bluuebunny/crossref_metadata_2025 huggingface dataset:
Susceptibility of Elizabethkingia spp. to commonly tested and novel antibiotics and concordance between broth microdilution and automated testing methods
Authors: Kuo Shu-Chen , Tan Mei-Chen , Huang Wei-Cheng , Wu Han-Chieh , Chen Feng-Jui , Liao Yu-Chieh , Wang Hui-Ying , Shiau Yih-Ru , Lauderdale Tsai-Ling
Published: November 2020

Objectives

We aimed to determine susceptibilities of Elizabethkingia spp. to 25 commonly tested and 8 novel antibiotics, and to compare the performance of different susceptibility testing methods.

Methods

Clinical isolates of Elizabethkingia spp., Chryseobacterium spp. and Flavobacterium spp. collected during 2002–18 (n = 210) in a nationwide surveillance programme in Taiwan were speciated by 16S rRNA sequencing. MICs were determined by broth microdilution. The broth microdilution results of 18 common antibiotics were compared with those obtained by the VITEK 2 automated system.

Results

Among the Elizabethkingia spp. identified (n = 108), Elizabethkingia anophelis was the most prevalent (n = 90), followed by Elizabethkingia meningoseptica (n = 7) and Elizabethkingia miricola cluster [E. miricola (n = 6), Elizabethkingia bruuniana (n = 3) and Elizabethkingia ursingii (n = 2)]. Most isolates were recovered from respiratory or blood specimens from hospitalized, elderly patients. PFGE showed two major and several minor E. anophelis clones. All isolates were resistant to nearly all the tested β-lactams. Doxycycline, minocycline and trimethoprim/sulfamethoxazole inhibited >90% of Elizabethkingia spp. Rifampin inhibited E. meningoseptica (100%) and E. anophelis (81.1%). Fluoroquinolones and tigecycline were active against E. meningoseptica and E. miricola cluster isolates. Novel antibiotics, including imipenem/relebactam, meropenem/vaborbactam, ceftazidime/avibactam, cefepime/zidebactam, delafloxacin, eravacycline and omadacycline were ineffective but lascufloxacin inhibited half of Elizabethkingia spp. The very major discrepancy rates of VITEK 2 were >1.5% for ciprofloxacin, moxifloxacin and vancomycin. Major discrepancy rates were >3% for amikacin, tigecycline, piperacillin/tazobactam and trimethoprim/sulfamethoxazole.

Conclusions

MDR, absence of standard interpretation criteria and poor intermethod concordance necessitate working guidelines to facilitate future research of emerging Elizabethkingia spp.
Species-specific patterns of the use of burrows of Upogebia Leach, 1814 (Decapoda: Gebiidea: Upogebiidae) by the symbiotic alpheid shrimps Stenalpheops anacanthus Miya, 1997 and Athanas japonicus Kubo, 1936 (Decapoda: Caridea: Alpheidae) as revealed by laboratory quantification
Authors: Henmi Yumi , Itani Gyo
Published: November 2020

Many alpheid shrimps live symbiotically on the body surface or inside the bodies of other invertebrates, while others use burrows made by other animals. The burrow symbiosis of alpheid shrimps is poorly studied in the context of ecology, probably because the cryptic infaunal nature of the relationship is hard to observe. The limited knowledge of the pattern of burrow use by alpheid shrimps leaves a gap in our understanding of their evolutionary history. We described and compared the behavior of Stenalpheops anacanthusMiya, 1997 and Athanas japonicusKubo, 1936, two alpheid species living symbiotically in the burrows of the same host, Upogebia yokoyaiMakarov, 1938. We found that both alpheid species used U. yokoyai burrows in aquaria, but their burrow use patterns were quite different. The average time taken for S. anacanthus to enter the burrow for the first time was much shorter (1 min) than that of A. japonicus (13 min). Subsequently, S. anacanthus made longer use of the burrow (80% of the observation period) than A. japonicus (49%). The tail-first exit frequency, which may indicate a sudden expulsion from the burrow by the host, was more frequent in A. japonicus (25%) than in S. anacanthus (7%). Such differences could be attributed to the nature of the symbiotic relationship, obligate in S. anacanthus but facultative in A. japonicus. Because of the diversity of symbiotic lifestyles, there is considerable potential to study the ecology and evolutionary biology of burrow-symbiotic alpheids further.
The persistence of apartheid regional wage disparities in South Africa
Authors: Mudiriza Gibson , Edwards Lawrence
Published: November 2020

In this article, we use a new economic geography (NEG) model to estimate the extent to which the persistence in apartheid regional wage disparities in South Africa is an outcome of economic forces such as market access. We estimate a structural wage equation derived directly from the NEG theory for 354 regions over the period 1996 to 2011. We find support for an augmented NEG model in explaining regional wage disparities across regions in South Africa, although the market access effects are highly localised in view of high distance coefficients. We also find, even after controlling for NEG and other region-specific characteristics, a persistent wage deficit in the former homelands, where under apartheid black South Africans were forcefully relocated according to their ethnic groups. Average wages of workers in homelands remained approximately 17% lower than predicted between 1996 and 2011, despite the reintegration of these regions into South Africa and the implementation of regional policies after the end of apartheid.
Measuring the impact of corn on mammalian omnivores
Authors: Hopkins John B , Ferguson Jake M , Frederick Cheryl , Jerina Klemen
Published: November 2020

