DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop ...extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
Abstract Motivation Hi-C is gaining prominence as a method for mapping genome organization. With declining sequencing costs and a growing demand for higher-resolution data, efficient tools for ...processing Hi-C datasets at different resolutions are crucial. Over the past decade, the .hic and Cooler file formats have become the de-facto standard to store interaction matrices produced by Hi-C experiments in binary format. Interoperability issues make it unnecessarily difficult to convert between the two formats and to develop applications that can process each format natively. Results We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python and R bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication. Availability and implementation The hictk library, Python bindings and CLI tools are released under the MIT license as a multi-platform application available at github.com/paulsengroup/hictk. Pre-built binaries for Linux and macOS are available on bioconda. Python bindings for hictk are available on GitHub at github.com/paulsengroup/hictkpy, while R bindings are available on GitHub at github.com/paulsengroup/hictkR.
This study evaluates the incidence and clinical features and associated risk factors of delayed gastric emptying (DGE) after pancreaticoduodenectomy, employing the International Study Group of ...Pancreatic Surgery (ISGPS) consensus definition.
Demographic, pathological and surgical details for 260 consecutive patients who underwent pylorus-preserving pancreaticoduodenectomy at a single institution were analysed using univariate and multivariate models.
Postoperative complications occurred in 108 (41.5%) and DGE was diagnosed in 36 (13.8%) of 260 patients. Among the 36 DGE patients, 16 had grade A, 18 grade B and two grade C DGE. Resumption of a solid diet (P < 0.001), time to passage of stool (P= 0.002) and hospital discharge (P < 0.001) occurred later in DGE patients. The need for total parenteral nutrition was significantly higher in DGE grade B/C patients (P < 0.001). In the univariate analysis, abdominal collections (P≤ 0.001), pancreatic fistula (PF) grades B and C (P < 0.001), biliary fistula (P= 0.002), pulmonary complications (P < 0.001) and sepsis (P= 0.002) were associated with DGE. Only abdominal collections (P= 0.009), PF grade B/C (P < 0.001) and sepsis (P= 0.024) were associated with clinically relevant DGE. In the multivariate analysis, PF grade B/C (P= 0.004) and biliary fistula (P= 0.039) were independent risk factors for DGE.
The ISGPS classification and grading systems correlate well with the clinical course of DGE and are feasible for patient management. The principal risk factors for DGE seem to be pancreatic and biliary fistulas.
To study the application of a fast-track care protocol in colorectal surgery for deep infiltrating endometriosis. Bowel endometriosis is an infrequent but not rare condition that often needs ...intestinal surgery and imposes a high economic burden on society.
Prospective randomized trial (Canadian Task Force classification I).
Tertiary referral center.
Two hundred twenty-seven patients with preoperative evidence of bowel endometriosis.
We randomly assigned 227 patients with preoperative evidence of bowel endometriosis to a fast-track protocol (no preoperative bowel preparation, early restoration of diet, no postoperative antibiotics, and early postoperative mobilization) or conventional care for laparoscopic intestinal surgery. Randomization was obtained on a double-blind, date-based schedule, and all procedures were performed by a homogenous group of expert surgeons. Surgical outcomes and a health economic evaluation were assessed.
The primary outcome was hospital stay. Patient's well-being and intraoperative and postoperative complications up to 30 days after surgery were also assessed. Subsequently, direct medical costs were analyzed. Patients assigned to the fast-track protocol were discharged earlier (median 3 vs 7 days, p < .001) with no significant differences in subjective well-being (p = .55). Operative details, postoperative complications, and need of temporary ileostomy were similar (p = .89) between groups as well as readmission rates within 30 days (p = .69). The application of a fast-track protocol resulted in an overall significant reduction of costs (USD 6699 vs 8674, p < .01), and differences were more evident in cases of protective stoma (7652 vs 8793, p < .05) and surgery with postoperative complications (10 835 vs 14 005, p < .01).
The application of a fast-track care protocol for laparoscopy in cases of pelvic and intestinal endometriosis does not increase the risk of complications and ensures a reduction of medical costs.
