Miracle-dz/UniFAR-FTUs huggingface dataset:
Development and Comparison of In-house Line Probe Assay (LiPA) and SYBR Green Real-time PCR Regarding the Detection of Periodontal Pathogens

Background: Periodontal disease, which can become a chronic condition, is an inflammatory disease that upsets the soft and hard structures supporting the teeth. The aim of the present study was to design and develop an in-house Line Probe Assay (LiPA), to detect putative periodontitis-related bacterial pathogens, and compare it with SYBR Green Real-time PCR. Methods: The LiPA method was launched using biotinylated 16s rRNA universal primers and specific probes for each of the five bacteria including Aggregatibacter acti-nomycetemcomitans, Prevotella intermedia, Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola. For this, optimized quantities of the primers and specific probes were dotted onto nylon membrane stripes in a defined pattern. Hybridization was performed between the probes and the single-stranded biotinylated PCR products. The stripes were developed via biotin-streptavidin reaction. Ultimately, the analytical and diagnostic sensitivity and specificity of the in-house LiPA was evaluated and compared with SYBR Green Real-time PCR. Results: The detection limit of the LiPA was 2760 copies of targeted genes. In testing analytical specificity, only signals corresponding to the specific biotinylated products were produced. The calculated diagnostic sensitivity of the LiPA for the five bacterial targets ranged from 96.4 to 100%, whereas the diagnostic specificity was between 90.9 and 100%. Comparing the results, no noticeable difference (p=0.4795) was observed between the two methods. Conclusion: To screen periodontal pathogens, a simple, inexpensive and accurate method is desirable. The in-house LiPA, having advantages such as high specificity and sensitivity, and the ability to detect five major periodontal pathogens, offers the option of evaluating samples without the need for a post-PCR platform.
Modification of fliposomes with a polycation can enhance the control of pH-induced release

Purpose Nowadays, the development of stimuli-sensitive nanocontainers for targeted drug delivery is of great value. Encapsulation of a drug in a pH-sensitive liposomal container not only provides protective and transport functions, but also helps to create a system with a controlled release mechanism. Methods In this study, we investigated the influence of a cationic polypeptide on the pH-induced release of anticancer drug doxorubicin (DXR) from the anionic fliposomes – liposomes consisting of a neutral lipid, an anionic lipid (prone to interact with a polycation), and a lipid trigger (imparting the pH-sensitivity). Results First, we showed the possibility to control the pH-induced release by the simple modification of the anionic fliposomes with linear polylysine. Second, we optimized the fliposomal composition such that the obtained fliposomes responded to the pH changes only when complexed with the polycation (“turning on” the release). Finally, pH-induced release from the polylysine-modified anionic fliposomes was tested on an anticancer drug DXR. Conclusion We have succeeded in developing “smart” stimuli-sensitive nanocontainers capable of tunable controlled release of a drug. Moreover, based on the data on release of a low molecular salt, one can predict the release profile of DXR.
Tracking down the lizards from Gravenhorst's collection at the University of Wrocław: type specimens of Callopistes maculatus Gravenhorst, 1838 and three Liolaemus species rediscovered

Johann Ludwig Christian Gravenhorst’s herpetological collection at the Museum of Natural History, University of Wrocław included numerous important specimens of amphibians and reptiles. The majority, if not the entirety, of this collection has long been thought to be lost. However, we were able to rediscover some type specimens of lizards. The rediscovered specimens include the holotypes of Liolaemus conspersus and L. hieroglyphicus, one syntype of Callopistes maculatus (here designated as the lectotype) and two syntypes of L. lineatus (one of which is herein designated as the lectotype). Reexamination of these specimens indicates that previous synonymies proposed for L. conspersus and two syntypes of L. hieroglyphicus are problematic; furthermore, more complex taxonomic work is needed to resolve this issue. Two rediscovered syntypes of L. lineatus differ in several scalation traits and are possibly not conspecific. The type specimens of several other species of lizards from Gravenhorst’s collection (Liolaemus marmoratus, L. unicolor and two other syntypes of L. lineatus, Leiocephalus schreibersii and Chalcides viridanus) were not found and are probably lost.
Recent studies in adsorption of Pb(II), Zn(II) and Co(II) using conventional and modified materials:a review

