bluuebunny/crossref_metadata_2025 huggingface dataset:
Deflating inflation: the connection (or lack thereof) between decisional and metacognitive processes and visual phenomenology
Authors: Abid Greyson
Published: November 2019

Vision presents us with a richly detailed world. Yet, there is a range of limitations in the processing of visual information, such as poor peripheral resolution and failures to notice things we do not attend. This raises a natural question: How do we seem to see so much when there is considerable evidence indicating otherwise? In an elegant series of studies, Lau and colleagues have offered a novel answer to this long-standing question, proposing that our sense of visual richness is an artifact of decisional and metacognitive deficits. I critically evaluate this proposal and conclude that it rests on questionable presuppositions concerning the relationship between decisional and metacognitive processes, on one hand, and visual phenomenology, on the other.
A general end-to-end diagnosis framework for manufacturing systems
Authors: Yuan Ye , Ma Guijun , Cheng Cheng , Zhou Beitong , Zhao Huan , Zhang Hai-Tao , Ding Han
Published: November 2019

The manufacturing sector is envisioned to be heavily influenced by artificial-intelligence-based technologies with the extraordinary increases in computational power and data volumes. A central challenge in the manufacturing sector lies in the requirement of a general framework to ensure satisfied diagnosis and monitoring performances in different manufacturing applications. Here, we propose a general data-driven, end-to-end framework for the monitoring of manufacturing systems. This framework, derived from deep-learning techniques, evaluates fused sensory measurements to detect and even predict faults and wearing conditions. This work exploits the predictive power of deep learning to automatically extract hidden degradation features from noisy, time-course data. We have experimented the proposed framework on 10 representative data sets drawn from a wide variety of manufacturing applications. Results reveal that the framework performs well in examined benchmark applications and can be applied in diverse contexts, indicating its potential use as a critical cornerstone in smart manufacturing.
Midline Craniotomy for Resection of Cavernous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: November 2019

This patient presented with a cavernous malformation in the inferior posterior third ventricle extending into the aqueduct. The patient was positioned supine on the operating room table with the head rotated into the horizontal plane. The choroidal fissure is opened lateral to the choroid plexus. This technique allows for the choroid plexus to serve as protection against forniceal manipulation. Rigid retraction was applied to the cerebral falx and corpus callosum to permit aqueductal visualization. The lighted instruments are paramount for adequate visualization of the third ventricle and during dissection of the lesion. Intraoperative visualization and postoperative imaging confirm gross total resection of the lesion. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute.
Environmental variables driving species and genus level changes in annual plankton biomass
Authors: Forsblom Louise , Engström-öst Jonna , Lehtinen Sirpa , Lips Inga , Lindén Andreas
Published: November 2019

Abiotic variables subject to global change are known to affect plankton biomasses, and these effects can be species-specific. Here, we investigate the environmental drivers of annual biomass using plankton data from the Gulf of Finland in the northern Baltic Sea, spanning years 1993–2016. We estimated annual biomass time-series of 31 nanoplankton and microplankton species and genera from day-level data, accounting for the average phenology and wind. We found wind effects on day-level biomass in 16 taxa. We subsequently used state-space models to connect the annual biomass changes with potential environmental drivers (temperature, salinity, stratification, ice cover and inorganic nutrients), simultaneously accounting for temporal trends. We found clear environmental effects influencing the annual biomasses of Dinobryon faculiferum, Eutreptiella spp., Protoperidinium bipes, Pseudopedinella spp., Snowella spp. and Thalassiosira baltica and indicative effects in 10 additional taxa. These effects mostly concerned temperature, salinity or stratification. Together, these 16 taxa represent two-thirds of the summer biomass in the sampled community. The inter-annual variability observed in salinity and temperature is relatively low compared to scenarios of predicted change in these variables. Therefore, the potential impacts of the presented effects on plankton biomasses are considerable.
Diffeomorphisms on the fuzzy sphere
Authors: Ishiki Goro , Matsumoto Takaki
Published: November 2019

