Enzymatic antioxidants activity in gingival crevicular fluid and saliva in advanced periodontitis.

AIM: Enzymatic antioxidants are the primary line of defense against oxidative and nitrosative stress. However, their involvement in the progression of periodontitis is still not well understood. The study aimed to determine the activity of enzymatic antioxidants in the gingival crevicular fluid (GCF) and saliva of patients with periodontitis. MATERIALS AND METHODS: The study group of 56 patients with periodontitis (stage III and IV) and 28 healthy controls were involved. The modified plaque index, probing depth, the clinical attachment level, the percentage of sites with bleeding on probing, papilla bleeding index, and maximum value of tooth mobility (Periotest®) were tested. Saliva (stimulated and non-stimulated) and GCF were collected from the participants, and activity of peroxidase, catalase, superoxide dismutase, and glutathione reductase were determined colorimetrically. RESULTS: Lower activity of peroxidase (p < 0.0001), catalase (p < 0.0001), superoxide dismutase (p = 0.0188), and glutathione reductase (p < 0.0001) was noted in non-stimulated saliva of patients with periodontitis compared to healthy subjects. Peroxidase (p < 0.0001), catalase (p < 0.0001) and superoxide dismutase (p < 0.0001) showed lower activity in stimulated saliva of patients with periodontitis compared to healthy subjects. The peroxidase (p < 0.0029), catalase (p < 0.0001), and glutathione reductase (p = 0.0028) activity in GCF of stage III + IV were significantly higher compared to healthy controls. Superoxide dismutase (p < 0.0001) showed lower activity in GCF of patients with periodontitis. CONCLUSIONS: The demonstrated decrease in activity of all analyzed enzymatic antioxidants in non-stimulated saliva may result from long-lasting periodontitis and exhaustion of the safeguard mechanism against reactive oxygen species.

Microbiota in sports.

The influence of microbiota on the human body is currently the subject of many studies. The composition of bacteria colonizing the gastrointestinal tract varies depending on genetic make-up, lifestyle, use of antibiotics or the presence of diseases. The diet is also important in the species diversity of the microbiota. This study is an analysis of the relationships between physical activity, diet, and the microbiota of the gastrointestinal tract in athletes. This review shows the differences in the microbial composition in various sports disciplines, the influence of probiotics on the microbiome, the consequence of which may be achieved even better sports results. Physical activity increases the number of bacteria, mainly of the Clostridiales order and the genus: Lactobacillus, Prevotella, Bacteroides, and Veillonella, and their number varies depending on the sports discipline. These bacteria are present in athletes in sports that require a high VO2 max. The players' diet also influences the composition of the microbiota. A diet rich in dietary fiber increases the amount of Lactobacillus or Bifidobacterium bacteria, probiotic microorganisms, which indicates the need to supplement the diet with probiotic preparations. It is impossible to suggest an unambiguous answer to how the microbiota of the gastrointestinal tract changes in athletes and requires further analyzes.

Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base.

Integrating reference datasets (e.g. from high-throughput experiments) with unstructured and manually-assembled information (e.g. notes or comments from individual researchers) has the potential to tailor bioinformatic analyses to specific needs and to lead to new insights. However, developing bespoke analysis pipelines from scratch is time-consuming, and general tools for exploring such heterogeneous data are not available. We argue that by treating all data as text, a knowledge-base can accommodate a range of bioinformatic data types and applications. We show that a database coupled to nearest-neighbor algorithms can address common tasks such as gene-set analysis as well as specific tasks such as ontology translation. We further show that a mathematical transformation motivated by diffusion can be effective for exploration across heterogeneous datasets. Diffusion enables the knowledge-base to begin with a sparse query, impute more features, and find matches that would otherwise remain hidden. This can be used, for example, to map multi-modal queries consisting of gene symbols and phenotypes to descriptions of diseases. Diffusion also enables user-driven learning: when the knowledge-base cannot provide satisfactory search results in the first instance, users can improve the results in real-time by adding domain-specific knowledge. User-driven learning has implications for data management, integration, and curation.

Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave.

The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300-2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.

Vitamin D receptor gene polymorphism influence on lumbar intervertebral disc degeneration.