ABSTRACT Heavy metal contamination and its detrimental effects on human health and environment have been a worldwide concern. Over the years, various technologies have been adapted to tackle this problem. Adsorption is still considered to be one of the most feasible and cost-effective methods for treating wastewater contaminated with heavy metals. Adsorbents such as activated carbon, clay, zeolites and silica have been studied extensively in the past. Modification of these conventional adsorbents and the synthesis of nonconventional adsorbents such as nanocomposites and metal organic frameworks (MOF’s) have been the main focus of study in recent times. This review article attempts to present a detailed account of various adsorbents and their removal efficiencies for the treatment of wastewater contaminated with lead(II), zinc(II) and cobalt(II) in the current decade. Influence of various parameters, adsorption isotherms and kinetics best described for their removal have also been reviewed in detail. It is observed that most of the adsorbents followed pseudo second order kinetics suggestive of a chemisorption process. After conducting a thorough review of more than 120 recently published papers, it can be inferred that nanomaterials and nanocomposites have shown excellent adsorption capacity for removal of these heavy metals.
Assessing an assessment: The review and redesign of a competency-based mid-degree evaluation

Introduction Little has been published about competency-based education in academic medicine, in particular how competencies are or should be assessed. This paper re-examines a competency-based assessment for M.S. students in clinical research, and “assesses the assessment” 4 years into its implementation. Methods Data were gathered from student surveys and interviews with program advisors, and common themes were identified. We then made refinements to the assessment, and student surveys were administered to evaluate the impact of the changes. Results Research results suggested the need to improve communication, time the assessment to align with skills development and opportunities for planning, streamline, and clarify expectations with examples and templates. After implementing these changes, data suggest that student satisfaction has improved without any reduction in academic rigor. Conclusion The effective implementation of competency-based training in clinical and translational research requires the development of a scholarly literature on effective methods of assessment. This paper contributes to that nascent body of research.
Complete Genome Sequence of a Lytic T7-Like Phage, Escherichia Phage vB_EcoP-Ro45lw, Isolated from Nonfecal Compost Samples

Although isolation of the bacteriophages (phages) specific to Shiga toxin-producing Escherichia coli (STEC) is increasing, the number of those specific to STEC non-O157 strains, instead of STEC O157, with whole-genome sequencing characterization is relatively low. Here, we announce the complete genome sequence of a T7-like lytic phage against STEC O45. ABSTRACT Although isolation of the bacteriophages (phages) specific to Shiga toxin-producing Escherichia coli (STEC) is increasing, the number of those specific to STEC non-O157 strains, instead of STEC O157, with whole-genome sequencing characterization is relatively low. Here, we announce the complete genome sequence of a T7-like lytic phage against STEC O45.
Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures

In the field of biology, researchers need to compare genes or gene products using semantic similarity measures (SSM). Continuous data growth and diversity in data characteristics comprise what is called big data; current biological SSMs cannot handle big data. Therefore, these measures need the ability to control the size of big data. We used parallel and distributed processing by splitting data into multiple partitions and applied SSM measures to each partition; this approach helped manage big data scalability and computational problems. Our solution involves three steps: split gene ontology (GO), data clustering, and semantic similarity calculation. To test this method, split GO and data clustering algorithms were defined and assessed for performance in the first two steps. Three of the best SSMs in biology [Resnik, Shortest Semantic Differentiation Distance (SSDD), and SORA] are enhanced by introducing threaded parallel processing, which is used in the third step. Our results demonstrate that introducing threads in SSMs reduced the time of calculating semantic similarity between gene pairs and improved performance of the three SSMs. Average time was reduced by 24.51% for Resnik, 22.93%, for SSDD, and 33.68% for SORA. Total time was reduced by 8.88% for Resnik, 23.14% for SSDD, and 39.27% for SORA. Using these threaded measures in the distributed system, combined with using split GO and data clustering algorithms to split input data based on their similarity, reduced the average time more than did the approach of equally dividing input data. Time reduction increased with increasing number of splits. Time reduction percentage was 24.1%, 39.2%, and 66.6% for Threaded SSDD; 33.0%, 78.2%, and 93.1% for Threaded SORA in the case of 2, 3, and 4 slaves, respectively; and 92.04% for Threaded Resnik in the case of four slaves.
The Role of the Voltage-Gated Potassium Channel Proteins Kv8.2 and Kv2.1 in Vision and Retinal Disease: Insights from the Study of Mouse Gene Knock-Out Mutations

