Species Delimitation

Species delimitation is the process of determining whether a group of sampled individuals belong to the same species or to different species. The criteria used to delimit species differ across taxonomic groups, and the methods for delimiting species have changed over time, with a dramatic rise in the popularity of genomic approaches recently. Because inferred species boundaries have ramifications that extend beyond systematics, affecting all fields that rely upon species as a foundational unit, controversy has unsurprisingly surrounded not only the practices used to delimit species boundaries, but also the idea of what species are, which varies across taxa (e.g., the use of subspecies varies across the tree of life). This lack of consensus has no doubt contributed to the appeal of genetic-based delimitation. Specifically, genomic data can be collected from any taxon. Moreover, it can be analyzed in a common statistical framework (as popularized by the multispecies coalescent as a model for species delimitation). With the ease of collecting genetic data, the power of genomics, and the purported standardization for diagnosing species limits, genetic-based species delimitation is displacing traditional time-honored (albeit time-consuming) taxonomic practices of species diagnosis. It has also become an invaluable tool for discovering species in understudied groups, and genetic-based approaches are the foundation of international endeavors to generate a catalogue of DNA barcodes to illuminate biodiversity for all of life on the planet. Yet, genomic applications, and especially the sole reliance upon genetic data for inferring species boundaries, are not without their own set of challenges.

Reading Through Emotions: An Affective Narratolological Approach to Alice Munro's Short Stories

The emergence of fields of study like emotionology, affective narratology, and psychonarratology in recent decades evidences a dramatic rise in research done on the meaning and interpretation of emotions. Affective Narratology as one of the recent fields in emotion studies attempts to identify and account for the figuration of emotions in works of literature. Focusing on three basic emotions (shame, jealousy and love) figuring in Alice Munro’s selected short stories this paper probes the significance of emotional registers in the writer's depiction of daily life. Examined is the way the stories' sincere tone and their comprehensible, ordinary language, contribute to the emotional identification of readers with characters. Applying affective narratological theories, the objective is to show how emotions contribute to plot development and characterization in these stories. Central to the analysis is interpreting emotional moments experienced by characters, especially female characters

Nyelőcső-adenocarcinoma.

Összefoglaló. Az 1970-es évek előtt a nyelőcsőrákok csupán 1–3%-a volt adenocarcinoma. A 70-es évek közepétől a nyelőcső-adenocarcinoma mutatta a legnagyobb növekedést az összes malignus daganat közül, és a 90-es évek közepétől már meghaladta a laphámrákok előfordulási gyakoriságát a nyugati világban. Ma a nyelőcső-adenocarcinoma relatív incidenciája Magyarországon 34,7%, míg a nyugati világban már 60% körül van. A nyelőcső-adenocarcinoma etiológiájában meghatároztak néhány kockázati tényezőt, így a gastrooesophagealis refluxot, a Barrett-nyelőcsövet, a kóros kövérséget, a dohányzást és a csökkenő Helicobacter pylori fertőzöttséget. Ezek a tényezők azonban jelen voltak már a 70-es évek előtt is. A kövérség előfordulásának gyakorisága és a következményes gastrooesophagealis reflux megduplázódott az elmúlt 40 évben, de ez egyedül nem magyarázza az adenocarcinomák szaporodásának ütemét. Egy új, hatékony savcsökkentő gyógyszercsoportnak, a H2-receptor-blokkolóknak a bevezetésére 1976-ban került sor, és ez egybeesik a szokatlanul nagy incidencianövekedéssel. Tom DeMeester teóriája szerint a savcsökkentő kezelés által létrehozott pH-változás okozhatja a refluxátum carcinogenitasának fokozódását. A Barrett-oesophagus és a nyelőcső-adenocarcinoma etiológiájában, megelőzésében és kezelésében számos ellentmondás és vitás kérdés tapasztalható, különösen a protonpumpagátló gyógyszerek (PPI-k) hosszú távú használata körül. A PPI-k hatásossága a gyógyszer túlzott alkalmazásához vezetett nem mindig megfelelő indikációban, kitéve a betegeket potenciális kockázatoknak. Összefoglalva, a nyelőcső-adenocarcinoma drámai növekedésében biztosan szerepet játszik az elhízás és a refluxbetegség ezzel párhuzamos terjedése. Fontos továbbá a H. pylori fertőzöttség csökkenése, és új szempont a hatásos savcsökkentő szerek széles körű alkalmazása, melyek a refluxátumban okozott pH-változással erősíthetik a carcinogenesist. Orv Hetil. 2021; 162(51): 2040–2046. Summary. Before the 1970s, only 1–3% of esophageal cancers were adenocarcinoma. Since the mid-70s, the incidence of esophageal adenocarcinoma has shown the greatest increase compared to all other cancer types and overtook squamous carcinoma incidence in the mid-90s in the Western countries. Today, the relative incidence of esophageal adenocarcinoma in Hungary is 34.7% and around 60% in the Western countries. Some risk factors for esophageal adenocarcinoma have been identified such as gastroesophageal reflux disease, Barrett’s esophagus, obesity, smoking and decreased prevalence of Helicobacter pylori infection, but these risk factors were already present before the 70s. The prevalence of obesity and the consequentially developed gastroesophageal reflux has doubled during the last 40 years, but it does not explain alone the dramatic rise in the esophageal adenocarcinoma incidence. The H2 blockers, as new effective antisecretory medication, were introduced in 1976, coinciding in time with the substantial rise of esophageal adenocarcinoma. According to the DeMeester theory, the change in the pH of gastric refluxate caused by acid suppression enhances its carcinogenic potential. There are a lot of controversies among the prevention, etiology and treatment of Barrett’s esophagus and esophageal adenocarcinoma, especially regarding the long-term use of proton pump inhibitors (PPIs), an even more effective group of acid suppressors. The effectiveness of PPIs has led to an overuse exceeding its regular indications with little benefit, exposing patients to a number of potential risks. In conclusion, in the dramatic rise of the esophageal adenocarcinoma incidence, obesity accompanied by reflux disease and the decreased incidence of H. pylori infection certainly play important roles. The introduction of modern antisecretory drugs in the treatment of acid-related diseases promoting carcinogenesis, arises as a new consideration. Orv Hetil. 2021; 162(51): 2040–2046.

