MS1Connect: a mass spectrometry run similarity measure

Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repos- itory, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires comput- ing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols. We propose a method, MS1Connect, that calculates the simi- larity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though this data is not used by MS1Connect.

Water Sensitivity of Hemp-Foam Concrete

The necessity to build energy-efficient and low environmental impact buildings favors the development of biobased light-weight materials as hemp-foam concretes. In this context, experimental protocols were developed to study the effects of hemp shiv and the production methods on the water sensitivity of bio-based foamed concrete (BBFC). Foam concrete incorporates several materials and compounds: cement, protein-based foaming agent, ground granulated blast–furnace slag, metakaolin as a binder, and hemp shiv as bio-based aggregates. The study investigated first the effect of the incorporation of hemp shiv (from 0 to 15 vol%) and then the elaboration method, comparing direct method versus preformed method on the resulting physical properties, the isotherms sorption-desorption and the capillary water absorption of hemp-foam concretes. We observe an increasing porosity of the concrete with hemp shives content. Additionally, hemp shives increase the adsorption and the capillary absorption of water. Moreover, the preformed method produces concretes more sensitive to water than the direct methods since it increases its porosities.

Evaluation of Oxidative Stress potential of some Nsaıds against Hydrogen Peroxide in experimental animal

Background: Oxidative stress is imbalance between aggressive and defensive system. Overproduction of oxidative stress contribute in pathogenesis of many diseasesincluding Parkinsonism, Alzheimer diseases, apoptosis, hepatic fibrosis ,chronic kidney failure and liver steatosis etc . There are several OTC drugs including NSAIDs that generate oxidative stress when administered. So there is a need to explore about these drugs. Therefore this study was designed to evaluate the oxidative stress potential of Acetaminophen, acetyl salicylic acid and Celecoxib NSAIDs. Objective: The present study is design to investigate the oxidative stress of NSAIDs of acetaminophen, aspirin and Celecoxib drug with reference to the hydrogen peroxide. Material and method: The Experimental protocol was designed for estimate the level of oxidative stress in NSAIDs treated animals against hydrogen peroxides. Animal of control group received only vehicle throughout experimental protocol. Rats of AAP group, ASA group ,CX group were exposed to acetaminophen (150mg/kg; orally) acetyl salicylic acid (300mg/kg ;orally) and Celecoxib (50mg/kg; orally) for forty two days . Rodent of HP group were challenged with Hydrogen peroxides (0.5%) with same schedule as above. At end of experimental protocols, all the animals were sacrificed and their organ were identified and collected for oxidative stress estimation and histological examination. Result: NSAIDs administration caused increase in oxidative stress measured in terms of SOD, CAT, MDA, GSH and GPx. HP administration produced maximum oxidative stress compare to all other groups. Oxidative parameter i.e. SOD, CAT, GSH and GPx were found to be decreased as compare to control rats. However MDA were found to be increased as compare to control rats. Additionally, CX produced less oxidative stress compare to other NDAIDs. Further, histological examinations support the biochemical results. Conclusion: From the above observations it can be concluded that NSAIDs have oxidative stress potential and generate oxidative stress and damage the organs when administrated chronically. Thus, these drugs should be used judiciously.

Investigating Sand Production Phenomena: An Appraisal of Past and Emerging Laboratory Experiments and Analytical Models

This paper provides an in-depth review of research developments on a common phenomenon in oil and gas exploration: sand production. Due to its significant impact to reservoir productivity and production efficiency, sand production has been widely researched in recent years. This paper focused on the review of historical progress in experimental and analytical studies which helped to understand the nature of the sanding mechanism and identify conditions that favour the process. Collation of the experimental data and analytical solutions and formulations enabled the authors to comment on effectiveness and also limitations of the existing experimental protocols and analytical models. Sand production models were then grouped into categories based on initiation of sanding, rate and amount of sanding as well as the failure criterion incorporated in their formulation so that it will be more convenient for future researchers to identify and adopt an appropriate model for their own research. The review also confirms that there are still some aspects of sand production requiring further investigation, and maybe a hybrid approach combining experimental, analytical and numerical methods could be the best solution for future explorations.

