Microorganisms are closely associated with human diseases and health. Understanding the composition and function of microbial communities requires extensive research. Metaproteomics has recently become an important method for throughout and in-depth study of microorganisms. However, major challenges in terms of sample processing, mass spectrometric data acquisition, and data analysis limit the development of metaproteomics owing to the complexity and high heterogeneity of microbial community samples. In metaproteomic analysis, optimizing the preprocessing method for different types of samples and adopting different microbial isolation, enrichment, extraction, and lysis schemes are often necessary. Similar to those for single-species proteomics, the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition (DDA) and data-independent acquisition (DIA). DIA can collect comprehensive peptide information from a sample and holds great potential for future development. However, data analysis for DIA is challenged by the complexity of metaproteome samples, which hinders the deeper coverage of metaproteomes. The most important step in data analysis is the construction of a protein sequence database. The size and completeness of the database strongly influence not only the number of identifications, but also analyses at the species and functional levels. The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database. A public database-filtering method based on an iterative database search has been proven to have strong practical value. The peptide-centric DIA data analysis method is a mainstream data analysis strategy. The development of deep learning and artificial intelligence will greatly promote the accuracy, coverage, and speed of metaproteomic analysis. In terms of downstream bioinformatics analysis, a series of annotation tools that can perform species annotation at the protein, peptide, and gene levels has been developed in recent years to determine the composition of microbial communities. The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches. Metaproteomics has become an important component of the multi-omics analysis of microbial communities, and has great development potential in terms of depth of coverage, sensitivity of detection, and completeness of data analysis.

UNASSIGNED: Scabies is the second most common cause of disability among skin diseases in the Philippines as of 2019. There is no large nationwide study describing the epidemiologic profile of scabies in the country.
UNASSIGNED: This study aimed to describe the demographic, seasonal, and geographic profile of scabies in the Philippines.
UNASSIGNED: We compared secondary data of two local patient registries (Philippine Dermatological Society, PDS, 2010 to 2021; and Philippine Pediatric Society, PPS, 2009 to 2021) for reported cases of scabies in the Philippines. We reported the frequency and percentage distribution according to age, sex, month, year, and type of diagnosis, and region.
UNASSIGNED: The median annual frequency of scabies cases (mostly outpatient) for PDS (from year 2010) was 4087 (range ([QR], 342-6422 [3271.5]), while it was 183 (range [IQR], 64-234 [96.5]) (all inpatient) for PPS (from year 2009). There was a reduction to one-third (PDS) and one-fourth (PPS) of pre-pandemic numbers during the pandemic years (2020-2021). The peak months for scabies cases were the cooler months: January (median, 12.1% of annual cases; range [IQR], 2.6%-31.4% [3.6%]) to February (median, 10.0% of annual cases; range [IQR], 1.5%-27.8% [2.5%]) based on PDS data, and November (median, 10.0% of annual cases; range [IQR], 0.0%-24.3% [7.0%]) to January (median, 9.0% of annual cases; range [IQR], 0.0%-24.3% [6.6%]) for PPS data. Overall, for PDS, age 1-4 years is the most affected age group (median, PDS, 17.5% of annual cases; range [IQR], 11.9%-25.4% [8.1%]), while it was the less than 1-year-olds (median annual cases, 48.9%; range [IQR], 29.1%-67.3% [13.20%]) among PPS pediatric population aged 0 to 18 years. Males (median, 53.9% of annual cases; range [IQR], 45.0%-67.2% [8.8%]) were more affected than females in PPS. While for PDS during earlier years (prior to 2015), males (median, 51.6% of annual cases from 2010 to 2014; range [IQR], 47.4%-52.9% [0.2%]) were more affected than females. However, males became less affected than females with median, 44.7% of annual cases from 2015 onwards (range [IQR], 43.4%-46.5% [1.2%]). NCR was the region with the highest frequency of cases in PPS (median, 52.6% of annual cases; range [IQR], 22.7%-75.0% [20.4%]). The 2nd most affected regions were Central/Eastern Visayas (34.2%, 2009-2013; range [IQR], 17.9%-54.1% [5.3%]), Bicol region (12%; 2014 to 2018; range [IQR], 17.9%-54.1% [7.4%]), Central Luzon (18%; 2019), Central/Eastern Visayas (29%, 2020), and Northern/Central Mindanao (17%, 2021).
UNASSIGNED: Scabies was commonly seen in the younger age group, slightly more in females in the PDS, while slightly more among males in the PPS, in the cooler months of the year, and in the urbanized NCR.