Releasing the Kraken

Ten years ago, the dramatic rise in the number of microbial genomes led to an inflection point, when the approach of finding short, exact matches in a comprehensive database became just as accurate as older, slower approaches. The new idea led to a method that was hundreds of times times faster than those that came before. Today, exact k-mer matching is a standard technique at the heart of many microbiome analysis tools.

Topological Data Analysis with Applications

The continued and dramatic rise in the size of data sets has meant that new methods are required to model and analyze them. This timely account introduces topological data analysis (TDA), a method for modeling data by geometric objects, namely graphs and their higher-dimensional versions: simplicial complexes. The authors outline the necessary background material on topology and data philosophy for newcomers, while more complex concepts are highlighted for advanced learners. The book covers all the main TDA techniques, including persistent homology, cohomology, and Mapper. The final section focuses on the diverse applications of TDA, examining a number of case studies drawn from monitoring the progression of infectious diseases to the study of motion capture data. Mathematicians moving into data science, as well as data scientists or computer scientists seeking to understand this new area, will appreciate this self-contained resource which explains the underlying technology and how it can be used.

Business Model Innovation and the Rise of Technology Giants

Technology giants owe much of their success to fundamental improvements in the science and technology of information and communications technology. However, complementary advancements were also necessary, and, much as firms had to learn to incorporate electricity in the last nineteenth and early twentieth centuries, we posit that the giant platforms have learned to harness the contributions of external actors in order to grow more rapidly than would otherwise have been possible. Thus, the drivers of the dramatic rise of the tech giant platform firm can be viewed as a business model innovation as well as a technical innovation. As orchestration business models become better understood, we expect that firms in non-platform sectors are increasingly likely to adapt practices that also allow them to participate in and benefit from external value creation. At the same time, we expect regulatory scrutiny to increase as the power and reach of technology giants increases and their influence is felt across the economy.

Vital signs of Cavia porcellus (Guinea pig) diagnosed with malignant hyperthermia using sevoflurane gas

Malignant hyperthermia (MH) is a life-threatening clinical syndrome of hypermetabolism involving the skeletal muscle. It is triggered in susceptible individuals primarily by volatile inhalational anesthetic agents and the muscle relaxant succinylcholine. MH affects humans, certain pig breeds, dogs, horses, and probably other animals. The classic signs of MH include A dramatic rise in body temperature, rigid or painful muscles, especially in the jaw, flushed skin, sweating, an abnormally rapid or irregular heartbeat, rapid breathing or uncomfortable breathing, brown or cola-colored urine, very low blood pressure (shock), confusion and muscle weakness or swelling after the event. The syndrome is likely to be fatal if untreated. This study therefore assessed the effects of sevoflurane gas on the vital signs of Cavia porcellus with malignant hyperthermia. For the determination of malignant hyperthermia, 50, 15 day-old weaned kits of Peru breed were placed in an anesthesia chamber for 5 minutes and subjected to a mixture of air with 3% sevoflurane gas. Only 6% of them reacted positively, while most of them, 94%, were negative. The average body temperature of the positive kits was 38.9ºC, oscillating between 38.7 and 39.1 ° C, while the negative ones averaged 37.9 ° C. The positive kits had an average of 142.3 breaths per minute compared to the negative ones, which was determined to be 83.7. The number of heart beats per minute in the kits with a positive reaction to sevoflurane averaged 205 and the negative ones 119.5. Muscle tremors were observed throughout the body during exposure of the positive kits to sevoflurane gas. It is concluded that for every 16 guinea pigs, 1 will react to the sevoflurane gas exposure positive due to the result obtained from the vital sign. Only the positive ones presented muscle tremors. L'hyperthermie maligne (HM) est un syndrome clinique d'hypermétabolisme mettant en jeu le pronostic vital impliquant le muscle squelettique. Elle est déclenchée chez les individus sensibles principalement par des agents anesthésiques volatils par inhalation et le relaxant musculaire succinylcholine. MH affecte les humains, certaines races de porcs, les chiens, les chevaux et probablement d'autres animaux. Les signes classiques de MH comprennent une augmentation spectaculaire de la température corporelle, des muscles rigides ou douloureux, en particulier dans la mâchoire, une peau rougeoyante, une transpiration, un rythme cardiaque anormalement rapide ou irrégulier, une respiration rapide ou une respiration inconfortable, une urine brune ou de couleur cola, très faible tension artérielle (choc), confusion et faiblesse ou gonflement musculaire après l'événement. Le syndrome estsusceptible d'être fatal s'il n'est pas traité. Cette étude a donc évalué les effets du gaz sévoflurane sur les signes vitaux de Cavia porcellus avec hyperthermie maligne. Pour la détermination de l'hyperthermie maligne, 50 chatons sevrés de 15 jours de race Pérou ont été placés dans une chambre d'anesthésie pendant 5 minutes et soumis à un mélange d'air avec 3% de sévoflurane. Seuls 6 % d'entre eux ont réagi positivement, alors que la plupart d'entre eux, 94 %, ont été négatifs. La température corporelle moyenne des kits positifs était de 38,9 ° C, oscillant entre 38,7 et 39,1 ° C, tandis que les kits négatifs étaient en moyenne de 37,9 ° C. Les kits positifs avaient une moyenne de 142,3 respirations par minute par rapport aux négatifs, ce qui a été déterminé à être 83,7. Le nombre de battements cardiaques par minute dans les kits avec une réaction positive au sévoflurane était en moyenne de 205 et ceux négatifs de 119,5. Des tremblements musculaires ont été observés dans tout le corps pendant l'exposition des kits positifs au sévoflurane. Il est conclu que pour 16 cobayes, 1 réagira positivement à l'exposition au gaz sévoflurane en raison du résultat obtenu à partir du signe vital. Seuls les positifs présentaient des tremblements musculaires.

