Incorporating Support Vector Machine for Identifying Protein Tyrosine Sulfation Sites

[[abstract]]Abstract: Tyrosine sulfation is a post-translational modification of many secreted and membrane-bound proteins. It governs protein-protein interactions that are involved in leukocyte adhesion, hemostasis, and chemokine signaling. However, the intrinsic feature of sulfated protein remains elusive and remains to be delineated. This investigation presents SulfoSite, which is a computational method based on a support vector machine (SVM) for predicting protein sulfotyrosine sites. The approach was developed to consider structural information such as concerning the secondary structure and solvent accessibility of amino acids that surround the sulfotyrosine sites. One hundred sixty-two experimentally verified tyrosine sulfation sites were identified using UniProtKB/SwissProt release 53.0. The results of a five-fold cross-validation evaluation suggest that the accessibility of the solvent around the sulfotyrosine sites contributes substantially to predictive accuracy. The SVM classifier can achieve an accuracy of 94.2% in fivefold cross validation when sequence positional weighted matrix (PWM) is coupled with values of the accessible surface area (ASA). The proposed method significantly outperforms previous methods for accurately predicting the location of tyrosine sulfation sites. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2526-2537, 200

Clinical characteristics and therapeutic outcomes of nosocomial super-infection in adult bacterial meningitis

<p>Abstract</p> <p>Background</p> <p>Super-infection in adult bacterial meningitis (ABM) is a condition wherein the cerebrospinal fluid (CSF) grows new pathogen(s) during the therapeutic course of meningitis. It is an uncommon but clinically important condition rarely examined in literature.</p> <p>Methods</p> <p>Twenty-seven episodes of super-infection states in 21 ABM patients collected in a 9.5-year study period (January 2001 to June 2010) were evaluated. The clinical characteristics, implicated pathogens, results of antimicrobial susceptibility tests, and therapeutic outcomes were analyzed.</p> <p>Results</p> <p>Twenty-one patients (13 men, 8 women) aged 25-73 years (median, 45 years) had post-neurosurgical state as the preceding event and nosocomial infection. The post-neurosurgical states included spontaneous intracranial hemorrhage (ICH) with craniectomy or craniotomy with extra-ventricular drainage (EVD) or ventriculo-peritoneal shunt (VPS) in 10 patients, traumatic ICH with craniectomy or craniotomy with EVD or VPS in 6 patients, hydrocephalus s/p VPS in 2 patients, and one patient each with cerebral infarct s/p craniectomy with EVD, meningeal metastasis s/p Omaya implant, and head injury. All 21 patients had EVD and/or VP shunt and/or Omaya implant during the whole course of ABM. Recurrent fever was the most common presentation and the implicated bacterial pathogens were protean, many of which were antibiotic resistant. Most patients required adjustment of antibiotics after the pathogens were identified but even with antimicrobial therapy, 33.3% (7/21) died. Morbidity was also high among survivors.</p> <p>Conclusions</p> <p>Super-infection in ABM is usually seen in patients with preceding neurosurgical event, especially insertion of an external drainage device. Repeat CSF culture is mandatory for diagnostic confirmation because most of the implicated bacterial strains are non-susceptible to common antibiotics used. Unusual pathogens like anaerobic bacteria and fungi may also appear. Despite antimicrobial therapy, prognosis remains poor.</p

Adult mortality of diseases and injuries attributable to selected metabolic, lifestyle, environmental, and infectious risk factors in Taiwan: A comparative risk assessment

Background: To facilitate priority-setting in health policymaking, we compiled the best available information to estimate the adult mortality (>30 years) burden attributable to 13 metabolic, lifestyle, infectious, and environmental risk factors in Taiwan. Methods: We obtained data on risk factor exposure from nationally representative health surveys, cause-specific mortality from the National Death Registry, and relative risks from epidemiological studies and meta-analyses. We applied the comparative risk assessment framework to estimate mortality burden attributable to individual risk factors or risk factor clusters. Results: In 2009, high blood glucose accounted for 14,900 deaths (95% UI: 11,850-17,960), or 10.4% of all deaths in that year. It was followed by tobacco smoking (13,340 deaths, 95% UI: 10,330-16,450), high blood pressure (11,190 deaths, 95% UI: 8,190-14,190), ambient particulate matter pollution (8,600 deaths, 95% UI: 7,370-9,840), and dietary risks (high sodium intake and low intake of fruits and vegetables, 7,890 deaths, 95% UI: 5,970-9,810). Overweight-obesity and physical inactivity accounted for 7,620 deaths (95% UI: 6,040-9,190), and 7,400 deaths (95% UI: 6,670-8,130), respectively. The cardiometabolic risk factors of high blood pressure, high blood glucose, high cholesterol, and overweight-obesity jointly accounted for 12,120 deaths (95% UI: 11,220-13,020) from cardiovascular diseases. For domestic risk factors, infections from hepatitis B virus (HBV) and hepatitis C virus (HCV) were responsible for 6,300 deaths (95% UI: 5,610-6,980) and 3,170 deaths (95% UI: 1,860-4,490), respectively, and betel nut use was associated with 1,780 deaths from oral, laryngeal, and esophageal cancer (95% UI: 1,190-2,360). The leading risk factors for years of life lost were similar, but the impact of tobacco smoking and alcohol use became larger because the attributable deaths from these risk factors occurred among young adults aged less than 60 years. Conclusions: High blood glucose, tobacco smoking, and high blood pressure are the major risk factors for deaths from diseases and injuries among Taiwanese adults. A large number of years of life would be gained if the 13 modifiable risk factors could be removed or reduced to the optimal level

The incidence of experimental smoking in school children: an 8-year follow-up of the child and adolescent behaviors in long-term evolution (CABLE) study

<p>Abstract</p> <p>Background</p> <p>Studies have established that most regular adult smokers become addicted in their adolescent years. We investigated the incidence of and risk factors associated with initial experimental smoking among a group of school children who were followed for 8 years.</p> <p>Methods</p> <p>We used cohort data collected as part of the Child and Adolescent Behaviors in Long-term Evolution (CABLE) study, which selected nine elementary schools each from an urban area (Taipei City) and a rural area (Hsingchu county) in northern Taiwan. From 2002 to 2008, children were asked annually whether they had smoked in the previous year. An accelerated lifetime model with Weibull distribution was used to examine the factors associated with experimental smoking.</p> <p>Results</p> <p>In 2001, 2686 4^th-graders participated in the study. For each year from 2002 to 2008, their incidences of trial smoking were 3.1%, 4.0%, 2.8%, 6.0%, 5.3%, 5.0% and 6.0%, respectively. There was an increase from 7^thto 8^thgrade (6.0%). Children who were males, lived in rural areas, came from single-parent families, had parents who smoked, and had peers who smoked were more likely to try smoking earlier. The influence of parents and peers on experimental smoking demonstrated gradient effects.</p> <p>Conclusions</p> <p>This study used a cohort to examine incidence and multiple influences, including individual factors, familial factors, and community factors, on experimental smoking in adolescents. The findings fit the social ecological model, highlighting the influences of family and friends. School and community attachment were associated with experimental smoking in teenagers.</p

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field