In human-dominated landscapes throughout the world, wildlife seek out anthropogenic foods because they are high in nutritional value and are consistently available. To investigate this mode of foraging, some researchers use stable isotope analysis to detect these animals in populations and estimate their individual diets. In this study, we develop an integrative approach to measure the proportion of corn, a C4 plant, in the diets of free-ranging mammalian omnivores in C3-dominated ecosystems. We fed captive mice corn, C3 plants, and meat until carbon stable isotopes (δ 13C) from each diet equilibrated in their hair. We then used carbon discrimination factors (Δ 13C; offsets between stable isotope values of consumer tissues and their foods) for mice from these feeding trials and a simple carbon stable isotope mixing model to estimate the corn-based diets of free-ranging American black bears in Wisconsin and brown bears in Slovenia. We used Δ 13C factors for mice to estimate the diets of bears because mouse models are used commonly to study mammalian diet and health, including humans and bears, and body mass has no effect on carbon discrimination factors in monogastric mammalian omnivores. In this study, we found that mice grew fastest, largest, and δ 13C values equilibrated quickest in the hair of mice fed meat versus plant-based diets, suggesting protein quantity (quality was the same) has an effect on Δ 13C. Evidence also suggests that Δ 13C did not increase with animal growth rate as all mice grew throughout the 109-day feeding trials, but isotopic equilibration occurred early while mice still were subadults and was maintained throughout their adult lives. We also found that Δ 13C was highest and most variable in the hair, serum, and liver, of mice fed a mixed diet of C3 plants, supporting our mixed diet hypothesis that states that Δ 13C varies more among tissues of animals fed mixed diets than animals fed nonmixed diets because the former are composed of multiple foods, each with different macromolecular and isotopic compositions. Lastly, we found that corn may have been a more important component of bear diets in Wisconsin than previously thought (adults: x¯ = 29%; x¯ = 33%; subadults: x¯ = 22%; x¯ = 28%), and male brown bears may have fed on 50% more corn (x¯ = 47% versus 31%) in autumn during a year when beechnut availability was low. In a world that is rapidly changing, it is more important than ever to develop the appropriate quantitative tools to measure the impact people have on wildlife. Here, we provide such a tool for monogastric mammalian omnivores and encourage other researchers to do the same for other taxa of interest.
Genotypic diversity and antifungal susceptibility of environmental isolates of Cryptococcus neoformans from the Yangtze River Delta region of East China
Authors: Chen Min , Wang Yan , Li Yingfang , Hong Nan , Zhu Xinlin , Pan Weihua , Liao Wanqing , Xu Jianping , Du Jingxia , Chen Jianghan
Published: November 2020

Although cryptococcosis is widely recognized as infection by Cryptococcus neoformans sensu lato from environmental sources, information concerning the characteristics of environmental isolates of C. neoformans s. l. and how they are related to clinical isolates is very limited, especially in East China. In this study, 61 environmental isolates of C. neoformans were recovered from pigeon (Columba livia) droppings from the Yangtze River Delta region of East China. These isolates were genotyped using the ISHAM-MLST consensus scheme and their antifungal drug susceptibilities were determined following the CLSI M27-A3 guidelines. The 61 isolates were found belonging to 13 sequence types (STs), including several novel STs such as ST254 and ST194. The dominant ST in this environmental sample was ST31, different from that of clinical strains (ST5) in this region. Azole-resistance, such as fluconazole (FLU)-resistance, was observed among our environmental C. neoformans isolates. The findings of this study expand our understanding of ecological niches, population genetic diversity, and azole-resistance characteristics of the yeast in East China. Our research lays the foundation for further comparative analysis the potential mechanisms for the observed differences between environmental and clinical populations of C. neoformans in China.

Lay Summary

Cryptococcosis is widely recognized as infection by Cryptococcus neoformans sensu lato from environmental sources. However, there is currently limited information about the genetic diversity and antifungal susceptibility of environmental C. neoformans s. l. isolates, including how they may differ from clinical samples. In this study, we collected 61 environmental C. neoformans isolates from domestic pigeon droppings from the Yangtze River Delta region of East China. These isolates were genotyped using multi-locus sequencing. We found a high genotypic diversity in this population of C. neoformans, with several novel genotypes and a distribution of genotypes different from that of clinical strains in this region. Azole-resistance, such as fluconazole (FLU)-resistance, was observed among our environmental C. neoformans isolates. The findings of this study expand our understanding of ecological niches, genetic diversity, and azole-resistance characteristics of the yeast in East China. Our research lays the foundation for phylogenomic analysis investigating why and how disparate population structures of C. neoformans isolates formed between environmental and clinical sources in the region.
The cloudy shape of hot Jupiter thermal phase curves
Authors: Parmentier Vivien , Showman Adam P , Fortney Jonathan J
Published: November 2020

Hot Jupiters have been predicted to have a strong day/night temperature contrast and a hotspot shifted eastward of the substellar point. This was confirmed by numerous phase curve observations probing the longitudinal brightness variation of the atmosphere. Global circulation models, however, systematically underestimate the phase curve amplitude and overestimate the shift of its maximum. We use a global circulation model including non-grey radiative transfer and realistic gas and cloud opacities to systematically investigate how the atmospheric circulation of hot Jupiters varies with equilibrium temperature from 1000 to 2200 K. We show that the heat transport is very efficient for cloudless planets cooler than 1600 K and becomes less efficient at higher temperatures. When nightside clouds are present, the day-to-night heat transport becomes extremely inefficient, leading to a good match to the observed low nightside temperatures. The constancy of this low temperature is, however, due to the strong dependence of the radiative time-scale with temperature. We further show that nightside clouds increase the phase curve amplitude and decrease the phase curve offset at the same time. This change is very sensitive to the cloud chemical composition and particle size, meaning that the diversity of observed phase curves can be explained by a diversity of nightside cloud properties. Finally, we show that phase curve parameters do not necessarily track the day/night contrast nor the shift of the hotspot on isobars, and propose solutions to to recover the true hotspot shift and day/night contrast.
Disentangling the multiphase circumgalactic medium shared between a dwarf and a massive star-forming galaxy at z∼0.4
Authors: Nateghi Hasti , Kacprzak Glenn G , Nielsen Nikole M , Muzahid Sowgat , Churchill Christopher W , Pointon Stephanie K , Charlton Jane C
Published: November 2020

