Structural polymorphism of the HIV-1 leader region explored by computational methods

Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations, branched (BMH) and ‘linearized’ (LDI) and switch between them to achieve different functionality. In this study we computationally explored in detail, with our massively parallel genetic algorithm (MPGAfold), the propensity of 13 HIV-1 5′-UTRs to fold into the BMH and the LDI conformation types. Besides the BMH conformations these results predict the existence of two functionally equivalent types of LDI conformations. One is similar to what has been shown in vitro to exist in HIV-1 LAI, the other is a novel conformation exemplified by HIV-1 MAL long-distance interactions. These novel MPGAfold results are further corroborated by a consensus probability matrix algorithm applied to a set of 155 HIV-1 sequences. We also have determined in detail the impact of various strain mutations, domain sizes and folds of elongating sequences simulating folding during transcription on HIV-1 RNA secondary structure folding dynamics

Permafrost Base Degradation : Characteristics and Unknown Thread With Specific Example From Hornsund, Svalbard

Permafrost degradation is one of the most pressing issues in the modern cryosphere related to climate change. Most attention is paid to the degradation of the top of the active permafrost associated with contemporary climate. This is the most popular issue because in the subsurface part of it there is usually the greatest accumulation of ground ice in direct relation to the changes taking place. The melting of ground ice is the cause of the greatest changes related to subsidence and other mass-wasting processes. The degradation of the subsurface permafrost layer is also responsible for the increased emission of CO2 and methane. However, this is not a fully comprehensive look at the issue of permafrost degradation, because depending on its thickness, changes in its thermal properties may occur more or less intensively throughout its entire profile, also reaching the base of permafrost. These changes can degrade permafrost throughout its profile. The article presents the basic principles of permafrost degradation in its overall approach. Both the melting of the ground ice and the thermal degradation of permafrost, as manifested in an increase in its temperature in part or all of the permafrost profile, are discussed. However, special attention is paid to the degradation characteristics from the permafrost base. In the case of moderately thick and warm permafrost in the zone of its sporadic and discontinuous occurrence, this type of degradation may particularly contribute to its disappearance, and surficial consequences of such degradation may be more serious than we expect on the basis of available research and data now. A special case of such degradation is the permafrost located in the coastal zone in the vicinity of the Hornsund Spitsbergen, where a multidirectional thermal impact is noted, also causing similar degradation of permafrost: from the top, side and bottom. Especially the degradation of permafrost from the permafrost base upwards is an entirely new issue in considering the evolution of permafrost due to climate change. Due to the difficulties in its detection, this process may contribute to the threats that are difficult to estimate in the areas of discontinuous and sporadic permafrost

Results of endovascular treatment of iliac and femoral symptomatic lesions. Identification of re-intervention risk factors

Introduction. The aim of the study was to assess a presence of peripheral arterial disease risk factors in patients with symptomatic femoral and iliac lesions treated with use of Jaguar and Supera nitinol stents and to estimate potential relation between these factors and reintervention rate. Material and methods. The study group consisted of 60 patients between 46 and 85 years of age who presented with typical symptoms of intermittent claudication or critical limb ischemia and underwent percuta­neous transluminal angioplasty with stenting. We examined and divided group into two subgroups — patients who experienced or did not experience need of reintervention in treated lesion. Results. During the follow-up 24 (40%) of patients underwent reintervention in treated artery due to re­current symptoms of disease. Need of target lesion revascularization occurred more frequent in patients with hypertension (OR = 2.5), patient older than 68 (OR = 1.75) and smokers (OR = 1.75). Patency of all three arteries below knee protected from reintervention. Conclusions. Jaguar and Supera self-expanding nitinol stents has several advantages and its use were char­acterized by high procedural success and moderate frequency of reintervention correlated to some clinical findings like hypertension. Further studies are necessary to estimate factors disturbing and interfering with long-term patency.Introduction. The aim of the study was to assess a presence of peripheral arterial disease risk factors in patients with symptomatic femoral and iliac lesions treated with use of Jaguar and Supera nitinol stents and to estimate potential relation between these factors or some angiographical conditions and reintervention rate. Material and methods. The study group consisted of 60 patients between 46 and 85 years of age who presented with typical symptoms of intermittent claudication or critical limb ischemia and underwent percutaneous transluminal angioplasty with stenting using Supera or Jaguar self-expanding nitinol stent. We examined and divided group into two subgroups – patients who experienced or didn’t experience need of reintervention in treated lesion.Results. In 33 patients (55%) nitinol stent Jaguar and in 27 patients (45%) Supera were implanted. During the follow-up 24 of patients (40%) underwent reintervention in treated artery due to recurrent symptoms of disease. Need of target lesion revascularization occurred more frequent in patients with hypertension (OR=2,5), patient older than 68 (OR=1,75) and smokers (OR=1,75). Patency of all three arteries below knee protected from reintervention. Diabetes mellitus type 2, chronic kidney disease, kind or size of implanted stent and antiplatelet therapy model didn’t determine a need of reintervention. Conclusions. Jaguar and Supera self-expanding nitinol stents has several andvantages and its use were characterized by high procedural success and moderate frequency of reintervention correlated to some clinical findings like hypertension. Further studies are necessary to estimate factors disturbing and interfering with long-term patency

