Identification of hot regions in protein-protein interactions by sequential pattern mining

<p>Abstract</p> <p>Background</p> <p>Identification of protein interacting sites is an important task in computational molecular biology. As more and more protein sequences are deposited without available structural information, it is strongly desirable to predict protein binding regions by their sequences alone. This paper presents a pattern mining approach to tackle this problem. It is observed that a functional region of protein structures usually consists of several peptide segments linked with large wildcard regions. Thus, the proposed mining technology considers large irregular gaps when growing patterns, in order to find the residues that are simultaneously conserved but largely separated on the sequences. A derived pattern is called a cluster-like pattern since the discovered conserved residues are always grouped into several blocks, which each corresponds to a local conserved region on the protein sequence.</p> <p>Results</p> <p>The experiments conducted in this work demonstrate that the derived long patterns automatically discover the important residues that form one or several hot regions of protein-protein interactions. The methodology is evaluated by conducting experiments on the web server MAGIIC-PRO based on a well known benchmark containing 220 protein chains from 72 distinct complexes. Among the tested 218 proteins, there are 900 sequential blocks discovered, 4.25 blocks per protein chain on average. About 92% of the derived blocks are observed to be clustered in space with at least one of the other blocks, and about 66% of the blocks are found to be near the interface of protein-protein interactions. It is summarized that for about 83% of the tested proteins, at least two interacting blocks can be discovered by this approach.</p> <p>Conclusion</p> <p>This work aims to demonstrate that the important residues associated with the interface of protein-protein interactions may be automatically discovered by sequential pattern mining. The detected regions possess high conservation and thus are considered as the computational hot regions. This information would be useful to characterizing protein sequences, predicting protein function, finding potential partners, and facilitating protein docking for drug discovery.</p

Equivalent efficacies of reverse hybrid and concomitant therapies in first- line treatment of Helicobacter pylori infection

Background and AimConcomitant therapy is a recommended first- line treatment for Helicobacter pylori infection in most national or international consensuses. Reverse hybrid therapy is a modified 14- day concomitant therapy without clarithromycin and metronidazole in the final 7 days. This study aims to test whether 14- day reverse hybrid therapy is non- inferior to 14- day concomitant therapy in the first- line treatment of H. pylori infection.MethodsHelicobacter pylori- infected adult patients were randomly assigned to receive either reverse hybrid therapy (dexlansoprazole 60 mg o.d. plus amoxicillin 1 g b.d. for 14 days, and clarithromycin 500 mg plus metronidazole 500 mg b.d. for initial 7 days) or concomitant therapy (dexlansoprazole 60 mg once o.d. plus amoxicillin 1 g, clarithromycin 500 mg, and metronidazole 500 mg b.d. for 14 days). H. pylori status was assessed 6 weeks after the end of treatment.ResultsHelicobacter pylori- infected participants (n = 248) were randomized to receive either 14- day reverse hybrid therapy (n = 124) or 14- day concomitant therapy (n = 124). Intention- to- treat analysis demonstrated that the two therapies had comparable eradication rate (95.2% vs 93.5%; 95% confidence interval, - 4.0% to 7.4%; P = 0.582). However, reverse hybrid therapy had a much lower frequency of adverse events than concomitant therapy (20.2% vs 38.7%, P = 0.001). The two therapies exhibited comparable drug adherence (93.5% vs 87.9%, P = 0.125).ConclusionsFourteen- day reverse hybrid therapy and 14- day concomitant therapy are equivalent in efficacy for the first- line treatment of H. pylori infection. However, reverse hybrid therapy has fewer adverse events compared with concomitant therapy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163472/2/jgh15034_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163472/1/jgh15034.pd

Management of Crohn’s disease in Taiwan: consensus guideline of the Taiwan Society of Inflammatory Bowel Disease updated in 2023