Abstract Mutations in the KCNV2 gene, which encodes the voltage-gated K+ channel protein Kv8.2, cause a distinctive form of cone dystrophy with a supernormal rod response (CDSRR). Kv8.2 channel subunits only form functional channels when combined in a heterotetramer with Kv2.1 subunits encoded by the KCNB1 gene. The CDSRR disease phenotype indicates that photoreceptor adaptation is disrupted. The electroretinogram (ERG) response of affected individuals shows depressed rod and cone activity, but what distinguishes this disease is the supernormal rod response to a bright flash of light. Here, we have utilized knock-out mutations of both genes in the mouse to study the pathophysiology of CDSRR. The Kv8.2 knock-out (KO) mice show many similarities to the human disorder, including a depressed a-wave and an elevated b-wave response with bright light stimulation. Optical coherence tomography (OCT) imaging and immunohistochemistry indicate that the changes in six-month-old Kv8.2 KO retinae are largely limited to the outer nuclear layer (ONL), while outer segments appear intact. In addition, there is a significant increase in TUNEL-positive cells throughout the retina. The Kv2.1 KO and double KO mice also show a severely depressed a-wave, but the elevated b-wave response is absent. Interestingly, in all three KO genotypes, the c-wave is totally absent. The differential response shown here of these KO lines, that either possess homomeric channels or lack channels completely, has provided further insights into the role of K+ channels in the generation of the a-, b-, and c-wave components of the ERG.
The impact of pathological high-frequency oscillations on hippocampal network activity in rats with chronic epilepsy

In epilepsy, brain networks generate pathological high-frequency oscillations (pHFOs) during interictal periods. To understand how pHFOs differ from normal oscillations in overlapping frequency bands and potentially perturb hippocampal processing, we performed high-density single unit and local field potential recordings from hippocampi of behaving rats with and without chronic epilepsy. In epileptic animals, we observed two types of co-occurring fast oscillations, which by comparison to control animals we could classify as ‘ripple-like’ or ‘pHFO’. We compared their spectral characteristics, brain state dependence, and cellular participants. Strikingly, pHFO occurred irrespective of brain state, were associated with interictal spikes, engaged distinct subnetworks of principal neurons compared to ripple-like events, increased the sparsity of network activity, and initiated both general and immediate disruptions in spatial information coding. Taken together, our findings suggest that events that result in pHFOs have an immediate impact on memory processes, corroborating the need for proper classification of pHFOs to facilitate therapeutic interventions that selectively target pathological activity.
Rat-borne diseases at the horizon. A systematic review on infectious agents carried by rats in Europe 1995–2016

ABSTRACT To investigate the spectrum of rat-borne pathogens circulating in Europe a systematic review spanning across 55 European countries during the years 1995–2016 was performed. The study surveyed viruses, bacteria, macroparasites and unicellular eukaryotes (protozoa). Fifty-three different infectious agents, all with zoonotic potential, were reported to be carried by commensal rats; 48 by the brown rat (Rattus norvegicus) and 20 by the black rat (R. rattus). There was a tendency for rural areas to harbour more rat-borne microbes than urban areas regarding the brown rat, but the opposite could be observed for the black rat. The study clearly indicated that an improved surveillance on wild rats is needed in Europe, and further indicated the pathogens and geographical areas where the major focus is required. For example, six zoonotic microbes seemed to be clearly more geographically widespread in Europe than others; virulent or resistant E. coli, pathogenic Leptospira spp. , Hymenolepis diminuta, H. nana, Capillaria hepatica and Toxoplasma gondii.
Medical Professionalism: A Series of Near-Peer Facilitated Workshops for First-Year Medical Students