The multiphase circumgalactic medium (CGM) arises within the complex environment around a galaxy, or collection of galaxies, and possibly originates from a wide range of physical mechanisms. In this paper, we attempt to disentangle the origins of these multiphase structures and present a detailed analysis of the quasar field Q0122−003 field using Keck/KCWI galaxy observations and HST/COS spectra probing the CGM. Our re-analysis of this field shows that there are two galaxies associated with the absorption. We have discovered a dwarf galaxy, G_27kpc (M⋆ = 108.7 M⊙), at z = 0.39863 that is 27 kpc from the quasar sightline. G_27kpc is only +21 km s−1 from a more massive (M⋆ = 1010.5 M⊙) star-forming galaxy, G_163kpc, at an impact parameter of 163 kpc. While G_163kpc is actively forming stars (SFR = 6.9 M⊙ yr−1), G_27kpc has a low star-formation rate (SFR = 0.08 ± 0.03 M⊙ yr−1) and star formation surface density (ΣSFR = 0.006 M⊙ kpc−2 yr−1), implying no active outflows. By comparing galaxy SFRs, kinematics, masses, and distances from the quasar sightline to the absorption kinematics, column densities, and metallicities, we have inferred the following: (1) Part of the low-ionization phase has a metallicity and kinematics consistent with being accreted on to G_27kpc. (2) The remainder of the low ionization phase has metallicities and kinematics consistent with being intragroup gas being transferred from G_27kpc to G_163kpc. (3) The high ionization phase is consistent with being produced solely by outflows originating from the massive halo of G_163kpc. Our results demonstrate the complex nature of the multiphase CGM, especially around galaxy groups, and that detailed case-by-case studies are critical for disentangling its origins.
Partitioned Gene-Tree Analyses and Gene-Based Topology Testing Help Resolve Incongruence in a Phylogenomic Study of Host-Specialist Bees (Apidae: Eucerinae)
Authors: Freitas Felipe V , Branstetter Michael G , Griswold Terry , Almeida Eduardo A B
Published: November 2020

Incongruence among phylogenetic results has become a common occurrence in analyses of genome-scale data sets. Incongruence originates from uncertainty in underlying evolutionary processes (e.g., incomplete lineage sorting) and from difficulties in determining the best analytical approaches for each situation. To overcome these difficulties, more studies are needed that identify incongruences and demonstrate practical ways to confidently resolve them. Here, we present results of a phylogenomic study based on the analysis 197 taxa and 2,526 ultraconserved element (UCE) loci. We investigate evolutionary relationships of Eucerinae, a diverse subfamily of apid bees (relatives of honey bees and bumble bees) with >1,200 species. We sampled representatives of all tribes within the group and >80% of genera, including two mysterious South American genera, Chilimalopsis and Teratognatha. Initial analysis of the UCE data revealed two conflicting hypotheses for relationships among tribes. To resolve the incongruence, we tested concatenation and species tree approaches and used a variety of additional strategies including locus filtering, partitioned gene-trees searches, and gene-based topological tests. We show that within-locus partitioning improves gene tree and subsequent species-tree estimation, and that this approach, confidently resolves the incongruence observed in our data set. After exploring our proposed analytical strategy on eucerine bees, we validated its efficacy to resolve hard phylogenetic problems by implementing it on a published UCE data set of Adephaga (Insecta: Coleoptera). Our results provide a robust phylogenetic hypothesis for Eucerinae and demonstrate a practical strategy for resolving incongruence in other phylogenomic data sets.
LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements
Authors: Gao Yue , Li Xin , Shang Shipeng , Guo Shuang , Wang Peng , Sun Dailin , Gan Jing , Sun Jie , Zhang Yakun , Wang Junwei , Wang Xinyue , Li Xia , Zhang Yunpeng , Ning Shangwei
Published: November 2020

We describe an updated comprehensive database, LincSNP 3.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), which aims to document and annotate disease or phenotype-associated variants in human long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) or their regulatory elements. LincSNP 3.0 has updated with several novel features, including (i) more types of variants including single nucleotide polymorphisms (SNPs), linkage disequilibrium SNPs (LD SNPs), somatic mutations and RNA editing sites have been expanded; (ii) more regulatory elements including transcription factor binding sites (TFBSs), enhancers, DNase I hypersensitive sites (DHSs), topologically associated domains (TADs), footprintss, methylations and open chromatin regions have been added; (iii) the associations among circRNAs, regulatory elements and variants have been identified; (iv) more experimentally supported variant-lncRNA/circRNA-disease/phenotype associations have been manually collected; (v) the sources of lncRNAs, circRNAs, SNPs, somatic mutations and RNA editing sites have been updated. Moreover, four flexible online tools including Genome Browser, Variant Mapper, Circos Plotter and Functional Annotation have been developed to retrieve, visualize and analyze the data. Collectively, LincSNP 3.0 provides associations among functional variants, regulatory elements, lncRNAs and circRNAs in diseases. It will serve as an important and continually updated resource for investigating functions and mechanisms of lncRNAs and circRNAs in diseases.
Interaction ofOIP5-AS1withMEF2CmRNA promotes myogenic gene expression
Authors: Yang Jen-Hao , Chang Ming-Wen , Pandey Poonam R , Tsitsipatis Dimitrios , Yang Xiaoling , Martindale Jennifer L , Munk Rachel , De Supriyo , Abdelmohsen Kotb , Gorospe Myriam
Published: November 2020

