bluuebunny/crossref_metadata_2025 huggingface dataset:
Moral Economy, Predatory Society
Authors: Farrall Stephen , Karstedt Susanne
Published: May 2020

This chapter takes us into the murky world of seeminglypetty crimes at work, dishonesty in paperwork, and cheating. These topics are often left at the margins of criminological thinking, theorizing, and enquiries, and this work is an attempt to bring these more fully into mainstream studies. This chapter relates our thinking and findings on this topic to the work of others in criminology and related fields. It introduces the reader to both the concept of economic morality and the notion of ‘crime in the marketplace’, as well as the history of research into white-collar crime. We describe the main topic of the research project on which the book is based, and the extent to which this has been ignored by previous generations of criminologists. The moral economy of the neo-liberal marketplace is outlined (drawing upon E.P. Thompson’s work), the research strategy is explained, and some of the key concepts later developed are discussed.
The Middling Sort
Authors: Farrall Stephen , Karstedt Susanne
Published: May 2020

The chapter focuses on the core concept of the ‘middle class’. For England and Wales, the former East Germany and the former West Germany, socio-economic positions and financial situations of citizens/consumers are identified along with the social and economic attitudes related to these. The chapter then embarks on an examination of the relationship between individual’s socio-economic position and financial situation and involvement in crime in the marketplace, both as victims and offenders. The findings demonstrate that those with higher levels of income are most heavily involved in these types of crimes, equally as victims and offenders.
Communicating Crime, Risk, and Blame
Authors: Farrall Stephen , Karstedt Susanne
Published: May 2020

This chapter assesses the ways in which citizens and consumers communicate about their experiences of victimization as well as about the offences they committed, and how they create and shape the moral climate of contemporary markets. It explores how individual citizens support each other in avoiding victimization, provide moral support for offending and offer help in committing offences, comparing these by country. It analyses the extent to which such social networks which support offending are associated with legal cynicism, intentions to offend, techniques of neutralization, and self-interestedness. As well as relying on qualitative data, vignettes from the survey undertaken are included.
Crime, Consumption, and Economic Morality
Authors: Farrall Stephen , Karstedt Susanne
Published: May 2020

This chapter summarizes the main findings from the study, reflects on the theoretical and substantive knowledge produced, and assess its importance for criminological theory and research. It outlines the unique methodology of combining in-depth comparison with large scale macro-level perspectives. It identifies the mechanisms and dynamics that shape the moral economy and victimization and offending in the marketplace across time and space. Building on these results, the futures of middle class crime are discussed. With a global increase of middle class populations, and driven by technology and the internet, the crimes of everyday life and shady practices will become ever more important. Criminologists need to pay attention.
The History of Negation in the Languages of Europe and the Mediterranean
Authors: Breitbarth Anne , Lucas Christopher , Willis David
Published: May 2020

The book constitutes the second volume of the two-volume work The history of negation in the languages of Europe and the Mediterranean. While the first volume united a rich collection of ten case studies, the current second volume turns to the patterns and processes in the historical development of the expression of negation and its interaction with indefinites from a more general theoretical perspective. The volume is subdivided into two parts, one dealing with Jespersen’s cycle and one dealing with developments affecting indefinites in the scope of negation (the quantifier and free-choice cycles), including the diachronic development of negative concord. In each case, there are relevant empirical observations across the languages of Europe and the Mediterranean. The book considers both language-internal and language-contact motivations for the changes observed, developing a generative account of the developments in terms of semantic change, reanalysis, and child-language acquisition, integrating insights from functionalist approaches that invoke language use as a motivation behind these cycles. Language contact is shown to have played a significant role in the spread of negation systems. The result is a holistic account of language change in the domain of negation, developed from comparing the diachronies of languages across Europe and incorporating insights from a wide range of theoretical perspectives.
Postmodern Works
Authors: Pakes Anna
Published: May 2020

Chapter 4 explores the continuing operation of the work-concept in postmodern and contemporary dance, as well as a range of ways in which that concept has been challenged. The institutionalisation of choreographic authorship within modern dance is contrasted with critiques of authorship developed through American postmodern and subsequently European conceptual dance, both of which place renewed emphasis on the creative role of the dancer. The chapter also highlights the range of subject matter tackled by Western theatre dance since the mid-twentieth century and the polysemic character of many contemporary dances. It explores how increasing interest in documentation, preservation, and authentic performance are counterbalanced by practices of reinvention and alternative scoring. The chapter argues that, despite explicit challenges to the dance work-concept, it still underpins dance-making and dissemination.
Are Dance Works Real?
Authors: Pakes Anna
Published: May 2020