Introduction Professionalism is a core competency of medical education. It impacts one's ability to generate rapport with patients, foster patient satisfaction, and enhance the overall well-being of the medical professional. Unprofessional attitudes among medical students have been associated with higher rates of career dissatisfaction and burnout. A group of faculty and medical students at our institution have developed a series of peer facilitated modules addressing a set of common themes relevant to medical professionalism: professionalism in the clinical setting, professional electronic communication, teamwork and community, and work-life integration. Methods Student discussions on professionalism were facilitated by senior medical students. Using a 5-point Likert scale, electronic pre- and postsurveys assessed the impact of the workshop on first-year medical students' understanding of various professionalism topics. Results Seventy-seven percent of first-year medical students (n = 131) felt the modules contributed to their learning. Pre- and postsurveys showed significant improvements in understanding of and comfort with the majority of topics discussed. Students felt that their knowledge improved as well. Narrative comments expressed approval of the modules and suggested they addressed unmet needs in the medical curriculum. Discussion These modules were successfully incorporated into the first-year medical school curriculum and led to improved student understanding and comfort around these topics. Senior medical student facilitators also found the experience useful in their own career development. Although these modules were designed for medical students, they may also be useful for other professional students (e.g., dental, nursing, etc.) or for interprofessional educational experiences.
Complete Sequences of Two Plasmids Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain

Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids. ABSTRACT Plasmids play a crucial role in the evolution of bacterial genomes by mediating horizontal gene transfer. In this work, we sequenced two plasmids found in a Brazilian Bacillus thuringiensis serovar israelensis strain which showed 100% nucleotide identities with Bacillus thuringiensis serovar kurstaki plasmids.
Epidemiological Features of Highly Pathogenic Avian Influenza in Cameroon

The epidemiology of avian influenza is unknown in Cameroon despite the two outbreaks that occurred in 2006 and 2016-2017, respectively. In order to fill the gap, an attempt was made to provide some basic information on the epidemiology of highly pathogenic avian influenza in Cameroon. Thus, data were collected from follow-up reports of the second HPAI outbreaks prepared by the veterinary health officials of Cameroon and sent to the World Organisation for Animal Health (OIE). Two HPAI virus strains (H5N1 and H5N8) turned out to occur, with H5N1 virus involved in the Center, South, West, and Adamawa regions outbreaks and H5N8 involved in the Far North outbreak only. The affected hosts were the laying hens, backyard chickens, turkeys, guinea fowls, ducks, broiler and layer breeders, and geese for the H5N1 virus and the Indian peafowl (Pavo cristatus), pigeon, ducks, backyard chickens, and guinea fowls for the H5N8 virus. The first outbreak took place in Mvog-Betsi poultry complex in the Center region on the 20th May 2016 and spread to other regions. The mortality rate varied from 8% to 72% for H5N1 virus and was 96.26% for the H5N8 strain in Indian peafowl. No human case was recorded. The potential supporting factors for disease dissemination identified on the field were the following: poultry and eggs dealers moving from one farm, market, or town to another without any preventive care; poor biosecurity measures on farms and live poultry markets. After the first HPAI H5N1 virus outbreak in 2006, the second HPAI outbreak ten years later (2016-2017) involving two virus strains is a cause of concern for the poultry industry. The Cameroon Epidemio-Surveillance Network needs to be more watchful.
Crystal structure of bromidopentakis(tetrahydrofuran-κO)magnesium bis[1,2-bis(diphenylphosphanyl)benzene-κ2 P,P′]cobaltate(−1) tetrahydrofuran disolvate