The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community

Recent years have witnessed a dramatic rise in interest towards cancer epitopes in general and particularly neoepitopes, antigens that are encoded by somatic mutations that arise as a consequence of tumorigenesis. There is also an interest in the specific T cell and B cell receptors recognizing these epitopes, as they have therapeutic applications. They can also aid in basic studies to infer the specificity of T cells or B cells characterized in bulk and single-cell sequencing data. The resurgence of interest in T cell and B cell epitopes emphasizes the need to catalog all cancer epitope-related data linked to the biological, immunological, and clinical contexts, and most importantly, making this information freely available to the scientific community in a user-friendly format. In parallel, there is also a need to develop resources for epitope prediction and analysis tools that provide researchers access to predictive strategies and provide objective evaluations of their performance. For example, such tools should enable researchers to identify epitopes that can be effectively used for immunotherapy or in defining biomarkers to predict the outcome of checkpoint blockade therapies. We present here a detailed vision, blueprint, and work plan for the development of a new resource, the Cancer Epitope Database and Analysis Resource (CEDAR). CEDAR will provide a freely accessible, comprehensive collection of cancer epitope and receptor data curated from the literature and provide easily accessible epitope and T cell/B cell target prediction and analysis tools. The curated cancer epitope data will provide a transparent benchmark dataset that can be used to assess how well prediction tools perform and to develop new prediction tools relevant to the cancer research community.

Plan Meets Reality

Chapter 2 evaluates the implementation of the reforms offered by international financial institutions and shows the propensity of these plans to foster corruption and extreme wealth inequality and, in many cases, an economic collapse that was far greater than what had been foreseen. Those connected to the old regimes or with significant outside financial backing were able to capitalize on misguided and poorly implemented privatization plans. The chapter also explores how corrupt incentive structures created the oligarch class that is the primary driver of economic inequality in the postsocialist world. Finally, it considers the depth and length of transitional recessions, analyzing economic data to show that, in many cases, recovery took decades, and for the worst hit countries, productive capacity has yet to reach pre-1989 levels. Highlighting the dramatic rise of poverty during transition, this chapter points to the failure of the international organizations’ “targeted” poverty-prevention strategy.

A second dramatic rise in seroprevalence rates of SARS-CoV-2 antibodies among adult healthy blood donors in Jordan; have we achieved herd immunity?

Objectives: To determine the impact of the second wave of COVID-19 and the vaccination campaign on the seroprevalence rates of SARS-CoV-2 antibodies among healthy blood donors in Jordan. Methods: Sera from 536 healthy adult blood donors collected in June -2021 were tested using a commercially available quantitative assay for the total antibodies including IgG against the spike (S) protein receptor binding domain (RBD) of the SARS-CoV-2. Results: 399 (74.4%) of the donors tested positive for the antibodies of whom 69 (17.3%) were confirmed to have been previously infected, 245(61.4%) have received at least one dose of the vaccine and 123(30.8%) were neither diagnosed nor vaccinated. The seropositive donors were significantly more likely to have been vaccinated or previously infected. Conclusion: The crude seroprevalence rate of 74.4% among this group of healthy donors may be encouraging in terms of approaching herd immunity, however with predominance of the delta variant and the uncertainty regarding the required level of herd immunity this goal appears to be far from full achievement in Jordan.