The chapter considers whether dance works, if they are norm-types, are creatable given that types are conventionally understood to be eternally existing abstracta. It explores whether an account of dance creation as discovery is plausible, critically examining the adaptability to dance of Julian Dodd’s defence of a Platonist ontology of musical works. Problems Dodd raises concerning the putative creatability of indicated types prompts discussion of alternative views, including Amie Thomasson’s arguments that multiple works are abstract artefacts. The chapter critically considers also a simple nominalist view of dance works as sets of performances, and sketches a fictionalist ontology of dance works (following Andrew Kania’s similar discussion of musical works). The fictionalist leanings of some dance discourse critical of the idea of the work is highlighted, and a claim made for the reality of dance works as social objects.
Drowning in Swan Lakes
Authors: Pakes Anna
Published: May 2020

The chapter continues the discussion of dance identity, examining the problem posed by a specific case, the ballet Swan Lake. This ballet is often invoked in the existing philosophical literature on identity but arguably with insufficient attention paid to its historical genesis and development. The chapter argues that nineteenth-century ballet ‘classics’ are not central or paradigm cases of choreographic works in the modern sense. It also makes the case that the variously authored, individual productions titled Swan Lake are works in their own right rather than tokens of some overarching work-type. If there is an overarching Swan Lake type, then this is a very “thin” entity on which it is problematic to model an account of the identity conditions of later works, since that misrepresents their identity constraints. The discussion illustrates how identity issues—and work ontology more generally—are intertwined with historically contingent conceptualisations and practices.
Films, Recordings, and Screendance Works
Authors: Pakes Anna
Published: May 2020

The chapter begins by noting the significance of the development of audiovisual recording technology for how dance works are conceptualised. Distinctions between different types of dance film are drawn, building on typology developed by Noël Carroll. The chapter discusses ontological and epistemological issues raised by these different types of dance film and video. It argues against sceptical views of recording that maintain the unreliability and undesirability of restaging dance works from film as distinct from notation. And the chapter develops an argument in support of the view that dances can genuinely be seen or experienced through film, drawing on the transparency thesis elaborated by Kendall Walton. The question of what kinds of things screendances are is also addressed, in the context of the ontological positions already explored in the book.
AVERAGE GLANDULAR DOSES AND NATIONAL DIAGNOSTIC REFERENCE LEVELS IN MAMMOGRAPHY EXAMINATIONS IN TURKEY
Authors: Parmaksız Aydın , Ataç Gökçe K , Bulur Emine , İnal Tolga , Alhan Aslıhan
Published: May 2020

In order to establish national diagnostic reference levels for mammography examinations, entrance skin air kerma, entrance skin dose and average glandular doses (AGDs) were calculated for a total of 25 624 cranio-caudal (CC) and mediolateral oblique (MLO) projections of 6309 patients for 40–49 and 50–64 age groups. The average entrance skin air kerma and entrance skin dose values for both age groups were found to be higher in MLO projections compared with CC projections. The minimum and maximum values of AGDs were determined as 0.4 and 7.9 mGy for both projections. The maximum numbers of AGDs for CC and MLO projections were calculated in the range of 1.1–1.5 and 1.6–2.0 mGy, respectively. The third quartile values of AGDs were calculated for each compressed breast thickness between 20 and 99 mm. The first national diagnostic reference levels of the country were established for each 10-mm compressed breast thickness in mammography examinations.
Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets
Authors: Neumann Johannes S , Desalle Rob , Narechania Apurva , Schierwater Bernd , Tessler Michael
Published: May 2020

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000–400,000 characters in size with $\sim $15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their “equivalent” under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10$\times $ in both likelihood and parsimony can in some cases “flip” which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically “swamp out” morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of “flipping points” (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.]
Evaluation of selected categories of pet treats using in vitro assay and texture analysis
Authors: He Fei , Holben Grace , de Godoy Maria R C
Published: May 2020

Treats are important contributors to the economics of the U.S. pet product industry. Not only do pet owners use them to build an emotional bond or interact with their pets, but treats also can deliver functional or health benefits. The objective of this study was to evaluate the digestion and safety of selected commercial treats by measuring their in vitro dry matter disappearance (DMD) using the modified in vitro method of Boisen and Eggum, which was developed to simulate in vivo digestibility of nonruminant animals. Twenty-five commercial treats were classified into six categories based on their appearance, size, and functionality. These categories included biscuit, chew, dental, meat product, rawhide, and cat treat. Each commercial product was analyzed in triplicate and in vitro DMD was calculated after enzymatic digestion and incubation. A wide variation in DMD was observed among and within different treat categories in both gastric and gastric + small intestinal phases of digestion. For the gastric phase, DMD ranged from 8.40% to 92.20%, whereas intestinal phase digestion had a DMD range of 35.10–100% (P < 0.05). In general, treats from meat products, dental, chew, biscuit, and cat treat categories had a high DMD (>85%) after the intestinal phase, whereas DMD of rawhide treats varied from 35.10% to 95.70%. Principal component analysis, in addition, has visually shown that rawhide treats displayed the largest portion of variation from the other treats. A low DMD at gastric phase is a concern because it may pose a risk for gastrointestinal blockage and intolerance, particularly for treats of large size that remained intact during this phase. In vitro DMD results can be used as a potential predictor of in vivo digestibility, facilitate recommendations about pet treat safety for professionals and manufacturers in the pet industry, and assist pet owners in the treat selection process and with treat purchasing decisions.
Postweaning mortality in commercial swine production. I: review of non-infectious contributing factors
Authors: Gebhardt Jordan T , Tokach Mike D , Dritz Steve S , DeRouchey Joel M , Woodworth Jason C , Goodband Robert D , Henry Steve C
Published: May 2020