Diffeomorphisms can be seen as automorphisms of the algebra of functions. In matrix regularization, functions on a smooth compact manifold are mapped to finite-size matrices. We consider how diffeomorphisms act on the configuration space of the matrices through matrix regularization. For the case of the fuzzy $$S^2$, we construct the matrix regularization in terms of the Berezin–Toeplitz quantization. By using this quantization map, we define diffeomorphisms on the space of matrices. We explicitly construct the matrix version of holomorphic diffeomorphisms on $$S^2$. We also propose three methods of constructing approximate invariants on the fuzzy $$S^2$. These invariants are exactly invariant under area-preserving diffeomorphisms and only approximately invariant (i.e. invariant in the large-$$N$ limit) under general diffeomorphisms.
The effects of dietary soybean hulls particle size and diet form on nursery and finishing pig performance1
Authors: Goehring Devin L , Wu Fangzhou , DeRouchey Joel M , Goodband Robert D , Tokach Mike D , Woodworth Jason C , Paulk Chad B , Dritz Steve S
Published: November 2019

Two experiments were conducted to investigate increasing unground and finely ground soybean hulls fed in meal or pelleted form on nursery and finishing pig performance. In experiment 1, 1,100 nursery pigs (initially 6.8 ± 0.1 kg and 28 d of age) were used in a 42-d study with 11 replicates per treatment. Treatments were arranged in a 2 × 2 × 2 factorial with main effects of soybean hulls (10% vs. 20%), grind type (unground, 617 µ vs. ground, 398 µ), and diet type (pelleted vs. meal form). No three-way or soybean hull level × grind type interactions were observed. Overall, average daily gain (ADG) was increased (P < 0.05) by pelleting, decreased (P < 0.05) by grinding, but unaffected by soybean hull levels. Grind type × diet form interactions were observed (P < 0.05) for gain:feed ratio (G:F) and a tendency for average daily feed intake (ADFI; P < 0.10). This was because grinding soybean hulls decreased (P < 0.05) ADFI and increased (P < 0.05) G:F when fed in meal form; however, grinding did not affect ADFI and decreased (P < 0.05) G:F when diets were pelleted. Increasing soybean hulls increased (P < 0.05) ADFI and decreased (P < 0.05) G:F when diets were fed in meal form, but these effects were not observed when diets were pelleted (diet form × soybean hull level interaction, P < 0.06). In experiment 2, 1,215 pigs (initially 21.1 ± 0.1 kg) were used in a 118-d study with nine replications per treatment. Treatments were a corn–soybean meal–based control diet and four diets arranged in a 2 × 2 factorial with the main effects of soybean hulls (7.5% vs. 15%) and grind type (unground, 787 µ vs. ground, 370 µ). All diets were fed in meal form. No soybean hull level × grind type interactions were observed for any growth or carcass responses. Increasing dietary soybean hulls from 0% to 15%, regardless of particle size, did not affect ADG or ADFI, but decreased (linear, P < 0.02) G:F. Carcass yield, hot carcass weight, and backfat depth decreased (linear, P < 0.03) whereas percentage lean increased (linear, P < 0.01) with increasing soybean hulls. Pigs fed ground soybean hulls had increased backfat depth (P < 0.01) and decreased (P < 0.01) percentage lean and fat-free lean index. In summary, increasing soybean hulls up to 20% decreased G:F in nursery and finishing pigs, whereas pelleting nursery diets improved ADG and eliminated the negative effect of increasing soybean hulls on G:F. Grinding soybean hulls reduced growth performance in nursery and finishing pigs.
Drivers of habitat partitioning among three Quercus species along a hydrologic gradient
Authors: Teshera-Levye Jennifer , Miles Brianna , Terwilliger Valery , Lovelock Catherine E , Cavender-Bares Jeannine
Published: November 2019

A critical process that allows multiple, similar species to coexist in an ecological community is their ability to partition local habitat gradients. The mechanisms that underlie this separation at local scales may include niche differences associated with their biogeographic history, differences in ecological function associated with the degree of shared ancestry and trait-based performance differences, which may be related to spatial or temporal variation in habitat. In this study we measured traits related to water-use, growth and stress tolerance in mature trees and seedlings of three oak species (Quercus alba L., Quercus falcata Michx. and Quercus palustris Münchh). which co-occur in temperate forests across the eastern USA but tend to be found in contrasting hydrologic environments. The three species showed significant differences in their local distributions along a hydrologic gradient. We tested three possible mechanisms that influence their contrasting local environmental distributions and promote their long-term co-existence: (i) differences in their climatic distributions across a broad geographic range, (ii) differences in functional traits related to water use, drought tolerance and growth and (iii) contrasting responses to temporal variation in water availability. We identified key differences between the species in both their range-wide climatic distributions (especially aridity index and mean annual temperature) and physiological traits in mature trees and seedlings, including daily water loss, hydraulic conductance, stress responses, growth rate and biomass allocation. Taken together, these differences explain the habitat partitioning that allows three closely related species to co-occur locally.
A “Far North Dixie Land”: Black Settlement, Discrimination, and Community in Urban Alaska
Authors: Hartman Ian C , Reamer David
Published: November 2019

