Chemical Names Research Articles

The Lithuanian Soviet Nomenclature as an Object and Subject of Control

The topic of nomenclature in the context of research on the Soviet period is usually associated with the power and influence exerted by a single group in society. While assessing the evolution of the post-Stalin system, the role of a separate ruling stratum rather than that of an individual leader becomes more apparent. Many studies hesitate to call the post-Stalin system totalitarian and secretary-generals of the Communist Party as unilateral leaders. In individual studies, nomenclature, particularly top ranking, is clearly perceived as an acting and influencing subject, capable of subjecting system resources to its articulated aims. However, the discussion of the role of Lithuanian nomenclature as a certain peripheral elite and its relationship with the system shows that it is impossible to treat it only as an acting subject. The interests and management style of the central government determined greater or lesser control of the Soviet republics. So it is interesting to consider which situations would define the Lithuanian Soviet nomenclature itself as an object of control, and in which areas it could express its own interests and be activity. The Soviet institutional environment was saturated with control. Control measures were designed not only to control processes in society; they were also applied to the system of nomenclature itself by applying hierarchical control principles both to the governing political party and lower executive ranks. Information was collected about ideological compliance and participation in the execution of plans. Transgressions recognised to be ideological were assessed most strictly. The tools of control were diverse: in addition to control bodies (people’s control, GLAVLIT, KGB) Communist party structures and ministries had their own divisions responsible for control of the activities of a particular area and even the suitability of people. In addition to routine planned activity, individual influential officials carried out controlling functions and exposed ad hoc cases. It can be stated that the system was essentially saturated with control activities – the same area was controlled by at least 3-4 levels different levels of officials and this obviously stifled the dynamics of any activity. In the late Soviet period, locality as a factor of social environment can be clearly distinguished whereby local representatives of the nomenclature would often reduce the effect of control by replacing the object ‘what and how to control’ with the consensus of higher ranking officials of the nomenclature regarding the areas and leaders to be controlled and possible consequences of control (including penalties for members of the Communist Party). This model complemented institutional regulation and was applied not only to ensure control inside a republic but also in relation to the supervision carried out by the centre. The government of the republic frequently faced hostility from some leaders controlling the manufacturing industry, but except for one incident, it managed to ‘localise’ both local and arriving leaders, thereby creating a certain closed social network of members of the nomenclature of the republic and simultaneously opening more opportunities for higher ranking officials of Lithuanian nomenclature to express their personal interests, assess the situation subjectively, and act in the area of control as a subject rather than an object. The social network of members of the nomenclature of the republic rather actively and using various measures sought to isolate their own circle therefore ensuring not only the integrity of the circle, but also control of the space subordinate to it, while at the same time maintaining good relations with the centre. The top ranking officials of the republic were very keen to maintain the stability of this network and their primary goal was to preserve the routine of governing, given that this status quo was in line with Brezhnev’s governing style.

Comprehensive Data Evaluation Methods Used in Developing the SWGDRUG Mass Spectral Reference Library for Seized Drug Identification.

The mass spectral library of the Scientific Working Group for the Analysis of Seized Drugs (SWGDRUG) is the most comprehensive free reference database of its kind in the world. It provides reliable mass spectra for identification of seized drugs, their metabolites, and related forensic compounds when using gas chromatography/mass spectrometry (GC/MS). The SWGDRUG library (version 3.13) contains spectra for 3598 compounds. All spectra are evaluated by the Mass Spectrometry Data Center (MSDC) at the National Institute of Standards and Technology (NIST). Over the past few years, new evaluation methods aided by improved software have been developed. First, all chemical information, such as chemical structure and name, is confirmed. Second, the product ions in each spectrum are verified to match the compound structure using the NIST MS Interpreter software tool. Subsequently, the mass spectra are compared to the same or similar compounds across six different mass spectral reference libraries using three distinct library search methods. Additionally, the NIST Artificial Intelligence Retention Indices (AIRI) software is used to help confirm the corresponding compounds of spectra, especially for those without molecular ions. Low-quality and incorrect spectra are rejected for inclusion in the library.

International Union of Basic and Clinical Pharmacology. CXVIII. Update on the Nomenclature for Atypical Chemokine Receptors including ACKR5.

