Repetitions in infinite palindrome-rich words

Rich words are characterized by containing the maximum possible number of distinct palindromes. Several characteristic properties of rich words have been studied; yet the analysis of repetitions in rich words still involves some interesting open problems. We address lower bounds on the repetition threshold of infinite rich words over 2 and 3-letter alphabets, and construct a candidate infinite rich word over the alphabet $\Sigma_2=\{0,1\}$ with a small critical exponent of $2+\sqrt{2}/2$. This represents the first progress on an open problem of Vesti from 2017.Comment: 12 page

Palindromic Decompositions with Gaps and Errors

Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient algorithms for the factorization of sequences into palindromes and maximal palindromes have been devised in recent years. We extend these studies by allowing gaps in decompositions and errors in palindromes, and also imposing a lower bound to the length of acceptable palindromes. We first present an algorithm for obtaining a palindromic decomposition of a string of length n with the minimal total gap length in time O(n log n * g) and space O(n g), where g is the number of allowed gaps in the decomposition. We then consider a decomposition of the string in maximal \delta-palindromes (i.e. palindromes with \delta errors under the edit or Hamming distance) and g allowed gaps. We present an algorithm to obtain such a decomposition with the minimal total gap length in time O(n (g + \delta)) and space O(n g).Comment: accepted to CSR 201

Activated MCTC mast cells infiltrate diseased lung areas in cystic fibrosis and idiopathic pulmonary fibrosis

<p>Abstract</p> <p>Background</p> <p>Although mast cells are regarded as important regulators of inflammation and tissue remodelling, their role in cystic fibrosis (CF) and idiopathic pulmonary fibrosis (IPF) has remained less studied. This study investigates the densities and phenotypes of mast cell populations in multiple lung compartments from patients with CF, IPF and never smoking controls.</p> <p>Methods</p> <p>Small airways, pulmonary vessels, and lung parenchyma were subjected to detailed immunohistochemical analyses using lungs from patients with CF (20 lung regions; 5 patients), IPF (21 regions; 7 patients) and controls (16 regions; 8 subjects). In each compartment the densities and distribution of MC_Tand MC_TCmast cell populations were studied as well as the mast cell expression of IL-6 and TGF-β.</p> <p>Results</p> <p>In the alveolar parenchyma in lungs from patients with CF, MC_TCnumbers increased in areas showing cellular inflammation or fibrosis compared to controls. Apart from an altered balance between MC_TCand MC_Tcells, mast cell in CF lungs showed elevated expression of IL-6. In CF, a decrease in total mast cell numbers was observed in small airways and pulmonary vessels. In patients with IPF, a significantly elevated MC_TCdensity was present in fibrotic areas of the alveolar parenchyma with increased mast cell expression of TGF-β. The total mast cell density was unchanged in small airways and decreased in pulmonary vessels in IPF. Both the density, as well as the percentage, of MC_TCcorrelated positively with the degree of fibrosis. The increased density of MC_TC, as well as MC_TCexpression of TGF-β, correlated negatively with patient lung function.</p> <p>Conclusions</p> <p>The present study reveals that altered mast cell populations, with increased numbers of MC_TCin diseased alveolar parenchyma, represents a significant component of the histopathology in CF and IPF. The mast cell alterations correlated to the degree of tissue remodelling and to lung function parameters. Further investigations of mast cells in these diseases may open for new therapeutic strategies.</p

Identification and in vitro Analysis of the GatD/MurT Enzyme-Complex Catalyzing Lipid II Amidation in Staphylococcus aureus