Some herbal extracts contain relatively high amounts of lipopolysaccharide (LPS). Because orally administered LPS activates innate immunity without inducing inflammation, it plays a role as an active ingredient in herbal extracts. However, the LPS content in herbal extracts remains extensively unevaluated. This study aimed to create a database of LPS content in herbal extracts; therefore, the LPS content of 414 herbal extracts was measured and the macrophage activation potential was evaluated. The LPS content of these hot water extracts was determined using the kinetic-turbidimetric method. The LPS concentration ranged from a few ng/g to hundreds of μg/g (Standard Escherichia coli LPS equivalent). Twelve samples had a high-LPS-content of > 100 μg/g, including seven samples from roots and three samples from leaves of the herbal extracts. These samples showed high phagocytosis and NO production capacity, and further investigation using polymyxin B, an LPS inhibitor, significantly inhibited macrophage activation. This study suggests that some herbal extracts contain sufficient LPS concentration to activate innate immunity. Therefore, a new approach to evaluate the efficacy of herbal extracts based on their LPS content was proposed. A database listing the LPS content of different herbal extracts is essential for this approach.

Due to the similarity and diversity among kinases, small molecule kinase inhibitors (SMKIs) often display multi-target effects or selectivity, which have a strong correlation with the efficacy and safety of these inhibitors. However, due to the limited number of well-known popular databases and their restricted data mining capabilities, along with the significant scarcity of databases focusing on the pharmacological similarity and diversity of SMIKIs, researchers find it challenging to quickly access relevant information. The KLIFS database is representative of specialized application databases in the field, focusing on kinase structure and co-crystallised kinase-ligand interactions, whereas the KLSD database in this paper emphasizes the analysis of SMKIs among all reported kinase targets. To solve the current problem of the lack of professional application databases in kinase research and to provide centralized, standardized, reliable and efficient data resources for kinase researchers, this paper proposes a research program based on the ChEMBL database. It focuses on kinase ligands activities comparisons. This scheme extracts kinase data and standardizes and normalizes them, then performs kinase target difference analysis to achieve kinase activity threshold judgement. It then constructs a specialized and personalized kinase database platform, adopts the front-end and back-end separation technology of SpringBoot architecture, constructs an extensible WEB application, handles the storage, retrieval and analysis of the data, ultimately realizing data visualization and interaction. This study aims to develop a kinase database platform to collect, organize, and provide standardized data related to kinases. By offering essential resources and tools, it supports kinase research and drug development, thereby advancing scientific research and innovation in kinase-related fields. It is freely accessible at: http://ai.njucm.edu.cn:8080.

The Saudi National Diabetes Registry focuses mainly on adult patients. In 2020, the National Guard Health Authority (NGHA) launched the Saudi Pediatric and Youth Diabetes Registry (SPYDR), for children and adolescents with diabetes. This report is about the first data and the challenges we faced during SPYDR initiation. Patients were identified from the electronic medical records of the Saudi NGHA hospitals using the International Classification of Disease (ICD-10). A trained coordinator verified the diagnosis and entered patients\' details into the registry and a random sample was validated by experienced endocrinologists. The data were analyzed according to patients\' demography, diabetes subtypes, duration, control, and complications. The challenges faced by the team were identified and addressed. At the time of manuscript submission, 2,344 individuals were enrolled. Their mean age at diagnosis was 9.08 (±4.27) years and 1,136 (48.46%) were females. Of these, 91.3% have type 1 (T1D), and 6.4% have type 2 diabetes (T2D). The mean HbA1c was 10.45% (±2.36) and duration of diabetes was 5.31 (±3.05) years. The main challenges included the COVID-19 pandemic, data validation, and centers\' participation. However, within 12 months of initiation enrolled subjects matched the expected number. Despite the challenges, the first step of SPYDR was achieved. The initial data confirmed that T1D is the most common form of childhood diabetes, and the frequency of T2D is comparable to regional and international data. SPYDR provides the infrastructure for data sharing and collaborative research with the enrollment of patients from other Saudi healthcare institutes.

