CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations.

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.

Colorectal cancer risk information presented by a nonphysician assistant does not increase screening rates.

OBJECTIVE: To determine the effectiveness of presenting individualized colorectal cancer (CRC) risk information for increasing CRC screening rates in primary care patients at above-average risk of CRC. DESIGN: Randomized controlled trial. SETTING: Georgia Regents University in Augusta-an academic family medicine clinic in the southeastern United States. PARTICIPANTS: Outpatients (50 to 70 years of age) scheduled for routine visits in the family medicine clinic who were determined to be at above-average risk of CRC. INTERVENTIONS: Individualized CRC risk information calculated from the Your Disease Risk tool compared with a standard CRC screening handout. MAIN OUTCOME MEASURES: Intention to complete CRC screening. Secondary measures included the proportions of subjects completing fecal occult blood tests, flexible sigmoidoscopy, and colonoscopy. RESULTS: A total of 1147 consecutive records were reviewed to determine eligibility. Overall, 210 (37.7%) of 557 eligible participants were randomized to receive either individualized CRC risk information (prepared by a research assistant) or a standard CRC screening handout. The intervention group had a mean (SD) age of 55.7 (4.8) years and the control group had a mean (SD) age of 55.6 (4.6) years. Two-thirds of the participants in each group were female. The intervention group and the control group were matched by race (P = .40). There was no significant difference between groups for intention to complete CRC screening (P = .58). Overall, 26.7% of the intervention participants and 27.7% of the control participants completed 1 or more CRC screening tests (P = .66). CONCLUSION: Presentation of individualized CRC risk information by a nonphysician assistant as a decision aid did not result in higher CRC screening rates in primary care patients compared with presentation of general CRC screening information. Future research is needed to determine if physician presentation of CRC risk information would result in increased screening rates compared with research assistant presentation.

Nonalcoholic fatty liver disease: diagnosis and management.

Nonalcoholic fatty liver disease is characterized by excessive fat accumulation in the liver (hepatic steatosis). Nonalcoholic steatohepatitis is characterized by steatosis, liver cell injury, and inflammation. The mechanism of nonalcoholic fatty liver disease is unknown but involves the development of insulin resistance, steatosis, inflammatory cytokines, and oxidative stress. Nonalcoholic fatty liver disease is associated with physical inactivity, obesity, and metabolic syndrome. Screening is not recommended in the general population. The diagnosis is usually made after an incidental discovery of unexplained elevation of liver enzyme levels or when steatosis is noted on imaging (e.g., ultrasonography). Patients are often asymptomatic and the physical examination is often unremarkable. No single laboratory test is diagnostic, but tests of liver function, tests for metabolic syndrome, and tests to exclude other causes of abnormal liver enzyme levels are routinely performed. Imaging studies, such as ultrasonography, computed tomography, and magnetic resonance imaging, can assess hepatic fat, measure liver and spleen size, and exclude other diseases. Liver biopsy remains the criterion standard for the diagnosis of nonalcoholic steatohepatitis. Noninvasive tests are available and may reduce the need for liver biopsy. A healthy diet, weight loss, and exercise are first-line therapeutic measures to reduce insulin resistance. There is insufficient evidence to support bariatric surgery, metformin, thiazolidinediones, bile acids, or antioxidant supplements for the treatment of nonalcoholic fatty liver disease. The long-term prognosis is not associated with an increased risk of all-cause mortality, cardiovascular disease, cancer, or liver disease.

Diagnosis and management of upper gastrointestinal bleeding.

Upper gastrointestinal bleeding causes significant morbidity and mortality in the United States, and has been associated with increasing nonsteroidal anti-inflammatory drug use and the high prevalence of Helicobacter pylori infection in patients with peptic ulcer bleeding. Rapid assessment and resuscitation should precede the diagnostic evaluation in unstable patients with severe bleeding. Risk stratification is based on clinical assessment and endoscopic findings. Early upper endoscopy (within 24 hours of presentation) is recommended in most patients because it confirms the diagnosis and allows for targeted endoscopic treatment, including epinephrine injection, thermocoagulation, application of clips, and banding. Endoscopic therapy results in reduced morbidity, hospital stays, risk of recurrent bleeding, and need for surgery. Although administration of proton pump inhibitors does not decrease mortality, risk of rebleeding, or need for surgery, it reduces stigmata of recent hemorrhage and the need for endoscopic therapy. Despite successful endoscopic therapy, rebleeding can occur in 10 to 20 percent of patients; a second attempt at endoscopic therapy is recommended in these patients. Arteriography with embolization or surgery may be needed if there is persistent and severe bleeding.