Long noncoding (lnc)RNAs potently regulate gene expression programs in physiology and disease. Here, we describe a key function for lncRNA OIP5-AS1 in myogenesis, the process whereby myoblasts differentiate into myotubes during muscle development and muscle regeneration after injury. In human myoblasts, OIP5-AS1 levels increased robustly early in myogenesis, and its loss attenuated myogenic differentiation and potently reduced the levels of the myogenic transcription factor MEF2C. This effect relied upon the partial complementarity of OIP5-AS1 with MEF2C mRNA and the presence of HuR, an RNA-binding protein (RBP) with affinity for both transcripts. Remarkably, HuR binding to MEF2C mRNA, which stabilized MEF2C mRNA and increased MEF2C abundance, was lost after OIP5-AS1 silencing, suggesting that OIP5-AS1 might serve as a scaffold to enhance HuR binding to MEF2C mRNA, in turn increasing MEF2C production. These results highlight a mechanism whereby a lncRNA promotes myogenesis by enhancing the interaction of an RBP and a myogenic mRNA.
Factors associated with workability in Spanish health centre workers
Authors: Mateo-Rodríguez I , Knox E , Daponte-Codina A ,   esTAR group, Moncada Ana , Ranchal Antonio , Oliver Coral , Queraltó Nuria , Ramblado Mercedes , Enriquez Francisca , Ramos Amalia , Márquez Rebeca , Javier Jiménez Antonio , Javier Rodríguez Francisco , Toro Silvia , Fernández Alberto , Cabrera Andrés , Sánchez Pablo
Published: November 2020

Background

The concept of workability provides a conceptual framework and proposes measures for the evaluation of relevant actions focused on a healthy workforce. In Spain, one of the countries with the highest life expectancy, there are practically no scientific studies on workability and its associated factors.

Aims

The objective of this study is to examine the associations between workability and variables related to health and work in a sample of workers from Spanish health centres.

Methods

Cross-sectional study including 1184 health centre workers who completed a questionnaire at baseline, comprising measures of workability, health and other work-related factors. Workability has been analysed as a one-factor construct, and as a two-factor construct. Multinomial logistic regression models were used to analyse factors associated with workability.

Results

As a one-dimensional construct, workability is associated with physical and mental health, number of hours of worked, insomnia, work and family life balance, adequate training, never having had an accident and type of contract. When the two-factor measure was used, sensitivity of findings increased, and it was identified that those participants who were older, lived alone and have more years of service in their profession also show worse workability.

Conclusions

The present study identified factors associated with the workability of health centre workers. The two-factor workability index (WAI) has better psychometric properties and used in combination with the global measure of WAI, identifies important additional aspects, specifically, age and years of professional experience as additional considerations for the intervention.
Depressants: Sedative-Hypnotic-Tranquilizing DrugsFrom Errant Yeast to Halcion and Its Relatives
Authors: Winter Jerrold
Published: November 2020

The agents we will consider in this chapter are a disparate bunch, but they are united in that most can induce a mild state of intoxication that many of us find to be pleasant; social drinkers of ethyl alcohol are familiar with the phenomenon. The darker side of these drugs is that all can induce physical dependence with a characteristic and sometimes life-threatening withdrawal syndrome. In addition, they are often agents of addiction; alcoholism is a prime example. Further uniting these drugs is the relatively recent recognition of a common mechanism of action. Their current primary medical uses are in anesthesiology, as anticonvulsants, and in the treatment of anxiety and sleep disorders. For many years, drugs of this class were referred to as sedative- hypnotics. Sedation implies the induction of a state of calmness, while hypnosis refers to sleep. However, with the discovery of meprobamate (Miltown), and the benzodiazepines, for example, Valium, which we will consider later, a third term was introduced. These drugs were to be called tranquilizers to distinguish them from earlier sedative-hypnotics. But whatever the drugs are called, the fact is that for most there is a dose-related continuum of action beginning with a state of calmness (call it tranquility, if you wish) to sleep, and, finally, for some, coma and death. An illustration of the long- recognized connectedness of sedation, hypnosis, and anxiety was provided us by Henry Behrend. He describes his patient as … … a gentleman, forty years of age… . He was of a most excitable and nervous temperament, and was engaged in mercantile transactions of great magnitude, the extent of which seemed quite to overwhelm him… . He had lost his natural sleep, was harassed and fatigued during the day, and sought my opinion as to whether he ought not at once to withdraw from business, although the sacrifice entailed thereby would be very great, and he was most anxious to avoid it… .
Hallucinogens: Magic Mushrooms, Ayahuasca, Mescal Buttons, and Dr. Hofmann’s Problem Child
Authors: Winter Jerrold
Published: November 2020

