Tell el-Murra (Northeastern Nile Delta Survey) : season 2010

Much of the work of the Northwestern Nile Delta Survey Project involved research at Tell el-Murra, a site in the northeastern part of the Nile Delta chosen for excavation on the basis of results from the 2008 survey season. Archaeological testing was coupled with magnetic prospection and geological core drillings in an effort to establish site stratigraphy and chronology. An analysis of the assemblage of finds (mainly pottery), confirmed occupation of the northeastern part of the site in the Old Kingdom period, after the southwestern part had already been abandoned. Core drilling results suggested the presence of Predynastic layers below the Protodynastic strata explored in 2010. A continued survey around Tell el-Murra comprised prospection at the sites of Tell Abu el-Halyat, Tell el-Akhdar, Minshat Radwan, Tell Gezira el-Faras, Gezira Sangaha, Mantiqat el-Qalaa and Kafr el-Hadidi. Naqada III pottery was confirmed at the first four of these sites

Benchmark of algorithms for multiple DNA sequence alignment across livestock species

Background: Due to the growing amount of biological data, it is often necessary to select the most optimal estimation method for DNA sequence alignment across livestock species. One of the most important benches of genomics is to modelling homology between considered DNA sequences. A multiple sequence alignment is a potent tool for molecular and evolutionary biology, and there are several programs and algorithms applicable for this purpose. The purpose of this paper was to study the most commonly used DNA alignment algorithms to select the optimal tool dedicated for short sequences.Methods: Four steps of bioinformatics pipelines were considered to benchmark the algorithms for multiple DNA sequence alignment across livestock species: 1) selection of reference genome sequences of ARS1.2 for cattle, EquCab3.0 for horse and vicPac2 for alpaca with a low E-value using TBLASTn 2) removing gaps for these sequences 3) alignment of obtained sequences using examined algorithms 4) matching the quality of aligned sequences with sequences of reference genomes by more software. The time of computation was archived for the whole analysis. The seven programs were utilized, each based on different alignment algorithms, namely: ClustalO, ClustalW, Kalign, MAFFT, MUSCLE, Probcons and T-Coffee.Results: The result obtained in this study showed that the fastest is progressive algorithms such as Kalign or MUSCLE-FAST. Moreover, the iterative algorithms like MAFFT and MUSCLE revealed a higher quality of the alignment. The T-Coffee and Probcons programs were computational cost-effective; simultaneously, they were generating a medium-quality calculation in a relatively long time. The best quality of alignment was shown by iterative variants of the MAFFT program; however, the speed of the calculations was relatively low. The fastest algorithm was Kalign, making alignment much faster than the competitors, but achieving average results in the quality of the alignment. The average speed ratio concerning the quality of the analyzed algorithms was obtained by the progressive version of MAFFT, NS1.Conclusions: We conclude that the results of this study can be used to re-alignment of variant primers in new livestock genome releases

Evaluation of analytical protocols of alignment mapping tools using high throughput next-generation genome sequencing data

Background: Ever since the development of first next-generation genome sequencer (NGS) in 2005, there are rapid developments of high throughput next-generation genome sequencing (HT-NGS) techniques and tools used in genetics and genomics has become much more comfortable and cheaper. The result is the generation of a massive amount of data sets, requiring detailed analysis, which becomes impossible without the use of appropriate bioinformatics tools. One of the crucial steps in the analysis of NGS data is to map readings to a reference sequence. Although the dominance of Illumina synthesis by sequencing (SBS) technology has been noticeable in recent years, the choice of the tools is hampered and the variety of input data and reference genomes. Moreover, the tools used are crucial for result files and further analysis.Methods: The subject of this paper is the three most frequently used alignment mapping programs, which have functions to allow working with many platforms: BWA, Bowtie2 and SMALT. The task of the tested aligners is to match short sequences coming from NGS with reference sequences. The most popular: BWA and Bowtie2 use for this purpose the Burrows-Wheeler transformation and SMALT maps the sequences using hashing and dynamic programming. The presented paper aimed to compare the quality and efficiency of the alignment mapping programs under examination, due to three criteria: i) the quality of the compared sequences of different lengths and from different platforms; ii) coefficient of wrongly compared sequences; iii) the computational resources used.Results: By comparing the results of the mapping analyses for all the programs used, the least popular SMALT is the best. Obtaining the highest percentage of mapped readings for each platform and maintaining the lowest computational memory usage, turns out to be the most optimal choice.Conclusions: The results presented in this paper can be used to verify and rebuild data analysis pipelines from NGS based so far on other tools. We conclude that by using the tools under appropriate conditions, it is possible to improve the quality of the analyses, speed them up and reduce their cost