Intervertebral disc (IVD) degeneration is a multifaceted pathology that is the main morphological cause of lower back pain. This study aimed to determine the link between the vitamin D receptor gene single nucleotide polymorphisms (SNPs) and degenerative processes of the lumbar spine. The complete lumbar spinal columns were collected from 100 Caucasian cadavers via ventral dissection. The specimens for the histological analysis were harvested from the L5/S1 IVDs and endplates. Then, the tissues were cut into slices, inserted into paraffin blocks, and stained. The histology was evaluated according to the Boos' protocol. Moreover, TaqI(rs731236), FokI(rs2228570), and ApaI(rs7975232) genotyping were performed. Lastly, the histological scores for different genotypes were analyzed. The overall Boos' score in the study group was 12.49. It consisted of a mean IVD score of 7.46 and endplate score of 5.39. The determination of the SNPs was successful in 99 specimens and had a distribution of all alleles in accordance with the Hardy-Weinberg equilibrium. No significant differences in overall histological degeneration scores were found between samples from donors with different genotypes. However, in subgroup analysis of specific regions on the IVD, the significant difference was found in posterior inner anulus fibrosus for ApaI. The results of this study suggest that one must be careful when interpreting the results of the clinical and/or radiological studies on vitamin D receptor gene polymorphisms and lumbar spine degeneration risk, because such a relationship, if present, is likely to be very subtle.

Incremental data integration for tracking genotype-disease associations.

Functional annotation of genes remains a challenge in fundamental biology and is a limiting factor for translational medicine. Computational approaches have been developed to process heterogeneous data into meaningful metrics, but often do not address how findings might be updated when new evidence comes to light. To address this challenge, we describe requirements for a framework for incremental data integration and propose an implementation based on phenotype ontologies and Bayesian probability updates. We apply the framework to quantify similarities between gene annotations and disease profiles. Within this scope, we categorize human diseases according to how well they can be recapitulated by animal models and quantify similarities between human diseases and mouse models produced by the International Mouse Phenotyping Consortium. The flexibility of the approach allows us to incorporate negative phenotypic data to better prioritize candidate genes, and to stratify disease mapping using sex-dependent phenotypes. All our association scores can be updated and we exploit this feature to showcase integration with curated annotations from high-precision assays. Incremental integration is thus a suitable framework for tracking functional annotations and linking to complex human pathology.

In Vivo Evaluation of Periodontal Phenotypes Using Cone-Beam Computed Tomography, Intraoral Scanning by Computer-Aided Design, and Prosthetic-Driven Implant Planning Technology.

BACKGROUND Two clinical parameters, the gingival thickness (GT) and the width of keratinized tissue (WKT), describe the gingival phenotype, which is defined as the 3-dimensional volume of the gingiva. The periodontal phenotype additionally includes the thickness of the labial plate of the alveolar crest (TLPAC). MATERIAL AND METHODS Thirty patients with healthy periodontium on the upper canines and incisors underwent measurements for crestal, supracrestal, free gingival thickness (FGT), the alveolar crest-gingival margin (AC-GM), alveolar crest-cementoenamel junction distance, and the TLPAC at 2, 4, and 8 mm apically from the edge of the alveolar crest using cone-beam computed tomography (CBCT) with computer-aided design and prosthetic-driven implant planning technology. For each tooth, the gingival and periodontal phenotype was evaluated on the basis of the gingival thickness, width of keratinized tissue (WKT), and TLPAC measurements. Each patient's periodontal phenotype was evaluated according to the coronal width/length ratio of both the upper central incisors. RESULTS The dentogingival units had varying average values for the 3 periodontal phenotypes (thin phenotype: FGT 0.65±0.06 mm, WKT 4.85±1.18 mm, AC-GM 3.17±0.64 mm, TLPAC2 0.66±0.28 mm; medium phenotype: FGT 0.87±0.07 mm, WKT 5.49±1.23 mm, AC-GM 3.36±0.65 mm, TLPAC2 0.76±0.37 mm; and thick phenotype: FGT 1.20 mm, WKT 6.00 mm, AC-GM 3.90 mm, TLPAC2 0.90 mm). Positive correlations were seen among WKT, FGT, AC-GM, and TLPAC2. CONCLUSIONS Positive correlations between the FGT and WKT, and the AC-GM distance confirm that measurements using CBCT with computer-aided design and prosthetic-driven implant planning technology can evaluate the gingival phenotype and TLPAC2 for the periodontal phenotype.

Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells.

In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.

Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity.

