RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a 'Structural View of Biology.'

EMDataBank unified data resource for 3DEM.

Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.

Healthcare-Associated Infections after Lower Urinary Tract Endoscopic Surgery: Analysis of Risk Factors, Associated Microorganisms and Patterns of Antibiotic Resistance.

OBJECTIVES: To review the incidence of healthcare-associated infections/urinary tract infection (UTI), risk factors, microorganisms isolated and antibiotic resistances in patients who underwent lower urinary tract endoscopic surgery (LUTES) in a tertiary care hospital. METHODS: A prospective observational study was carried out including 1,498 patients who undergo LUTES. Patients with and without UTI after surgery were compared. We analysed infection incidence, risk factors, microorganisms isolated and antibiotic resistances. RESULTS: Postoperative UTI incidence was 4.7%. Risk factors found: higher American Society of Anesthesiologists classification (OR 2.82; 95% CI 1.8-4.5; p < 0.00), immunosuppression (OR 2.89; 95% CI 1.2-7.2; p = 0.01), indwelling urinary catheter prior admission (OR 2.6; 95% CI 1.6-4.2; p < 0.00) and postoperative catheterization longer than 2 days (OR 1.74; 95% CI 1.7-4.3; p < 0.00). Transurethral resection of the bladder (TURB) had the highest infection rates (5.5%). Microorganisms isolated were Pseudomonas aeruginosa (23.5%), Escherichia coli (17.6%), Klebsiella pneumoniae and Enterococcus spp (11.8%). Resistance rates for flourquinolones varied between 28 and 80%, and Carbapenem-resistant Enterobacteriaceae rose up 20%. CONCLUSIONS: Low percentage of UTI after endoscopic surgery was registered. TURB was the procedure with highest infection rate. Pseudomonas aeruginosa stands out as the most frequently isolated microorganism. Patient comorbidities, previous urinary catheter and postoperative catheter were identified as risk factors.

Urinary Infections in Patients with Catheters in the Upper Urinary Tract: Microbiological Study.

BACKGROUND: Infections related to catheters in the upper urinary tract (CUUT) are associated with specific characteristics. METHODS: A prospective observational study was carried out from 2012 to 2015 to evaluate infections in patients with CUUT. RESULTS: A total of 209 infections were included (99 with double-J, 81 with nephrostomy, and 29 with internal/external nephroureteral stents). Among nephrostomy tube carriers, the most frequently isolated microorganisms were Pseudomonas and Enterococcus. In those with an internal/external nephroureteral stent, Klebsiella was the most common, and 57.1% were extended-spectrum beta-lactamase-producing Klebsiella. In double-J carriers, Escherichia coli and Enterococcus were the most common microorganisms. Multiple-drug resistance (MDR) microorganisms were isolated in 28.6, 47.1, and 58.3% of patients with double-J, nephrostomy, and internal-external nephroureteral stents. A percutaneous CUUT (p = 0.005) and immunosuppression (p = 0.034) were risk factors for MDR microorganisms. CONCLUSIONS: Non-E. coli bacteria are commonly isolated in patients with CUUT. MDR microorganisms are frequent, mainly in percutaneous approach or immunosuppression.

Progress and remaining challenges for cancer control in Latin America and the Caribbean.

Cancer is one of the leading causes of mortality worldwide, and an increasing threat in low-income and middle-income countries. Our findings in the 2013 Commission in The Lancet Oncology showed several discrepancies between the cancer landscape in Latin America and more developed countries. We reported that funding for health care was a small percentage of national gross domestic product and the percentage of health-care funds diverted to cancer care was even lower. Funds, insurance coverage, doctors, health-care workers, resources, and equipment were also very inequitably distributed between and within countries. We reported that a scarcity of cancer registries hampered the design of credible cancer plans, including initiatives for primary prevention. When we were commissioned by The Lancet Oncology to write an update to our report, we were sceptical that we would uncover much change. To our surprise and gratification much progress has been made in this short time. We are pleased to highlight structural reforms in health-care systems, new programmes for disenfranchised populations, expansion of cancer registries and cancer plans, and implementation of policies to improve primary cancer prevention.

Extended-Spectrum Beta-Lactamase-Producing Bacteria in a Urology Ward: Epidemiology, Risk Factors and Antimicrobial Susceptibility Patterns.