Diagnosis and management of IBS in adults.

Irritable bowel syndrome is defined as abdominal discomfort or pain associated with altered bowel habits for at least three days per month in the previous three months, with the absence of organic disease. In North America, the prevalence of irritable bowel syndrome is 5 to 10 percent with peak prevalence from 20 to 39 years of age. Abdominal pain is the most common symptom and often is described as a cramping sensation. The absence of abdominal pain essentially excludes irritable bowel syndrome. Other common symptoms include diarrhea, constipation, or alternating diarrhea and constipation. The goals of treatment are symptom relief and improved quality of life. Exercise, antibiotics, antispasmodics, peppermint oil, and probiotics appear to improve symptoms. Over-the-counter laxatives and antidiarrheals may improve stool frequency but not pain. Treatment with antidepressants and psychological therapies are also effective for improving symptoms compared with usual care. Lubiprostone is effective for the treatment of constipation-predominant irritable bowel syndrome, and alosetron (restrictions for use apply in the United States) and tegaserod (available only for emergency use in the United States) are approved for patients with severe symptoms in whom conventional therapy has been ineffective.

Acute-on-chronic liver failure: extracorporeal liver assist devices.

PURPOSE OF REVIEW: Acute-on-chronic liver failure (ACLF), a syndrome precipitated by acute liver injury in patients with advanced cirrhosis, is associated with multiorgan dysfunction and high rates of mortality. Liver support systems have been developed in an attempt to improve survival of patients with ACLF by providing a bridge until recovery of the native liver function. RECENT FINDINGS: Nonbiological devices such as molecular adsorbent recirculating system (MARS) and fractionated plasma separation and adsorption (Prometheus) are effective in improving severe hepatic encephalopathy and cholestasis, have good safety and tolerability profiles and are frequently employed in patients with ACLD; however, randomized controlled trials (RCTs) failed to show improvement in survival. Biologic devices that incorporate hepatic cells in bioreactors are also under development. Recent data from pilot studies suggested improvement in survival rates in some groups of patients with ACLF; however, their effect on patient survival in RCT is still unknown. SUMMARY: Liver support systems are safe and well tolerated when used in management of patients with ACLF. Their use should continue in controlled clinical trials to explore their role in bridging patients to liver transplantation or recovery in well defined patient groups.

Face and construct validity of a computer-based virtual reality simulator for ERCP.

BACKGROUND: Currently, little evidence supports computer-based simulation for ERCP training. OBJECTIVE: To determine face and construct validity of a computer-based simulator for ERCP and assess its perceived utility as a training tool. DESIGN: Novice and expert endoscopists completed 2 simulated ERCP cases by using the GI Mentor II. SETTING: Virtual Education and Surgical Simulation Laboratory, Medical College of Georgia. MAIN OUTCOME MEASUREMENTS: Outcomes included times to complete the procedure, reach the papilla, and use fluoroscopy; attempts to cannulate the papilla, pancreatic duct, and common bile duct; and number of contrast injections and complications. Subjects assessed simulator graphics, procedural accuracy, difficulty, haptics, overall realism, and training potential. RESULTS: Only when performance data from cases A and B were combined did the GI Mentor II differentiate novices and experts based on times to complete the procedure, reach the papilla, and use fluoroscopy. Across skill levels, overall opinions were similar regarding graphics (moderately realistic), accuracy (similar to clinical ERCP), difficulty (similar to clinical ERCP), overall realism (moderately realistic), and haptics. Most participants (92%) claimed that the simulator has definite training potential or should be required for training. LIMITATIONS: Small sample size, single institution. CONCLUSIONS: The GI Mentor II demonstrated construct validity for ERCP based on select metrics. Most subjects thought that the simulated graphics, procedural accuracy, and overall realism exhibit face validity. Subjects deemed it a useful training tool. Study repetition involving more participants and cases may help confirm results and establish the simulator's ability to differentiate skill levels based on ERCP-specific metrics.