Though it never ranked among the top destinations of the Great Migration, Alaska nevertheless enticed thousands of African Americans during the postwar decades. On the one hand, Black Alaskans experienced the lamentable patterns that defined American race relations in the twentieth century: housing and job discrimination alongside marginalization and racial violence. On the other hand, Black men and women also found in Alaska a place to make their own. This article presents a case study of urban history in the American West and demonstrates that despite its distance from other metropolitan centers, Alaska’s largest city, Anchorage, was not excluded from major postwar trends. Rather, many of the defining through-lines of midcentury U.S. history—mass migration, racial discrimination, community formation, urban planning, and civic activism, to name a few—were present and comprise a dynamic story that until now has never been told.
Melanopsidae (Caenogastropoda: Cerithioidea) from the eastern Mediterranean: another case of morphostatic speciation
Authors: Falniowski Andrzej , Heller Joseph , Cameron Robert A D , Pokryszko Beata M , Osikowski Artur , Rysiewska Aleksandra , Hofman Sebastian
Published: November 2019

Melanopsidae were collected from 23 localities in central and south-eastern Europe, the Aegean Islands and Israel. This study considered Melanopsis from the Aegean Islands, the Peloponnese and Israel, and Esperiana esperi, Holandriana holandrii and Microcolpia from continental Europe. Shells and radulae were described and illustrated, showing continuous variation of shell characters and differences in radulae among genera. Phylogenetic analyses were conducted on single-locus datasets (COI, 18S, 28S, ITS2 and H3) and on a concatenated dataset. Molecular data showed a differentiation not paralleled in morphology, reflecting morphostatic evolution. In all species with ribbed shell-forms, the ribbed and unribbed forms did not differ genetically. Within Melanopsis, four clades representing five species were distinguished. Melanopsis buccinoidea is found in Khios and Lesbos Islands, M. astropaliae in Naxos, Samos and Tinos Islands, M. wagneri in Rhodes Island and the Peloponnese, and M. costata and M. saulcyi in Israel. Molecular results and the ICZN rule of priority restrict the range of M. buccinoidea to the North Aegean Islands. ‘Melanopsis’ parreyssi belongs to the genus Microcolpia. Esperiana esperi belongs to a clade separate from Microcolpia.
A New Mutation Genotype of K218T in Myosin-5 Confers Resistance to Phenamacril in Rice Bakanae Disease in the Field
Authors: Wu J. Y. , Sun Y. N. , Zhou X. J. , Zhang C. Q.
Published: November 2019

In 2017 and 2018, a total of 294 Fusarium fujikuroi isolates were collected from bakanae-diseased rice plants in Jinhua, Shaoxing, and Jiaxing in Zhejiang Province, China. Phenamacril sensitivity of these isolates was determined by the 50% effective concentration value or minimum inhibitory concentration methods. Our results indicated that the phenamacril resistance frequency of F. fujikuroi increased from 18% in 2017 to 47% in 2018, and rice plants infected with F. fujikuroi-resistant isolates could not be protected effectively with 50 mg/liter of phenamacril. Phenamacril-resistant F. fujikuroi isolates obtained from rice fields showed stable resistance, because their fitness levels (i.e., mycelial growth, sporulation, and pathogenicity) were similar to the phenamacril-sensitive isolates. In addition to the point mutation at codon 219 in the myosin-5 gene that conferred resistance to phenamacril, our results also showed another point mutation at codon 218 (AAG→ACG) in myosin-5 that also conferred resistance to phenamacril. In this study, we found rapid development and persistence of diversified genotypes of phenamacril resistance, highlighting the importance of proper use of phenamacril in rice fields. Our results may also help researchers develop new fungicides or new control strategies using combinations of different fungicides in the control of phenamacril-resistant F. fujikuroi isolates.
Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring
Authors: Valle-Inclan Jose Espejo , Stangl Christina , de Jong Anouk C. , van Dessel Lisanne F. , van Roosmalen Markus J. , Helmijr Jean C.A. , Renkens Ivo , de Blank Sam , de Witte Chris J. , Martens John W.M. , Jansen Maurice P.H.M. , Lolkema Martijn P. , Kloosterman Wigard P.
Published: November 2019

Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of circulating tumor DNA (ctDNA) in liquid biopsies. However, affordable and fast identification of such SV biomarkers is challenging, which hinders routine use in the clinic. Here, we developed a novel approach - termed SHARC - for rapid discovery of somatic SVs as personalized tumor biomarkers. SHARC combines low coverage cancer genome sketching by using Oxford Nanopore sequencing with random forest classification and a dedicated filtering pipeline to enrich for somatic SVs. Our method leverages the real-time and long-read capabilities of nanopore sequencing to identify somatic SV breakpoints at nucleotide resolution from a tumor tissue biopsy within three days. We applied SHARC to tumor samples of high-grade ovarian and prostate cancer and validated on average ten somatic SVs per sample with PCR mini-amplicons. An accompanying method for SV breakpoint detection from liquid biopsies was devised based on digital PCR, enabling detection of cancer in a quantitative manner. Using this method, we retrospectively monitored treatment response in patients with metastatic prostate cancer. Our work demonstrates that SHARC forms a universal framework for rapid development of personalized biomarker assays for blood-based monitoring of any cancer type.
Cellular Fitness Phenotypes of Cancer Target Genes from Oncobiology to Cancer Therapeutics
Authors: George Bijesh , Paul Aswathy Mary , Pillai P. Mukundan , Amjesh Ravikumar , Leitzel Kim , Ali Suhail M. , Sandiford Oleta , Lipton Allan , Rameshwar Pranela , Hortobagyi Gabriel N. , Pillai Madhavan Radhakrishna , Kumar Rakesh
Published: November 2019

To define the growing significance of cellular targets of cancer drugs, we examined the fitness dependency of cellular targets or effectors of cancer drug targets across human cancer cells from 19 cancer types. We observed that the deletion of 35 out of 47 cellular mediators or targets of oncology drugs did not result in the expected loss of cell fitness in appropriate cancer types for which drugs targeting or utilizing these molecules were approved. Additionally, our analysis recognized 43 cellular targets as fitness genes in several cancer types in which these drugs were not approved, and thus, providing clues repurposing approved oncology drugs in cancer types. For example, we found the widespread upregulation and fitness dependency of the components of the mevalonate and purine biosynthesis pathways (currently targeted by bisphosphonates, statins, and pemetrexed in certain cancers) and an association between the overexpression of these targets and reduction in the overall survival duration of patients with breast and other hard-to-treat cancers, for which such drugs are not approved. In brief, the present analysis raised cautions about off-target and undesirable effects of certain oncology drugs in a subset of cancers where the in-tended cellular effectors of drug might not be fitness genes and offers a potential rationale for repurposing certain approved oncology drugs for targeted therapeutics in additional cancer types.
Midbrain activity supports high-level visual properties in primate temporal cortex
Authors: Bogadhi Amarender R. , Katz Leor N. , Bollimunta Anil , Leopold David A. , Krauzlis Richard J.
Published: November 2019

The evolution of the primate brain is marked by a dramatic increase in the number of neocortical areas that process visual information 1. This cortical expansion supports two hallmarks of high-level primate vision – the ability to selectively attend to particular visual features 2 and the ability to recognize a seemingly limitless number of complex visual objects 3. Given their prominent roles in high-level vision for primates, it is commonly assumed that these cortical processes supersede the earlier versions of these functions accomplished by the evolutionarily older brain structures that lie beneath the cortex. Contrary to this view, here we show that the superior colliculus (SC), a midbrain structure conserved across all vertebrates 4, is necessary for the normal expression of attention-related modulation and object selectivity in a newly identified region of macaque temporal cortex. Using a combination of psychophysics, causal perturbations and fMRI, we identified a localized region in the temporal cortex that is functionally dependent on the SC. Targeted electrophysiological recordings in this cortical region revealed neurons with strong attention-related modulation that was markedly reduced during attention deficits caused by SC inactivation. Many of these neurons also exhibited selectivity for particular visual objects, and this selectivity was also reduced during SC inactivation. Thus, the SC exerts a causal influence on high-level visual processing in cortex at a surprisingly late stage where attention and object selectivity converge, perhaps determined by the elemental forms of perceptual processing the SC has supported since before there was a neocortex.
Combining multiple functional connectivity methods to improve causal inferences
Authors: Sanchez-Romero Ruben , Cole Michael W.
Published: November 2019