INTRODUCTION: Our aim was to describe the incidence and risk factors associated with extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and their resistance rate in a urological ward. MATERIAL AND METHODS: We carried out a prospective observational study from November 2011 to December 2014, reviewing healthcare-associated infections (HAIs) in our department. We evaluated the infections caused by ESBL-producing Enterobacteriaceae. RESULTS: The incidence of HAIs in our urology ward was 6.8%. Enterobacteriaceae including Escherichia coli (24.9%), Klebsiella spp. (12.1%), Enterobacter spp. (5.9%), Morganella spp. (1.5%), Proteus spp. (1.5%), and Citrobacter spp. (1.5%) represented 47.4% of the isolated pathogens. The percentage of ESBL-producing Enterobacteriaceae was 26.4. Risk factors associated with a higher incidence of ESBL-producing bacteria were prior urinary tract infection (UTI; p < 0.001), hypertension (p = 0.042), immunosuppression (p = 0.004), and urinary stone (p = 0.027). The multivariable analysis confirmed prior UTI, immunosuppression and urinary stone as risk factors. ESBL-producing strains showed resistance rates of 85.3% for fluoroquinolones and 11.8% for carbapenems. Moreover, 16.7% of ESBL-Klebsiella were resistant to carbapenems. CONCLUSIONS: ESBL-producing enterobacteria are associated with higher cross resistance to antibiotics such as quinolones. Higher resistance rates are reported in ESBL-producing Klebsiella. Among patients admitted in a urology ward, risk factors for ESBL-producing strains were previous UTI, immunosuppression, and urinary stone.

EMDataBank.org: unified data resource for CryoEM.

Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) and Protein Data Bank (PDB), and facilitates use of EM structural data of macromolecules and macromolecular complexes by the wider scientific community.

Attitudes and beliefs of Argentinian medical oncologists regarding palliative care referral.

INTRODUCTION: Local evidence suggests insufficient access to palliative care (PC) for advanced cancer patients. The objective was to investigate the attitudes and beliefs of Argentinian medical oncologists regarding PC referral of their patients. METHODS: All medical oncologists listed in the main national Clinical Oncology Associations (N = 831) were invited to participate in a telephone survey. RESULTS: Fifty nine percent (N = 489) completed the survey. Most reported being informed about the scopes of PC (83%) and having accessible PC service/specialists (71%). However, 53% did not work collaboratively, and 55% exceptionally or never referred their patients. Oncologists who usually referred their patients did so mainly due to uncontrolled pain (67%) or absence of curative treatment (48%). Only 19% supported early-referral criteria. Those who exceptionally referred their patients argued that PC was not meaningful/beneficial/a priority (78%) or that they preferred to handle the patient's problems by themselves (55%). End-of-life care (33%) and improvement in quality of life (32%) were stated as primary benefits of PC for cancer patients. Addressing psychological aspects was considered the least important item (2%). Having an accessible PC service (P = 0.002) and being well informed about PC (P = 0.008) were associated with frequent referral. Having =10 years or >30 years from graduation were associated with exceptional or no referral (P = 0.012 and 0.001, respectively). DISCUSSION: Oncologists report awareness of the potential advantages of PC and have accessible PC services, but rarely refer patients. They mainly use late-referral criteria. Younger and older age are negatively associated with referral. More research is needed to improve the referral rate and timing of cancer patients to PC.

Introducción: La evidencia local sugiere un acceso insuficiente a los cuidados paliativos (CP) para los pacientes con cáncer avanzado. El objetivo fue investigar las actitudes y creencias de médicos oncólogos argentinos respecto de la derivación de sus pacientes a CP. Métodos: Todos los médicos oncólogos registrados en las principales Asociaciones Nacionales de Oncología Clínica (N = 831) fueron invitados a participar en una encuesta telefónica. Resultados: El 59% (N = 489) completó la encuesta. La mayoría informó estar informado sobre los alcances de CP (83%) y tener especialistas/servicios de CP acce sibles (71%). Sin embargo, el 53% no trabajaba de forma colaborativa y el 55% excepcionalmente o nunca derivaba a sus pacientes. Los oncólogos que habitualmente derivan a sus pacientes lo hacen principalmente por dolor no controlado (67%) o ausencia de tratamiento curativo (48%). Solo el 19% mencionó criterios de derivación temprana. Aquellos que excepcionalmente derivan a sus pacientes argumentaron que los CP no era significativos, beneficiosos o prioritarios (78%) o que preferían manejar los problemas del paciente por sí mismos (55%). La atención al final de la vida (33 %) y la mejora de la calidad de vida (32 %) se señalaron como los principales beneficios de los CP para los pacientes con cáncer. El abordaje de los aspectos psicológicos fue el ítem menos señalado (2%). Tener un servicio de CP accesible (P= 0,002) y estar bien informado sobre CP (P = 0,008) se asociaron con la derivación frecuente. Tener =10 años o >30 años desde la graduación se asoció con una derivación excepcional o nula (P = 0,012 y 0,001, respectivamente). Discusión: Los oncólogos refieren conocer las ventajas potenciales de los CP y tienen servicios de CP accesibles, pero rara vez derivan pacientes. Utilizan principalmente criterios de derivación tardía. Las edades más jóvenes y mayores se asocian negativamente con la derivación. Se necesita más investigación para mejorar la tasa y momento de derivación de los pacientes con cáncer a CP.