The reduction of CoBr2 by the Grignard reagent p-tolylmagnesium bromide in the presence of 1,2-bis(diphenylphosphanyl)benzene (dbpz) resulted in the d 10, formally Co−1 anion, [Co(dpbz)2]−. The crystal structure of the [MgBr(THF)5]+ (THF is tetrahydrofuran) salt showed the anion to be pseudotetrahedral and packed in alternating layers of anions and cations.
Pain Beliefs and Perceptions and Their Relationship with Coping Strategies, Stress, Anxiety, and Depression in Patients with Cancer

Objective: The current study was conducted aiming at the investigation of pain beliefs and perceptions and their relationship with coping strategies, stress, anxiety, and depression in patients with cancer. Materials and Methods: Study design: This was a descriptive-correlational and cross-sectional study. Data collection tools – Demographic questionnaire, Pain Beliefs and Perceptions Inventory, Pain Coping Strategies Questionnaire (Rosenstiel and Keefe), and Depression, Anxiety, and Stress Scale were used in this study. The dataset was analyzed using descriptive and infreretial statistics that included the chi-square and one-way ANOVA with software SPSS v.16 analysis. Results: Findings of the study indicated that the most common belief about pain in patients is pain permanence. In addition, the most commonly used strategies for coping pain in patients were praying/hoping (25.82 ± 7.86) and self-statements (22.3 ± 10.34). Results indicated that there is a significant difference between pain coping strategies and pain control (P = 0.02). No significant difference was observed between the pain beliefs and the coping strategies (P = 0.15). Depression and anxiety level of patients was estimated as moderate, and their stress was estimated as mild. It was specified that there is a significant difference between self-blame belief and depression of patients (P = 0.01). Conclusion: Understanding and identifying emotional-psychological variables in patients with chronic pains may provide a basis for implementing educational cognitive-behavioral programs for patients and the ground for increasing the ability to control the pain in nonpharmacological methods leading to promoting quality of life in these patients.
Most sleep does not serve a vital function: Evidence from Drosophila melanogaster

Sleepless fruit flies live, an unexpected finding that provides a new perspective on sleep for this and perhaps other species. Sleep appears to be a universally conserved phenomenon among the animal kingdom, but whether this notable evolutionary conservation underlies a basic vital function is still an open question. Using a machine learning–based video-tracking technology, we conducted a detailed high-throughput analysis of sleep in the fruit fly Drosophila melanogaster, coupled with a lifelong chronic and specific sleep restriction. Our results show that some wild-type flies are virtually sleepless in baseline conditions and that complete, forced sleep restriction is not necessarily a lethal treatment in wild-type D. melanogaster. We also show that circadian drive, and not homeostatic regulation, is the main contributor to sleep pressure in flies. These results offer a new perspective on the biological role of sleep in Drosophila and, potentially, in other species.
Inducible pesticide tolerance in Daphnia pulex influenced by resource availability

Abstract Pesticides are a ubiquitous contaminant in aquatic ecosystems. Despite the relative sensitivity of aquatic species to pesticides, growing evidence suggests that populations can respond to pesticides by evolving higher baseline tolerance or inducing a higher tolerance via phenotypic plasticity. While both mechanisms can allow organisms to persist when faced with pesticides, resource allocation theory suggests that tolerance may be related to resource acquisition by the organism. Using Daphnia pulex, we investigated how algal resource availability influenced the baseline and inducible tolerance of D. pulex to a carbamate insecticide, carbaryl. Individuals reared in high resource environments had a higher baseline carbaryl tolerance compared to those reared in low resource environments. However, D. pulex from low resource treatments exposed to sublethal concentrations of carbaryl early in development induced increased tolerance to a lethal concentration of carbaryl later in life. Only individuals reared in the low resource environment induced carbaryl tolerance. Collectively, this highlights the importance of considering resource availability in our understanding of pesticide tolerance.