Postweaning mortality is a complex causal matrix involving animal, environment, and infectious etiologic factors. Despite advances in swine productivity such as total pigs born, growth rate, feed intake, and efficiency, there have been modest to no improvements in postweaning mortality rates over the last several years. Industry averages for postweaning mortality range from four to eight percent for each the nursery, grow-finish, or wean-finish stages. Retrospective mortality causal analyses of individual databases have been performed. However, little information derived from meta-analysis, systematic review, or comprehensive literature reviews are available. In order to develop and evaluate strategies to comprehensively manage and reduce postweaning mortality, addressing the complexity and range of impact that factors have on mortality is necessary to identify and prioritize such contributing factors. Our objective is to describe the current state of knowledge regarding non-infectious causes of postweaning mortality, focusing on estimates of frequency and magnitude of effect where available. Postweaning mortality can be generalized into non-infectious and infectious causes, with non-infectious factors further classified into anatomic abnormalities, toxicity, animal factors, facility factors, nutritional inadequacies, season, and management factors. Important non-infectious factors that have been identified through review of literature include birth weight, pre-weaning management, weaning age and weight, and season. Additionally, reasons for mortality with a low incidence but a high magnitude include abdominal organ torsion/volvulus, sodium ion or ionophore toxicosis, or dietary imbalance due to feed formulation or manufacture error. Many interactive effects are present between and among infectious and non-infectious factors, but an important trend is the impact that non-infectious factors have on the incidence, severity, and resolution of infectious disease. Strategies to reduce postweaning mortality must consider the dynamic, complex state that forms the causal web. Control of postweaning mortality through understanding of the complexity, evaluation of mortality reduction strategies through rigorous scientific evaluation, and implementation remains an area of opportunity for continued growth and development in the global swine industry.
Effects of switching from corn distillers dried grains with solubles- to corn- and soybean meal-based diets on finishing pig performance, carcass characteristics, and carcass fatty acid composition
Authors: Lerner Annie B , Tokach Mike D , DeRouchey Joel M , Dritz Steve S , Goodband Robert D , Woodworth Jason C , Allerson Matt
Published: May 2020

Corn distillers dried grains with solubles (DDGS) are known to negatively impact carcass yield and fat quality, thus finishing pigs may need to be switched from diets containing DDGS to corn–soybean meal (CSBM) diets before marketing (DDGS withdrawal). A total of 860 finishing pigs (PIC C48 or L42 × 327; initially 66.2 kg body weight, BW) were used in a 76-day experiment to evaluate the effects of DDGS withdrawal periods at increasing intervals before harvest. Pen served as the experimental unit, and there were seven replicate pens per treatment with 23 to 25 pigs per pen. Pens were blocked by BW and allotted to one of five dietary treatments differentiated by the DDGS withdrawal period: 76, 42, 27, 15, or 0 day before harvest. Diets contained 40% DDGS from 22 to 66 kg prior to the experiment, 0% or 35% DDGS during the experiment from ~66 to 82 kg, and 0% or 30% DDGS until the completion of the trial. Diets were not balanced for net energy. Linear and quadratic response to time following dietary switch was evaluated using PROC GLIMMIX. For the overall period (day 76 prior to market to day 0), as withdrawal period increased, average daily gain (ADG) and final BW increased (linear, P < 0.002) and feed efficiency (G:F) improved (quadratic, P = 0.019). Average daily feed intake increased (quadratic, P = 0.030) as withdrawal period increased. There was an increase (linear P = 0.010) in hot carcass weight (HCW), with a marginally significant increase in carcass yield (linear, P = 0.094) with increasing withdrawal period. Loin depth and lean percentage did not demonstrate any evidence for treatment differences (P > 0.132). Backfat increased (linear, P = 0.030) with increasing withdrawal period. Finally, iodine value (IV) of belly fat was decreased (linear, P = 0.001) with increased withdrawal period. In conclusion, switching from a DDGS-based diet to a CSBM-based diet for longer periods before slaughter increased ADG and improved G:F, resulting in increased HCW. After diets were switched from DDGS to CSBM, pigs demonstrated an increase in intake, likely due to the ability to consume high volumes of feed after consuming high fiber (DDGS) diets. Belly fat IV was decreased as the length of time after dietary change was increased, with the lowest IV resulting from pigs that consumed CSBM for the entire experimental period.
Effects of corn distillers dried grains with solubles in finishing diets on pig growth performance and carcass yield with two different marketing strategies
Authors: Lerner Annie B , Tokach Mike D , DeRouchey Joel M , Dritz Steve S , Goodband Robert D , Woodworth Jason C , Hastad Chad W , Coble Kyle F , Arkfeld Emily , Cartagena Hilda C , Vahl Christopher
Published: May 2020