Current Scenario of Clinical Cancer Research in Latin America and the Caribbean.

In Latin America and the Caribbean (LAC), progress has been made in some national and regional cancer control initiatives, which have proved useful in reducing diagnostic and treatment initiation delays. However, there are still significant gaps, including a lack of oncology clinical trials. In this article, we will introduce the current status of the region's clinical research in cancer, with a special focus on academic cancer research groups and investigator-initiated research (IIR) initiatives. Investigators in LAC have strived to improve cancer research despite drawbacks and difficulties in funding, regulatory timelines, and a skilled workforce. Progress has been observed in the representation of this region in clinical trial development and conduct, as well as in scientific productivity. However, most oncology trials in the region have been sponsored by pharmaceutical companies, highlighting the need for increased funding from governments and private foundations. Improvements in obtaining and/or strengthening the LAC cancer research group's financing will provide opportunities to address cancer therapies and management shortcomings specific to the region. Furthermore, by including this large, ethnic, and genetically diverse population in the world's research agenda, one may bridge the gap in knowledge regarding the applicability of results of clinical trials now mainly conducted in populations from the Northern Hemisphere.

Enhanced validation of small-molecule ligands and carbohydrates in the Protein Data Bank.

The Worldwide Protein Data Bank (wwPDB) has provided validation reports based on recommendations from community Validation Task Forces for structures in the PDB since 2013. To further enhance validation of small molecules as recommended from the 2016 Ligand Validation Workshop, wwPDB, Global Phasing Ltd., and the Noguchi Institute, recently formed a public/private partnership to incorporate some of their software tools into the wwPDB validation package. Augmented wwPDB validation report features include: two-dimensional (2D) diagrams of small-molecule ligands and carbohydrates, highlighting geometric validation outcomes; 2D topological diagrams of oligosaccharides present in branched entities generated using 2D Symbol Nomenclature for Glycan representation; and views of 3D electron density maps for ligands and carbohydrates, illustrating the goodness-of-fit between the atomic structure and experimental data (X-ray crystallographic structures only). These improvements will impact confidence in ligand conformation and ligand-macromolecular interactions that will aid in understanding biochemical function and contribute to small-molecule drug discovery.

Impact of the COVID-19 Pandemic on Oncology Clinical Research in Latin America (LACOG 0420).

PURPOSE: COVID-19 has affected cancer care worldwide. Clinical trials are an important alternative for the treatment of oncologic patients, especially in Latin America, where trials can be the only opportunity for some of them to access novel and, sometimes, standard treatments. METHODS: This was a cross-sectional study, in which a 22-question survey regarding the impact of the COVID-19 pandemic on oncology clinical trials was sent to 350 representatives of research programs in selected Latin American institutions, members of the Latin American Cooperative Oncology Group. RESULTS: There were 90 research centers participating in the survey, with 70 of them from Brazil. The majority were partly private or fully private (n = 77; 85.6%) and had confirmed COVID-19 cases at the institution (n = 57; 63.3%). Accruals were suspended at least for some studies in 80% (n = 72) of the responses, mostly because of sponsors' decision. Clinical trials' routine was affected by medical visits cancelation, reduction of patients' attendance, reduction of other specialties' availability, and/or alterations on follow-up processes. Formal COVID-19 mitigation policies were adopted in 96.7% of the centers, including remote monitoring and remote site initiation visits, telemedicine visits, reduction of research team workdays or home office, special consent procedures, shipment of oral drugs directly to patients' home, and increase in outpatient diagnostic studies. Importantly, some of these changes were suggested to be part of future oncology clinical trials' routine, particularly the ones regarding remote methods, such as telemedicine. CONCLUSION: To our knowledge, this was the first survey to evaluate the impact of COVID-19 on Latin American oncology clinical trials. The results are consistent with surveys from other world regions. These findings may endorse improvements in clinical trials' processes and management in the postpandemic period.