Crohn’s disease (CD) is a chronic, fluctuating inflammatory condition that primarily affects the gastrointestinal tract. Although the incidence of CD in Taiwan is lower than that in Western countries, the severity of CD presentation appears to be similar between Asia and the West. This observation indicates the urgency for devising revised guidelines tailored to the unique reimbursement system, and patient requirements in Taiwan. The core objectives of these updated guidelines include the updated treatment choices and the integration of the treat-to-target strategy into CD management, promoting the achievement of deep remission to mitigate complications and enhance the overall quality of life. Given the diversity in disease prevalence, severity, insurance policies, and access to medical treatments in Taiwan, a customized approach is imperative for formulating these guidelines. Such tailored strategies ensure that international standards are not only adapted but also optimized to local contexts. Since the inception of its initial guidelines in 2017, the Taiwan Society of Inflammatory Bowel Disease (TSIBD) has acknowledged the importance of continuous revisions for incorporating new therapeutic options and evolving disease management practices. The latest update leverages international standards and recent research findings focused on practical implementation within the Taiwanese healthcare system

Management of ulcerative colitis in Taiwan: consensus guideline of the Taiwan Society of Inflammatory Bowel Disease updated in 2023

Ulcerative colitis (UC) is a chronic inflammation of the gastrointestinal tract and is characterized by alternating periods of inflammation and remission. Although UC incidence is lower in Taiwan than in Western countries, its impact remains considerable, demanding updated guidelines for addressing local healthcare challenges and patient needs. The revised guidelines employ international standards and recent research, emphasizing practical implementation within the Taiwanese healthcare system. Since the inception of the guidelines in 2017, the Taiwan Society of Inflammatory Bowel Disease has acknowledged the need for ongoing revisions to incorporate emerging therapeutic options and evolving disease management practices. This updated guideline aims to align UC management with local contexts, ensuring comprehensive and context-specific recommendations, thereby raising the standard of care for UC patients in Taiwan. By adapting and optimizing international protocols for local relevance, these efforts seek to enhance health outcomes for patients with UC

Dynamic Set Planning for Coordinated Multi-Point in B4G/5G Networks

Coordinated Multi-Point (CoMP) is an important technique in B4G/5G networks. With CoMP, multiple base stations can be clustered to compose a cooperating set to improve system throughput, especially for the users in cell edges. Existed studies have discussed how to mitigate overloading scenarios and enhance system throughput with CoMP statically. However, static cooperation fixes the set size and neglects the fast-changing of B4G/5G networks. Thus, this paper provides a full study of off-peak hours and overloading scenarios. During off-peak hours, we propose to reduce BSs’ transmission power and use the free radio resource to save energy while guaranteeing users’ QoS. In addition, if large-scale activities happen with crowds gathering or in peak hours, we dynamically compose the cooperating set based on instant traffic requests to adjust base stations’ BSs’ transmission power; thus, the system will efficiently offload the traffic to the member cells which have available radio resources in the cooperating set. Experimental results show that the proposed schemes enhance system throughput, radio resource utilization, and energy efficiency, compared to other existing schemes

Bile aspiration enhances the diagnostic accuracy of Clonorchis sinensis : A case report

Clonorchis sinensis is endemic to Southeast Asia, Japan, China, and Taiwan. Those infected often have a history of consumption of raw fresh fish. Its manifestations can be asymptomatic of cholangitis, biliary stones, or cholangiocarcinoma. A 69-year-old male living in Chishan, Taiwan visited our hospital with obstructive jaundice. Noninvasive analyses, such as stool examination, abdominal ultrasound, and an abdominal computed tomography scan did not reveal clues of clonorchiasis. As the obstructive jaundice was unexplained, endoscopic retrograde cholangiopancreatography (ERCP) was then performed and a hepatic fluke was seen via aspiration of bile. Subsequently, the ova of C. sinensis were detected via microscopic examination of bile samples. Bile aspiration is not routine during an ERCP procedure, however, we suggest the bile aspiration can be diagnostically accurate for clonorchiasis, especially for patients with a suspicious infection

Blood Cadmium Levels and Oxygen Desaturation during the 6-Minute Walk Test in Patients with Chronic Obstructive Pulmonary Disease