Cognition and behavior emerge from brain network interactions, suggesting that causal interactions should be central to the study of brain function. Yet approaches that characterize relationships among neural time series—functional connectivity (FC) methods—are dominated by methods that assess bivariate statistical associations rather than causal interactions. Such bivariate approaches result in substantial false positives since they do not account for confounders (common causes) among neural populations. A major reason for the dominance of methods such as bivariate Pearson correlation (with functional MRI) and coherence (with electrophysiological methods) may be their simplicity. Thus, we sought to identify an FC method that was both simple and improved causal inferences relative to the most popular methods. We started with partial correlation, showing with neural network simulations that this substantially improves causal inferences relative to bivariate correlation. However, the presence of colliders (common effects) in a network resulted in false positives with partial correlation, though this was not a problem for bivariate correlations. This led us to propose a new combined functional connectivity method (combinedFC) that incorporates simple bivariate and partial correlation FC measures to make more valid causal inferences than either alone. We release a toolbox for implementing this new combinedFC method to facilitate improvement of FC-based causal inferences. CombinedFC is a general method for functional connectivity and can be applied equally to resting-state and task-based paradigms.
Solo: doublet identification via semi-supervised deep learning
Authors: Bernstein Nicholas , Fong Nicole , Lam Irene , Roy Margaret , Hendrickson David G. , Kelley David R.
Published: November 2019

Abstract

Single cell RNA-seq (scRNA-seq) measurements of gene expression enable an unprecedented high-resolution view into cellular state. However, current methods often result in two or more cells that share the same cell-identifying barcode; these “doublets” violate the fundamental premise of single cell technology and can lead to incorrect inferences. Here, we describe Solo, a semi-supervised deep learning approach that identifies doublets with greater accuracy than existing methods. Solo can be applied in combination with experimental doublet detection methods to further purify scRNA-seq data to true single cells beyond any previous approach.
Genetic Deletion of TrpV1 and TrpA1 Does not Alter Avoidance of or Patterns of Brainstem Activation to Citric Acid in Mice
Authors: Yu Tian , Wilson Courtney E. , Stratford Jennifer M. , Finger Thomas E
Published: November 2019

Exposure of the oral cavity to acidic solutions evokes not only a sensation of sour, but also of sharp or tangy. Acidic substances potentially stimulate both taste buds and acid-sensitive mucosal free nerve endings. Mice lacking taste function (P2X2/P2X3 double-KO mice) refuse acidic solutions similarly to wildtype mice and intraoral infusion of acidic solutions in these KO animals evokes substantial c-Fos activity within orosensory trigeminal nuclei as well as of the nucleus of the solitary tract (nTS) (Stratford et. al 2017). This residual acid-evoked, non-taste activity includes areas that receive inputs from trigeminal and glossopharyngeal peptidergic (CGRP-containing) nerve fibers that express TrpA1 and TrpV1 both of which are activated by low pH. We compared avoidance responses in wildtype (WT) and TrpA1/V1 double KO (TRPA1/V1Db1-/-) mice in brief-access behavioral assay (lickometer) to 1, 3, 10, 30 mM citric acid, along with 100 μM SC45647 and H2O. Both WT and TRPA1/V1Db1-/- show similar avoidance, including to higher concentrations of citric acid (10 and 30 mM; pH 2.62 and pH 2.36 respectively), indicating that neither TrpA1 nor TrpV1 is necessary for the acid avoidance behavior in animals with an intact taste system. Similarly, induction of c-Fos in the nTS and dorsomedial spinal trigeminal nucleus was similar in the WT and TRPA1/V1Db1-/-animals. Taken together these results suggest non-TrpV1 and non-TrpA1 receptors underlie the residual responses to acids in mice lacking taste function.
Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication inBrassica rapa
Authors: Qi Xinshuai , An Hong , Hall Tara E. , Di Chenlu , Blischak Paul D. , McKibben Michael T. W. , Hao Yue , Conant Gavin C. , Pires J. Chris , Barker Michael S.
Published: November 2019

Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication.

To test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties ofBrassica rapa. Like all “diploid” flowering plants,B. rapahas a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivatedB. rapaaccessions.

Using a combination of approaches, we identified more than 3,000 candidate genes associated with the domestication of four majorB. rapacrop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs.

Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication ofB. rapaand provide support for its importance in the success of modern agriculture.
Junctophilin-4 is essential for signalling at plasma membrane-endoplasmic reticulum junctions in sensory neurons
Authors: Hogea Alexandra , Shah Shihab , Jones Frederick , Carver Chase M , Hao Han , Liang Ce , Huang Dongyang , Du Xiaona , Gamper Nikita
Published: November 2019

Junctions of endoplasmic reticulum and plasma membrane (ER-PM junctions) serve as signaling hubs in prokaryotic cells. ER-PM junctions are present in peripheral sensory neurons and are necessary for pro-inflammatory G protein coupled receptor signalling and for inflammatory pain generation. Yet, the principles of ER-PM junctions assembly and maintenance, as well as their role in inflammatory signaling in sensory neurons are only beginning to emerge. Here we discovered that a member of the junctophilin family of proteins, JPH4, is abundantly expressed in rat dorsal root ganglion (DRG) neurons and is necessary for the formation of store operated Ca2+ entry (SOCE) complex at the ER-PM junctions in response to the G-protein induced ER Ca2+ store depletion. Furthermore, we demonstrate a key role of the JPH4 and ER Ca2+ stores in the maintenance of inflammatory pain. Indeed, knockdown of JPH4 expression in DRG in vivo significantly reduced the duration of pain produced by inflammatory mediator bradykinin. Since the ER supplies Ca2+ for the excitatory action of multiple inflammatory mediators, we suggest that junctional Ca2+ signalling maintained by JPH4 is an important contributor to the inflammatory pain mechanisms.
Fate of developmental mechanisms of myocardial plasticity in the postnatal heart
Authors: Hatzistergos Konstantinos E. , Durante Michael A. , Valasaki Krystalenia , Harbour J. William , Hare Joshua M.
Published: November 2019

Whether the heart’s organ-founding, progenitor cell gene regulatory networks (CPC-GRNs) are sustained after birth and can be therapeutically evoked for regeneration in response to disease, remains elusive. Here, we report a spatiotemporally resolved analysis of CPC-GRN deployment dynamics, through the pan-CPC-GRN gene Isl1. We show that the Isl1-CPC-GRNs that are deployed during early cardiogenesis and generate the cardiomyocyte majority from mesoderm, undergo programmed silencing through proteasome- and PRC2-mediated Isl1 repression, selectively in the arterial pole. In contrast, we identify a neural crest (CNC)-specific Wnt/β-catenin/Isl1-CPC-GRN that is deployed through the venous pole during cardiac growth and partitioning, and contributes a minority of cardiomyocytes which, in turn, expand massively to build ~10% of the biventricular myocardium. These “dorsal CNCs” continue to sporadically generate cardiomyocytes throughout postnatal growth which, however, are non-proliferative, suggesting that partitioning-like, fetal proliferation signals could be therapeutically targeted to evoke clonal expansion capacity in postnatal CNC-cardiomyocytes for heart regeneration.
von Willebrand Factor D and EGF Domains is an evolutionarily conserved and required feature of blastemas capable of multi-tissue appendage regeneration
Authors: Leigh N.D. , Sessa S. , Dragalzew A.C. , Payzin-Dogru D. , Sousa J.F. , Aggouras A.N. , Johnson K. , Dunlap G.S. , Haas B.J. , Levin M. , Schneider I. , Whited J.L.
Published: November 2019

Regenerative ability varies tremendously across species. A common feature of regeneration of appendages such as limbs, fins, antlers, and tails is the formation of a blastema--a transient structure that houses a pool of progenitor cells that regenerate the missing tissue. We have identified the expression of von Willebrand Factor D and EGF Domains (vwde) as a common feature of blastemas capable of regenerating limbs and fins in a variety of highly regenerative species. Further, vwde expression is tightly linked to the ability to regenerate appendages. Functional experiments demonstrate a requirement for vwde in regeneration and indicate that Vwde is a potent mitogen in the blastema. These data identify a key role for vwde in regenerating blastemas and underscore the power of an evolutionarily-informed approach for identifying conserved genetic components of regeneration.
Human pseudoislet system enables detection of differences in G-protein-coupled-receptor signaling pathways between α and β cells
Authors: Walker John T. , Haliyur Rachana , Nelson Heather A. , Ishahak Matthew , Poffenberger Gregory , Aramandla Radhika , Reihsmann Conrad , Luchsinger Joseph R. , Saunders Diane C. , Wang Peng , Garcia-Ocaña Adolfo , Bottino Rita , Agarwal Ashutosh , Powers Alvin C. , Brissova Marcela
Published: November 2019