There are about 400,000 species of plants in this world. Only a small fraction, perhaps 100 in number, contain hallucinogenic chemicals. Nearly a century ago, Lewis Lewin, professor of pharmacology at the University of Berlin, in speaking of drugs he called phantasticants, said “The passionate desire which … leads man to flee from the monotony of daily life … has made him discover strange substances (which) have been integral to human evolution both societal and cultural for thousands of years.” An unusual problem presents itself to me in writing about these drugs: They straddle the worlds of science and mysticism. The Encyclopedia Britannica defines mysticism as the practice of religious ecstasies (religious experiences during alternate states of consciousness), together with whatever ideologies, ethics, rites, myths, legends, and magic may be related to them. Science I am comfortable with; mysticism not so much. Yet in our exploration of the agents found in this chapter, we will encounter many persons speaking of drug-induced mystical experiences. I have attempted to get around my unease by first providing the history and the pharmacology of these agents and then touching only lightly on mysticism, allowing readers to draw their own conclusions. What shall we call these chemicals? Hallucinogen, a substance that induces perception of objects with no reality, is the term most commonly encountered and the one that I have settled on for the title of this chapter. However, it comes with a caveat. Albert Hofmann, the discoverer of LSD, our prototypic hallucinogen, has pointed out that a true hallucination has the force of reality, but the effects of LSD only rarely include this feature. Two additional terms that we will find useful are psychotomimetic and psychedelic. We have already considered the former, an ability to mimic psychosis, in our discussion of amphetamine-induced paranoid psychosis in chapter 4 and the effects of phencyclidine in chapter 6. A psychedelic was defined in 1957 by Humphrey Osmond, inventor of the word, as a drug like LSD “which enriches the mind and enlarges the vision.”
When a Daring Chemistry Meets a Boring Chemistry: The Reception of Mendeleev’s Periodic System in Sweden
Authors: Lundgren Anders
Published: November 2020

The reception of Mendeleev’s periodic system in Sweden was not a dramatic episode. The system was accepted almost without discussion, but at the same time with no exclamation marks or any other outbursts of enthusiasm. There are but a few weak short-lived critical remarks. That was all. I will argue that the acceptance of the system had no overwhelming effect on chemical practice in Sweden. At most, it strengthened its characteristics. It is actually possible to argue that chemistry in Sweden was more essential for the periodic system than the other way around. My results might therefore suggest that we perhaps have to reevaluate the role of Mendeleev’s system in the history of chemistry. Chemistry in Sweden at the end of the nineteenth century can be characterized as a classifying science, with chemists very skilled in analysis, and as mainly an atheoretical science, which treated theories at most only as hypothesis—the slogan of many chemists being “facts persist, theories vanish.” Thanks to these characteristics, by the end of the nineteenth century, chemistry in Sweden had developed into, it must be said, a rather boring chemistry. This is obviously not to say that it is boring to study such a chemistry. Rather, it gives us an example of how everyday science, a part of science too often neglected but a part that constitutes the bulk of all science done, is carried out. One purpose of this study is to see how a theory, considered to be important in the history of chemistry, influenced everyday science. One might ask what happened when a daring chemistry met a boring chemistry. What happened when a theory, which had been created by a chemist who has been described as “not a laboratory chemist,” met an atheoretical experimental science of hard laboratory work and, as was said, the establishment of facts? Furthermore, could we learn something about the role of the periodic system per se from the study of such a meeting? Mendeleev’s system has often been considered important for teaching, and his attempts to write a textbook are often taken as the initial step in the chain of thoughts that led to the periodic system.
Popular Science, Textbooks, and Scientists: The Periodic Law in Italy
Authors: Ciardi Marco , Taddia Marco
Published: November 2020

This essay deals with an issue that has never before been the focus of attention in the field of research on the history of chemistry in Italy: the diffusion of Mendeleev’s periodic system in our nation. In the following text we will analyze the situation in the period preceding the arrival of Mendeleev’s theory in Italy with regard to the matter of classifying elements. By doing so, it will be possible to demonstrate that—despite the superficiality and lack of accuracy of certain studies—Italian chemistry was already very willing to consider new proposals relating to the classification of elements. We will then attempt to illustrate how Mendeleev’s work not only attracted the attention of the most renowned Italian chemists, such as Augusto Piccini and Giacomo Ciamician, but also became widely used in university texts and secondary school textbooks. In order to understand the classification criteria for elements adopted by Italian chemists before Mendeleev and therefore the cultural terrain the law of periodicity was to take root in, it would be better to refer to a number of texts used widely for teaching in universities. We will examine four of these, published between 1819 and 1867. In all these texts, the term “simple bodies” appears, with the expression “simple substances” used less frequently, while Antoine-Laurent Lavoisier (1743–94), in his 1789 Traité élémentaire de chimie (Traité thereafter), uses the same term “simple substances” or “simple substances … which may be considered as the elements of bodies.” It is interesting to note that Vincenzo Dandolo’s Italian translation (first edition 1792) uses the expression “sostanze semplici,” interpreting quite literally the Frenchman’s choice of term. Thirty years after publication of the Traité, Antonio Santagata (1774–1858), professor of general chemistry at the Pontificia Università di Bologna, published his Lezioni di chimica elementare [Lessons in elementary chemistry], derived from Lezioni di chimica elementare: applicata alla medicina e alle arti [Lessons in Elementary Chemistry: Applied to Medicine and the Arts] (Bologna, 1804), written by his predecessor in the university chair, Pellegrino Salvigni (1777–1841).
Functional Group Interconversion
Authors: Lambert Tristan H.
Published: November 2020

