The underlying principle governing the natural phenomena of life is one of the critical issues receiving due importance in recent years. A key feature of the scale-free architecture is the vitality of the most connected nodes (hubs). The major objective of this article was to analyze the protein-protein and metabolic interaction networks of Drosophila melanogaster by considering the architectural patterns and the consequence of removal of hubs on the topological parameter of the two interaction systems. Analysis showed that both interaction networks follow a scale-free model, establishing the fact that most real world networks,from varied situations, conform to the small world pattern. The average path length showed a two-fold and a three-fold increase (changing from 9.42 to 20.93 and from 5.29 to 17.75, respectively) for the protein-protein and metabolic interaction networks, respectively, due to the deletion of hubs. On the contrary, the arbitrary elimination of nodes did not show any remarkable disparity in the topological parameter of the protein-protein and metabolic interaction networks (average path length: 9.42±0.02 and 5.27±0.01, respectively). This aberrant behavior for the two cases underscores the significance of the most linked nodes to the natural topology of the networks.

Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain interactions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as "interacting". In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis elegans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area under the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs increased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on average 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.
Animals ; Caenorhabditis elegans Proteins ; chemistry ; genetics ; metabolism ; Confidence Intervals ; Databases, Protein ; Gene Expression Profiling ; statistics & numerical data ; Humans ; Likelihood Functions ; Phylogeny ; Protein Array Analysis ; methods ; statistics & numerical data ; Protein Interaction Mapping ; methods ; statistics & numerical data ; Protein Structure, Tertiary ; ROC Curve ; Saccharomyces cerevisiae Proteins ; chemistry ; genetics ; metabolism ; Sensitivity and Specificity

A concept of unique peptides(CUP)was proposed and implemented to identify whole-cell proteins from tandem mass spectrometry(MS/MS)ion spectra.A unique peptide is defined as a peptide,irrespective of its length,that exists only in one protein of a proteome of interest,despite the fact that this peptide may appear more than once in the same protein.Integrating CUP,a two-step whole-cell protein identification strategy was developed to further increase the confidence of identified proteins.A dataset containing 40,243 MS/MS ion spectra of Saccharomyces cerevisiae and protein identification tools including Mascot and SEQUEST were used to illustrate the proposed concept and strategy.Without implementing CUP,the proteins identified by SEQUEST are 2.26 fold of those identified by Mascot.When CUP was applied,the proteins bearing unique peptides identified by SEQUEST are3.89 fold of those identified by Mascot.By cross-comparing two sets of identified proteins,only 89 common proteins derived from CUP were found.The key discrepancy between identified proteins was resulted from the filtering criteria employed by each protein identification tool.According to the origin of peptides classified by CUP and the commonality of proteins recognized by protein identification tools,all identified proteins were cross-compared,resulting in four groups of proteins possessing different levels of assigned confidence.

Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain inter- actions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as "interacting". In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis ele- gans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area un- der the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs in- creased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on aver- age 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.

PURPOSE: Professional hemodialysis (HD) nursing tends to be task-oriented and lack consideration of the client's viewpoint. This study aims to interpret the process of psychosocial adaptation to dealing with HD in people with end-stage renal disease (ESRD). METHODS: A grounded theory guided this study. Theoretical sampling included 15 people receiving HD at the HD center of a hospital from July to November 2010. Participants received an information sheet in writing, a verbal invitation, and informed consent forms before interviews were conducted. A constant comparative data analysis was analyzed using open, axial and selective coding. The computer software ATLAS.ti assisted data management. Credibility, transferability, dependability, and confirmability ensured the rigor of study process. RESULTS: This study identified "adopting life with hemodialysis", which captures the process of the psychosocial adaptation in people with ESRD as one transformation. Four categories that evolved from "adopting HD life" are (a) slipping into, (b) restricted to a renal world, (c) losing self control, and (d) stuck in an endless process. CONCLUSIONS: The findings of this investigation indicate the multidimensional requirements of people receiving maintenance dialysis, with an emphasis on the deficiency in psychosocial and emotional care. The study's findings contribute to clinical practice by increasing the understanding of the experience of chronic HD treatment from the recipient's viewpoint. The better our understanding, the better the care provided will meet the needs of the people receiving HD.
*Adaptation, Psychological ; Adult ; Aged ; Female ; Humans ; Kidney Failure, Chronic/*psychology/therapy ; Male ; Middle Aged ; Qualitative Research ; Renal Dialysis/*psychology

PURPOSE: This study aims to gain in-depth understanding of nurses' perspectives of working in an overcrowded emergency. METHODS: Symbolic interactionism and Charmaz's construction of grounded theory were used. Purposive sampling at the start of the study and a further theoretical sampling by snowball technique were used to recruit 40 registered nurses (RN) to participate in in-depth, semi-structured interviews betweenMay and November, 2014. Data analysis included analytic techniques of initial, focused and theoretical coding. RESULTS: Study findings showed searching for work role is derived by the themes of Finding the role of positioning in Emergency Department (ED), Recognizing causes of ED overcrowding, and Confined working environment. Nurses' work experience which represents the RNs not gained control over their work, as care actions influenced by the problematic overcrowded circumstance of the ED environment. CONCLUSION: The findings fill a gap in knowledge about how RNs experience their work role in the context of an overcrowded Emergency Department in Taiwan. Arising from the study result include taking account of nurses' perspectives when planning staff/patient ratios, strategies to reduce waiting time and ensure that clients receive appropriate care.
Clinical Coding ; Crowding ; Emergencies* ; Emergency Service, Hospital* ; Grounded Theory ; Humans ; Nurses ; Statistics as Topic ; Taiwan*