Feeding diets high in corn distillers dried grains with solubles (DDGS) before market can negatively impact carcass yield, hot carcass weight (HCW), and belly fat iodine value (IV). Two experiments were conducted to evaluate the effects of switching from DDGS-based to corn-soybean meal (CSBM)-based diets at increasing intervals (withdrawal periods) before harvest on finishing pig performance and carcass characteristics. Diets in both experiments contained either 0% or 30% DDGS and were balanced for net energy (NE). In Exp. 1, 985 pigs (initially 99.6 kg body weight [BW]) were used with 12 pens per treatment. The four treatments were increasing DDGS withdrawal periods: 28, 21, 14, or 0 d (no dietary switch) before marketing. All pens were marketed by removing the 17% heaviest pigs 21 d before slaughter and the remaining 83% all slaughtered 21 d later. Overall, there was no evidence for treatment differences on final BW, average daily feed intake, or feed efficiency (G:F;P > 0.10); however, average daily gain (ADG) increased (linear, P = 0.022) and belly fat IV decreased (linear, P = 0.001) the longer pigs were fed CSBM diets. There was no evidence for differences for HCW (P > 0.10); however, carcass yield increased (linear, P = 0.001) with increasing time following the switch to CSBM. Backfat depth decreased and percentage lean increased as CSBM feeding time increased (quadratic; P < 0.05). In Exp. 2, 1,158 pigs (initially 105 kg BW) were used in a 35-d study. There were 15 pens per treatment and four treatments of increasing DDGS withdrawal periods: 35, 28, 14, or 0 d (no dietary switch). All pens were marketed by removing the 15% heaviest pigs on day 28, the 28% heaviest pigs on day 14, and a final marketing of approximately 57% of starting barn inventory. There was no evidence that final BW, ADG, G:F, or HCW differed among dietary treatments (P > 0.10). Average daily feed intake and carcass yield increased and belly fat IV decreased (P < 0.050); the longer pigs were fed CSBM. In conclusion, growth performance was minimally impacted following dietary switch from DDGS- to CSBM-based diets, possibly due to similar dietary NE. For carcass yield and belly fat IV, the optimal time to make a dietary switch from high to low fiber appears to be linear in nature and at least 28 d before marketing.
Calmodulin inhibition as a mode of action of antifungal imidazole pharmaceuticals in non-target organisms
Authors: Breitholtz Magnus , Ivanov Pavel , Ek Karin , Gorokhova Elena
Published: May 2020

To improve assessment of risks associated with pharmaceutical contamination of the environment, it is crucial to understand effects and mode of action of drugs in non-target species. The evidence is accumulating that species with well-conserved drug targets are prone to be at risk when exposed to pharmaceuticals. An interesting group of pharmaceuticals released into the environment is imidazoles, antifungal agents with inhibition of ergosterol synthesis as a primary mode of action in fungi. However, imidazoles have also been identified as competitive antagonists of calmodulin (CaM), a calcium-binding protein with phylogenetically conserved structure and function. Therefore, imidazoles would act as CaM inhibitors in various organisms, including those with limited capacity to synthesize sterols, such as arthropods. We hypothesized that effects observed in crustaceans exposed to imidazoles are related to the CaM inhibition and CaM-dependent nitric oxide (NO) synthesis. To test this hypothesis, we measured (i) CaM levels and its gene expression, (ii) NO accumulation and (iii) gene expression of NO synthase (NOS1 and NOS2), in the cladoceran Daphnia magna exposed to miconazole, a model imidazole drug. Whereas significantly increased CaM gene expression and its cellular allocation were observed, supporting the hypothesized mode of action, no changes occurred in either NO synthase expression or NO levels in the exposed animals. These findings suggest that CaM inhibition by miconazole leads to protein overexpression that compensates for the loss in the protein activity, with no measurable downstream effects on NO pathways. The inhibition of CaM in D. magna may have implications for effect assessment of exposure to mixtures of imidazoles in aquatic non-target species.
Traumatic Brain Injury among football players in 2017 Series A Brazilian Football Championship – The gap between concussion protocols and the current medical practices
Authors: Salvarani Cármine Porcelli , de Medeiros Lucas Ribeiro , Sotocorno Leonardo Henrique Micheletti , Tomazini Vinícius Simon , de Castro Diego Ciotta , Dias Eduardo Almeida , da Costa Paulo Sérgio Teixeira , Pimenta Bruno Bueno , de Oliveira Diego Almeida , da Silva Eduardo Vinícius Colman , Sapatero Fernando Henrique
Published: May 2020

Background

Sideline assessment of football players with a potential concussion is a challenging concern. Video analysis is an important tool to recognize traumatic brain injury (TBI), including sports-related concussions, among football players.

