specificity. After the onset of symptoms, the sensitivity of the immunoassay varies considering of blood collection day. The antigen detection test showed the highest specificity reached, however is sensitivity is lower compared to NAAT assays. Conclusions In summary, RT-PCR still considered the gold standard and precisely detects the presence of virus RNA, although with some flaws in sensitivity, while the serological tests identify a previous infection by the virus, detecting antibodies, allowing the kinetic and immunological studies, not being able to use as a diagnostic method. The molecular point of care testing equipment’s revelled be the future in the rapid and accurately diagnosis of SARS-CoV-2.

Reproductive Anatomy of Chondrichthyans: Notes on Specimen Handling and Sperm Extraction. II. Sharks and Chimaeras

The chondrichthyan fishes, which comprise sharks, rays, and chimaeras, are one of the most threatened groups of vertebrates on the planet. Given this situation, an additional strategy for the protection of these species could be the ex situ conservation projects developed in public aquaria and research centers. Nevertheless, to increase sustainability and to develop properly in situ reintroduction strategies, captive breeding techniques, such as sperm extraction and artificial insemination, should be developed. These techniques are commonly used in other threatened species and could be also used in chondrichthyans. However, the different reproductive morphologies found in this group can complicate both processes. Therefore, a comparison of the reproductive anatomy of eight distinct chondrichthyans, with an emphasis on those important differences when performing sperm extraction or artificial insemination, is carried out herein. Sharks and chimaeras belonging to the Scyliorhinidae, Carcharhinidae, Centrophoridae, Etmopteridae, Hexanchidae, and Chimaeridae families were obtained from commercial fisheries, public aquaria, and stranding events. In addition, the process of obtaining viable sperm samples through cannulation, abdominal massage, and oviducal gland extraction is described in detail for both living and dead animals.

Reproductive Anatomy of Chondrichthyans: Notes on Specimen Handling and Sperm Extraction. I. Rays and Skates

The superorder Batoidea (rays, skates, and relatives), constitutes one of the most threatened group of vertebrates. Strengthening ex situ conservation programs developed in research centers and public aquaria could be a way of addressing this situation. However, captive breeding programs must be improved to prevent the capture of wild animals and to develop proper in situ reintroduction strategies. Sperm extraction and artificial insemination are two techniques commonly used in other threatened species, which could also be used in rays and the like. However, the different reproductive morphologies present within this group of animals may hamper both processes. Here, we present a comparison of the reproductive anatomies of 11 distinct batoid species, emphasizing the important differences between the species when performing sperm extraction or artificial insemination. Both male and female animals, belonging to the Rajidae, Dasyatidae, Torpedinidae and Myliobatidae families, from the Mediterranean Sea were studied. In addition, we describe the procedure to extract sperm using both cannulation and abdominal massage, either from live or dead batoids Finally, the obtention of motile sperm recovered from the oviducal gland of females is described. These techniques generate a new range of possibilities for the conservation of these threatened species.

Neoadjuvant Chemotherapy for Breast Cancer: Moving Beyond Pathological Complete Response in the Molecular Age

<p>This review focuses on neoadjuvant chemotherapy for breast cancer which introduces practical issues for pathologists, including predicting response, optimising specimen handling, size measurement and assessment of residual disease, and recent advances in management of the axilla. The role of neoadjuvant chemotherapy in breast cancer is increasing, and it has become standard of care for high risk Human Epidermal Growth Factor Receptor 2 positive and triple negative breast cancers. The benefits of the neoadjuvant approach extend beyond pathological complete response to tumour downstaging permitting conservative surgi- cal options in the breast and axilla, and assessment of response provides valuable prognostic information to enable escalation and de-escalation of adjuvant therapy to optimise oncological outcomes. Hence histopathologists play a vital role in patient management in the neoadjuvant setting. Optimal patient selection for neoadjuvant chemotherapy requires consideration of pre- treatment histopathological and molecular tumour characteristics. Post chemotherapy, tumour staging can be challenging, and changes in criteria for measurement of primary tumour and metastases in the 7th and 8th editions of the TNM have led to confu- sion amongst pathologists. This review offers practical guidance on specimen handling and measurement of lesion size. Mov- ing forwards more detailed information on degree of response will be required for adjuvant therapy decision making, and the Residual Cancer Burden is emerging as the preferred method for quantifying residual disease not just within clinical trials but in routine practice. Recent advances in management of the axilla are discussed, including the significance of minimal residual disease in the form of isolated tumour cells and micrometastases which portend a worse prognosis in the neoadjuvant setting.</p><p><strong>Conclusion</strong>. Neoadjuvant chemotherapy now forms part of routine breast cancer management, and detailed histopathological assessment and an understanding of the importance of molecular tumour biology is essential for clinical decision making.</p>