Metabolic dysfunction-associated fatty liver disease (MAFLD) is an increasingly common liver disease worldwide. MAFLD is diagnosed based on the presence of steatosis on images, histological findings, or serum marker levels as well as the presence of at least one of the three metabolic features: overweight/obesity, type 2 diabetes mellitus, and metabolic risk factors. MAFLD is not only a liver disease but also a factor contributing to or related to cardiovascular diseases (CVD), which is the major etiology responsible for morbidity and mortality in patients with MAFLD. Hence, understanding the association between MAFLD and CVD, surveillance and risk stratification of MAFLD in patients with CVD, and assessment of the current status of MAFLD management are urgent requirements for both hepatologists and cardiologists. This Taiwan position statement reviews the literature and provides suggestions regarding the epidemiology, etiology, risk factors, risk stratification, nonpharmacological interventions, and potential drug treatments of MAFLD, focusing on its association with CVD.

Repetitive transcranial magnetic stimulation (rTMS) and intermittent theta-burst stimulation (iTBS) are evidenced-based treatments for patients with major depressive disorder (MDD) who fail to respond to standard first-line therapies. However, although various TMS protocols have been proven to be clinically effective, the response rate varies across clinical applications due to the heterogeneity of real-world psychiatric comorbidities, such as generalized anxiety disorder, posttraumatic stress disorder, panic disorder, or substance use disorder, which are often observed in patients with MDD. Therefore, individualized treatment approaches are important to increase treatment response by assigning a given patient to the most optimal TMS treatment protocol based on his or her individual profile. This literature review summarizes different rTMS or TBS protocols that have been applied in researches investigating MDD patients with certain psychiatric comorbidities and discusses biomarkers that may be used to predict rTMS treatment response. Furthermore, we highlight the need for the validation of neuroimaging and electrophysiological biomarkers associated with rTMS treatment responses. Finally, we discuss on which directions future efforts should focus for developing the personalization of the treatment of depression with rTMS or iTBS.

Repetitive transcranial magnetic stimulation (rTMS) and intermittent theta-burst stimulation (iTBS) are evidenced-based treatments for patients with major depressive disorder (MDD) who fail to respond to standard first-line therapies. However, although various TMS protocols have been proven to be clinically effective, the response rate varies across clinical applications due to the heterogeneity of real-world psychiatric comorbidities, such as generalized anxiety disorder, posttraumatic stress disorder, panic disorder, or substance use disorder, which are often observed in patients with MDD. Therefore, individualized treatment approaches are important to increase treatment response by assigning a given patient to the most optimal TMS treatment protocol based on his or her individual profile. This literature review summarizes different rTMS or TBS protocols that have been applied in researches investigating MDD patients with certain psychiatric comorbidities and discusses biomarkers that may be used to predict rTMS treatment response. Furthermore, we highlight the need for the validation of neuroimaging and electrophysiological biomarkers associated with rTMS treatment responses. Finally, we discuss on which directions future efforts should focus for developing the personalization of the treatment of depression with rTMS or iTBS.

Background/Aims: Hypopharyngeal multichannel intraluminal impedance-pH (HMII-pH) technology incorporating 2 trans-upper esophageal sphincter impedance channels has been developed to detect pharyngeal reflux. We used the HMII-pH technique to validate the candidate pharyngeal acid reflux (PAR) episodes based on the dual-pH tracings and determined the interobserver reproducibility. Methods: We conducted a cross-sectional study in tertiary centers in Taiwan. Ninety patients with suspected laryngopharyngeal reflux and 28 healthy volunteers underwent HMII-pH test when off acid suppressants. Candidate PAR episodes were characterized by pharyngeal pH drops of at least 2 units and reaching a nadir pH of 5 within 30 seconds during esophageal acidification. Two experts manually independently identified candidate PAR episodes based on the dual-pH tracings. By reviewing the HMII-pH tracings, HMII-pH-proven PAR episodes were subsequently confirmed. The consensus reviews of HMII-pH-proven PAR episodes were considered to be the reference standard diagnosis. The interobserver reproducibility was assessed. Results: A total of 105 candidate PAR episodes were identified. Among them 84 (80.0%; 95% CI, 71.0-87.0%) were HMII-pH-proven PAR episodes (82 in 16 patients and 2 in 1 healthy subject). Patients tended to have more HMII-pH-proven PAR episodes than healthy controls (median and percentile values [25th, 75th, and 95th percentiles]: 0 [0, 0, 3] vs 0 [0, 0, 0], P = 0.067). The concordance rate in diagnosing HMII-pH-proven PAR episodes between 2 independent observers was 92.2%. Conclusion Our preliminary data showed that 80.0% (71.0-87.0%) of the proposed candidate PAR episodes were HMII-pH-proven PAR episodes, among which the interobserver reproducibility was good.