Chemokines signal through classical G protein-coupled receptors (GPCRs) to induce cell migration during development, immune homeostasis and multiple diseases. Over the last decade a subfamily of atypical chemokine receptors (ACKRs) was delineated from GPCRs based on their inability to trigger conventional G protein signaling or mediate cell migration in response to chemokines. These receptors nevertheless play an important role within the chemokine system by sequestering, transporting or internalizing chemokines thereby regulating their availability and shaping their gradients. GPR182, the recently deorphanized chemokine receptor, shares about 30% of sequence similarity with its closest relative ACKR3. GPR182 is mainly expressed on endothelial cells and was proposed to act as a scavenger regulating the availability of a large set of chemokines from the CXC, CC and XC families and to act cooperatively with ACKR3 and ACKR4. Unlike other ACKRs, GPR182 was shown to have a strong constitutive interaction with β-arrestins that is required for intracellular receptor trafficking and chemokine scavenging. Chemokine ligation of GPR182 has no additional detectable impact on β-arrestin recruitment. Genetic ablation of GPR182 affects spleen size, myelopoiesis, and serum chemokine levels, indicating its role in chemokine homeostasis and immune regulation. GPR182 was also reported to regulate immune responses to bloodborne antigens and tumorigenesis. Taken together, compelling cumulative evidence indicates that GPR182 does not trigger G protein-mediated signaling but acts as a scavenger for chemokines in vitro and in vivo strongly supporting its inclusion as ACKR5 in the systematic nomenclature of chemokine receptors. Significance Statement The summarized presented findings strongly support the designation of GPR182 as ACKR5 and its formal inclusion in the family of atypical chemokine receptors.

A systematic evidence map protocol for mapping global exposure to bisphenols and their alternatives and social and environmental justice implications

BackgroundBisphenol A (BPA) is one of the highest-volume chemicals produced worldwide, and human exposure to BPA is thought to be ubiquitous. Stricter regulations around the use of BPA have led many manufacturers to switch to other bisphenol chemicals with similar functions such as bisphenol S and F. Even though exposure to BPA, other bisphenol chemicals and bisphenol alternatives poses a health risk for humans, very little is known about the granular exposure levels of different populations around the world. AimThis systematic evidence map (SEM) will identify human studies reporting concentrations of bisphenols and their alternatives measured in human bio-samples with the aim to chart the global human exposure levels by country and population characteristics to identify research gaps and discuss any social and environmental injustice implications. Search strategy and eligibility criteriaMEDLINE®, Embase and Web of Science (WoS) databases as well as grey literature sources will be searched using predefined search strings. The database search results will be supplemented by backward and forward citation tracking on included studies. A scoping exercise conducted during planning identified 90 bisphenol chemicals and alternatives used in plastics. These include BPA, other bisphenol chemicals with/without similar functions to BPA as well as alternatives with similar functions to bisphenol chemicals. Eligible studies must report concentrations of at least one relevant bisphenol chemical/alternative measured in human bio-samples. Study selectionOnly primary studies published in English since 2010 will be considered. The title, abstract and keywords will be screened by the DistillerAI tool and two independent reviewers. Grey literature will be screened by two reviewers for inclusion and exclusion. The full text of the included studies will then be screened by two independent reviewers. Study appraisalStudy quality will not be evaluated in this SEM. Data extraction and codingData extraction and coding will be performed by two independent reviewers. Parameters of interest will include the following: study characteristics (e.g., year of publication, sampling timepoints and study design), population information (e.g., country, age, sex, ethnicity, number of participants) and exposure information (sources of exposure, bio-sample analyzed, chemical name, concentration, and detection frequencies). Synthesis and visualizationThe results will be presented using a narrative summary, tables, bar plots and color-coded maps. The interactive database will be available on a dedicated freely accessible website. Systematic map protocol registry and registration numberThis protocol has been registered on Open Science Framework (OSF) and is available at https://doi.org/10.17605/OSF.IO/MNWTD.

Poor Acceptance of the Revised Classification of Premalignant Anal Lesions Following the LAST Standardized Project.