A Gravimetria contemporânea vale-se de gravímetros para encontrar o módulo da aceleração gravitacional (g) de forma pontual na superfície terrestre. Esse trabalho considerou a pertinência da ...determinação de g no laboratório didático por intermédio do pêndulo, fazendo atenciosa análise dos fenômenos que afetam o dispositivo em oscilação, trazendo contribuições para o ensino da Física Clássica. A primeira, embora modesta, é eficaz, e propõe medir o período de oscilação empregando dois smartphones. A segunda, uma análise teórica acerca do efeito da amplitude angular correlacionada ao arrasto, sobre o período de oscilação do pêndulo. A terceira, refere-se à validação de duas equações que fornecem o valor de g em função da latitude e da altitude, com os dados gravimétricos disponíveis no site do IBGE. No campus Londrina da UTFPR, realizaram-se ensaios independentes, permitindo que se obtivesse o valor g U T F P R − L d = ( 9,7873 ± 0,0012 ) m ⋅ s − 2. Para a validação da metodologia e verificação da acuracidade, as duas equações que fornecem g em função da altitude e da latitude foram confrontadas com dados gravimétricos para definir qual seria mais adequada para gerar o valor de referência. Assim feito, verificou-se que o valor obtido experimentalmente divergia em 0,001 m ⋅ s − 2 (0,01%).
Contemporary gravimetry uses gravimeters to find the magnitude of gravitational acceleration (g) in a punctual manner on the Earth’s surface. This work considered the relevance of determining g in the didactic laboratory using the pendulum, making a careful analysis of the phenomena that affect the oscillating device, bringing contributions to the teaching of Classical Physics. The first, although modest, is effective, and proposes measuring the oscillation period using two smartphones. The second, a theoretical analysis of the effect of angular amplitude correlated to drag, on the period of pendulum oscillation. The third refers to the validation of two equations that provide the value of g like a function of latitude and altitude, with gravimetric data available on the IBGE website. At the Londrina campus of UTFPR, independent tests were carried out, allowing the value g U T F P R − L d = ( 9.7873 ± 0.0012 ) m ⋅ s − 2 to be obtained. To validate the methodology and verify its accuracy, the two equations that provide g as a function of altitude and latitude were compared with gravimetric data to define which would be most suitable for generating the reference value. This done, it was found that the experimentally obtained value differed by 0.001 m ⋅ s − 2 (0.01%).
Esse artigo descreve uma proposta de atividade prática para a graduação, envolvendo um estudo teórico-experimental sobre a influência do ar no movimento de queda dos corpos. Para isso, analisou-se a ...dinâmica do movimento de objetos esféricos em queda vertical no ar, considerando-se a força de arrasto, apreciando-se a relação entre um intervalo de tempo característico e o comportamento da velocidade e da aceleração, comparando-se a previsão do modelo teórico com os dados experimentais. Para a obtenção dos dados, realizou-se um ensaio utilizando-se de filmagem da queda com aparelho celular e posterior tratamento com o Tracker. Os resultados apontaram que o movimento de queda de um corpo esférico de isopor com diâmetro da ordem de dois centímetros serviria ao propósito, permitindo verificar-se a presença do arrasto inercial e a tendência a uma velocidade limite em uma queda inferior a três metros, em acordo com as previsões teóricas. Além disso, verificou-se não haver correlação entre o módulo da velocidade inicial com a magnitude da velocidade terminal, implicando que a transição ocorrida do regime viscoso para o inercial, nos primeiros instantes, não afetaria o comportamento da velocidade nos instantes seguintes. Palavras-chave: Ensino de Física, queda no ar, velocidade terminal, força de arrasto, resistência do ar, viscosidade.
This article describes a practical activity proposal for graduation, involving a theoretical and experimental study on the influence of air on the falling motion of bodies. For this, the dynamics of the movement of spherical objects in vertical fall in the air were analyzed, considering the drag force, appreciating the relationship between a characteristic time interval and the behavior of speed and acceleration, comparing the prediction of the theoretical model with the experimental data. To obtain the data, a test was performed using video footage of the fall with a cell phone and subsequent treatment with the Tracker. The results showed that the falling movement of a spherical styrofoam body with a diameter of the order of two centimeters would serve the purpose, allowing to verify the presence of inertial drag and the tendency to a limit speed in a fall of less than three meters, in according to theoretical predictions. In addition, it was found that there is no correlation between the initial velocity module and the magnitude of the terminal velocity, implying that the transition from the viscous to the inertial regime, in the first moments, would not affect the behavior of the velocity in the following moments.