Background and Objectives: chronic obstructive pulmonary disease (COPD) is characterized by persistent airflow limitation and a history of exposure to noxious stimuli. Cigarette smoking is the most important causal factor for developing COPD. Cadmium, a minor metallic element, is one of the main inorganic components in tobacco smoke. Inhaled cadmium was associated with a decline in lung function, gas exchange impairment, and the development of obstructive lung disease. Patients with COPD who had oxygen desaturation during the 6-min walk test (6MWT) had a significantly worse prognosis than non-desaturation in COPD patients. Nonetheless, few studies have addressed the influence of blood cadmium levels on exercise-induced oxygen desaturation in COPD patients. Our objective was to assess the potential impact of blood cadmium levels on oxygen desaturation during the 6MWT among COPD patients. Materials and Methods: we performed a retrospective analysis of patients with COPD who were examined for blood cadmium levels in a tertiary care referral center in Taiwan, between March 2020 and May 2021. The 6-min walk test was performed. Normal control subjects who had no evidence of COPD were also enrolled. Results: a total of 73 COPD patients were analyzed and stratified into the high-blood cadmium group (13 patients) and low-blood cadmium group (60 patients). A total of 50 normal control subjects without a diagnosis of COPD were enrolled. The high-blood cadmium group had a significantly higher extent of desaturation than the low-blood cadmium group. The frequency of desaturation during 6MWT revealed a stepwise-increasing trend with an increase in blood cadmium levels. A multivariable logistic regression model revealed that blood cadmium levels were independently associated with desaturation during the 6MWT (odds ratio 12.849 [95% CI 1.168–141.329]; p = 0.037). Conclusions: our findings indicate that blood cadmium levels, within the normal range, were significantly associated with desaturation during 6MWT in patients with COPD

Not only hysterectomy but also cesarean section can predict incomplete flexible sigmoidoscopy among patients with prior abdominal or pelvic surgery

Background: Flexible sigmoidoscopy (FS) is a safe and effective method for colorectal cancer (CRC) screening. Several studies have demonstrated that individuals who have undergone surgery are at a greater risk of having incomplete FS. This study explored predictors of incomplete FS and reduced polyp detection rates for participants who had undergone abdominal or pelvic surgery. Methods: From January 2009 to December 2009, individuals participating in health examinations and who had undergone abdominal or pelvic surgery were invited to participate in this investigation. Four experienced gastroenterologists performed examinations using a 60-cm Olympus video sigmoidoscope. Factors associated with incomplete FS insertions and reduced polyp detection rates were analyzed using logistic regression models. Results: Overall, 106 eligible individuals were analyzed, and 45 (42%) incomplete FS insertions were reviewed. Fifty participants (47%) had undergone pelvic surgery, and the other 56 (53%) had undergone abdominal surgery. Pelvic surgeries were cesarean section (25%) and hysterectomy (15%); appendectomy (36%) was the most common abdominal surgery. The main pathological FS findings were hemorrhoids (54%) and adenomatous polyps (18%). Multivariate analysis indicated that only prior pelvic surgery [odds ratio (OR), 3.54; p = 0.01] was an independent risk factor for incomplete FS insertion. Incomplete examinations were inversely related to adenomatous polyp detection rates (OR, 0.23; p = 0.03). Conclusion: Prior pelvic surgery, particularly cesarean section and hysterectomy, is an independent factor for incomplete FS insertion in a selected adult population. In addition, incomplete FS can increase the risk of missing polyps, particularly in individuals who underwent pelvic surgery

The pattern discovered for the PDB chain PDB:, chain A, where the pattern blocks are shown in with different blocks plotted in distinct colors, protein LCI in , and zinc ions in crimson spheres

<p><b>Copyright information:</b></p><p>Taken from "Identification of hot regions in protein-protein interactions by sequential pattern mining"</p><p>http://www.biomedcentral.com/1471-2105/8/S5/S8</p><p>BMC Bioinformatics 2007;8(Suppl 5):S8-S8.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1892096.</p><p></p> This maximum-size pattern hits the contact regions when interacting with the protein LCI, where the ligand GLU is plotted in representation and colored in CPK mode

Example used to illustrate how the patterns generated by MAGIIC-PRO facilitate the study of identifying hot regions

<p><b>Copyright information:</b></p><p>Taken from "Identification of hot regions in protein-protein interactions by sequential pattern mining"</p><p>http://www.biomedcentral.com/1471-2105/8/S5/S8</p><p>BMC Bioinformatics 2007;8(Suppl 5):S8-S8.</p><p>Published online 24 May 2007</p><p>PMCID:PMC1892096.</p><p></p> The protruding residue Arg15 of 5L15 (chain I) falls in the first block of the derived pattern and the structurally conserved residues in the complemented pocket of VIIa (chain H) can be found in the three blocks of the derived pattern. The patterns are plotted as representation on the structure and colored in the same way as in their regular expression form