Patterns of somatic mutations in cancer genes provide information about their functional role in tumourigenesis, and thus indicate their potential for therapeutic exploitation. Yet, the classical distinction between oncogene and tumour suppressor may not always apply. For instance, TP53 has been simultaneously associated with tumour suppressing and promoting activities. Here, we uncover a similar phenomenon for GATA3, a frequently mutated, yet poorly understood, breast cancer gene. We identify two functional classes of frameshift mutations that are associated with distinct expression profiles in tumours, differential disease-free patient survival and gain- and loss-of-function activities in a cell line model. Furthermore, we find an estrogen receptor-independent synthetic lethal interaction between a GATA3 frameshift mutant with an extended C-terminus and the histone methyltransferases G9A and GLP, indicating perturbed epigenetic regulation. Our findings reveal important insights into mutant GATA3 function and breast cancer, provide the first potential therapeutic strategy and suggest that dual tumour suppressive and oncogenic activities are more widespread than previously appreciated.

Reasons and risk indicators tor tooth loss in the Polish cross-sectional gerodontological study

INTRODUCTION: The number of teeth in the elderly is the most essential epidemiological data in gerodontological studies. It depends mainly on two medical causes in the form of caries and periodontitis, as well as many risk factors and indicators for tooth preservation and loss. The goals of the cross-sectional study among the residents of Wroclaw and Olawa aged 65-74 have been to assess the number of preserved teeth, severe tooth loss and edentulism in a 30-year trend and in relation to current European regional data. In addition, the most important risk indicators for tooth preservation and loss in the assessed population will be determined. MATERIAL AND METHODS: After applying the two-tier stratification method from a group of 1,200 people, 387 volunteered for the study. The examination was conducted in dental offices in Wroclaw and Olawa, it consisted from clinical and anamnestic parts. The average number of preserved teeth in the entire group was 13.07 (median 15), there were 21.2% persons with functional dentition, 21.4% with severe tooth loss and 14.2% with edentulism. The main direct reason of tooth loss was caries and its complications, which concerned 81.9% of the teeth removed, on average over 12 teeth in the examined person. RESULTS: Referring the results of the obtained study to previous observations can be seen, that in the 30-year trend for Wroclaw in people aged 65 to 74 years, the average number of teeth as well as the percentage of edentulism have improved, but they are still worse than the results of regional European studies. The main risk indicators of earlier loss of teeth by seniors in Lower Silesia are low income, past incorrect pro-health behaviours towards the oral cavity as well as current smoking and history of cardiovascular incidence.

Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line.

Near-haploid human cell lines are instrumental for genetic screens and genome engineering as gene inactivation is greatly facilitated by the absence of a second gene copy. However, no completely haploid human cell line has been described, hampering the genetic accessibility of a subset of genes. The near-haploid human cell line HAP1 contains a single copy of all chromosomes except for a heterozygous 30-megabase fragment of Chromosome 15. This large fragment encompasses 330 genes and is integrated on the long arm of Chromosome 19. Here, we employ a CRISPR/Cas9-based genome engineering strategy to excise this sizeable chromosomal fragment and to efficiently and reproducibly derive clones that retain their haploid state. Importantly, spectral karyotyping and single-nucleotide polymorphism (SNP) genotyping revealed that engineered-HAPloid (eHAP) cells are fully haploid with no gross chromosomal aberrations induced by Cas9. Furthermore, whole-genome sequence and transcriptome analysis of the parental HAP1 and an eHAP cell line showed that transcriptional changes are limited to the excised Chromosome 15 fragment. Together, we demonstrate the feasibility of efficiently engineering megabase deletions with the CRISPR/Cas9 technology and report the first fully haploid human cell line.

Comparison of genetic variants in matched samples using thesaurus annotation.

MOTIVATION: Calling changes in DNA, e.g. as a result of somatic events in cancer, requires analysis of multiple matched sequenced samples. Events in low-mappability regions of the human genome are difficult to encode in variant call files and have been under-reported as a result. However, they can be described accurately through thesaurus annotation-a technique that links multiple genomic loci together to explicate a single variant. RESULTS: We here describe software and benchmarks for using thesaurus annotation to detect point changes in DNA from matched samples. In benchmarks on matched normal/tumor samples we show that the technique can recover between five and ten percent more true events than conventional approaches, while strictly limiting false discovery and being fully consistent with popular variant analysis workflows. We also demonstrate the utility of the approach for analysis of de novo mutations in parents/child families. AVAILABILITY AND IMPLEMENTATION: Software performing thesaurus annotation is implemented in java; available in source code on github at GeneticThesaurus (https://github.com/tkonopka/GeneticThesaurus) and as an executable on sourceforge at geneticthesaurus (https://sourceforge.net/projects/geneticthesaurus). Mutation calling is implemented in an R package available on github at RGeneticThesaurus (https://github.com/tkonopka/RGeneticThesaurus). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: tomasz.konopka@ludwig.ox.ac.uk.