Aim

To report the characteristics of TBI among football players in 2017 Brazilian Series A Football Championship and to discuss the evaluation protocols of football players with concussion.

Methods

This is an observational study concerning video analysis of all matches on 2017 Series A Brazilian Football Championship. The videos were first analyzed by a team of 10 trained medical students. All suspected TBIs were reviewed by the research’s coordinator. Concussion diagnosis was defined by one of the following events: lying motionless, loss of responsiveness, impact seizure, disorientation and motor incoordination. The length of sideline medical assessment was systematically recorded.

Results

In a whole of 380 matches, it was verified 374 TBIs. The most common etiology was “head-to-head” impact. Twelve players were replaced after TBI. Thirteen players (3,5% of TBIs) had concussion, but only four of them were replaced. The overall mean time for medical assessment was 1’35” (range: 48” to 7’40”). Considering the twelve players who had a concussion and the thirteen players who were replaced, the mean time for medical evaluation was 3’19” and 3’26”, respectively.

Conclusion

This study confirms that there is a gap between formal protocols for concussion assessment on sideline in Brazilian Elite Football and current medical practices. It also discusses changes on football rules of player replacement to an adequate sideline medical evaluation.
T cells expanded from renal cell carcinoma are tumor-reactive but fail to produce IFN-γ, TNF-α or IL-2
Authors: van Asten Saskia D. , de Groot Rosa , van Loenen Marleen M. , de Jong Jeroen , Monkhorst Kim , Haanen John B.A.G. , Amsen Derk , Bex Axel , Spaapen Robbert M. , Wolkers Monika C.
Published: May 2020

Metastatic renal cell carcinoma (RCC) has a poor prognosis. Recent advances have shown beneficial responses to immune checkpoint inhibitors, such as anti-PD-1 or anti-PD-L1 antibodies. As only a subset of RCC patients respond, alternative strategies should be explored. Patients refractory to anti-PD-1 therapy may benefit from autologous tumor infiltrating lymphocyte (TIL) therapy. Even though efficient TIL expansion was reported from RCC lesions, it is not well established how many RCC TIL products are tumor-reactive, how well they produce pro-inflammatory cytokines in response to autologous tumors, and whether their response correlates with the presence of specific immune cells in the tumor lesions.

We here compared the immune infiltrate composition of RCC lesions with that of autologous kidney tissue of 18 RCC patients. T cell infiltrates were increased in the tumor lesions, and CD8+T cell infiltrates were primarily of effector memory phenotype. Nine out of 16 (56%) tested TIL products we generated were tumor-reactive, as defined by CD137 upregulation after exposure to autologous tumor digest. Tumor reactivity was found in particular in TIL products originating from tumors with a high percentage of infiltrated T cells compared to autologous kidney, and coincided with increasedex vivoCD25 expression on CD8+T cells. Importantly, although TIL products had the capacity to produce the key effector cytokines IFN-γ, TNF-α or IL-2, they failed to do so in response to autologous tumor digests. In conclusion, TIL products from RCC lesions contain tumor-reactive T cells. Their lack of tumor-specific cytokine production requires further investigation of immunosuppressive factors in RCC and subsequent optimization of RCC-derived TIL culture conditions.
Unique habitat and macroinvertebrate assemblage structures in spring-fed stream: a comparison among clastic lowland tributaries and mainstreams in northern Japan
Authors: Sakai Masaru , Iwabuchi Katsuya , Bauman David
Published: May 2020

The stable flow and temperature regimes of spring-fed streams are distinct from the dynamic regimes of other streams. We investigated differences in habitat and macroinvertebrate assemblages among three stream types (spring-fed tributary, non-spring-fed tributary and mainstream) in a clastic lowland of northern Japan. Current velocity was the slowest in the spring-fed reach, where the percent of fine sediment deposition was also 3.8–11.4 times higher than in the other stream types. The standing stock of detritus was also greater in the spring-fed reach. These results suggest that the stable flow regime in the spring-fed stream leads to the accumulation of fine sediment and detritus on the streambed. Oligochaeta and chironomids, which are burrower-gatherers, were remarkably abundant in the spring-fed reach. Total macroinvertebrate abundance was 3.8–12.2 times greater in the spring-fed reach than in the other stream types. Sprawler-grazer ephemeropterans were the most abundant in the mainstream reaches, likely due to higher primary productivity.Allomyiasp, which depend on cool spring-fed habitats, were found only in the spring-fed reach. The indicator species analysis also indicated multiple taxa of detritivores andAllomyiasp. for the spring-fed tributary. The macroinvertebrate assemblage in the spring-fed reach was characterized by numerous burrowers, collector-gatherers, and crenobiont taxa, highlighting the uniqueness and its contribution to enhance beta diversity in river networks.
Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19
Authors: Juno Jennifer A , Tan Hyon-Xhi , Lee Wen Shi , Reynaldi Arnold , Kelly Hannah G , Wragg Kathleen , Esterbauer Robyn , Kent Helen E , Batten C Jane , Mordant Francesca L , Gherardin Nicholas A , Pymm Phillip , Dietrich Melanie H , Scott Nichollas E , Tham Wai-Hong , Godfrey Dale I , Subbarao Kanta , Davenport Miles P , Kent Stephen J , Wheatley Adam K
Published: May 2020