The peptidoglycan of Staphylococcus aureus is characterized by a high degree of crosslinking and almost completely lacks free carboxyl groups, due to amidation of the D-glutamic acid in the stem peptide. Amidation of peptidoglycan has been proposed to play a decisive role in polymerization of cell wall building blocks, correlating with the crosslinking of neighboring peptidoglycan stem peptides. Mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin. We identified the enzymes catalyzing the formation of D-glutamine in position 2 of the stem peptide. We provide biochemical evidence that the reaction is catalyzed by a glutamine amidotransferase-like protein and a Mur ligase homologue, encoded by SA1707 and SA1708, respectively. Both proteins, for which we propose the designation GatD and MurT, are required for amidation and appear to form a physically stable bi-enzyme complex. To investigate the reaction in vitro we purified recombinant GatD and MurT His-tag fusion proteins and their potential substrates, i.e. UDP-MurNAc-pentapeptide, as well as the membrane-bound cell wall precursors lipid I, lipid II and lipid II-Gly5. In vitro amidation occurred with all bactoprenol-bound intermediates, suggesting that in vivo lipid II and/or lipid II-Gly5 may be substrates for GatD/MurT. Inactivation of the GatD active site abolished lipid II amidation. Both, murT and gatD are organized in an operon and are essential genes of S. aureus. BLAST analysis revealed the presence of homologous transcriptional units in a number of gram-positive pathogens, e.g. Mycobacterium tuberculosis, Streptococcus pneumonia and Clostridium perfringens, all known to have a D-iso-glutamine containing PG. A less negatively charged PG reduces susceptibility towards defensins and may play a general role in innate immune signaling

Intraperitoneal drain placement and outcomes after elective colorectal surgery: international matched, prospective, cohort study

Despite current guidelines, intraperitoneal drain placement after elective colorectal surgery remains widespread. Drains were not associated with earlier detection of intraperitoneal collections, but were associated with prolonged hospital stay and increased risk of surgical-site infections.Background Many surgeons routinely place intraperitoneal drains after elective colorectal surgery. However, enhanced recovery after surgery guidelines recommend against their routine use owing to a lack of clear clinical benefit. This study aimed to describe international variation in intraperitoneal drain placement and the safety of this practice. Methods COMPASS (COMPlicAted intra-abdominal collectionS after colorectal Surgery) was a prospective, international, cohort study which enrolled consecutive adults undergoing elective colorectal surgery (February to March 2020). The primary outcome was the rate of intraperitoneal drain placement. Secondary outcomes included: rate and time to diagnosis of postoperative intraperitoneal collections; rate of surgical site infections (SSIs); time to discharge; and 30-day major postoperative complications (Clavien-Dindo grade at least III). After propensity score matching, multivariable logistic regression and Cox proportional hazards regression were used to estimate the independent association of the secondary outcomes with drain placement. Results Overall, 1805 patients from 22 countries were included (798 women, 44.2 per cent; median age 67.0 years). The drain insertion rate was 51.9 per cent (937 patients). After matching, drains were not associated with reduced rates (odds ratio (OR) 1.33, 95 per cent c.i. 0.79 to 2.23; P = 0.287) or earlier detection (hazard ratio (HR) 0.87, 0.33 to 2.31; P = 0.780) of collections. Although not associated with worse major postoperative complications (OR 1.09, 0.68 to 1.75; P = 0.709), drains were associated with delayed hospital discharge (HR 0.58, 0.52 to 0.66; P &lt; 0.001) and an increased risk of SSIs (OR 2.47, 1.50 to 4.05; P &lt; 0.001). Conclusion Intraperitoneal drain placement after elective colorectal surgery is not associated with earlier detection of postoperative collections, but prolongs hospital stay and increases SSI risk

ТРАНСПЛАНТАЦИЯ СЕРДЦА У ПАЦИЕНТКИ С ПОСТТРАВМАТИЧЕСКОЙ АНЕВРИЗМОЙ ЛЕГОЧНОЙ АРТЕРИИ

Right heart catheterization (RHC) should be performed on all candidates in preparation for listing for cardiac transplantation. Patient, 64 y. o., with chronic heart failure NYHA III class, had developed a rare complication while performing that procedure – a rupture of segmental branch of pulmonary artery (PA) with pulmonary haemorrhage. The episode of pulmonary bleeding was stopped conservatively without surgical management. There was a pseudoaneurysm formation of segmental branch of PA 2,7 × 2,8 cm with signs of thrombosis. Afterfi ve months the patient underwent heart transplantation without severe complications in perioperative period. No more recurrent episodes of pulmonary haemorrhage were identifi ed.Обязательной процедурой, выполняемой перед включением кандидата на трансплантацию сердца в лист ожидания, является катетеризация правых отделов сердца и легочной артерии (ЛА). У пациентки 64 летс хронической сердечной недостаточностью III функционального класса по NYHA при выполнении данной манипуляции возникло редкое осложнение – разрыв сегментарной ветви ЛА с развитием легочного кровотечения. На фоне комплексной интенсивной терапии эпизод легочного кровотечения был купирован, не потребовав хирургического лечения. Сформировалась ложная аневризма сегментарной ветви ЛА размерами 2,7 × 2,8 см с признаками тромбирования. Спустя пять месяцев пациентка перенесла трансплантацию сердца, периоперационный период протекал без развития тяжелых осложнений, повторных эпизодов легочного кровотечения зафиксировано не было