Glenn M. Samm is at the University of British Columbia reported (Angew. Chem. Int. Ed. 2012, 51, 10804) the photofluorodecarboxylation of aryloxyacids such as 1 using Selectfluor 2. Jean-François Paquin at the Université Laval found (Org. Lett. 2012, 14, 5428) that the halogenation of alcohols (e.g., 4 to 5) could be achieved with [Et2NSF2]BF4 (XtalFluor-E) in the presence of the appropriate tetraethylammonium halide. A method for the reductive bromination of carboxylic acid 6 to bromide 7 was developed (Org. Lett. 2012, 14, 4842) by Norio Sakai at the Tokyo University of Science. Professor Sakai also reported (Org. Lett. 2012, 14, 4366) a related method for the reductive coupling of acid 8 with octanethiol to produce thioether 9. The esterification of primary alcohols in water-containing solvent was achieved (Org. Lett. 2012, 14, 4910) by Michio Kurosu at the University of Tennessee Health Science Center using the reagent 11, such as in the conversion of alcohol 10 to produce 12 in high yield. Hosahudya N. Gopi discovered (Chem. Commun. 2012, 48, 7085) that the conversion of thioacid 13 to amide 14 was rapidly promoted by CuSO4. A ruthenium-catalyzed dehydrative amidation procedure using azides and alcohols, such as the reaction of 15 with phenylethanol to produce 16, was reported (Org. Lett. 2012, 14, 6028) by Soon Hyeok Hong at Seoul National University. An alternative oxidative amidation was developed (Tetrahedron Lett. 2012, 53, 6479) by Chengjian Zhu at Nanjing University and the Shanghai Institute of Organic Chemistry who utilized catalytic tetrabutylammonium iodide and disubstituted formamides to convert alcohols such as 17 to amides 18. A redox catalysis strategy was developed (Angew. Chem. Int. Ed. 2012, 51, 12036) by Brandon L. Ashfeld at Notre Dame for the triphenylphosphine-catalyzed Staudinger ligation of carboxylic acid 19 to furnish amide 20. For direct catalytic amidation of carboxylic acids and amines such as in the conversion of 21 to 23, Dennis G. Hall at the University of Alberta reported (J. Org. Chem. 2012, 77, 8386) that the boronic acid 22 was a highly effective catalyst that operated at room temperature.
C–H Functionalization: The Hatakeyama Synthesis of (–)-Kaitocephalin
Authors: Taber Douglass F.
Published: November 2020

John F. Hartwig of the University of California, Berkeley showed (Nature 2012, 483, 70) that intramolecular C–H silylation of 1 selectively gave, after oxidation and acetylation, the bis acetate 2. Gong Chen of Pennsylvania State University coupled (J. Am. Chem. Soc. 2012, 134, 7313) 3 with 4 to give the ether 5. M. Christina White of the University of Illinois effected (J. Am. Chem. Soc. 2012, 134, 9721) selective oxidation of the taxane derivative 6 to the lactone 7. Most of the work on C–H functionalization has focused on the formation of C–C, C–O, and C–N bonds. Donald A. Watson of the University of Delaware developed (Angew. Chem. Int. Ed. 2012, 51, 3663) conditions for the complementary conversion of an alkene 8 to the allyl silane 9, a powerful and versatile nucleophile. Kilian Muniz of ICIQ Tarragona oxidized (J. Am. Chem. Soc. 2012, 134, 7242) the enyne 10 selectively to the amine 11. Phil S. Baran of Scripps/La Jolla devised (J. Am. Chem. Soc. 2012, 134, 2547) a protocol for the OH-directed amination of 12 to 13. Professor White developed (J. Am. Chem. Soc. 2012, 134, 2036) a related OH-directed amination of 14 to 15 that proceeded with retention of absolute configuration. Tom G. Driver of the University of Illinois, Chicago showed (J. Am. Chem. Soc. 2012, 134, 7262) that the aryl azide 16 could be cyclized directly to the amine, which was protected to give 17. As illustrated by the conversion of 18 to 20 devised (Adv. Synth. Catal. 2012, 354, 701) by Martin Klussmann of the Max-Planck-Institut, Mülheim, C–H functionalization can be accomplished by hydride abstraction followed by coupling of the resulting carbocation with a nucleophile. Olafs Daugulis of the University of Houston used (Angew. Chem. Int. Ed. 2012, 51, 5188) a Pd catalyst to couple 21 with 22 to give 23 with high diastereocontrol. Yoshiji Takemoto of Kyoto University cyclized (Angew. Chem. Int. Ed. 2012, 51, 2763) the chloroformate 24 directly to the oxindole 25.
Enantioselective Synthesis of Alcohols and Amines: The Ichikawa Synthesis of (+)-Geranyllinaloisocyanide
Authors: Taber Douglass F.
Published: November 2020

Shuichi Nakamura of the Nagoya Institute of Technology reduced (Angew. Chem. Int. Ed. 2011, 50, 2249) the α-oxo ester 1 to 2 with high ee. Günter Helmchen of the Universität-Heidelberg optimized (J. Am. Chem. Soc. 2011, 133, 2072) the Ir*-catalyzed rearrangement of 3 to the allylic alcohol 4. D. Tyler McQuade of Florida State University effected (J. Am. Chem. Soc. 2011, 133, 2410) the enantioselective allylic substitution of 5 to give the secondary allyl boronate, which was then oxidized to 6. Kazuaki Kudo of the University of Tokyo developed (Org. Lett. 2011, 13, 3498) the tandem oxidation of the aldehyde 7 to the α-alkoxy acid 8. Takashi Ooi of Nagoya University prepared (Synlett 2011, 1265) the secondary amine 10 by the enantioselective addition of an aniline to the nitroalkene 9. Yixin Lu of the National University of Singapore assembled (Org. Lett. 2011, 13, 2638) the α-quaternary amine 13 by the addition of the aldehyde 11 to the azodicarboxylate 10. Chan-Mo Yu of Sungkyunkwan University added (Chem. Commun. 2011, 47, 3811) the enantiomerically pure 2-borylbutadiene 15 to the aldehyde 14 to give 16 in high ee. Because the allene is readily dragged out to the terminal alkyne, this is also a protocol for the enantioselective homopropargylation of an aldehyde. Lin Pu of the University of Virginia devised (Angew. Chem. Int. Ed. 2011, 50, 2368) a protocol for the enantioselective addition of 17 to the aldehyde 18 to give 19. Xiaoming Feng of Sichuan University developed (Angew. Chem. Int. Ed. 2011, 50, 2573) a Mg catalyst for the enantioselective addition of 21 to the α-oxo ester 20. Tomonori Misaka and Takashi Sugimura of the University of Hyogo added (J. Am. Chem. Soc. 2011, 133, 5695) 23 to 24 to give the Z-amide 25 in high ee. Marc L. Snapper and Amir H. Hoveyda of Boston College developed (J. Am. Chem. Soc. 2011, 133, 3332) a Cu catalyst for the enantioselective allylation of the imine 26. Jonathan Clayden of the University of Manchester effected (Org. Lett. 2010, 12, 5442) the enantioselective rearrangement of the amide 29 to the α-quaternary amine 30.
Arrays of Stereogenic Centers: The Davies Synthesis of Acosamine
Authors: Taber Douglass F.
Published: November 2020