Hepatitis B: diagnosis and treatment.

Although an estimated 1 million persons in the United States are chronically infected with hepatitis B virus, the prevalence of hepatitis B has declined since the implementation of a national vaccination program. Hepatitis B virus is transmitted in blood and secretions. Acute infection may cause nonspecific symptoms, such as fatigue, poor appetite, nausea, vomiting, abdominal pain, low-grade fever, jaundice, and dark urine; and clinical signs, such as hepatomegaly and splenomegaly. Fewer than 5 percent of adults acutely infected with hepatitis B virus progress to chronic infection. The diagnosis of hepatitis B virus infection requires the evaluation of the patient's blood for hepatitis B surface antigen, hepatitis B surface antibody, and hepatitis B core antibody. The goals of treatment for chronic hepatitis B virus infection are to reduce inflammation of the liver and to prevent complications by suppressing viral replication. Treatment options include pegylated interferon alfa-2a administered subcutaneously or oral antiviral agents (nucleotide reverse transcriptase inhibitors). Persons with chronic hepatitis B virus infection should be monitored for disease activity with liver enzyme tests and hepatitis B virus DNA levels; considered for liver biopsy; and entered into a surveillance program for hepatocellular carcinoma.

Hepatitis C: diagnosis and treatment.

Hepatitis C, a common chronic bloodborne infection, is found in approximately 2 percent of adults in the United States. Chronic infection is associated with serious morbidity and mortality (e.g., cirrhosis, hepatocellular carcinoma). Testing for hepatitis C is recommended for at-risk populations, and confirmatory testing includes quantification of virus by polymerase chain reaction. The U.S. Preventive Services Task Force recommends against routine screening for hepatitis C virus infection in asymptomatic adults who are not at increased risk of infection (general population). It found insufficient evidence to recommend for or against routine screening in adults at high risk of infection. Current therapy for chronic hepatitis C virus includes pegylated interferon and ribavirin. Therapy is based on factors that predict sustained virologic response, and the goal of therapy is to slow or halt progression of fibrosis and prevent the development of cirrhosis. In the future, multidrug regimens in combination with current therapies may be developed. Patients with chronic hepatitis C virus infection should be advised to abstain from alcohol use. Currently, there is no vaccine available to prevent hepatitis C virus infection; however, persons infected with hepatitis C virus should be vaccinated for hepatitis A and B. The American Association for the Study of Liver Diseases recommends ultrasound surveillance for hepatocellular carcinoma in persons with chronic hepatitis C virus infection and cirrhosis.

The current state of proteomics in GI oncology.

Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.

Hydrogen peroxide improves the visibility of ulcer bases in acute non-variceal upper gastrointestinal bleeding: a single-center prospective study.

BACKGROUND: Acute non-variceal upper gastrointestinal bleeding (ANVB) or hemorrhage (used interchangeably) is an emergency. Endoscopically applied hydrogen peroxide (H2O2) has been shown to improve visualization of the ulcer base. AIMS: To test the hypothesis that ulcer base clot clearance with 3% H2O2 improves the visualization of ANVB lesions compared to water alone. METHODS: In this single-center prospective study, 320 patients with ANVB were examined, of which 81 met the entry criteria for evaluation. All patients with ANVB underwent urgent endoscopy. Those with adherent clots on the ulcer base were sprayed with 250 ml of water, followed by up to 100 ml of 3% H2O2. The main outcome measurement was Kalloo"s Visual Scores of the ulcer base before and after water and H2O2. RESULTS: Eighty-one patients with gastric ulcers (GU; 34) and duodenal ulcers (DU; 47) met the entry criteria. The mean improvement in grade from water to H2O2 was 2.04 (95% confidence interval [CI] (1.86, 2.23)). The mean volume of H2O2 used to clear clots was higher (70 ml) in patients who were negative for both Helicobacter pylori and non-steroidal anti-inflammatory drug (NSAID) use than in those who were positive for both (31 ml) (P = 0.00). More DU patients (72%) had visible vessels than GU patients (44%) (P = 0.01). CONCLUSIONS: H2O2 improved the visualization of ulcer bases in ANVB. A smaller volume of H2O2 was required to clear clots in patients who used NSAIDs and had H. pylori infection. H2O2 identified more DU vessels. The use of H2O2 should be considered as a standard therapy in the management of clots in ANVB.