Nonunion of ulnar diaphysis after Monteggia fracture of a right forearm in a 55-year-old patient - Are all methods effective? Case report

Fractures of the forearm make up about 10-14% of all fractures. Monteggia lesions account for 1-6% of the forearm fractures. The eponym “Monteggia fracture” is a term used for fracture of ulnar proximal shaft with concomitant dislocation of the radial head in the proximal radioulnar joint [1]. Its clinical symptoms are: pain, edema, local sensitivity, friction between bone fragments, deformation of the limb, loss of function in elbow joint and the forearm. Radiographs in AP and lateral views of the entire forearm, with wrist and elbow joint, are mandatory for successful diagnosis [2]. There are four types of fractures in the Bado classification system of the Monteggia lesion [3]. All Monteggia fractures in adults require surgical procedure of open reduction and internal fixation as a method of choice [4]. Delayed bone adhesion, nonunion, synostosis, instability of the radial head, nerve damage and restriction of movement are main complications of surgical intervention. We present a case of a 55-year-old patient with Monteggia fracture of a right forearm with a complication of a nonunion of the ulnar shaft, despite undergoing surgical procedure of open reduction and internal fixation. We describe consecutive methods of treatment that resulted in complete bone adhesion. Nonunion typically occurs due to technical mistakes in initial surgical intervention. Application of the correct reparative technique with autogenous bone graft and compression plates allows to fully heal nonunion of the bone

CFD numerical modelling of a PV–TEG hybrid system cooled by air heat sink coupled with a single-phase inverter

This study presents full transient, three-dimensional numerical models of a PV–TEG hybrid module coupled with single-phase inverter by co-simulation. The influence of factors, such as wind speed, solar radiation intensity, or ambient temperature on the PV–TEG system, was also examined. The numerical model was implemented using Ansys software which accounted the phenomena of Thomson, Seebeck, and Joule’s heat place on the TEG system. Furthermore, its impact on total electrical efficiency was studied. The heat transfer surface of the passive heat sink and forced air circulation positively affected the total heat transfer, and therefore helped to maintain the electrical efficiency at a higher level. Simulation of the single-phase inverter with a PV–TEG system allows the determination of the power characteristics of the system in real time. The results of the study presented may provide a basis for performance optimization of a practical PV–TEG-inverter hybrid system co-design

Early, posttraumatic, frontal instability of the knee joint deriving from injured medial collateral ligament, after total knee arthroplasty, complicated by wound dehiscence and Clostridium difficile infection in a 70-year-old patient

Gonarthrosis is a joint disease in which a balance between regenerative and degenerative processes of articular cartilage is impaired. Its main symptoms are: pain, swelling, rigidity, function restraint as well as articular deformation [1]. It is estimated that about 40% of the knee joint degeneration is a consequence of ageing of the body. 60% of remaining cases of gonarthrosis is a result of excessive strain, contusion and injury. Patients with advanced arthrosis are qualified for total arthroplasty of the knee. Medial collateral ligament (MCL) is responsible for the medial stability of the knee joint, it prevents from valgus deformity and restraints external rotation of tibia relative to the femur. Injury, most often distorting the knee, may lead to straining as well as complete rupture of the MCL [2,3]. We present a case of a 70-year-old patient with MCL injury that happened three weeks after total knee arthroplasty, complicated by wound dehiscence. Insufficiency of the medial collateral ligament in our patient had an effect in longer healing process and rehabilitation. Main treatment options are: revision surgery with use of constrained implants and injured medial collateral ligament reconstruction. Constrained implants may have reduced longevity in some patients through aseptic loosening. Our patient underwent a MCL reconstruction. Reconstruction of MCL without revision arthroplasty has good results for injured MCL after total arthroplasty of the knee

Pilon fracture of the tibia with severe complications in a 42-year-old patient – case report.