The rapid global spread of SARS-CoV-2 and resultant mortality and social disruption have highlighted the need to better understand coronavirus immunity to expedite vaccine development efforts. Multiple candidate vaccines, designed to elicit protective neutralising antibodies targeting the viral spike glycoprotein, are rapidly advancing to clinical trial. However, the immunogenic properties of the spike protein in humans are unresolved. To address this, we undertook an in-depth characterisation of humoral and cellular immunity against SARS-CoV-2 spike in humans following mild to moderate SARS-CoV-2 infection. We find serological antibody responses against spike are routinely elicited by infection and correlate with plasma neutralising activity and capacity to block ACE2/RBD interaction. Expanded populations of spike-specific memory B cells and circulating T follicular helper cells (cTFH) were detected within convalescent donors, while responses to the receptor binding domain (RBD) constitute a minor fraction. Using regression analysis, we find high plasma neutralisation activity was associated with increased spike-specific antibody, but notably also with the relative distribution of spike-specific cTFH subsets. Thus both qualitative and quantitative features of B and T cell immunity to spike constitute informative biomarkers of the protective potential of novel SARS-CoV-2 vaccines.
Neurophysiologic evidence for increased memory suppression among negative ruminators
Authors: Nair Aarti , Eyer Joshua C , Faust Mark E
Published: May 2020

Events (e.g., seeing a familiar face) may initiate retrieval of associated information (e.g., persons name), but not all cue initiated memory retrieval is welcome (e.g., trauma). Memory suppression refers to the ability to halt unwanted retrieval, and any erosion of memory associations in response to repeatedly excluding a memory from consciousness. The current study sought to examine event related potential (ERP, averaged scalp electrical recordings) correlates of inhibitory cognitive control of memory retrieval and any linkage of such control to ruminative memory styles. Participants (N=23) first learned face-picture pairings. ERPs were then recorded as they viewed face cues while either bringing the associated picture to mind (think trial), or not allowing the associated picture to come to mind (no-think trial). Emotional valence of learned pictures (negative vs neutral) modulated a posterior (P1, 100-150 ms) ERP associated with attention to the face cue. Memory strategy (think vs no-think) modulated a frontal (P3, 350-450 ms) associated with alerting of the need to control retrieval. Both valence and strategy worked in combination to modulate a late posterior (LC, 450-550 ms) ERP associated with successful memory retrieval. Brooding, a negative form of rumination, was found to be positively correlated with the LC ERP. The results suggest early separation of emotional and strategic control of retrieval, but later combined control over access to working memory. Moreover, the positive correlation of brooding and the LC suggest that individuals who are high in application of perseverative strategies to memory retrieval will show greater modulation of the retrieval-related LC ERP.
Fuzzy Autocatalytic analysis of Covid-19 outbreak in Malaysia
Authors: Ahmad Tahir , Ashaari Azmirul , Awang Siti Rahmah , Mamat Siti Salwana , Wan Mohamad Wan Munirah , Ahmad Fuad Amirul Aizad , Hassan Nurfarhana
Published: May 2020

The objective of this research is to demonstrate a mathematical technique to analyze the Covid-19 outbreak, particularly with respect to Malaysia. The technique is able to accommodate scarcity, quantity, and availability of the data set. The obtained results can offer descriptive insight for reflecting and strategizing actions in combating the pandemic.
Visualizing the itch-sensing skin arbors
Authors: Xing Yanyan , Steel Haley R. , Hilley Henry B. , Lawson Katy , Niehoff Taylor , Han Liang
Published: May 2020