Babak Borhan of Michigan State University found (Angew. Chem. Int. Ed. 2011, 50, 2593) that the ligand developed for asymmetric osmylation worked well for the enantioselective cyclization of 1 to 2. Kyungsoo Oh of IUPUI devised (Org. Lett. 2011, 13, 1306) a Co catalyst for the stereocontrolled addition of 4 to 3 to give 5. Michael J. Krische of the University of Texas Austin prepared (Angew. Chem. Int. Ed. 2011, 50, 3493) 8 by Ir*-mediated oxidation/addition of 7 to 6. Yixin Lu of the National University of Singapore employed (Angew. Chem. Int. Ed. 2011, 50, 1861) an organocatalyst to effect the stereocontrolled addition of 10 to 9. Naoya Kumagai and Masakatsu Shibasaki of the Institute of Microbial Chemistry, Tokyo took advantage (J. Am. Chem. Soc. 2011, 133, 5554) of the soft Lewis basicity of 13 to effect stereocontrolled condensation with 12. Yujiro Hayashi of the Tokyo University of Science found (Angew. Chem. Int. Ed. 2011, 50, 2804, not illustrated) that aqueous chloroacetaldehyde participated well in crossed aldol condensations. Andrew V. Malkov, now at Loughborough University, and Pavel Kocovsky of the University of Glasgow showed (J. Org. Chem. 2011, 76, 4800) that the inexpensive mixed crotyl silane 16 could be added to 15 with high stereocontrol. Shigeki Matsunaga of the University of Tokyo and Professor Shibasaki opened (J. Am. Chem. Soc. 2011, 133, 5791) the meso aziridine 18 with malonate 19 to give 20. Masahiro Terada of Tohoku University effected (Org. Lett. 2011, 13, 2026) the conjugate addition of 22 to 21 with high stereocontrol. Jinxing Ye of the East China University of Science and Technology reported (Angew. Chem. Int. Ed. 2011, 50, 3232, not illustrated) a related conjugate addition. Kian L. Tian of Boston College observed (Org. Lett. 2011, 13, 2686) that the kinetic hydroformylation of 24 set the relative configuration of two stereogenic centers. Alexandre Alexakis and Clément Mazet of the Université de Genève established (Angew. Chem. Int. Ed. 2011, 50, 2354) a tandem one-pot procedure for the addition of 26 to 27 to give 28.
Alkaloid Synthesis: (–)-α-Kainic Acid (Cohen), Hyacinthacine A2 (Fox), (–)-Agelastatin A (Hamada), (+)-Luciduline (Barbe), (+)-Lunarine (Fan), (–)-Runanine (Herzon)
Authors: Taber Douglass F.
Published: November 2020

The intramolecular ene cyclization is still little used in organic synthesis. Theodore Cohen of the University of Pittsburgh trapped (J. Org. Chem. 2011, 76, 7912) the cyclization product from 1 with iodine to give 2, setting the stage for an enantiospecific total synthesis of (–)-α-kainic acid 3. Intramolecular alkene hydroamination has been effected with transition metal catalysts. Joseph M. Fox of the University of Delaware isomerized (Chem. Sci. 2011, 2, 2162) 4 to the trans cyclooctene 5 with high diastereocontrol. Deprotection of the amine led to spontaneous cyclization, again with high diastereocontrol to hyacinthacine A2 6. Yasumasa Hamada of Chiba University devised (Org. Lett. 2011, 13, 5744) a catalyst system for the enantioselective aziridination of cyclopentenone 7. The product 8 was carried on to the tricyclic alkaloid (–)-agelastatin A 9. Guillaume Barbe, now at Novartis in Cambridge, MA, effected (J. Org. Chem. 2011, 76, 5354) the enantioselective Diels-Alder cycloaddition of acrolein 11 to the dihydropyridine 10. Ring-opening ring-closing metathesis later formed one of the carbocyclic rings of (+)-luciduline 13, and set the stage for an intramolecular aldol condensation to form the other. Chun-An Fan of Lanzhou University employed (Angew. Chem. Int. Ed. 2011, 50, 8161) a Cinchona-derived catalyst for the enantioselective Michael addition to prepare 14. Although 14 and 15 were only prepared in 77% ee, crystallization to remove the racemic component of a later intermediate led to (+)-lunarine 16 in high ee. Seth B. Herzon of Yale University used (Angew. Chem. Int. Ed. 2011, 50, 8863) the enantioselective Diels-Alder addition with 18 to block one face of the quinone 17. Reduction of 19 followed by methylation delivered an iminium salt, only one face of which was open for the addition of an aryl acetylide. Thermolysis to remove the cyclopentadiene gave an intermediate that was carried on to (+)-runanine 20.
Synthesis of Heteroaromatics
Authors: Lambert Tristan H.
Published: November 2020