The Lower Anogenital Squamous Terminology (LAST) Project recommended unified classification for HPV-associated squamous lesions of the lower anogenital tract, using a 2-tiered nomenclature in 2013. Adherence to the new nomenclature worldwide is unknown. This study aims to assess the trend of the use of the two-tiered High Squamous Intraepithelial Lesion and Low Squamous Intraepithelial Lesion (HSIL/LSIL) as opposed to the traditional three-tiered Anal Intraepithelial Neoplasia (AIN I/II/III) classification as suggested by the LAST Project. A literature search on full-text English language studies of premalignant anal lesion was performed on PubMed from 2002-2022. The studies were categorized by continent, and the prevalence of HSIL/LSIL classification vs AIN I/II/III was calculated. 546 studies and 251 studies were identified using the AIN I/II/II and the HSIL/LSIL classification respectively. Global trend suggested a statistically significant downward trend in the use of the two-tiered nomenclature system in publications globally. Regional trend including North America, Europe, and other (Asia and Latin America) showed variance in adoption of the two-tiered nomenclature system. Despite multidisciplinary collaborative effort, adherence to the recommendations to use the two-tiered system for HPV-associated premalignant anal lesions continues to be suboptimal. Further efforts are needed to identify the cause of poor adherence to be able to create strategies that reinforces unification of terminology and integration of LAST the recommendations.

Simplified Nomenclature and Projection Diagrams of Chiral Cubane Analogs.

A simplified nomenclature for chiral cubane analogs is proposed where analogs with a clockwise systematic continuous numbering of the cubane core are designated as (C)-, and analogs with an anticlockwise continuous numbering of the cubane core are designated as (A)-. This method is accurate, allows for the rapid conversion of the chemical name to a structure, and it eliminates the need to designate the stereochemistry of each of the 8 carbons of cubane.

Ferredoxins: Functions, Evolution, Potential Applications, and Challenges of Subtype Classification.

Ferredoxins are proteins found in all biological kingdoms and are involved in essential biological processes including photosynthesis, lipid metabolism, and biogeochemical cycles. Ferredoxins are classified into different groups based on the iron-sulfur (Fe-S) clusters that they contain. A new subtype classification and nomenclature system, based on the spacing between amino acids in the Fe-S binding motif, has been proposed in order to better understand ferredoxins' biological diversity and evolutionary linkage across different organisms. This new classification system has revealed an unparalleled diversity between ferredoxins and has helped identify evolutionarily linked ferredoxins between species. The current review provides the latest insights into ferredoxin functions and evolution, and the new subtype classification, outlining their potential biotechnological applications and the future challenges in streamlining the process.

Metabolic Pathways of Acylcarnitine Synthesis.

Acylcarnitines are important markers in metabolic studies of many diseases, including metabolic, cardiovascular, and neurological disorders. We reviewed analytical methods for analyzing acylcarnitines with respect to the available molecular structural information, the technical limitations of legacy methods, and the potential of new mass spectrometry-based techniques to provide new information on metabolite structure. We summarized the nomenclature of acylcarnitines based on historical common names and common abbreviations, and we propose the use of systematic abbreviations derived from the shorthand notation for lipid structures. The transition to systematic nomenclature will facilitate acylcarnitine annotation, reporting, and standardization in metabolomics. We have reviewed the metabolic origins of acylcarnitines important for the biological interpretation of human metabolomic profiles. We identified neglected isomers of acylcarnitines and summarized the metabolic pathways involved in the synthesis and degradation of acylcarnitines, including branched-chain lipids and amino acids. We reviewed the primary literature, mapped the metabolic transformations of acyl-CoAs to acylcarnitines, and created a freely available WikiPathway WP5423 to help researchers navigate the acylcarnitine field. The WikiPathway was curated, metabolites and metabolic reactions were annotated, and references were included. We also provide a table for conversion between common names and abbreviations and systematic abbreviations linked to the LIPID MAPS or Human Metabolome Database.

Regenerative Retinal Laser and Light Therapies (RELITE): Proposal of a New Nomenclature, Categorization, and Trial Reporting Standard.