Attitudes and beliefs of argentinian medical oncologists regarding palliative care referral / Actitudes y creencias de los médicos oncólogos argentinos sobre la derivación a cuidados paliativos

Abstract Introduction: Local evidence suggests insufficient access to palliative care (PC) for advanced cancer patients. The objective was to investigate the attitudes and beliefs of Argentinian medical oncologists regarding PC referral of their patients. Methods: All medical oncologists listed in the main national Clinical Oncology Associations (N = 831) were invited to participate in a telephone survey. Results: Fifty nine percent (N = 489) completed the survey. Most reported being informed about the scopes of PC (83%) and having accessible PC service/specialists (71%). However, 53% did not work collaboratively, and 55% exceptionally or never referred their patients. Oncologists who usually referred their patients did so mainly due to uncontrolled pain (67%) or absence of curative treatment (48%). Only 19% supported early-referral criteria. Those who exception ally referred their patients argued that PC was not meaningful/beneficial/a priority (78%) or that they preferred to handle the patient's problems by themselves (55%). End-of-life care (33%) and improvement in quality of life (32%) were stated as primary benefits of PC for cancer patients. Addressing psychological aspects was consid ered the least important item (2%). Having an accessible PC service (P = 0.002) and being well informed about PC (P = 0.008) were associated with frequent referral. Having ≤10 years or >30 years from graduation were associated with exceptional or no referral (P = 0.012 and 0.001, respectively). Discussion: Oncologists report awareness of the potential advantages of PC and have accessible PC services, but rarely refer patients. They mainly use late-referral criteria. Younger and older age are negatively associated with referral. More research is needed to improve the referral rate and timing of cancer patients to PC.

Resumen Introducción: La evidencia local sugiere un acceso insuficiente a los cuidados paliativos (CP) para los pacien tes con cáncer avanzado. El objetivo fue investigar las actitudes y creencias de médicos oncólogos argentinos respecto de la derivación de sus pacientes a CP. Métodos: Todos los médicos oncólogos registrados en las principales Asociaciones Nacionales de Oncología Clínica (N = 831) fueron invitados a participar en una encuesta telefónica. Resultados: El 59% (N = 489) completó la encuesta. La mayoría informó estar informado sobre los alcances de CP (83%) y tener especialistas/servicios de CP acce sibles (71%). Sin embargo, el 53% no trabajaba de forma colaborativa y el 55% excepcionalmente o nunca derivaba a sus pacientes. Los oncólogos que habi tualmente derivan a sus pacientes lo hacen principalmente por dolor no controlado (67%) o ausencia de trata miento curativo (48%). Solo el 19% mencionó criterios de derivación temprana. Aquellos que excepcionalmente derivan a sus pacientes argumentaron que los CP no era significativos, beneficiosos o prioritarios (78%) o que preferían manejar los problemas del paciente por sí mismos (55%). La atención al final de la vida (33 %) y la mejora de la calidad de vida (32 %) se señalaron como los principales beneficios de los CP para los pacientes con cáncer. El abordaje de los aspectos psicológicos fue el ítem menos señalado (2%). Tener un servicio de CP accesible (P= 0,002) y estar bien informado sobre CP (P = 0,008) se asociaron con la derivación frecuente. Tener ≤10 años o >30 años desde la graduación se asoció con una derivación excepcional o nula (P = 0,012 y 0,001, respectivamente). Discusión: Los oncólogos refieren conocer las ventajas potenciales de los CP y tienen servicios de CP accesibles, pero rara vez derivan pacientes. Utilizan principalmente criterios de derivación tardía. Las edades más jóvenes y mayores se asocian negativamente con la derivación. Se necesita más investigación para mejorar la tasa y momento de derivación de los pacientes con cáncer a CP.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Database URL: https://www.wwpdb.org/.

Prospective study analyzing risk factors and characteristics of healthcare-associated infections in a Urology ward.