Diverse sensory neurons exhibit distinct neuronal morphologies with a variety of axon terminal arborizations used to subserve their functions. Due to its clinical significance, the molecular and cellular mechanisms of itch are being intensely studied. However, a complete analysis of itch-sensing terminal arborization morphology is missing. Using a novelMrgprC11CreERT2transgenic mouse line, we labeled a small subset of itch-sensing neurons that express multiple itch-related molecules including MrgprA3, MrgprC11, histamine receptor H1, IL-31 receptor, 5-HT receptor 1F, natriuretic precursor peptide B, and neuromedin B. By combining sparse genetic labeling and whole-mount PLAP histochemistry, we found that itch-sensing skin arbors exhibit free endings with extensive axonal branching in the superficial epidermis and large receptive fields. These results revealed the unique morphological characteristics of itch-sensing neurons and provide novel insights into the basic mechanisms of itch transmission.
GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers
Authors: Bianco Gaia , Coto-Llerena Mairene , Gallon John , Taha-Mehlitz Stephanie , Kancherla Venkatesh , Konantz Martina , Srivatsa Sumana , Montazeri Hesam , Panebianco Federica , De Menna Marta , Paradiso Viola , Ercan Caner , Dahmani Ahmed , Montaudon Elodie , Beerenwinkel Niko , Kruithof-de Julio Marianna , Terracciano Luigi M. , Lengerke Claudia , Bidard François-Clément , Jeselsohn Rinath M. , Marangoni Elisabetta , Ng Charlotte K. Y. , Piscuoglio Salvatore
Published: May 2020

Synthetic lethal interactions, where the simultaneous but not individual inactivation of two genes is lethal to the cell, have been successfully exploited to treat cancer.GATA3is frequently mutated in estrogen receptor (ER)-positive breast cancers and its deficiency defines a subset of patients with poor response to hormonal therapy and poor prognosis. However, GATA3 is not targetable. Here we show thatGATA3andMDM2are synthetically lethal in ER-positive breast cancer. Depletion and pharmacological inhibition of MDM2 induce apoptosis inGATA3-deficient modelsin vitro, in vivoand in patient-derived organoids (PDOs) harboringGATA3somatic mutation. The synthetic lethality requires p53 and acts via the PI3K/Akt/mTOR pathway. Our results present MDM2 as a novel therapeutic target in the substantial cohort of ER-positive,GATA3-mutant breast cancer patients. With MDM2 inhibitors widely available, our findings can be rapidly translated into clinical trials to evaluate in-patient efficacy.
Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod
Authors: Russell Aubrie , Borrelli Sevarin , Fontana Rose , Laricchiuta Joseph , Pascar Jane , Becking Thomas , Giraud Isabelle , Cordaux Richard , Chandler Christopher H.
Published: May 2020

Sex chromosomes are highly variable in some taxonomic groups, but the evolutionary mechanisms underlying this diversity are not well understood. In terrestrial isopod crustaceans, evolutionary turnovers in sex chromosomes are frequent, possibly caused byWolbachia, a vertically-transmitted endosymbiont causing male-to-female sex reversal. Here, we use surgical manipulations and genetic crosses, plus genome sequencing, to examine sex chromosomes in the terrestrial isopodTrachelipus rathkei. Although an earlier cytogenetics study suggested a ZZ/ZW sex chromosome system in this species, we surprisingly find multiple lines of evidence that in our study population, sex is determined by an XX/XY system. Consistent with a recent evolutionary origin for this XX/XY system, the putative male-specific region of the genome is small. The genome shows evidence of Y-linked duplications of the gene encoding the androgenic gland hormone, a major component of male sexual differentiation in isopods. Our analyses also uncover sequences horizontally acquired from pastWolbachiainfections, consistent with the hypothesis thatWolbachiamay have interfered with the evolution of sex determination inT. rathkei. Overall, these results provide evidence for the co-occurrence of multiple sex chromosome systems withinT. rathkei, further highlighting the relevance of terrestrial isopods as models for the study of sex chromosome evolution.
A homodimeric aptamer variant generated from ligand-guided selection activates T-cell receptor cluster of differentiation three complex
Authors: Freage Lina , Jamal Deana , Williams Nicole , Mallikaratchy Prabodhika R.
Published: May 2020

Recently, immunotherapeutic modalities with engineered cells and monoclonal antibodies have been effective in treating several malignancies. However, growing evidence suggests that immune-related adverse events (irAE) lead to severe and long-term side effects. Most iRAEs involve prolonged circulation of antibodies. To address this problem, nucleic acid aptamers can serve as alternative molecules to design immunotherapeutics with high functional diversity and predictable circulation times. Here, we report the first synthetic prototype consisting of DNA aptamers, which can activate T-cell receptor cluster of differentiation 3 (TCR-CD3) complex in cultured T-cells. We show that activation potential is similar to that of a monoclonal antibody (mAb) against TCR-CD3, suggesting the potential of aptamers in developing efficacious synthetic immunomodulators. The synthetic prototype of anti-TCR-CD3ε, as described herein, was designed using aptamer ZUCH-1 against TCR-CD3ε, generated by Ligand Guided Selection (LIGS). Aptamer ZUCH-1 was truncated and modified with nuclease-resistant RNA analogs to enhance stability. Several dimeric analogs with truncated and modified variants were designed with variable linker lengths to investigate the activation potential of each construct. Among them, dimeric aptamer with approximate dimensions similar to those of an antibody showed the highest T-cell-activation, suggesting the importance of optimizing linker lengths in engineering functional aptamers. The observed activation potential of dimeric aptamers shows the vast potential of aptamers in designing synthetically versatile immunomodulators with tunable pharmacokinetic properties, expanding immunotherapeutic designs with the use of nucleic acid-based ligands such as aptamers.
Microbubble-Mediated Cavitation Promotes Apoptosis and Suppresses Invasion in AsPC-1 Cells
Authors: Cao J. , Zhou H. , Qiu F. , Chen J. , Diao F. , Huang P.
Published: May 2020