G-protein-coupled-receptors (GPCRs) modulate insulin secretion from β cells and glucagon secretion from α cells. Here, we developed an integrated approach to study the function of primary human islet cells using genetically modified pseudoislets that resemble native islets across multiple parameters. We studied the Gi and Gq GPCR pathways by expressing the designer receptors exclusively activated by designer drugs (DREADDs) hM4Di or hM3Dq. Activation of Gi signaling reduced insulin and glucagon secretion, while activation of Gq signaling stimulated glucagon secretion but had both stimulatory and inhibitory effects on insulin secretion. Further, we developed a microperifusion system that allowed synchronous acquisition of GCaMP6f biosensor signal and hormone secretory profiles and showed that the dual effects for Gq signaling occur through changes in intracellular Ca2+. By combining pseudoislets with a microfluidic system, we co-registered intracellular signaling dynamics and hormone secretion and demonstrated differences in GPCR signaling pathways between human β and α cells.
Demonstration of RNA interference by bacterial feeding in Stentor polymorphus
Authors: Slabodnick Mark M.
Published: November 2019

Stentor is a genus of large trumpet-shaped unicellular organisms in the ciliate phylum. Classically they have been used as models of cellular morphogenesis due to their large size and ability to regenerate, but some Stentor species have features that make them useful models for other types of studies as well. Stentor polymorphus is a widely distributed species that harbors green algal endosymbionts from the Chlorella genus. While interesting phenomenology in this species has been described, molecular tools have never been developed in this system. As technology has advanced, the use of emerging models like S. polymorphus has become more prevalent, and recently a set of transcriptomes for S. polymorphus was published. However, there are still technical hurdles to using S. polymorphus as an effective experimental system in the lab. Here I describe the identification and culture of a S. polymorphus population from North Carolina as well as the identification and cloning of homologs of α-tubulin and the morphogenesis gene mob-1. Additionally, I demonstrate that RNA interference (RNAi) by feeding is effective against both of these homologs in S. polymorphus. The phenotypes observed in S. polymorphus were similar to phenotypes previously validated in S. coeruleus, a related Stentor species. A direct comparison of feeding RNAi between the two species revealed that RNAi appeared to be less effective in S. polymorphus. The ability to perform RNAi in S. polymorphus strengthens its use as an emerging model for exploring mechanisms of unicellular morphogenesis and regeneration or host-symbiont interactions and suggests that RNAi by bacterial feeding might be more broadly effective across the Stentor genus.
Evaluation of yield, yield stability and yield-protein trade-off in commercial faba bean cultivars
Authors: Skovbjerg Cathrine Kiel , Knudsen Jens Nørgaard , Füchtbauer Winnie , Stougaard Jens , Stoddard Frederick L. , Janss Luc , Andersen Stig Uggerhøj
Published: November 2019

Faba bean is a legume crop with high protein content and large potential for cultivation in the Northern latitudes. However, it has a reputation for being an unstable crop with large inter-annual variability, mostly explained by yearly variation in rainfall. Consequently, the objective is to breed cultivars with high seed yield and high yield stability. In this study, 17 commercial cultivars of faba bean were evaluated for seed yield, yield stability and trade-off between seed yield and protein content in four locations in Denmark and Finland during 2016-2018. We found that location and year effects accounted for 72% of the total seed yield variation. Cultivar by environment interactions (G×E) were found to be small and did not cause re-ranking of cultivars in different environments. Yield stability contributed little to the mean yield of the cultivars because high-yielding cultivars consistently outperformed the lower yielding genotypes, even under the most adverse conditions. The latter was also the case for total protein yield quantified as total yield multiplied by seed protein percentage. Although we found a strong negative correlation of −0.64 between yield and protein content, a few cultivars produced high yields while maintaining a relatively high protein content, suggesting that these traits may to some degree be genetically separable.
Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases
Authors: Guevara Tibisay , Rodriguez-Banqueri Arturo , Ksiazek Miroslaw , Potempa Jan , Gomis-Rüth F. Xavier
Published: November 2019

Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54–Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1′. Moreover, residue Cys23 within a conserved cysteine–glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1′ to S6′. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.
Crystal structure of pyridinium tetraisothiocyanatodipyridinechromium(III) pyridine monosolvate
Authors: Neumann Tristan , Jess Inke , Näther Christian
Published: November 2019