Efficacy of videothoracoscopic talc pleurodesis and intrapleural administration of Vibramicin in palliative treatment of neoplasmatic pleural effusion - a comparative study

Wstęp. U wielu pacjentów z pierwotnym rakiem płuca lub przerzutami innych nowotworów do płuc występuje nawracający wysięk opłucnowy, który znacznie zaburza komfort życia w schyłkowej fazie choroby. Celem niniejszej pracy było porównanie skuteczności 2 metod leczenia paliatywnego prowadzących do zamierzonej sklerotyzacji obu listków opłucnej, zapobiegającej nawrotowi wysięku. Materiał i metody. W grupie I (n = 45) zastosowano sproszkowany talk, który podawano doopłucnowo w czasie wideotorakoskopii. W grupie II (n = 30) wprowadzano doopłucnowy dren i po opróżnieniu opłucnej oraz rozprężeniu płuca kilkakrotnie podawano przez niego Vibramycynę. Wyniki i wniosek. Obie metody postępowania były bardzo skuteczne. Ograniczyły gromadzenie się wysięku u 65% chorych w 3-miesięcznym okresie obserwacji. W grupie I odsetek nawrotów był jednak wyraźnie mniejszy (22% vs. 33%), wskazując na większą trwałość pleurodezy uzyskanej za pomocą wideotorakoskopowego talkowania opłucnej.Background. Recurrent pleural effusion is a common finding in patients with primary or metastatic pulmonary neoplasm which worsen their quality of life at the end-stage disease. The aim of our study was the assessment of two comparable methods of pleurodesis.Material and methods. In group I (n = 45) videothoracoscopic approach was used for evacuation of the fluid and talc poudrage. In group II (n = 30) pleural effusion was evacuated with chest tubing. When the lung was fully expanded chest tubes were used for rinsing of pleural space with Vibramycin. Results and conclusion. Both methods showed comparable efficacy and 65% of patients at the third month of follow-up were free from pleural effusion. However, in group I (videothoracoscopic talc poudrage) recurrence rate of effusion was markedly lower than in group II (Vibramycin in pleural rinsing) (22% vs. 33%). We conclude that the use of videothoracoscopic talc poudrage provides longer and better results of pleurodesis than administration of Vibramycin to the pleural space

Polysaccharides and mucin 5AC (MUC5AC) expression in gallbladder mucosa of young patients with gallstones as evaluated by spatial visualization and quantification