Numerous laser and light therapies have been developed to induce regenerative processes in the choroid/retinal pigment epithelium (RPE)/photoreceptor complex, leaving the neuroretina undamaged. These therapies are applied to the macula for the treatment of various diseases, most prominently diabetic maculopathy, retinal vein occlusion, central serous chorioretinopathy, and age-related macular degeneration. However, the abundance of technologies, treatment patterns, and dosimetry protocols has made understanding these therapies and comparing different approaches increasingly complex and challenging. To address this, we propose a new nomenclature system with a clear categorization that will allow for better understanding and comparability between different laser and light modalities. We propose this nomenclature system as an open standard that may be adapted in future toward new technical developments or medical advancements. A systematic literature review of reported macular laser and light therapies was conducted. A categorization into a standardized system was proposed and discussed among experts and professionals in the field. This paper does not aim to assess, compare, or evaluate the efficacy of different laser or dosimetry techniques or treatment patterns. The literature search yielded 194 papers describing laser techniques, 50 studies describing dosimetry, 272 studies with relevant clinical trials, and 82 reviews. Following the common therapeutic aim, we propose "regenerative retinal laser and light therapies (RELITE)" as the general header. We subdivided RELITE into four main categories that refer to the intended physical and biochemical effects of temperature increase (photothermal therapy, PTT), RPE regeneration (photomicrodisruption therapy, PMT), photochemical processes (photochemical therapy, PCT), and photobiomodulation (photobiomodulation therapy, PBT). Further, we categorized the different dosimetry approaches and treatment regimens. We propose the following nomenclature system that integrates the most important parameters to enable understanding and comparability: Pattern-Dosimetry-Exposure Time/Frequency, Duty Cycle/Irradiation Diameter/Wavelength-Subcategory-Category. Regenerative retinal laser and light therapies are widely used for different diseases and may become valuable in the future. A precise nomenclature system and strict reporting standards are needed to allow for a better understanding, reproduceable and comparable clinical trials, and overall acceptance. We defined categories for a systematic therapeutic goal-based nomenclature to facilitate future research in this field.

Medication Management Strategies to Support Medication Adherence: Interview Study With Older Adults.

Home medication management has been insufficiently studied, including the factors that impact the development and effectiveness of adherence strategies under both routine and anomalous circumstances. Older adults are a particularly important population to study due to the greater likelihood of taking medication in combination with the desire to "age in place." This interview study aims to understand how older adults develop medication management strategies, identify when and why such strategies succeed or fail, learn more about how older adults think about their medication, and explore interventions that increase medication adherence. This study used a qualitative, semistructured interview design to elicit older adults' experiences with home medication management. Overall, 22 participants aged ≥50 years taking 1 to 3 prescription medications were recruited and interviewed. Interview responses were recorded, and thematic, qualitative analysis was performed by reviewing recordings and identifying recurring patterns and themes. Responses were systematically coded, which not only facilitated the identification of these themes but also allowed us to quantify the prevalence of behaviors and perceptions, providing a robust understanding of medication management and medication adherence. Participants reported developing home medication management strategies on their own, with none of the participants receiving guidance from health care providers and 59% (13/22) of the participants using trial and error. The strategies developed by study participants were all unique and generally encompassed prescription medication and vitamins or supplements, with no demarcation between what was prescribed or recommended by a physician and what they selected independently. Participants thought about their medications by their chemical name (10/22, 45%), by the appearance of the pill (8/22, 36%), by the medication's purpose (2/22, 9%), or by the medication's generic name (2/22, 9%). Pill cases (17/22, 77%) were more popular than prescription bottles (5/22, 23%) for storage of daily medication. Most participants (19/22, 86%) stored their pill cases or prescription bottles in visible locations in the home, and those using pill cases varied in their refill routines. Participants used ≥2 routines or objects as triggers to take their medication. Nonadherence was associated with a disruption to their routine. Finally, only 14% (3/22) of the participants used a time-based reminder or alarm, and none of the participants used a medication adherence device or app. Participants in our study varied considerably in their home medication management strategies and developed unique routines to remember to take their medication as well as to refill their pill cases. To reduce trial and error in establishing a strategy, there are opportunities for physicians and pharmacists to provide adherence guidance to older adults. To minimize the impact of disruptions on adherence, there are opportunities to develop more durable strategies and to design aids to medication adherence that leverage established daily routines.