Normal values for pharyngeal pH monitoring.

OBJECTIVES: We performed a prospective study of asymptomatic adult volunteers to establish normative values of pharyngeal pH using a novel pH probe. METHODS: The Dx-pH probe is a novel pH device capable of measuring liquid and aerosolized acid levels. Twenty asymptomatic patients (Reflux Symptom Index less than 10 and Reflux Finding Score less than 6) underwent simultaneous investigation with this probe placed in the oropharynx and a dual antimony probe placed in the hypopharynx and esophagus. The reflux parameters measured from the oropharyngeal probe included the percentage of time and the number of events in which the pH was less than 5.5,5.0,4.5, and 4.0. RESULTS: The upper limits of normal (95th percentile) for the number of events below pH of 5.5, 5.0, 4.5, and 4.0 per 24-hour period were 16.6, 10.7, 7.4, and 0.2, respectively. The upper limits of normal (95th percentile) for an acid exposure time below pH of 5.5, 5.0, 4.5, and 4.0 per 24-hour period were 820 seconds, 385 seconds, 75 seconds, and 3 seconds, respectively. CONCLUSIONS: Normative pharyngeal pH values are presented. Further studies are required to determine clinical relevance.

Diverticular bleeding.

Diverticular bleeding is a common cause of lower gastrointestinal hemorrhage. Patients typically present with massive and painless rectal hemorrhage. If bleeding is severe, initial resuscitative measures should include airway maintenance and oxygen supplementation, followed by measurement of hemoglobin and hematocrit levels, and blood typing and crossmatching. Patients may need intravenous fluid resuscitation with normal saline or lactated Ringer's solution, followed by transfusion of packed red blood cells in the event of ongoing bleeding. Diverticular hemorrhage resolves spontaneously in approximately 80 percent of patients. If there is severe bleeding or significant comorbidities, patients should be admitted to the intensive care unit. The recommended initial diagnostic test is colonoscopy, performed within 12 to 48 hours of presentation and after a rapid bowel preparation with polyethylene glycol solutions. If the bleeding source is identified by colonoscopy, endoscopic therapeutic maneuvers can be performed. These may include injection with epinephrine or electrocautery therapy. If the bleeding source is not identified, radionuclide imaging (i.e., technetium-99m-tagged red blood cell scan) should be performed, usually followed by arteriography. For ongoing diverticular hemorrhage, other therapeutic modalities such as selective embolization, intra-arterial vasopressin infusion, or surgery, should be considered.

Attitudes toward performance of endoscopic colon cancer screening by family physicians.

BACKGROUND AND OBJECTIVES: This study's purpose was to examine attitudes of family physicians and gastroenterologists toward family physician performance of lower endoscopy in general practice. METHODS: A mailed survey was sent to 1,563 board-certified physicians in Georgia (1,303 family physicians, 260 gastroenterologists). Respondents were asked to describe their practice of lower endoscopy procedures and colorectal (CRC) screening preferences. RESULTS: Fifty-one percent (801) of the surveys were returned. For CRC screening, family physicians recommend fecal occult blood testing most frequently (51.7%), while gastroenterologists recommended colonoscopy most frequently (89.5%). Most family physicians believe that family physicians should perform flexible sigmoidoscopy (FS) (81.4%) and colonoscopy (CS) (71.3%). A total of 71.2% of surveyed gastroenterologists believe that family physicians should perform FS, but only a minority (4.5%) believe that family physicians should perform screening CSs. Approximately 28% (186) of family physicians report performing FS (mean=.8 FS per month). Only 3.7 % (25) of family physicians reported performing CS (mean=8.2 CSs per month). CONCLUSIONS: Although most family physicians believe that they should perform lower endoscopy, only a minority of gastroenterologists believe family physicians should perform CS. Our results show that family physician performance of lower endoscopic CRC screening is limited in general practice. Future research might consider exploring these issues from both the gastroenterologist and family physician perspective.