The study aimed at examination of tissue expression of polysaccharides and secretory mucin 5AC (MUC5AC)in young patients (up to 25 years of age) with a symptomatic gallstones. For comparison, patients most frequently subjectedto cholecystectomy were studied, i.e. patients of approximately 50 years of age with the same diagnosis. In quantitativestudies on tissue expression of both mucus components, the modern technique of spatial visualization was applied for thefirst time. Application of the technique permitted to demonstrate significant positive relationships between expression ofglycoproteins (immunocytochemical ABC technique for detection of MUC5AC) and expression of sugar components inmucus (PAS technique) and to confirm suitability of the technique for quantitative appraisal of both histochemical andimmunocytochemical reactions. An even higher expression of polysaccharides in the entire mucosa and of MUC5AC wasdetected in gallbladder epithelium of 50-year-old patients, as compared to young patients with symptomatic gallstones. Inthe young patients, expression of polysaccharides correlated with inflammatory activity (grading), width of gallbladder walland PLT level in peripheral blood. A significantly higher expression of polysaccharides in gallbladder epithelium wasdemonstrated in young patients admitted in the emergency mode to the hospital. These correlations in young patients maysuggest a role of both mucus components in pathogenesis of cholelithiasis in this age group. A quantitative appraisal ofmucus component expression in the two parts of gallbladder mucosa (epithelium vs. entire mucosa) using spatial visualizationtechnique permitted to more accurately compare production of glycoproteins and of polysaccharides in patients withcholelithiasis and to demonstrate additional correlations of a potential clinical significance

Polysaccharides and mucin 5AC (MUC5AC) expression in gallbladder mucosa of young patients with gallstones as evaluated by spatial visualization and quantification.

The study aimed at examination of tissue expression of polysaccharides and secretory mucin 5AC (MUC5AC) in young patients (up to 25 years of age) with a symptomatic gallstones. For comparison, patients most frequently subjected to cholecystectomy were studied, i.e. patients of approximately 50 years of age with the same diagnosis. In quantitative studies on tissue expression of both mucus components, the modern technique of spatial visualization was applied for the first time. Application of the technique permitted to demonstrate significant positive relationships between expression of glycoproteins (immunocytochemical ABC technique for detection of MUC5AC) and expression of sugar components in mucus (PAS technique) and to confirm suitability of the technique for quantitative appraisal of both histochemical and immunocytochemical reactions. An even higher expression of polysaccharides in the entire mucosa and of MUC5AC was detected in gallbladder epithelium of 50-year-old patients, as compared to young patients with symptomatic gallstones. In the young patients, expression of polysaccharides correlated with inflammatory activity (grading), width of gallbladder wall and PLT level in peripheral blood. A significantly higher expression of polysaccharides in gallbladder epithelium was demonstrated in young patients admitted in the emergency mode to the hospital. These correlations in young patients may suggest a role of both mucus components in pathogenesis of cholelithiasis in this age group. A quantitative appraisal of mucus component expression in the two parts of gallbladder mucosa (epithelium vs. entire mucosa) using spatial visualization technique permitted to more accurately compare production of glycoproteins and of polysaccharides in patients with cholelithiasis and to demonstrate additional correlations of a potential clinical significance

Influence of cardiac resynchronization therapy on oxidative stress markers in patients with chronic heart failure

Background: The aim of the study was to assess changes of substances of oxidative stress in patients treated with cardiac resynchronization therapy (CRT).Methods: The study comprised 51 patients with median age of 66 years. The presence, severity, and changes of oxidative stress during CRT were assessed and expressed as malondialdehyde (MDA) concentration in plasma or in red blood cells. Antioxidant activity was assessed by the activity of catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GPx) in red blood cells. The concentration and activities were analyzed directly prior to implantation, 2–5 days after the procedure and after 6 months. Follow-up (6 months) included clinical, echocardiographic and implanted device assessments.Results: During the follow-up, 14% patients died. The median percentage of biventricular pacing was 99.29%. After 6 months 88% of patients improved NYHA, 12% remained as non-responders. Left ventricular ejection fraction increased from median 21.5% to 29% (p < 0.05). Left ventricular end-diastolic diameter decreased significantly from a median of 69.5 mm to 63 mm (p < 0.05). After a 6-month study, MDA plasma concentration and the activity levels of each antioxidant enzymes (CAT, SOD, GPx) showed a statistically significant reduction (p < 0.05). Changes concerning MDA concentrations in red blood cells remained statistically insignificant.Conclusions: Resynchronization effect oxidative stress by reducing plasma concentration of MDA, CAT, SOD and GPX