Anatomical classification of canine congenital extrahepatic portosystemic shunts based on CT angiography: A SVSTS and VIRIES multi-institutional study in 1082 dogs.

Canine congenital extrahepatic portosystemic shunt (EHPSS) morphologies have not been fully elucidated. The goal of this retrospective, multi-institutional study was to use CT angiography to create an anatomical-based nomenclature system for canine congenital EHPSS. These shunt morphologies were then evaluated to identify any significant association with patient age, sex, breed, weight, or subjective portal perfusion score. Data collected respectively from the SVSTS and VIRIES list-serves included patient DOB, sex, breed, weight, CT date, and reported diagnosis. A single author (C.W.) viewed all CT scans and classified shunts based on the shunt portal vessel(s) of origin, the shunt systemic vessel(s) of insertion, and any substantial portal vessels contributing to the shunt. Additionally, hepatic portal perfusion was subjectively scored between one (poor/none) and five (good/normal) based on the caliber of the intrahepatic portal veins. A total of 1182 CT scans were submitted from 13 different institutions. Due to exclusion criteria, 100 (8.5%) were removed, leaving 1082 CT scans to be included. Forty-five different EHPSS anatomies were identified with five classifications accounting for 85% of all shunts (left gastric-phrenic [27%], left gastric-azygos [19%], left gastric-caval [15%], aberrant left gastric-caval with right gastric vein [12%], and aberrant left gastric-caval with right gastric vein and short gastric vein [11%]). Shunt origin involved the left gastric vein in 95% of the described classifications. Significant differences were identified among the five most common shunt types with respect to age at the time of the CT scan (P<.001), sex (P=.009), breed (P<.001), weight (P<.001), and subjective portal perfusion score (P<.001). An anatomical classification system for canine EHPSS may enable improved understanding, treatment comparisons, and outcome prediction for these patients.

Proposal for a Global Classification and Nomenclature System for A/H9 Influenza Viruses.

Influenza A/H9 viruses circulate worldwide in wild and domestic avian species, continuing to evolve and posing a zoonotic risk. A substantial increase in human infections with A/H9N2 subtype avian influenza viruses (AIVs) and the emergence of novel reassortants carrying A/H9N2-origin internal genes has occurred in recent years. Different names have been used to describe the circulating and emerging A/H9 lineages. To address this issue, an international group of experts from animal and public health laboratories, endorsed by the WOAH/FAO Network of Expertise on Animal Influenza, has created a practical lineage classification and nomenclature system based on the analysis of 10,638 hemagglutinin sequences from A/H9 AIVs sampled worldwide. This system incorporates phylogenetic relationships and epidemiologic characteristics designed to trace emerging and circulating lineages and clades. To aid in lineage and clade assignment, an online tool has been created. This proposed classification enables rapid comprehension of the global spread and evolution of A/H9 AIVs.

Cultures as types and the utility of viable specimens for fungal nomenclature

The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.

A Review On : To Develop and Validate Analytical Method for Determination of Methimazole in Bulk and Pharmaceutical Dosage Form

Hyperthyroidism is a condition characterized by increased in synthesis and secretion of thyroid hormones from thyroid gland. Methimazole is an anti-hyperthyroidism drug. It is of great importance and significance for life science. Up to now, various different methods have been applied for the determination of methimazole, such as spectrophotometry1-3, LC4, HPLC6, RP-HPLC7, HPLC-UV8, electrochemical analysis9, kinetic method10. In this paper, a new UV-Spectrophotometric method for the determination of methimazole has been established. The chemical name of Methimazole is (1-methylimidazole-2-thiol). The chemical formula of Methimazole is C4H6N2S and the molecular weight is 114.17 g/mol. The structure of Methimazole features a 5 membered imidazole ring with a methyl group at position 1st and thione group at position 2nd. Methimazole is white colour powder and has melting point 1440 C.

DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance.

