Stmol: A component for building interactive molecular visualizations within streamlit web-applications.

Streamlit is an open-source Python coding framework for building web-applications or "web-apps" and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists.

Autograft Anatomic, Double-Bundle Posterior Cruciate Ligament Reconstruction.

It is well known that the posterior cruciate ligament (PCL) is the main stabilizer to posterior tibial translation in the knee. Anatomic double-bundle reconstruction has recently been proposed to best restore posterior and rotational tibial instability, especially compared with a single-bundle PCL reconstruction (PCLR). Most publications in the peer-reviewed literature on double-bundle PCLR have used allografts. However, in many countries, allografts are not available. This Technical Note describes an all-autograft arthroscopic technique for PCLR using the quadriceps and semitendinosus tendons.

Mortality-related factors in gastroschisis - a Jamaican perspective.

OBJECTIVE: To determine the mortality rate of patients treated with gastroschisis at a Jamaican pediatric hospital, and to identify factors that contribute significantly to mortality. METHODS: Eighty-five patients were treated with gastroschisis between November 1, 2006 and November 30, 2015. Of these, 80 records were recovered and reviewed retrospectively. Records were analyzed for maternal and patient characteristics, and details of the clinical course. Death during admission was the primary outcome measure. RESULTS: 63 of the 80 patients died during admission, giving a mortality rate of 78.8%. Sepsis was the main cause of death (82.4%). 27 patients (33.8%) had complicated gastroschisis (necrosis, perforation and/or atresia), all of whom died. Only preterm gestational age, complicated gastroschisis, and the lack of parenteral nutrition were found to be statistically associated with increased mortality. CONCLUSION: Our mortality rate is higher than those quoted in high-income countries, and correlates to those found in low- to middle-income countries. Mortality in our cohort was significantly associated with prematurity, complicated gastroschisis, and the lack of parenteral nutrition. Efforts to improve outcome must focus on improving antenatal care, establishing transfer protocols, and optimizing nutrition for all patients with gastroschisis. STUDY TYPE: Prognostic/Retrospective Study LEVEL OF EVIDENCE: Level II.

Anatomy and biomechanics of the medial side of the knee and their surgical implications.

In order to reconstruct the medial knee to restore the original biomechanical function of its ligamentous structures, a thorough understanding of its anatomic placement and relationship with surrounding structures is required. To restore the knee to normal kinematics, the diagnosis and surgical approach have to be aligned, to successfully reconstruct the area of injury. Three important ligaments maintain primary medial knee stability: the superficial medial collateral ligament, posterior oblique ligament, and deep medial collateral ligament. It is important not to exclude the assistance that other ligaments of the medial knee provide, including support of patellar stability by the medial patellofemoral ligament and multiligamentous hamstring tendon attachments. Valgus gapping and medial knee stability is accounted for collectively by every primary medial knee stabilizing structure. The following will review the principal medial knee anatomic and biomechanical properties.

Assessment of urinary metals following exposure to a large vegetative fire, New Mexico, 2000.

INTRODUCTION: In May 2000, a vegetative fire burned 47,000 acres in northern New Mexico, including 7500 acres of land administered by the Los Alamos National Laboratory. We evaluated potential human exposures from the fire. METHODS: We surveyed two populations (firefighters and the general population) in four cities for urine heavy metal concentrations. Reference concentrations were based on the Third National Health and Nutrition Examination Survey (NHANES III). Multivariate linear regression assessed the association of urinary metal concentrations with smoke exposure. We also performed isotopic analysis of uranium and cesium on a subset of specimens. RESULTS: A total of 92 firefighters and 135 nonfirefighters participated. In both populations, urinary nickel, cesium, chromium, and uranium concentrations were greater than expected compared with NHANES III reference values. No values required immediate medical follow-up. Regression analysis demonstrated that for National Guard members, arsenic and cadmium levels were significantly related to smoke exposure, and for firefighters, cesium and arsenic levels were significantly related to exposure; however, only for cesium in National Guard members was this association in the positive direction. Isotopic analysis demonstrated that the cesium and uranium were naturally occurring. CONCLUSIONS: Some people had spot urine metal concentrations above nationally derived reference values, and values for some metals were associated with smoke exposure. These associations had little public health or clinical importance. Studies of exposures resulting from vegetative fires are difficult, and careful consideration should be given to the technical and communication processes at the outset of a fire exposure investigation. Recommendations for future investigations include testing as soon as possible during or after a fire, and early clinical consultation with a medical toxicologist.

Sinus node dysfunction and atrial tachycardia after the Fontan procedure: The scope of the problem.