Racial disparities and barriers to colorectal cancer screening in rural areas.

INTRODUCTION: This study examined barriers to colorectal cancer (CRC) screening in people living in rural areas. METHODS: We identified 2 rural counties with high rates of CRC and randomly contacted county residents by telephone using a published listing. RESULTS: Six hundred thirty-five of the 1839 eligible respondents (34.5%) between the ages of 50 and 79 years living in McDuffie and Screven counties, Georgia, agreed to complete the survey. The mean age was 62.2 years (SD, ±7.5 years); 72.4% were women, 79.4% were white, and 19.5% were African American. African-American respondents had lower CRC screening rates (50.4%) than whites (63.4%; P = .009). Significantly more African Americans compared with whites reported barriers to CRC screening. Based on logistic regression analyses, having a physician recommend CRC screening had the strongest association with having a current CRC screening, regardless of race. CONCLUSIONS: Important racial differences existed between African Americans and whites regarding the barriers to CRC screening and factors impacting current screening. However, endorsement of a small set of questionnaire items--not race--had the strongest association with being current with screening. Physician recommendation for CRC screening had the strongest association with being current with CRC screening.

Salmonella newport bacteremia in a 12-day-old infant.

In the United States, Salmonella infections (salmonellosis) cause multiple medical problems. Although the most common presenting symptom is diarrhea, bacteremia can also occur. An estimated 1.4 million cases of salmonellosis occur annually in the United States. We present a case of Salmonella bacteremia in a 12-day old infant. We discuss the presenting signs, symptoms, and management strategies for a patient younger than 28 days old (neonate) presenting with fever and diarrhea.

Eosinophilic ascites, an unusual presentation of eosinophilic gastroenteritis: A case report and review.

Eosinophilic ascites (EA) is a rare disorder of unknown etiology that has been reported in both adult and pediatric patients. It is a part of the syndrome of eosinophilic gastroenteritis, which is characterized by eosinophilic infiltration of any or all layers of the gut wall and may involve any segment of the gastrointestinal tract. Peripheral eosinophilia may or may not be present. We report a case of EA that developed post partum.

Hepatic failure caused by plasma cell infiltration in multiple myeloma.

Although plasma cell infiltration is not rare in autopsy of patients with multiple myeloma (MM), it is very rarely detected in living patients. This is because MM rarely causes significant liver dysfunction that requires further evaluation. A 49-year-old man presented with acute renal failure and was diagnosed with kappa light chain MM stage IIB. Thalidomide and dexamethasone were initiated. The patient developed a continuous increase in bilirubin that led to severe cholestasis. A liver biopsy revealed plasma cell infiltration. He then rapidly progressed to liver failure and died. Treatment options are limited in MM with significant liver dysfunction. Despite new drug therapies in MM, those patients with rapidly progressive liver failure appear to have a dismal outcome.

What every gastroenterologist needs to know about common anorectal disorders.

Anorectal complaints are very common and are caused by a variety of mostly benign anorectal disorders. Many anorectal conditions may be successfully treated by primary care physicians in the outpatient setting, but patients tend not to seek medical attention due to embarrassment or fear of cancer. As a result, patients frequently present with advanced disease after experiencing significant decreases in quality of life. A number of patients with anorectal complaints are referred to gastroenterologists. However, gastroenterologists' knowledge and experience in approaching these conditions may not be sufficient. This article can serve as a guide to gastroenterologists to recognize, evaluate, and manage medically or non-surgically common benign anorectal disorders, and to identify when surgical referrals are most prudent. A review of the current literature is performed to evaluate comprehensive clinical pearls and management guidelines for each topic. Topics reviewed include hemorrhoids, anal fissures, anorectal fistulas and abscesses, and pruritus ani.