This study aimed to identify the potential and mechanisms of microbubble-mediated cavitation in promoting apoptosis and suppressing invasion in cancer cells. AsPC-1 cells were used and divided into four groups: control group, microbubble-only (MB) group, ultrasound-only (US) group, and ultrasound combined with microbubbles (US+MB) group. Pulse ultrasound was used with a frequency of 360 kHz and an intensity of 0.7 W/cm2for 1 min (duty rate=50%). Then cells in four groups were cultured for 24 h. Cell counting kit‑8 illustrated that US+MB could decrease cell viability. Western blot confirmed that US+MB increased cleaved Caspase‑3, Bcl-2-associated X protein (BAX), and decreased the B‑cell lymphoma‑2 (Bcl-2) levels. Besides, US+MB increased intracellular calcium ions and down-regulated cleaved Caspase-8. For proliferation ability, cells in US+MB group had a lower expression of Ki67 and the weakened colony formation ability. The transwell invasion assay showed that US+MB could decrease invasion ability in AsPC-1 cells. Further evidence showed that cells conducted with US+MB had the lower level of hypoxia-inducible factor-1α (HIF-1α) and Vimentin and the higher expression of E-cadherin than the other three groups. Finally, cells conducted with US+MB had less invadopodia formation. In conclusion, these results suggested that microbubble-mediated cavitation promoted apoptosis and suppressed invasion in AsPC-1 cells.

Significance

Cancer cells have a high rate of cell division and a high rate of cell division can speed up the development of hypoxia which lead to promote cancer invasion and metastasis. Here we used microbubble-mediated cavitation to generate a mechanical shock wave which could effectively kill cancer cells through physical damage and intrinsic signaling pathway. Furthermore, effective killing of cancer cells could restrain the development of hypoxia and prevent invasion ability of cancer cells.
A Purkinje cell model that simulates complex spikes
Authors: Burroughs Amelia , Cerminara Nadia L. , Apps Richard , Houghton Conor
Published: May 2020

Purkinje cells are the principal neurons of the cerebellar cortex. One of their distinguishing features is that they fire two distinct types of action potential, called simple and complex spikes, which interact with one another. Simple spikes are stereotypical action potentials that are elicited at high, but variable, rates (0 – 100 Hz) and have a consistent waveform. Complex spikes are composed of an initial action potential followed by a burst of lower amplitude spikelets. Complex spikes occur at comparatively low rates (~ 1 Hz) and have a variable waveform. Although they are critical to cerebellar operation a simple model that describes the complex spike waveform is lacking. Here, a novel single-compartment model of Purkinje cell electrodynamics is presented. The simpler version of this model, with two active conductances and a leak channel, can simulate the features typical of complex spikes recordedin vitro. If calcium dynamics are also included, the model can capture the pause in simple spike activity that occurs after complex spike events. Together, these models provide an insight into the mechanisms behind complex spike spikelet generation, waveform variability and their interactions with simple spike activity.
O-Pair Search with MetaMorpheus for O-glycopeptide Characterization
Authors: Lu Lei , Riley Nicholas M. , Shortreed Michael R. , Bertozzi Carolyn R. , Smith Lloyd M.
Published: May 2020

We report O-Pair Search, a new approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. O-Pair Search is freely available:https://github.com/smith-chem-wisc/MetaMorpheus.
sangeranalyseR: simple and interactive analysis of Sanger sequencing data in R
Authors: Chao Kuan-Hao , Barton Kirston , Palmer Sarah , Lanfear Robert
Published: May 2020

sangeranalyseR is an interactive R/Bioconductor package and two associated Shiny applications designed for analysing Sanger sequencing from data from theABIFfile format in R. It allows users to go from loading reads to saving aligned contigs in a few lines of R code. sangeranalyseR provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, viewing chromatograms, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. sangeranalyseR comes with extensive online documentation, and outputs detailed interactive HTML reports.

Availability and implementation

sangeranalyseR is implemented in R and released under an MIT license. It is available for all platforms on Bioconductor (https://bioconductor.org/packages/sangeranalyseR) and on Github (https://github.com/roblanf/sangeranalyseR).

Contact

kuanhao.chao@gmail.com

Supplementary information

Documentation athttps://sangeranalyser.readthedocs.io/.