Gene expression is dynamic and varies at different stages of processes. The identification of gene profiles with temporal-specific expression patterns can provide valuable insights into ongoing biological processes, such as the cell cycle, cell development, circadian rhythms, or responses to external stimuli such as drug treatments or viral infections. However, currently, no database defines, identifies or archives gene profiles with temporal-specific expression patterns. Here, using a high-throughput regression analysis approach, eight linear and nonlinear parametric models were fitted to gene expression profiles from time-series experiments to identify eight types of gene profiles with temporal-specific expression patterns. We curated 2684 time-series transcriptome datasets and identified 2644,370 gene profiles exhibiting temporal-specific expression patterns. The results were stored in the database GeTeSEPdb (gene profiles with temporal-specific expression patterns database, http://www.inbirg.com/GeTeSEPdb/). Moreover, we implemented an online tool to identify gene profiles with temporal-specific expression patterns from user-submitted data. In summary, GeTeSEPdb is a comprehensive web service that can be used to identify and analyse gene profiles with temporal-specific expression patterns. This approach facilitates the exploration of transcriptional changes and temporal patterns of responses. We firmly believe that GeTeSEPdb will become a valuable resource for biologists and bioinformaticians.

Fungi is a highly diverse group of eukaryotic organisms that live under an extremely wide range of environmental conditions. Nowadays, there is a fundamental focus on observing how biodiversity varies on different spatial scales, in addition to understanding the environmental factors which drive fungal biodiversity. Metabarcoding is a high-throughput DNA sequencing technology that has positively contributed to observing fungal communities in environments. While the DNA sequencing data generated from metabarcoding studies are available in public archives, this valuable data resource is not directly usable for fungal biodiversity investigation. Additionally, due to its fragmented storage and distributed nature, it is not immediately accessible through a single user interface. We developed the MycoDiversity DataBase User Interface (https://mycodiversity.liacs.nl) to provide direct access and retrieval of fungal data that was previously inaccessible in the public domain. The user interface provides multiple graphical views of the data components used to reveal fungal biodiversity. These components include reliable geo-location terms, the reference taxonomic scientific names associated with fungal species and the standard features describing the environment where they occur. Direct observation of the public DNA sequencing data in association with fungi is accessible through SQL search queries created by interactively manipulating topological maps and dynamic hierarchical tree views. The search results are presented in configurable data table views that can be downloaded for further use. With the MycoDiversity DataBase User Interface, we make fungal biodiversity data accessible, assisting researchers and other stakeholders in using metabarcoding studies for assessing fungal biodiversity.