The reliable and timely recognition of outbreaks is a key component of public health surveillance for foodborne diseases. Whole genome sequencing (WGS) offers high resolution typing of foodborne bacterial pathogens and facilitates the accurate detection of outbreaks. This detection relies on grouping WGS data into clusters at an appropriate genetic threshold. However, methods and tools for selecting and adjusting such thresholds according to the required resolution of surveillance and epidemiological context are lacking. Here we present DODGE (Dynamic Outbreak Detection for Genomic Epidemiology), an algorithm to dynamically select and compare these genetic thresholds. DODGE can analyse expanding datasets over time and clusters that are predicted to correspond to outbreaks (or "investigation clusters") can be named with established genomic nomenclature systems to facilitate integrated analysis across jurisdictions. DODGE was tested in two real-world Salmonella genomic surveillance datasets of different duration, 2 months from Australia and 9 years from the United Kingdom. In both cases only a minority of isolates were identified as investigation clusters. Two known outbreaks in the United Kingdom dataset were detected by DODGE and were recognized at an earlier timepoint than the outbreaks were reported. These findings demonstrated the potential of the DODGE approach to improve the effectiveness and timeliness of genomic surveillance for foodborne diseases and the effectiveness of the algorithm developed. DODGE is freely available at https://github.com/LanLab/dodge and can easily be installed using Conda.

Personal Names of 14-16th Century Armenian Lapidary Inscriptions (Region of Present-Day Ukraine)

The personal names in the lithographic inscriptions of the 14th-16th centuries there are some personal names, which in some cases are a novelty in our Armenian personal nomenclature system. Studing those, Acharyan's dictionary of personal names can be supplemented with not only numerical personal names (Khachum, Khatrshay, Malkhas, Nor Paron, Satat, Sarupeh, Aziz Khatun, Chihan, Pey Meliq, Sirakhatun, Tilshat), but also new phonetic versions of personal names (Raqel, Ulpek, Tagorshah), and new personal names (Ataka, Armushqah, Badiar, Yeaulik, Tulayd, Khachkarapet, Hundish, Merhider, Mikhno, Mutakh). The existence of new personal names also testifies to the literary Armenian that in the middle period of the development of the Armenian, the process of personal identification continued in the life of the Armenians of the colony, which is mentioned by the lithographic inscriptions. Referring only to the records of the region of present-day Ukraine, it’s noticeable that the local Armenians migrated mainly from Ani in the order of inheritance preserving their personal nomenclature system. Some of them (Sargis, Meliq, Petros, Ghazar, Grigor) were handed down from the ancient period of development of literary Armenian and are stil used nowdays, others (Asli, Babah, Badiar), present a new layer in the middle literary Armenian due to the influence of the foreign environment.

Investigating diversity and similarity between CBM13 modules and ricin-B lectin domains using sequence similarity networks

BackgroundThe CBM13 family comprises carbohydrate-binding modules that occur mainly in enzymes and in several ricin-B lectins. The ricin-B lectin domain resembles the CBM13 module to a large extent. Historically, ricin-B lectins and CBM13 proteins were considered completely distinct, despite their structural and functional similarities.ResultsIn this data mining study, we investigate structural and functional similarities of these intertwined protein groups. Because of the high structural and functional similarities, and differences in nomenclature usage in several databases, confusion can arise. First, we demonstrate how public protein databases use different nomenclature systems to describe CBM13 modules and putative ricin-B lectin domains. We suggest the introduction of a novel CBM13 domain identifier, as well as the extension of CAZy cross-references in UniProt to guard the distinction between CAZy and non-CAZy entries in public databases. Since similar problems may occur with other lectin families and CBM families, we suggest the introduction of novel CBM InterPro domain identifiers to all existing CBM families. Second, we investigated phylogenetic, nomenclatural and structural similarities between putative ricin-B lectin domains and CBM13 modules, making use of sequence similarity networks. We concluded that the ricin-B/CBM13 superfamily may be larger than initially thought and that several putative ricin-B lectin domains may display CAZyme functionalities, although biochemical proof remains to be delivered.ConclusionsRicin-B lectin domains and CBM13 modules are associated groups of proteins whose database semantics are currently biased towards ricin-B lectins. Revision of the CAZy cross-reference in UniProt and introduction of a dedicated CBM13 domain identifier in InterPro may resolve this issue. In addition, our analyses show that several proteins with putative ricin-B lectin domains show very strong structural similarity to CBM13 modules. Therefore ricin-B lectin domains and CBM13 modules could be considered distant members of a larger ricin-B/CBM13 superfamily.