No presente trabalho, apresenta-se uma proposta de atividade didática para estudantes de graduação dos cursos de Física e de Engenharia, visando a determinação do módulo de elasticidade do aço e do ...alumínio, empregando-se hastes constituídas por estes metais e um smartphone para se obterem os valores das frequências ressonantes dos harmônicos que se nelas estabelecem. A fundamentação teórica considerou a oscilação destas hastes submetidas a flexões simples, com extremos livres. Resolveu-se a equação da dinâmica do movimento para se obter as localizações dos nós, as frequências dos harmônicos, e a relação com o módulo de Young. Os ensaios práticos empregam técnicas de medida bastante simples, equipamentos altamente disponíveis e de muito baixo custo. Os resultados demonstraram a viabilidade da proposta que, além de explorar o ensino por meio de representações múltiplas, possui um forte apelo lúdico e sensorial, inclusive para estudantes com deficiência auditiva. Também há um viés de aplicabilidade para o ensino médio.
In the present work, a didactic activity proposal is presented for undergraduate students of Physics and Engineering courses, aiming at determining the elasticity module of steel and aluminum, using rods constituted by these metals and a smartphone to obtain the values of the resonant frequencies of the harmonics that are established in them. The theoretical foundation considered the oscillation of these rods submitted to simple flexions, with free ends. The motion dynamics equation was solved to obtain the locations of the nodes, the frequencies of the harmonics, and the relationship with the Young’s modulus. The practical tests employ simple measurement techniques, highly available equipment and very low cost. The results demonstrate the feasibility of the proposal, which, in addition to exploring teaching through multiple representations, has a strong playful and sensory appeal, including for students with hearing disabilities. There is also an applicability bias for high school.
To present the outcome of laparoscopic resection for bowel endometriosis.
In the last 12 months, numerous articles have been published to demonstrate and underline the efficiency and feasibility of ...the laparoscopic approach in the treatment of bowel endometriosis.
Endometriosis is a common condition that can affect women in their reproductive age. It can have an intestinal involvement, and when it occurs rectum and rectosigmoid junction are the most frequent sites; other lesser frequent sites are the appendix, the distal ileum, and the cecum. It is widely agreed that surgical management is the primary treatment for symptomatic bowel endometriosis. Laparoscopic bowel resection has become increasingly popular because it represents a well tolerated and feasible technique.
Background
Bowel endometriosis is the most common pattern of Deep Endometriosis (DE). Arising from the posterior portion of the cervix and spreading to the recto-vaginal septum, utero-sacral and ...parametrial ligaments could lead to a distortion of normal pelvic anatomy, causing pain and infertility. Hormonal therapy is the first-line treatment in non-symptomatic patient. Conversely, laparoscopic surgical treatment has to be considered when symptoms relief are not optimal or with signs of bowel occlusion.
Methods
Retrospective experience of consecutive series of patients who referred to a third-level referral center with suspected bowel DE and failure of multiple medical treatments. After an intraoperative evaluation of nodule size with a rectal shaving of its external portion, patients underwent radical DE eradication with concomitant disc excision in rectal nodules < 3 cm with no signs of substantial full-thickness infiltration.
Results
A total of 371 patients were considered eligible for analysis, with a median age of 37 years. The median operative time of was 180 min, with an estimated blood loss of 100 mL and a median diameter of removed rectal nodule of 25 mm. Early postoperative procedure-related complications were 47 cases of acute rectal bleeding (12.7%), that were managed by rectal endoscopy, 3 bowel anastomotic dehiscence (0.8%), 8 hemoperitoneum (2.2%) and 3 ureteral fistula (0.8%). 22 patients experienced postoperative hyperpyrexia (5.9%), while 17 women underwent transient bladder deficiency (4.6%). Median follow-up was 60 months with a bowel recurrence rate of 2.2%. There was an improvement of all symptoms in the immediate postoperative follow-up (
p
< 0.0001). Among all patients with childbearing desire, the pregnancy rate found was 42.2% and was obtained by in vitro fertilization (IVF) techniques in 32% of cases.
Conclusions
Laparoscopic disc excision for bowel endometriosis is an effective surgical treatment in selected residual rectal nodules < 3.0 cm. The concomitant radical DE excision contributes to a significant improvement of symptoms with an acceptable complications’ rate.
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