Article-Level Metrics.

In the era of digitization and Open Access, article-level metrics are increasingly employed to distinguish influential research works and adjust research management strategies. Tagging individual articles with digital object identifiers allows exposing them to numerous channels of scholarly communication and quantifying related activities. The aim of this article was to overview currently available article-level metrics and highlight their advantages and limitations. Article views and downloads, citations, and social media metrics are increasingly employed by publishers to move away from the dominance and inappropriate use of journal metrics. Quantitative article metrics are complementary to one another and often require qualitative expert evaluations. Expert evaluations may help to avoid manipulations with indiscriminate social media activities that artificially boost altmetrics. Values of article metrics should be interpreted in view of confounders such as patterns of citation and social media activities across countries and academic disciplines.

Loss of PKD1/polycystin-1 impairs lysosomal activity in a CAPN (calpain)-dependent manner.

Mutations in the PKD1 gene result in autosomal dominant polycystic kidney disease (ADPKD), the most common monogenetic cause of end-stage renal disease (ESRD) in humans. Previous reports suggested that PKD1, together with PKD2/polycystin-2, may function as a receptor-cation channel complex at cilia and on intracellular membranes and participate in various signaling pathways to regulate cell survival, proliferation and macroautophagy/autophagy. However, the exact molecular function of PKD1 and PKD2 has remained enigmatic. Here we used Pkd1-deficient mouse inner medullary collecting duct cells (mIMCD3) genetically deleted for Pkd1, and tubular epithelial cells isolated from nephrons of doxycycline-inducible conditional pkd1fl/fl;Pax8rtTA;TetOCre+ knockout mice to show that the lack of Pkd1 caused diminished lysosomal acidification, LAMP degradation and reduced CTSB/cathepsin B processing and activity. This led to an impairment of autophagosomal-lysosomal fusion, a lower delivery of ubiquitinated cargo from multivesicular bodies (MVB)/exosomes to lysosomes and an enhanced secretion of unprocessed CTSB into the extracellular space. The TFEB-dependent lysosomal biogenesis pathway was however unaffected. Pkd1-deficient cells exhibited increased activity of the calcium-dependent CAPN (calpain) proteases, probably due to a higher calcium influx. Consistent with this notion CAPN inhibitors restored lysosomal function, CTSB processing/activity and autophagosomal-lysosomal fusion, and blocked CTSB secretion and LAMP degradation in pkd1 knockout cells. Our data reveal for the first time a lysosomal function of PKD1 which keeps CAPN activity in check and ensures lysosomal integrity and a correct autophagic flux.Abbreviations: acCal: acetyl-calpastatin peptide; ADPKD: autosomal dominant polycystic kidney disease; CI-1: calpain inhibitor-1; CQ: chloroquine; Dox: doxycycline; EV: extracellular vesicles; EXO: exosomes; LAMP1/2: lysosomal-associated membrane protein 1/2; LGALS1/GAL1/galectin-1: lectin, galactose binding, soluble 1; LMP: lysosomal membrane permeabilization; mIMCD3: mouse inner medullary collecting duct cells; MV: microvesicles; MVB: multivesicular bodies; PAX8: paired box 8; PKD1/polycystin-1: polycystin 1, transient receptor potential channel interacting; PKD2/polycystin-2: polycystin 2, transient receptor potential cation channel; Tet: tetracycline; TFEB: transcription factor EB; VFM: vesicle-free medium; WT: wild-type.

Comprehensive Approach to Open Access Publishing: Platforms and Tools.

The Open Access Initiative is gaining momentum due to the worldwide availability of advanced digital tools, online publishing platforms, and systems for tracking academic contributions. Several declarations and initiatives, including Plan S, have already laid a foundation for moving away from subscription to full and immediate open-access publishing. The global initiatives imply targeting journals satisfying the upgraded quality and visibility criteria. To meet these criteria, a comprehensive approach to Open Access is recommended. This article overviews the essential components of the comprehensive approach, increasing transparency, adherence to ethical standards, and diversification of evaluation metrics. With the increasing volume of quality open-access journals, their indexing with free databases and search engines is becoming increasingly important. The Directory of Open Access Journals and PubMed Central currently free searches of open-access sources. These services, however, cannot fully satisfy the increasing demands of the users, and attempts are underway to upgrade the indexing and archiving of open-access sources in China, Japan, Korea, Russia, and elsewhere. The wide use of identifiers is essential for transparency of scholarly communications. Peer reviewers are now offered credits from Publons. These credits are transferrable to their Open Researcher and Contributor iDs. Various social media channels are increasingly used by scholars to comment on articles. All these comments are tracked by related metric systems, such as Altmetrics. Combined with traditional citation evaluations, the alternative metrics can help timely identify and promote publications influencing education, research, and practice.