Challenges for assessing replicability in preclinical cancer biology

We conducted the Reproducibility Project: Cancer Biology to investigate the replicability of preclinical research in cancer biology. The initial aim of the project was to repeat 193 experiments from 53 high-impact papers, using an approach in which the experimental protocols and plans for data analysis had to be peer reviewed and accepted for publication before experimental work could begin. However, the various barriers and challenges we encountered while designing and conducting the experiments meant that we were only able to repeat 50 experiments from 23 papers. Here we report these barriers and challenges. First, many original papers failed to report key descriptive and inferential statistics: the data needed to compute effect sizes and conduct power analyses was publicly accessible for just 4 of 193 experiments. Moreover, despite contacting the authors of the original papers, we were unable to obtain these data for 68% of the experiments. Second, none of the 193 experiments were described in sufficient detail in the original paper to enable us to design protocols to repeat the experiments, so we had to seek clarifications from the original authors. While authors were extremely or very helpful for 41% of experiments, they were minimally helpful for 9% of experiments, and not at all helpful (or did not respond to us) for 32% of experiments. Third, once experimental work started, 67% of the peer-reviewed protocols required modifications to complete the research and just 41% of those modifications could be implemented. Cumulatively, these three factors limited the number of experiments that could be repeated. This experience draws attention to a basic and fundamental concern about replication – it is hard to assess whether reported findings are credible.

Ecological Entomology: How Is Gibson’s Framework Useful?

To date, numerous studies have demonstrated the fundamental role played by optic flow in the control of goal-directed displacement tasks in insects. Optic flow was first introduced by Gibson as part of their ecological approach to perception and action. While this theoretical approach (as a whole) has been demonstrated to be particularly suitable for the study of goal-directed displacements in humans, its usefulness in carrying out entomological field studies remains to be established. In this review we would like to demonstrate that the ecological approach to perception and action could be relevant for the entomologist community in their future investigations. This approach could provide a conceptual and methodological framework for the community in order to: (i) take a critical look at the research carried out to date, (ii) develop rigorous and innovative experimental protocols, and (iii) define scientific issues that push the boundaries of the current scientific field. After a concise literature review about the perceptual control of displacement in insects, we will present the framework proposed by Gibson and suggest its added value for carrying out research in the field of behavioral ecology in insects.

Reporting Data on Auditory Brainstem Responses (ABR) in Rats: Recommendations Based on Review of Experimental Protocols and Literature

Research in hearing science is accelerating, and a wealth of data concerning auditory brainstem responses (ABR) in various animal models is published in peer-reviewed journals every year. Recently, we reviewed studies using ABR measurements in tinnitus rat models. We found significant discrepancies in the outcomes of these studies, some due to different research approaches and others due to different methodologies. Thus, the present work aimed to collect comprehensive information on all factors influencing ABR recordings in rats and compile recommendations on ABR data reporting. A questionnaire with queries about animal husbandry, transfer, handling, and the exact test conditions before, during, and after ABR recordings was sent to 125 researchers who published the relevant studies between 2015 and 2021. Eighteen researchers provided detailed answers on factors related to ABR measurements. Based on the analysis of the returned questionnaires, we identified three domains reflecting animal-, equipment-, and experiment-dependent factors that might influence the ABR outcome, thus requiring reporting in published research. The analysis of survey results led to the compilation of recommendations for reporting ABR outcomes supported by a literature review. Following these recommendations should facilitate comparative and meta-analyses of ABR results provided by various research groups.

Drug Release Kinetics of DOX-Loaded Graphene-Based Nanocarriers for Ovarian and Breast Cancer Therapeutics

Cancer remains one of the leading causes of death worldwide despite extensive efforts at developing curative treatments. Chemotherapy, one of the most common forms of treatment, lacks specificity and can induce collateral damages to healthy surrounding tissues/cells and elicit off-target toxic side effects. The carbon-based nanomaterial graphene, can load aromatic drugs with high efficiency, has good biocompatibility, and can be easily functionalised with targeting ligands, antibodies, and biomolecules to increase the accuracy of targeting specific areas; graphene has therefore been explored as a nanocarrier for classical chemotherapy drugs. In this work, seventeen publications that report the release of doxorubicin (DOX) from 2D graphene-based nanohybrids (graphene oxide and reduced graphene oxide) for the treatment of breast and ovarian cancers have been identified based on a range of inclusion and exclusion criteria. To aid in the clinical translation of proof-of-concept studies, this work identifies the pre-clinical experimental protocols and analyses the release kinetics of these publications. Fifteen of the papers utilised a change in pH as the stimulus for drug release, and two utilised either near infrared (NIR) or ultrasound as the stimulus. The extracted drug release data from these publications were fit to four known kinetic models. It was found that the majority of these data best fit the Weibull kinetic model. The agreement between the kinetic data in previously published literature provides a predictable estimation of DOX release from graphene-based nanocarriers. This study demonstrates the potential conjugation of graphene and DOX in drug delivery applications, and this knowledge can help improve to the design and formulation of future graphene-based nanocarriers. In addition, the use of further experimental testing and the standardisation of experimental protocols will be beneficial for future work. The incorporation of computational modelling prior to pre-clinical testing will also aid in the development of controlled and sustained DOX release systems that offer efficient and efficacious results.