Protecting stable biological nomenclatural systems enables universal communication: A collective international appeal.

The fundamental value of universal nomenclatural systems in biology is that they enable unambiguous scientific communication. However, the stability of these systems is threatened by recent discussions asking for a fairer nomenclature, raising the possibility of bulk revision processes for "inappropriate" names. It is evident that such proposals come from very deep feelings, but we show how they can irreparably damage the foundation of biological communication and, in turn, the sciences that depend on it. There are four essential consequences of objective codes of nomenclature: universality, stability, neutrality, and transculturality. These codes provide fair and impartial guides to the principles governing biological nomenclature and allow unambiguous universal communication in biology. Accordingly, no subjective proposals should be allowed to undermine them.

PubChem synonym filtering process using crowdsourcing

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most requested tasks in PubChem and other chemical databases is to search chemicals by name (also commonly called a “chemical synonym”). PubChem performs this task by looking up chemical synonym-structure associations provided by individual depositors to PubChem. In addition, these synonyms are used for many purposes, including creating links between chemicals and PubMed articles (using Medical Subject Headings (MeSH) terms). However, these depositor-provided name-structure associations are subject to substantial discrepancies within and between depositors, making it difficult to unambiguously map a chemical name to a specific chemical structure. The present paper describes PubChem’s crowdsourcing-based synonym filtering strategy, which resolves inter- and intra-depositor discrepancies in synonym-structure associations as well as in the chemical-MeSH associations. The PubChem synonym filtering process was developed based on the analysis of four crowd-voting strategies, which differ in the consistency threshold value employed (60% vs 70%) and how to resolve intra-depositor discrepancies (a single vote vs. multiple votes per depositor) prior to inter-depositor crowd-voting. The agreement of voting was determined at six levels of chemical equivalency, which considers varying isotopic composition, stereochemistry, and connectivity of chemical structures and their primary components. While all four strategies showed comparable results, Strategy I (one vote per depositor with a 60% consistency threshold) resulted in the most synonyms assigned to a single chemical structure as well as the most synonym-structure associations disambiguated at the six chemical equivalency contexts. Based on the results of this study, Strategy I was implemented in PubChem’s filtering process that cleans up synonym-structure associations as well as chemical-MeSH associations. This consistency-based filtering process is designed to look for a consensus in name-structure associations but cannot attest to their correctness. As a result, it can fail to recognize correct name-structure associations (or incorrect ones), for example, when a synonym is provided by only one depositor or when many contributors are incorrect. However, this filtering process is an important starting point for quality control in name-structure associations in large chemical databases like PubChem.

Aldo-keto reductase (AKR) superfamily website and database: An update

The aldo-keto reductase (AKR) superfamily is a large family of proteins found across the kingdoms of life. Shared features of the family include 1) structural similarities such as an (α/β)8-barrel structure, disordered loop structure, cofactor binding site, and a catalytic tetrad, and 2) the ability to catalyze the nicotinamide adenine dinucleotide (phosphate) reduced (NAD(P)H)-dependent reduction of a carbonyl group. A criteria of family membership is that the protein must have a measured function, and thus, genomic sequences suggesting the transcription of potential AKR proteins are considered pseudo-members until evidence of a functionally expressed protein is available. Currently, over 200 confirmed AKR superfamily members are reported to exist. A systematic nomenclature for the AKR superfamily exists to facilitate family and subfamily designations of the member to be communicated easily. Specifically, protein names include the root “AKR”, followed by the family represented by an Arabic number, the subfamily-if one exists-represented by a letter, and finally, the individual member represented by an Arabic number. The AKR superfamily database has been dedicated to tracking and reporting the current knowledge of the AKRs since 1997, and the website was last updated in 2003. Here, we present an updated version of the website and database that were released in 2023. The database contains genetic, functional, and structural data drawn from various sources, while the website provides alignment information and family tree structure derived from bioinformatics analyses.