Updated Editorial Guidance for Quality and Reliability of Research Output.

Over the past few years, updated editorial policy statements of several associations have provided a platform for improving the quality of scientific research and publishing. The updates have particularly pointed to the need for following research reporting standards, authorship and contributorship regulations, implementing digital tools for the identification and crediting academic contributors, and moving towards optimal ethical open-access models. This article overviews some of the recent editorial policy statements of global editorial associations and reflects on the role of the regional counterparts in advancing scholarly publishing. One of the globally promoted documents is the Recommendations of the International Committee of Medical Journal Editors (ICMJE). Its latest versions contain statements on proper research reporting, reviewing, editing, and publishing. Points on ethical target journals and 'predatory' sources are also available. This year, in a move to update its editorial policy, the Committee on Publication Ethics (COPE) released the Core Practices, comprehensively reflecting on the major issues in publication ethics. Updated joint statements of medical writers associations are also available to implement transparent policy on contributorship in sponsor-supported research projects and related reports. Several suggestions are put forward to improve global editorial statements on online profiling, crediting, and referencing. It is also highlighted that knowledge and implementation of updated editorial guidance is essential for editors' good standing.

Researcher and Author Profiles: Opportunities, Advantages, and Limitations.

Currently available online profiling platforms offer various services for researchers and authors. Opening an individual account and filling it with scholarly contents increase visibility of research output and boost its impact. This article overviews some of the widely used and emerging profiling platforms, highlighting their tools for sharing scholarly items, crediting individuals, and facilitating networking. Global bibliographic databases and search platforms, such as Scopus, Web of Science, PubMed, and Google Scholar, are widely used for profiling authors with indexed publications. Scholarly networking websites, such as ResearchGate and Academia.edu, provide indispensable services for researchers poorly visible elsewhere on the Internet. Several specialized platforms are designed to offer profiling along with their main functionalities, such as reference management and archiving. The Open Researcher and Contributor Identification (ORCID) project has offered a solution to the author name disambiguation. It has been integrated with numerous bibliographic databases, platforms, and manuscript submission systems to help research managers and journal editors select and credit the best reviewers, and other scholarly contributors. Individuals with verifiable reviewer and editorial accomplishments are also covered by Publons, which is an increasingly recognized service for publicizing and awarding reviewer comments. Currently available profiling formats have numerous advantages and some limitations. The advantages are related to their openness and chances of boosting the researcher impact. Some of the profiling websites are complementary to each other. The underutilization of various profiling websites and their inappropriate uses for promotion of 'predatory' journals are among reported limitations. A combined approach to the profiling systems is advocated in this article.

The Pressure to Publish More and the Scope of Predatory Publishing Activities.

This article overviews unethical publishing practices in connection with the pressure to publish more. Both open-access and subscription publishing models can be abused by 'predatory' authors, editors, and publishing outlets. Relevant examples of 'prolific' scholars are viewed through the prism of the violation of ethical authorship in established journals and indiscriminately boosting publication records elsewhere. The instances of ethical transgressions by brokering editorial agencies and agents, operating predominantly in non-Anglophone countries, are presented to raise awareness of predatory activities. The scheme of predatory publishing activities is presented, and several measures are proposed to tackle the issue of predatory publishing. The awareness campaigns by professional societies, consultations with information facilitators, implementation of the criteria of best target journals, and crediting of scholars with use of integrative citation metrics, such as the h-index, are believed to make a difference.

Statement on Publication Ethics for Editors and Publishers.

The digitization and related developments in journal editing and publishing necessitate increasing the awareness of all stakeholders of science communication in the emerging global problems and possible solutions. Journal editors and publishers are frequently encountered with the fast-growing problems of authorship, conflicts of interest, peer review, research misconduct, unethical citations, and inappropriate journal impact metrics. While the number of erroneous and unethical research papers and wasteful, or 'predatory', journals is increasing exponentially, responsible editors are urged to 'clean' the literature by correcting or retracting related articles. Indexers are advised to implement measures for accepting truly influential and ethical journals and delisting sources with predatory publishing practices. Updating knowledge and skills of authors, editors and publishers, developing and endorsing recommendations of global editorial associations, and (re)drafting journal instructions can be viewed as potential tools for improving ethics of academic journals. The aim of this Statement is to increase awareness of all stakeholders of science communication of the emerging ethical issues in journal editing and publishing and initiate a campaign of upgrading and enforcing related journal instructions.

Specialist Bibliographic Databases.

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

Preserving the Integrity of Citations and References by All Stakeholders of Science Communication.