Parallel reverse genetic screening in mutant human cells using transcriptomics.

Reverse genetic screens have driven gene annotation and target discovery in model organisms. However, many disease-relevant genotypes and phenotypes cannot be studied in lower organisms. It is therefore essential to overcome technical hurdles associated with large-scale reverse genetics in human cells. Here, we establish a reverse genetic approach based on highly robust and sensitive multiplexed RNA sequencing of mutant human cells. We conduct 10 parallel screens using a collection of engineered haploid isogenic cell lines with knockouts covering tyrosine kinases and identify known and unexpected effects on signaling pathways. Our study provides proof of concept for a scalable approach to link genotype to phenotype in human cells, which has broad applications. In particular, it clears the way for systematic phenotyping of still poorly characterized human genes and for systematic study of uncharacterized genomic features associated with human disease.

A thesaurus of genetic variation for interrogation of repetitive genomic regions.

Detecting genetic variation is one of the main applications of high-throughput sequencing, but is still challenging wherever aligning short reads poses ambiguities. Current state-of-the-art variant calling approaches avoid such regions, arguing that it is necessary to sacrifice detection sensitivity to limit false discovery. We developed a method that links candidate variant positions within repetitive genomic regions into clusters. The technique relies on a resource, a thesaurus of genetic variation, that enumerates genomic regions with similar sequence. The resource is computationally intensive to generate, but once compiled can be applied efficiently to annotate and prioritize variants in repetitive regions. We show that thesaurus annotation can reduce the rate of false variant calls due to mappability by up to three orders of magnitude. We apply the technique to whole genome datasets and establish that called variants in low mappability regions annotated using the thesaurus can be experimentally validated. We then extend the analysis to a large panel of exomes to show that the annotation technique opens possibilities to study variation in hereto hidden and under-studied parts of the genome.

Anatomical variability and histological structure of the ulnar nerve in the Guyon's canal.

OBJECTIVES: The goal of our study was to analyze the prevalence of variations, branching patterns, and histology of the ulnar nerve (UN) in Guyon's canal to address its importance in hand surgery, particularly decompression of the UN. METHODS: Fifty fresh cadavers were dissected bilaterally, and the nerve in the area of Guyon's canal was visualized. Samples for histology were also taken and prepared. The collected data were then analyzed. RESULTS: Morphometric measurements of the hands and histological studies were not found to have significant differences when compared by left or right side or by sex. Three major branching patterns were found, with division into deep and superficial UN being the most common (85%). Additional findings included a majority (70%) presenting with a cutaneous branch within the canal and/or with an anastomosis of its distant branches with those of the median nerve (57%). CONCLUSION: The UN is most commonly found to divide into a superficial and deep ulnar branch within Guyon's canal. However, additional branches and anastomoses are common and should be taken into careful consideration when approached during surgery in the area, particularly during decompression procedures of Guyon's canal.

Effectiveness of orthodontic miniscrew implants in anchorage reinforcement during en-masse retraction: A systematic review and meta-analysis.

INTRODUCTION: The aim of this systematic review was to compare the effectiveness of orthodontic miniscrew implants-temporary intraoral skeletal anchorage devices (TISADs)-in anchorage reinforcement during en-masse retraction in relation to conventional methods of anchorage. METHODS: A search of PubMed, Embase, Cochrane Central Register of Controlled Trials, and Web of Science was performed. The keywords were orthodontic, mini-implants, miniscrews, miniplates, and temporary anchorage device. Relevant articles were assessed for quality according to Cochrane guidelines and the data extracted for statistical analysis. A meta-analysis of raw mean differences concerning anchorage loss, tipping of molars, retraction of incisors, tipping of incisors, and treatment duration was carried out. RESULTS: Initially, we retrieved 10,038 articles. The selection process finally resulted in 14 articles including 616 patients (451 female, 165 male) for detailed analysis. Quality of the included studies was assessed as moderate. Meta-analysis showed that use of TISADs facilitates better anchorage reinforcement compared with conventional methods. On average, TISADs enabled 1.86 mm more anchorage preservation than did conventional methods (P <0.001). CONCLUSIONS: The results of the meta-analysis showed that TISADs are more effective than conventional methods of anchorage reinforcement. The average difference of 2 mm seems not only statistically but also clinically significant. However, the results should be interpreted with caution because of the moderate quality of the included studies. More high-quality studies on this issue are necessary to enable drawing more reliable conclusions.