Pilon type fractures of the distal tibia are among the most difficult injuries of the lower extremity. They occur due to the axial loading injury which drives the talus into the tibial plafond, mainly because of high energy traumas such as car accidents and falls, but may arise from low energy traumas also. Due to specific conditions in the area of the injury: where skin and subcutaneous tissue is delicate, soft tissues are usually severely damaged, it is crucial to choose the correct timing for surgical intervention. There are several surgical options regarding treatment of the pilon fractures, however treatment plan of pilon fractures has not yet been unified. Surgical methods include open reduction with internal fixation and external fixation. Main purpose of the treatment of pilon fractures are the preservation of length and restoration of the joint surfaces. Great risks for the successful treatment are skin and soft tissue infections, that occur quite commonly due to specific anatomy of the fractured area. Wound infection may have potentially catastrophic consequences. Here we present a case of our 42-year-old patient, with a pilon fracture of the tibia who suffered multiple complications due to obtained tauma as well as his concurrent diseases: diabetes, alcohol and nicotine abuse, also as a result of his lack of compliance with medical advice. Despite the complications that occurred, outcome of the overall treatment was satisfactory both to the patient as well as orthopedic team. This example shows that treatment method should be chosen wisely not only on the type of the fracture, but also with patient’s ability to comply with doctors’ recommendation

Comprehensive cardiac rehabilitation as the keystone in the secondary prevention of cardiovascular disease

Comprehensive cardiac rehabilitation (CR) is a mainstay of the secondary prevention of cardiovascular disease. In the European Society of Cardiology guidelines, comprehensive cardiovascular rehabilitation has the highest class of recommendation and level of evidence as an effective method for the treatment of patients with ST-segment elevation myocardial infarction, after myocardial revascularization, with chronic coronary syndrome, for CVD prevention in clinical practice, and in patients with heart failure (HF). This document presents an expert opinion of the Cardiac Rehabilitation and Exercise Physiology Section of the Polish Cardiac Society concerning the definition, goals, target population, organization of rehabilitation services, standard clinical indications and methods of implementation. Moreover, it describes psychosocial risk factors influencing the course of CR and secondary prevention of cardiovascular disease in patients undergoing CR. Comprehensive CR is as a process that should be implemented as soon as possible, continued without interruption, and consist of multiple stages. Moreover, it should be tailored to the individual clinical situation and should be accepted by the patient and their family, friends, and caregivers

Slavic beliefs in Poland. Outline of collective identity.

Celem pracy jest zarysowanie tożsamości zbiorowej dla grupy rodzimowierców działających na terenie Polski. Precyzując, rozważania dotyczą Rodzimowierstwa Słowiańskiego. W pierwszych rozdziałach czytelnik może zapoznać się ze strukturą rodzimej religii i historią ruchu rodzimowierczego. W następnym fragmencie pracy dotyczącym teorii oraz metodologii przeprowadzonych badań, zapoznać się można ze definicją tożsamości zbiorowej oraz z przebiegiem badań i użytych w nich technikach. Kolejna część służy przedstawieniu materiału zebranego podczas pracy i jego analizie. Pozwala to zestawić rozważania teoretyczne z praktyką i wysnuć wnioski na temat badanego problemu. W ostatniej części przedstawione zostało podsumowanie rozważań.The purpose of this work is to attempt to outline a group identity for a groups of believers in native Slavic beliefs. In the first chapters, the reader can become familiar with the structure of the native religion functioning in Poland and the history of that movement. Next part of the licentiate work is focused on theoretical issues and research methodology.The penultimate chapter is the interpretive part in which the analysis of field studies is approximated. This allowed to combine theoretical considerations with practice. The last chapter contains conclusions from previous analyzes