UNASSIGNED: This second harvest of the Congenital Heart Surgery Database intended to compare current results with international databases.
UNASSIGNED: This retrospective study examined a total of 4007 congenital heart surgery procedures from 15 centers in the Congenital Heart Surgery Database between January 2018 and January 2023. International diagnostic and procedural codes were used for data entry. STAT (Society of Thoracic Surgeons and European Association for Cardiothoracic Surgery) mortality scores and categories were used for comparison of the data. Surgical priority status was modified from American Society of Anesthesiologist guidelines. Centers that sent more than 5 cases to the database were included to the study.
UNASSIGNED: Cardiopulmonary bypass and cardioplegic arrest were performed in 2,983 (74.4%) procedures. General risk factors were present in 22.6% of the patients, such as genetic anomaly, syndrome, or prematurity. Overall, 18.9% of the patients had preoperative risk factors (e.g., mechanical ventilation, renal failure, and sepsis). Of the procedures, 610 (15.2%) were performed on neonates, 1,450 (36.2%) on infants, 1,803 (45%) on children, and 144 (3.6%) on adults. The operative timing was elective in 56.5% of the patients, 34.4% were urgent, 8% were emergent, and 1.1% were rescue procedures. Extracorporeal membrane oxygenation support was used in 163 (4%) patients, with a 34.3% survival rate. Overall mortality in this series was 6.7% (n=271). Risk for mortality was higher in patients with general risk factors, such as prematurity, low birth weight neonates, and heterotaxy syndrome. Mortality for patients with preoperative mechanical ventilation was 17.5%. Pulmonary hypertension and preoperative circulatory shock had 11.6% and 10% mortality rates, respectively. Mortality for patients who had no preoperative risk factor was 3.9%. Neonates had the highest mortality rate (20.5%). Intensive care unit and hospital stay time for neonates (median of 17.8 days and 24.8 days, respectively) were also higher than the other age groups. Infants had 6.2% mortality. Hospital mortality was 2.8% for children and 3.5% for adults. Mortality rate was 2.8% for elective cases. Observed mortality rates were higher than expected in the fourth and fifth categories of the STAT system (observed, 14.8% and 51.9%; expected, 9.9% and 23.1%; respectively).
UNASSIGNED: For the first time, outcomes of congenital heart surgery in Türkiye could be compared to the current world experience with this multicenter database study. Increased mortality rate of neonatal and complex heart operations could be delineated as areas that need improvement. The Congenital Heart Surgery Database has great potential for quality improvement of congenital heart surgery in Türkiye. In the long term, participation of more centers in the database may allow more accurate risk adjustment.

UNASSIGNED: As state, regional, and national registries have rapidly expanded, the goal of this study is to assess the frequency of registry abstracts accepted for both podium and poster presentations at the American Association of Hip and Knee Surgeons between 2012 and 2022.
UNASSIGNED: Final programs and poster e-collections were examined over the past 11 years. Two reviewers evaluated each abstract to determine if they utilized large datasets and the location of each registry. Studies were excluded if they used institutional registries. Reviewers also identified the most frequently utilized registries to determine how their use has fluctuated over this time frame.
UNASSIGNED: A total of 3354 abstracts were reviewed and included. Of those, 577 abstracts utilized data obtained from orthopaedic registries (17.2%): 450 of which were poster presentations (16.5% of total poster acceptances), and 127 were podium presentations (20.5% of accepted podiums). The National Surgical Quality Improvement Program (NSQIP) was the most frequent dataset utilized, with 118 (20.5%) abstracts. Of note, NSQIP\'s use peaked between 2018 and 2020 and has since slowly trended downward. On the other hand, use of both American Joint Replacement Registry (AJRR) and PearlDiver registry have drastically increased since 2019, with only 6 abstracts chosen in 2019 and 28 abstracts in 2022 (10 AJRR [3 podiums] and 18 PearlDiver [6 podiums]). The proportion of registry data has increased, with the registry abstracts peaking in 2022 as 24% of posters and 37% of podium utilized data from large registry data sets (P < .001).
UNASSIGNED: There has been a significant increase in the number of studies utilizing registry data for both podium and poster presentations at the American Association of Hip and Knee Surgeons annual meeting. While NSQIP was the most utilized, its use has steadily declined while AJRR and PearlDiver use have increased over the past 3 years. Individuals should understand the strengths and weaknesses of each registry before making conclusions on study results.
UNASSIGNED: Level IV.

Compound databases (DBs) are essential tools for drug discovery. The number of DBs in public domain is increasing, so it is important to analyze these DBs. In this article, the main characteristics of 64 DBs will be presented. The methodological strategy used was a literature search. To analyze the characteristics obtained in the review, the DBs were categorized into two subsections: Open Access and Commercial DBs. Open access includes generalist DBs (containing compounds of diverse origins), DBs with specific applicability, DBs exclusive to natural products and those containing compounds with specific pharmacological action. The literature review showed that there are challenges to making these repositories available, such as standardizing information curation practices and funding to maintain and sustain them.
[Box: see text].