Citations to scholarly items are building bricks for multidisciplinary science communication. Citation analyses are currently influencing individual career advancement and ranking of academic and research institutions worldwide. This article overviews the involvement of scientific authors, reviewers, editors, publishers, indexers, and learned associations in the citing and referencing to preserve the integrity of science communication. Authors are responsible for thorough bibliographic searches to select relevant references for their articles, comprehend main points, and cite them in an ethical way. Reviewers and editors may perform additional searches and recommend missing essential references. Publishers, in turn, are in a position to instruct their authors over the citations and references, provide tools for validation of references, and open access to bibliographies. Publicly available reference lists bear important information about the novelty and relatedness of the scholarly items with the published literature. Few editorial associations have dealt with the issue of citations and properly managed references. As a prime example, the International Committee of Medical Journal Editors (ICMJE) issued in December 2014 an updated set of recommendations on the need for citing primary literature and avoiding unethical references, which are applicable to the global scientific community. With the exponential growth of literature and related references, it is critically important to define functions of all stakeholders of science communication in curbing the issue of irrational and unethical citations and thereby improve the quality and indexability of scholarly journals.

Rewarding peer reviewers: maintaining the integrity of science communication.

This article overviews currently available options for rewarding peer reviewers. Rewards and incentives may help maintain the quality and integrity of scholarly publications. Publishers around the world implemented a variety of financial and nonfinancial mechanisms for incentivizing their best reviewers. None of these is proved effective on its own. A strategy of combined rewards and credits for the reviewers1 creative contributions seems a workable solution. Opening access to reviews and assigning publication credits to the best reviews is one of the latest achievements of digitization. Reviews, posted on academic networking platforms, such as Publons, add to the transparency of the whole system of peer review. Reviewer credits, properly counted and displayed on individual digital profiles, help distinguish the best contributors, invite them to review and offer responsible editorial posts.

Systematic and open identification of researchers and authors: focus on open researcher and contributor ID.

Unique identifiers of researchers and authors can help all stakeholders of scientific communications improve their workflows. There have been several attempts to establish professional networks of scholars and list their scholarly achievements on digital platforms. Some of these platforms such as Google Scholar, Web of Knowledge and PubMed are searched to pick relevant peer reviewers, assess authors' publication history or choose suitable candidates for research and academic projects. However, each of these hubs has its specific applications, limiting the universal use for permanent tagging of researcher profiles. The Open Researcher and Contributor ID (ORCID) initiative, launched in 2012, is aimed at registering scholarly contributors and averting the persistent ambiguity of recorded author names. The ORCID registry is growing fast and integrating with other ID-generating platforms, thereby increasing the functionality of the integrated systems. ORCID identifiers are increasingly used for selecting peer reviewers and acknowledging various scholarly contributions (e.g., published articles, reviewer comments, conference presentations). The initiative offers unique opportunities for transparent disclosures of author contributions and competing interests and improving ethical standards of research, editing, and publishing.

Vertebrate evolution reflected in the evolution of nuclear ribosomal internal transcribed spacer 2.

In eukaryotes, mature rRNA sequences are produced from single large (45S) precursor (pre-rRNA) as the result of successive removal of spacers through a series of rapid and intricate actions of endo- and exonucleases. The excision of internal transcribed spacer (ITS2), a eukaryotic-specific insertion, remains the most elusive processing step. ITS2 is the element mandatory for all eukaryotic pre-rRNAs that contain at least three processing cleavage sites for precise 5.8S and 28S formation. Conserved core sequences (cis-elements) binding to trans-factors provide for precise rRNA processing, whereas rapidly diverging regions between the core sequences preserve internal complementarity, which guarantees the spatial integrity of ITS2. Characteristic differences in the formation of such insertions during evolution should reflect the relationships between taxa. The phylogeny of the reptiles and the relationships between taxa proposed by scientists are controversial. To delineate the structural and functional features preserved among reptilian ITS2s, we cloned and sequenced 58 ITS2s belonging to four reptile orders: Squamata, Crocodilians, Aves, and Testudines. We studied the subsequent alignment and folding of variable regions. The sizes and packing of the loop-stems between conserved consensus segments in reptiles vary considerably between taxa. Our phylogenetic trees constructed on the basis of the reptile ITS2s primary structural alignments revealed a split between Iguania clade and all other taxa. True lizards (suborder Scleroglossa) and snakes (suborder Serpentes) show sister relationships, as well as the two other reptilian orders, Crocodilia+Aves and Testudines. In summary, our phylogenetic trees exhibit a mix of specific features deduced or, to the contrary, rejected earlier by other authors.