Tissue expression of S100 proteins in gallbladder mucosa of the patients with calculous cholecystitis

 Proteins of S100 group, produced by phagocytes represent endogenous activators of innate immune responses. Role of these proteins in the etiopathogenesis of cholelithiasis remains unknown. The studies aimed at the morphometric evaluation of S100A8 and S100A9 protein expression in gallbladder mucosa in patients with acute and chronic calculous cholecystitis (n = 71). The presence of proteins was detected by immunohistochemistry while quantitative analysis employed the spatial visualization technique. We found the immunopositive expression of the two studied S100 proteins in neutrophils and monocytes/macrophages of the gallbladder’s wall and a higher expression in acute cholecystitis. Quantitative study revealed higher immunoexpression of S100A9 over S100A8 in both studied groups of patients. Moreover, a reciprocal linear relationship between the expression of the studied proteins and a positive correlation between expression of either S100A8 or S100A9 and inflammatory activity (grading) in the gallbladder wall were found. The expression of S100A8 protein in the chronic cholecystitis group and in older patients correlated with leukocytosis, which suggests the role of S100A8 particularly at the chronic stage of cholecystitis. The obtained results indicated close relationship between S100A8 and S100A9 proteins in their proinflammatory functions. The increased expression of only one of them can be recognized as a useful index of local inflammatory activity in calculous cholecystitis.

Nowy pacjent, stare problemy? : kontekst diagnozowania uzależnienia od internetu

Pacjenci, ich rodziny i społeczeństwo coraz częściej „umawiają się”, żeby różnorodne problemowe funkcjonowanie adolescentów konceptualizować jako uzależnienie od internetu. W artykule umieszczono to zjawisko w kulturowym kontekście rosnącego wpływu mediów cyfrowych na procesy rozwojowe dojrzewających pokoleń, których przedstawiciele bywają określani jako „cyfrowi tubylcy”. Używanie internetu u tej grupy współdefiniuje sposób uczestniczenia w rodzinie, sposób budowania więzi z otoczeniem społecznym, sposób udziału w rytuałach codzienności oraz korzystania z psychoterapii. Pociąga to za sobą nowe wyzwania dla praktyków w zakresie tworzenia rzeczywistości terapeutycznej oraz definiowania „normalnego” korzystania z internetu. Artykuł stawia pytania o użyteczność „prostych” diagnoz, wywodzących się z języka terapii uzależnień, wcześniej adresowanego do uzależnień od substancji czy uzależnień behawioralnych. Co tak postawiona „diagnoza” wnosi do myślenia o problematyce pacjentów adolescencyjnych z trudnościami relacyjnymi, różnorodną psychopatologią, nieoptymalnym funkcjonowaniem w rodzinie? Czy nie jest nadmiernym uproszczeniem, niosącym ryzyko zbyt redukcjonistycznego spojrzenia na zjawiska złożone, wieloaspektowe, niejednoznaczne? Może przeciwnie, poszerza możliwości rozumienia tej trudnej grupy pacjentów i wyposaża praktyków w nowe narzędzia? Autorzy sygnalizują możliwości pogłębionego rozumienia uzależnienia od internetu płynące z uwzględniania myślenia systemowego, funkcji objawu nadużywania internetu w rodzinie, roli, jaką odgrywa w jej narracjach, miejsca, jakie zajmuje w jej dążeniach socjoekonomicznych

Sequential algorithms for DNA sequencing

Abstract Reconstruction of the original DNA sequence in sequencing by hybridization approach (SBH) due to a large number of possible combinations requires a computational support. In the paper, a new method of sequencing has been proposed. Two algorithms based on its idea have been implemented and tested: for the case of an ideal hybridization experiment (complete data) and for more general case, when some data are missing, like in the real experiment. Authentic DNA sequences have been used for testing. A parallel version of the second algorithm has been also implemented and tested. The quality of the reconstruction is satisfactory for the library of oligunucleotides of length 9, and 100, 200 and 300-bp long sequences. A way to a further decrease of the computation time is also suggested