Residua of thymus in the mediastinum - clinical aspects - cadaveric study.

The main goal of this study was to investigate possible residua of thymic tissue in 100 adult cadavers with no thoracic pathology known before, by dissection of standard locations of thymic tissue in perithyroid, periaortic, peritracheal and retrotracheal spaces, as well as areas located next to the course of phrenic, vagus and left recurrent laryngeal nerves. Thus obtained tissue samples were studied by two pathologists independently. The remnants of the thymic tissue were found in 61 out of 100 specimens studied. It means that residua of ectopic thymic tissue is common, which may have a huge impact on the results of treatment of many diseases i.e. myasthenia gravis in course of thymoma.

A reversible gene trap collection empowers haploid genetics in human cells.

Knockout collections are invaluable tools for studying model organisms such as yeast. However, there are no large-scale knockout collections of human cells. Using gene-trap mutagenesis in near-haploid human cells, we established a platform to generate and isolate individual 'gene-trapped cells' and used it to prepare a collection of human cell lines carrying single gene-trap insertions. In most cases, the insertion can be reversed. This growing library covers 3,396 genes, one-third of the expressed genome, is DNA-barcoded and allows systematic screens for a wide variety of cellular phenotypes. We examined cellular responses to TNF-α, TGF-ß, IFN-γ and TNF-related apoptosis-inducing ligand (TRAIL), to illustrate the value of this unique collection of isogenic human cell lines.

Homicides with corpse dismemberment in the material collected by the Department of Forensic Medicine, Krakow, Poland.

Aim of the study: To determine the circumstances which can be useful for offenders profiling in homicide cases with victim's body dismemberment. Material and methods: Study of all homicide cases with victim's corpse dismemberment examined in Krakow Department of Forensic Medicine over the last 50 years. Results: Within the past 50 years, a total number of 30 cases of homicides with dismembered bodies were examined in Krakow. 22 cases represent defensive mutilations performed by offender, 3 cases can be classified as offensive muti-lations and 3 cases represent aggressive mutilations - decapitation as a method of committing homicide. In this period the only 1 case of necrophilic mutilations was examined, when the body was dismembered without murder. In most cases the background of homicide was the family conflict, 6 was cause of mental illness of perpetrator and in 3 was sexual motive. Only in 3 cases (from 25 when the offender was known) perpetrator kill a stranger. In the other the offender belonged to the family or friends of the victim. In all cases where the perpetrator was determined, homicide and dismemberment was performed in his place of residence. The findings of the Police investigations indicate that in most cases homicides were not planned, occurred under the influence of emotion, only two have been previously scheduled. Conclusions: Homicides with corpses dismemberment usually are committed by offenders who is in close relationship with victim (family or friend). Dismemberment is almost always performed in the same place as murder - home of perpetrator. This type of homicide usually is not planned.

Analysis of the nature of injuries in victims of fall from height

AIM OF STUDY: To assess the types and extent of injuries sustained by victims of fall from height depending on the height of fall. MATERIAL AND METHODS: The study included 338 bodies of victims of fatal falls from different heights (from the 1st to 10th floors) who were subjected to medico-legal autopsy at the Department of Forensic Medicine, Jagiellonian University Medical College, between 1995 and 2014. For each individual, selected data were collected including gender, age, body height, injury types and presence of alcohol or other intoxicants in blood. The analysis comprised injuries to the brain, thoracic and abdominal organs, fractures of the skull, extremities, ribs and spine, and fractures of the scapula, clavicle and sternum (considered together). The study focused on determining the frequency of occurrence of different injuries in relation to one another and depending on the height of fall. RESULTS: The number and extent of injuries was found to increase along with the height of fall. Three injury types, including injuries to the mesentery and both kidneys and fractures of upper extremity small bones, were shown to occur from the threshold heights of the 3rd, 4th and 6th floors. Eleven injuries demonstrated a statistically significant correlation with the height of fall. The study also revealed a number of correlations between the frequencies of occurrence of different injuries. CONCLUSIONS: Injuries found from the threshold value may suggest the minimal height of fall. The presence of injuries which correlate with increasing height, and the overall number of injuries observed in victims of fall from height, may be useful for inferring the height of the fall.