The International System for Reporting Serous Fluid Cytopathology: How to Incorporate Molecular Data in Cytopathology Reports

Serous effusion cytology is widely employed in the initial evaluation of the etiology of effusions with a high diagnostic sensitivity. To standardize practices, The International System for Reporting Serous Fluid Cytology (TIS) was developed following best international practices, the most up-to-date literature, and expert consensus. In the context of this system, ancillary techniques play an important role. Besides defining basic principles in laboratory specimen handling, adequacy criteria, and a standardized reporting terminology with five diagnostic categories, TIS provides an actionable framework for using immunohistochemical and molecular testing in effusion samples, namely, in atypical, suspicious of malignant samples. For diagnostic purposes, these tests may be employed to distinguish between a primary and secondary neoplasm, to confirm a diagnosis of malignant mesothelioma vs. reactive mesothelial hyperplasia, and to correctly classify and determine the primary location of a metastasis. Theranostic molecular tests may also be used for these samples to evaluate potential therapeutic targets. Pathologists play a central role in guiding this process by determining adequacy and selecting appropriate ancillary tests. The activity in this area of research should increase in the near future as new therapeutic targets are discovered and new drugs enter the clinical practice.

A systematic review on improving implementation of the revitalised integrated disease surveillance and response system in the African region: A health workers’ perspective

Background The revised integrated disease surveillance and response (IDSR) guidelines adopted by African member states in 2010 aimed at strengthening surveillance systems critical capacities. Milestones achieved through IDSR strategy implementation prior to adopting the revised guidelines are well documented; however, there is a dearth of knowledge on the progress made post-adoption. This study aimed to review key recommendations resulting from surveillance assessment studies to improve implementation of the revitalised IDSR system in the African region based on health workers’ perspectives. The review focused on literature published between 2010 and 2019 post-adopting the revised IDSR guidelines in the African region. Methods A systematic literature search in PubMed, Web of Science and Cumulative Index for Nursing and Allied Health Literature was conducted. In addition, manual reference searches and grey literature searches using World Health Organisation Library and Information Networks for Knowledge databases were undertaken. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement checklist for systematic reviews was utilised for the review process. Results Thirty assessment studies met the inclusion criteria. IDSR implementation under the revised guidelines could be improved considerably bearing in mind critical findings and recommendations emanating from the reviewed surveillance assessment studies. Key recommendations alluded to provision of laboratory facilities and improved specimen handling, provision of reporting forms and improved reporting quality, surveillance data accuracy and quality, improved knowledge and surveillance system performance, utilisation of up-to-date information and surveillance system strengthening, provision of resources, enhanced reporting timeliness and completeness, adopting alternative surveillance strategies and conducting further research to improve surveillance functions. Conclusion Recommendations on strengthening IDSR implementation in the African region post-adopting the revised guidelines mainly identify surveillance functions focused on reporting, feedback, training, supervision, timeliness and completeness of the surveillance system as aspects requiring policy refinement. Systematic review registration PROSPERO registration number CRD42019124108.

The Rate of Sample Rejection and Pre-Analytical Errors at KCMC Clinical Laboratory in Moshi, Kilimanjaro

Background: Over the years, modern medicine has been able to provide a better quality services to patients. However, medical error is still prevalent and has a lot of negative consequences on patients’ outcome. These may include delayed treatment, longer hospital stays, or even worsening of the patient’s condition. The aim of this study was to determine the rate of sample rejection at KCMC Clinical Laboratory and the different pre-analytical errors that contribute to it. Methods: Data extraction sheet was used to collect information from rejection forms from January to December 2016. Information on types of sample rejected, the wards/departments from which they were collected and the clinical laboratory section in which they were to be analysed were collected. Results: Out of the 117181 samples received from January to December 2016, 234 were rejected, giving a 0.19% rate of rejection. The highest rates of rejection were from haematology section 78 (33.3%). The major type of rejected sample was blood (86.3%) and 20% of the rejected samples came from internal medicine department, mainly from its inpatient department (13.6%). The commonest reason for rejection was unpaid specimens 84 (35.9%). Conclusion: The impact of pre-analytical errors on patient care is not negligible. A joint collaboration of all the stakeholders involved in patient care, specimen handling and analysis, and policymaking is necessary to arrive at quick and tangible solutions. Better communication between laboratory staff and other health care personnel is essential.