Similar to other atrial baffling procedures, the Fontan procedure exposes patients to ongoing morbidity and mortality. The development of the bradycardia-tachycardia syndrome can have adverse effects on already-marginal hemodynamics and ventricular function. Patients with Fontan physiology and sinus node dysfunction can be managed with antibradycardic pacemakers. Atrial arrhythmias after "completion Fontan" are difficult to treat and usually require either antiarrhythmic agents, antitachycardic pacemakers, or radiofrequency catheter ablation of the re-entrant circuit. Successful treatment of atrial flutter occurs in only 50% to 70% of patients. There is a high recurrence rate of atrial flutter with any of the accepted management strategies. Copyright 1998 by W.B. Saunders Company

Economic evaluation of respiratory syncytial virus infection in Canadian children: a Pediatric Investigators Collaborative Network on Infections in Canada (PICNIC) study.

OBJECTIVES: To quantify the cost and distribution of health care resources consumed annually in management of Canadian children from birth to 4 years of age with respiratory syncytial virus (RSV) infection. STUDY DESIGN: Estimates of direct medical expenditures (in 1993 U.S. dollars) were collected from a prospective cohort study of hospitalized children with RSV and from national and provincial databases. RESULTS: The annual cost of RSV-associated illness was almost $18 million. The largest component of direct expenditures (62%) was for inpatient care for the estimated 0.7% of all infected children ill enough to require admission. Physician fees comprised only 4% of inpatient expenses. Expenditures for ambulatory patients accounted for 38% of direct costs. CONCLUSIONS: The greatest reductions in the economic cost of RSV infections will be found in interventions that reduce duration of or prevent hospital stay. Costs for management of RSV infection in children in the Canadian health care system are considerably less than charges reported in the United States.

Pediatric Investigators Collaborative Network on Infections in Canada (PICNIC) study of admission and management variation in patients hospitalized with respiratory syncytial viral lower respiratory tract infection.

OBJECTIVE: To describe differences in patients hospitalized with respiratory syncytial virus (RSV) lower respiratory tract infection (LRI) at nine Canadian tertiary care hospitals. In addition, this study describes the variation in use of drug and other interventions. METHODS: Data on patients hospitalized with RSV LRI and their outcomes were prospectively collected. Demographic data were obtained on enrollment by center study nurses. Data recorded daily included clinical assessment, oxygen saturation determination, and interventions (bronchodilators, steroids, ribavirin, antibiotics, intensive care, and mechanical ventilation) received during the day. Patients were divided into those with underlying diseases including congenital heart disease, chronic lung disease, immunodeficiency, or multiple congenital anomalies and those who were previously healthy. Mean RSV-associated length of stay and the proportion of patients receiving each intervention in each group were determined by hospital. RESULTS: A total of 1516 patients were enrolled at nine hospitals during January 1 to June 30, 1993, and January 1 to April 30, 1994. Significant differences were observed among hospitals in the proportion of patients with underlying disease, postnatal age less than 6 weeks, hypoxia, and pulmonary infiltrate on chest radiograph. The mean length of stay varied among hospitals from 8.6 to 11.8 days and 4.6 to 6.7 days in compromised and previously healthy patients, respectively. Except for receipt of bronchodilators, compromised patients were significantly more likely to receive interventions than previously healthy patients. There was variation among hospitals in receipt of most interventions in compromised and previously healthy patients. This variation was statistically significant for previously healthy patients but not statistically significant in those with underlying disease, because the numbers of patients in the latter group were much smaller. The magnitude of the variation for each intervention, however, was not different between those with underlying disease compared with previously healthy patients. CONCLUSION: Differences exist among tertiary pediatric hospitals in the nature of the patients admitted with RSV LRI. Variation occurred in the use of five interventions among the hospitals, regardless of whether the patient had underlying illness or was previously healthy. Given their current widespread use, high cost, and potential side effects, randomized clinical trials are needed to determine the efficacy of different drug treatments used to treat infants hospitalized with RSV.

Bronchial hyperreactivity in cystic fibrosis and asthma.

We studied 113 patients with CF and compared their responsiveness to inhaled methacholine to that of 50 asthmatic children and 26 normal children. Positive responses to MCh occurred in 51% of the patients with CF and 98% of those with asthma. There was a significant correlation between a positive response to MCh in CF and poor pulmonary function. There was no relationship between allergic rhinitis or positive allergen skin tests and a positive MCh response. Dose-response curves and time course to MCh challenge differed in CF and asthma. Bronchial hyperreactivity is thus common in CF but is different from that in asthma.