PURPOSE: Healthcare-associated infections (HAIs) in urological patients have special features due to specific risk factors. Our objective was to evaluate the characteristics and risk factors for HAIs in patients hospitalized in a Urology ward. MATERIALS AND METHODS: We evaluated prospectively, from 2012 to 2015, the incidence, types and risk factor for HAIs, microbiological and resistance patterns. RESULTS: The incidence of HAIs was 6.3%. The most common types were urinary infections (70.5%) and surgical site infections (22.1%). Univariate analysis showed an increased risk of HAIs among patients with American Society of Anesthesiologists physical status classification system III-IV (odds ratio [OR], 1.39; p<0.001), immunosuppression (OR, 1.80; p=0.013), previous urinary infection (OR, 4.46; p<0,001), and urinary catheter before admission (OR, 1.74; p<0.001). The surgical procedures with the highest incidence of HAIs were radical cystectomy (54.2%) and renal surgery (8.7%). The most frequently isolated microorganisms were Escherichia coli (25.1%), Enterococcus spp. (17.5%), Klebsiella spp. (13.5%) and Pseudomonas aeruginosa (12.3%). Enterococcus sp was the most common microorganism after radical cystectomy and in surgical site infections, E. coli showed resistance rates of 53.5% for fluoroquinolones, 9.3% for amikacin. The percentage of extended-spectrum betalactamase producing E. coli was 24.7%. Klebsiella spp. showed resistance rates of 47.8% for fluoroquinolones, 7.1% for amikacin and 4.3% for carbapenems. Enterococcus spp showed resistance rates of 1.7% for vancomycin and; P. aeruginosa of 33.3% for carbapenems and 26.2% for amikacin. CONCLUSIONS: Comorbidities, previous urinary infections, and urinary catheter are risk factors for HAIs. The microorganisms most commonly isolated were E. coli, Enterococcus and P. aeruginosa. Prospective monitoring may decrease the incidence of infections.

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive, has been developed as a global collaboration by the worldwide PDB (wwPDB) partners. This new system was designed to ensure that the wwPDB could meet the evolving archiving requirements of the scientific community over the coming decades. OneDep unifies deposition, biocuration, and validation pipelines across all wwPDB, EMDB, and BMRB deposition sites with improved focus on data quality and completeness in these archives, while supporting growth in the number of depositions and increases in their average size and complexity. In this paper, we describe the design, functional operation, and supporting infrastructure of the OneDep system, and provide initial performance assessments.

Effects of parenteral hydration in terminally ill cancer patients: a preliminary study.

PURPOSE: Most patients with cancer develop decreased oral intake and dehydration before death. This study aimed to determine the effect of parenteral hydration on overall symptom control in terminally ill cancer patients with dehydration. PATIENTS AND METHODS: Patients with clinical evidence of mild to moderate dehydration and a liquid oral intake less than 1,000 mL/day were randomly assigned to receive either parenteral hydration with 1,000 mL (treatment group) or placebo with 100 mL normal saline administered over 4 hours for 2 days. Patients were evaluated for target symptoms (hallucinations, myoclonus, fatigue, and sedation), global well-being, and overall benefit. RESULTS: Twenty-seven patients randomly assigned to the treatment group had improvement in 53 (73%) of their 73 target symptoms versus 33 (49%) of 67 target symptoms in the placebo group (n=22; P = .005). Fifteen (83%) of 18 and 15 (83%) of 18 patients had improved myoclonus and sedation after hydration versus eight (47%) of 17 and five (33%) of 15 patients after placebo (P = .035 and P = .005, respectively). There were no significant differences of improvement in hallucinations or fatigue between groups. When blinded to treatment, patients (17 [63%] of 77) and investigators (20 [74%] of 27) perceived hydration as effective compared with placebo in nine (41%) of 22 patients (P = .78) and 12 (54%) of 22 investigators (P = .15), respectively. The intensity of pain and swelling at the injection site were not significantly different between groups. CONCLUSION: Parenteral hydration decreased symptoms of dehydration in terminally ill cancer patients who had decreased fluid intake. Hydration was well tolerated, and a placebo effect was observed. Studies with larger samples and a longer follow-up period are justified.

Nebulized versus subcutaneous morphine for patients with cancer dyspnea: a preliminary study.