ШЕСТИЛЕТНИЙ ОПЫТ ТРАНСПЛАНТАЦИИ СЕРДЦА В ФГБУ «СЕВЕРО-ЗАПАДНЫЙ ФЕДЕРАЛЬНЫЙ МЕДИЦИНСКИЙ ИССЛЕДОВАТЕЛЬСКИЙ ЦЕНТР ИМЕНИ В.А. АЛМАЗОВА»

Aim. To estimate the results of 6-year experience of heart transplantation (HT) in Federal Almazov North-West Medical Research Centre. Methods. From 2010 to 2015 we have performed 65 HT. Mean age was 44.3 ± 14 years old (from 10 to 64 years old). We used biventricular assist device (BIVAD, Berlin Heart Excor) support in 7 heart transplant candidates before HT. 19 patients (29%) received thymoglobulin, whereas 46 patients (71%) had basiliximab to induce immunosuppression.Results. Extracorporeal membrane oxygenation machines were implanted in 5 patients (7.7%) after HT due to acute right ventricular failure. Suture annuloplasty (the Batista procedure) for tricuspid valve repair was carried out in 3 cases (4.6%). Venovenous hemodiafi ltration was used in 11 patients (16.9%). A total of 598 endomyocardial biopsies (EMB) were performed after HT. Evidence of cellular rejection (R1 and R2) was presented in 286 biopsies (48%). The 30-day in-hospital mortality rate was 3.1%. The 6-month survival rate after HT was 92%, 1-year – 91% and overall survival for the 6-year period of observation – 89.2%. Maximum observation period was 71 months.Conclusions. The 6-year experience of HT in our Center has shown a high level of survival. BIVAD Excor support can be effectively used as a «bridge» to HT. Prevention of graft loss due to acute rejection in heart transplant recipients can be achieved only through regular EMB monitoring. The rate of viral infection increased in 2 months after HT.Цель исследования. Оценить результаты трансплантаций сердца (ТС), выполненных в ФГБУ «Северо-Западный федеральный медицинский исследовательский центр имени В.А. Алмазова» за шесть лет.Материалы и методы. В период с 2010-го по 2015 год в Центре было выполнено 65 ТС. Средний возраст реципиентов составил 44,3 ± 14 лет (от 10 до 64 лет). В качестве «моста» к ТС у 7 пациентов перед пересадкой были имплантированы устройства вспомогательного кровообращения (УВК) Excor. Для индукции иммуносупрессивной терапии у 19 пациентов (29%) применялся антитимоцитарный иммуноглобулин, у 46 пациентов (71%) – базиликсимаб.Результаты. У 5 (7,7%) пациентов, в связи с тяжелой правожелудочковой недостаточностью, в раннем периоде после ТС была установлена система ЭКМО. У 3 (4,6%) больных ввиду развития трикуспидальной недостаточности была выполнена пластика трикуспидального клапана по Батиста. Проведение сеансов заместительной почечной терапии после ТС потребовалось у 11 (16,9%) реципиентов. Всего за шестилетний период наблюдения у всех пациентов было выполнено 598 эндомиокардиальных биопсий (ЭМБ). В 286 (48%) случаях диагностировано клеточное отторжение трансплантата стадии R1 или R2. 30-дневная госпитальная летальность составила 3,1% (2 пациента). Выживаемость в отдаленном периоде составила: через 6 месяцев – 92%, через 1 год – 91%, общая выживаемость за 6 лет наблюдения – 89%. Максимальный срок наблюдения – 71 месяц.Заключение. Шестилетний опыт ТС в нашем Центре показал высокий уровень выживаемости после операции. Имплантация УВК является «мостом» к ТС у больных с терминальной стадией ХСН. ЭМБ остается единственным эффективным методом диагностики острого отторжения трансплантата сердца. Через два месяца после ТС в структуре инфекционных осложнений увеличивается частота вирусной инфекции