Peter Wipf at the University of Pittsburgh utilized (J. Org. Chem. 2013, 78, 167) an alkynol-furan Diels-Alder reaction to convert 1 into the hydroxyindole 2. An intramolecular Larock indole synthesis was employed (Angew. Chem. Int. Ed. 2013, 52, 4902) by Yanxing Jia at Peking University for the conversion of aniline 3 to tricyclic indole 4. The reaction of boronodiene 5 with nitrosobenzene to produce pyrrole 6 was reported (Chem. Commun. 2013, 49, 5414) by Bertrand Carboni at CNRS University of Rennes and Andrew Whiting at Durham University. The merger of imine 7 with propargyl amine 8 in the presence of a strong base, leading to pyrrole 9, was disclosed (Org. Lett. 2013, 15, 3146) by Boshun Wan at the Chinese Academy of Sciences. Bin Li and Baiquan Wang at Nankai University found (Org. Lett. 2013, 15, 136) that pyrrole 12 could be prepared by the oxidative annulation of enamide 10 with alkyne 11 via ruthenium catalysis in the presence of copper(II). Naohiko Yoshikai at Nanyang Technological University demonstrated (Org. Lett. 2013, 15, 1966) that N-allyl imine 13 could be cyclized to pyrrole 14 via dehydrogenative intramolecular Heck cyclization. Rhett Kempe at the University of Bayreuth developed (Nature Chem. 2013, 5, 140) a “sustainable” pyrrole synthesis in which iridium complex 17 catalyzed the dehydrogenative coupling of alcohol 15 and phenylalaninol (16) to produce pyrrole 18. In a related process, David Milstein at the Weizmann Institute of Science found (Angew. Chem. Int. Ed. 2013, 52, 4012) that the ruthenium complex 20 effected the transformation of 2-octanol (19) and 16 to furnish pyrrole 21. An alternative ruthenium-catalyzed pyrrole synthesis from readily available components was developed (Angew. Chem. Int. Ed. 2013, 52, 597) by Matthias Beller, allowing for the preparation of 25 from ketone 22, diol 23, and amine 24. Meanwhile, with a bit of hetero-aromatic alchemy, Huw M.L. Davies at Emory University converted (J. Am. Chem. Soc. 2013, 135, 4716) the furan 26 to pyrrole 28 by reaction with triazole 27 under rhodium catalysis. Professor Kempe also developed (Angew. Chem. Int. Ed. 2013, 52, 6326) a method for the synthesis of pyridine 30 from amino alcohol 29 and propanol using an iridium catalyst closely related to 17.
Intramolecular Diels-Alder Cycloaddition: 7-Isocyanoamphilecta- 11(20),15-diene (Miyaoka), (–)-Scabronine G (Kanoh), Basiliolide B (Stoltz), Hirsutellone B (Uchiro), Echinopine A (Chen)
Authors: Taber Douglass F.
Published: November 2020

The amphilectane diterpenes, exemplified by 7-isocyanoamphilecta-11(20),15-diene 3, have been little investigated. In the course of a synthesis of 3, Hiroaki Miyaoka of the Tokyo University of Pharmacy and Life Sciences took advantage (Synlett 2011, 547) of the kinetic enolization and silylation of 1 to convert it into a trienone that spontaneously cyclized to 2. Scabronine G 6, isolated from the mushroom Sarcodon scabrosus, was found to enhance the secretion of neurotrophic factors from 1321N1 astrocytoma cells. To set the absolute configuration of the two quaternary centers that are 1, 4 on the cyclohexane ring of 6, Naoki Kanoh and Yoshiharu Iwabuchi of Tohoku University cyclized (Org. Lett. 2011, 13, 2864) 4 to 5. Although described by the authors as a double Michael addition, this transformation has the same connectivity as an intramolecular Diels-Alder cycloaddition. The diterpenes isolated from the genus Thapsia, represented by basiliolide B 9, induce rapid mobilization of intracellular Ca2+ stores. Brian M. Stoltz of Caltech effected (Angew. Chem. Int. Ed. 2011, 50, 3688) Claisen rearrangement of 7 to give an intermediate that cyclized to 8 as a mixture of diastereomers. A significant challenge in the synthesis was the assembly of the delicate enol ether/lactone of 9. Hirsutellone B 12, isolated from Hirsutella nivea, shows significant antituberculosis activity. Hiromi Uchiro of the Tokyo University of Science found it useful (Org. Lett. 2011, 13, 6268) to protect the intermediate unsaturated keto ester by intermolecular cycloaddition with pentamethylcyclopentadiene before constructing the triene of 10. Simple thermolysis reversed the intermolecular addition, opening the way to intramolecular cycloaddition to give 11. The tetracyclic ring system of the diterpene echinopine A 15 represents a substantial synthetic challenge. David Y.-K. Chen of Seoul National University approached this problem (Org. Lett. 2011, 13, 5724) by Pd-mediated cyclization of 13 to the diene, which then underwent intramolecular Diels-Alder cycloaddition to give 14, with control of the relative configuration of two of the three ternary centers of 15. Double bond migration followed by oxidative cleavage of the resulting cyclohexenone then set the stage for the intramolecular cyclopropanation that completed the synthesis of 15.