This study compared the effects of nebulized versus subcutaneous morphine on the intensity of dyspnea in cancer patients. Patients with a resting dyspnea intensity > or =3 on a 0-10 scale (0=no dyspnea, 10=worst possible dyspnea) who received regular oral or parenteral opioids were included. On day 1, patients received either subcutaneous (SC) morphine plus nebulized placebo or nebulized morphine plus SC placebo. On day 2, a crossover was made. Dyspnea intensity, side effects, and blinded preference of treatment were assessed. Eleven patients completed the study. Dyspnea decreased from a median of 5 (range, 3-8) to 3 (range, 0-7) after SC morphine (P=0.025) and from 4 (range, 3-9) to 2 (range, 0-9) after nebulized morphine (P=0.007). There was no significant difference in dyspnea intensity between nebulized and subcutaneous morphine at 60 minutes. Unfortunately, due to limited sample size, there was insufficient power to rule out a significant difference between both routes of administration. Nebulized morphine offered dyspnea relief similar to that of SC morphine. Larger randomized controlled trials in patients with both continuous dyspnea and earlier stages of dyspnea are justified.

[Healthcare-associated urinary tract infections in patients with a urinary catheter: Risk factors, microbiological characteristics and patterns of antibiotic resistance]. / INFECCIONES DEL TRACTO URINARIO DE ORIGEN HOSPITALARIO EN PACIENTES PORTADORES DE CATÉTER URINARIO: FACTORES DE RIESGO, CARACTERÍSTICAS MICROBIOLÓGICAS Y RESISTENCIAS A ANTIBIÓTICOS.

OBJECTIVE: Catheter-associated urinary tract infections (CAUTIs) are the most common nosocomial acquired infections, with high resistance rates. CAUTIs are a potentially severe complication in hospitalized patients and imply higher costs. Our aim was to analyze the characteristics of CAUTIs in our Urology department. METHODS: Between November 2011 and October 2013, a prospective observational study was carried out analyzing the incidence of healthcare-associated urinary tract infections in patients admitted to the urology ward with an indwelling urinary catheter. Furthermore, we evaluated associated risks factors and comorbidities such as urinary catheter at the time of admission or urological surgery during the hospitalization. We also presented our results regarding the microbiological characteristics and patterns of resistance to antibiotics in patients with CAUTI admitted in our service. RESULTS: The incidence of CAUTI was 8.2% (189/2283 patients who had urinary catheter). Mean age was 67.4±14.26 years, 90.2% underwent a surgical procedure (p<0.001), 14.8% had a urinary stone (p=0.058) and 46% had a urinary catheter before admission (p<0.001). The most commonly isolated pathogens were Escherichia coli (22.6%), Enterococcus (21.9%) and Pseudomonas aeruginosa (13.9%). E.coli showed resistance rates of 41.9% for quinolones, 33.3% of them produced extended spectrum Β-lactamase (ESBL). P.aeruginosa showed resistance rates of 42.1% for quinolones and 21.1% for carbapenems. CONCLUSIONS: Healthcare-associated CAUTI in patients hospitalized in a urology ward are related to risks factors such as having a urinary catheter before admission and undergoing a surgical procedure. Moreover, CAUTIs have higher incidence of pathogens with antibiotic resistances and non-common pathogens such as Enterococcus spp.

Dexamethasone in addition to metoclopramide for chronic nausea in patients with advanced cancer: a randomized controlled trial.

Chronic nausea occurs in most patients with advanced cancer. This study was done to assess the antiemetic effects of dexamethasone in patients with chronic nausea refractory to metoclopramide. Secondary outcomes included appetite, fatigue, and pain. Fifty-one patients who had nausea (> or = 3/10 on a 0-10 scale) for > or = 2 weeks despite 48 hours of oral metoclopramide therapy (40-60 mg/day) were enrolled. Patients received 20 mg/day dexamethasone (DM) orally (n = 25) or placebo (n = 26) for severe nausea in addition to metoclopramide (60 mg/day orally). At baseline the mean nausea intensity ratings in the DM and placebo groups were 8.0 and 7.4. At Day 8 they were 2.1 and 2.0, respectively. At Day 3 and Day 8, the mean difference in nausea intensity for the DM and placebo groups was 4.5 and 2.9 (P = 0.16) and 5.9 and 5.7 (P = 0.85), respectively. Improvement in appetite and fatigue were observed on Day 3 and Day 8 in both groups as compared with the baseline. Pain, vomiting, well-being, and quality of life remained unchanged in both groups at both times. We conclude that DM was not superior to placebo in the management of chronic nausea in our patients with advanced cancer.

Chemical annotation of small and peptide-like molecules at the Protein Data Bank.

Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org.