In the crystal structure of the title compound, (C5H6N)[Cr(NCS)4(C5H5N)2]·C5H5N, the CrIII ions are octahedrally coordinated by four N-bonding thiocyanate anions and two pyridine ligands into discrete negatively charged complexes, with the CrIII ion, as well as the two pyridine ligands, located on crystallographic mirror planes. The mean planes of the two pyridine ligands are rotated with respect to each other by 90°. Charge balance is achieved by one protonated pyridine molecule that is hydrogen bonded to one additional pyridine solvent molecule, with both located on crystallographic mirror planes and again rotated by exactly 90°. The pyridinium H atom was refined as disordered between both pyridine N atoms in a 70:30 ratio, leading to a linear N—H...N hydrogen bond. In the crystal, discrete complexes are linked by weak C—H...S hydrogen bonds into chains that are connected by additional C—H...S hydrogen bonding via the pyridinium cations and solvent molecules into layers and finally into a three-dimensional network.
Synthesis, crystal structure and Hirshfeld surface analysis of diethyl 2,6-dimethyl-4-(thiophen-3-yl)-1,4-dihydropyridine-3,5-dicarboxylate
Authors: Vu Quoc Trung , Tran Thi Thuy Duong , Phung Ngoc Thanh , Vu Quoc Manh , Nguyen Hien , Duong Khanh Linh , Tu Quang Anh , Van Meervelt Luc
Published: November 2019

In the title compound, C17H21NO4S, the 1,4-dihydropyridine ring has an envelope conformation with the Csp
3 atom at the flap. The thiophene ring is nearly perpendicular to the best plane through the 1,4-dihydropyridine ring, the dihedral angle being 82.19 (13)°. In the crystal, chains running along the b-axis direction are formed through N—H...O interactions between the 1,4-dihydropyridine N atom and one of the O atoms of the ester groups. Neighbouring chains are linked by C—H...O and C—H...π interactions. A Hirshfeld surface analysis shows that the most prominent contributuion to the surface contacts are H...H contacts (55.1%).
Crystal structure of a new polymorph of 3-acetyl-8-methoxy-2H-chromen-2-one
Authors: Gonzalez-Carrillo Gabino , Muñiz-Valencia Roberto , García-Báez Efren V. , Martínez-Martínez Francisco J.
Published: November 2019

A new polymorphic form of the title compound, C12H10O4, is described in the orthorhombic space group Pbca and Z = 8, as compared to polymorph I, which crystallizes in the monoclinic space group C2/c and Z = 8 [Li et al. (2012). Chin. J. Struct. Chem.
31, 1003–1007.]. In polymorph II, the coumarin ring system is almost planar (r.m.s. deviation = 0.00129 Å). In the crystal, molecules are connected by Csp
3—H...O and Car—H...O hydrogen bonds, forming molecular sheets linked into zigzag shaped layers along the b-axis direction. The three-dimensional lattice is assembled through stacking of the zigzag layers by π–π interactions with a centroid-to-centroid distance of 3.600 (9) Å and antiparallel C=O...C=O interactions with a distance of 3.1986 (17) Å, which give rise to a helical supramolecular architecture.
Crystal structure of [K(18-crown-6)]+2[Pt(CN)4]2−
Authors: Sellin Malte , Malischewski Moritz
Published: November 2019

In the title compound, di-μ-cyanato-1:2κ2N:C;2:3κ2C:N-dicyanato-2κ2C-bis(1,4,7,10,13,16-hexaoxacyclooctadecane)-1κ6O;3κ6O-1,3-dipotassium(I)-2-platinum(II), [K2Pt(CN)4(C12H24O6)2] or [K(18-crown-6)]2·[Pt(CN)4], twotrans-orientated cyano groups of the square-planar [Pt(CN)4]2−dianion (Pt site symmetry \overline{1}) bind to one potassium ion each, which are additionally coordinated by the six O atoms of 18-crown-6. No Pt...Pt interactions occur in the crystal, but very weak Pt...H contacts (2.79 Å) are observed.
5-(3-Hydroxyphenyl)-1,3,4-oxadiazole-2(3H)-thione hemihydrate
Authors: Razzoqova Surayyo Razzoqovna , Kadirova Shaxnoza , Ashurov Jamshid Mengnorovich , Rakhmonova Dilnoza Salamovna , Ziyaev Abdukhakim , Parpiev Nusrat Agzamovich
Published: November 2019

The title 1,3,4-oxadiazole derivative crystallizes as a hemihydrate, C8H6N2O2S·0.5H2O, with the water molecule located on a twofold rotation axis. The 1,3,4-oxadiazole molecule is essentially planar, the r.m.s. deviation of the non-H atoms being 0.0443 Å. The dihedral angle between the mean planes of the phenyl and oxadiazole rings is 6.101 (17)°. In the crystal, molecules are linked via O—H...S and N—H...O hydrogen bonds involving the water molecule, the N—H group and the thione S atom into undulating ribbons. Additional π–π interactions generate a two-dimensional supramolecular framework extending parallel to (001).
An empirical investigation of the relationship between the real exchange rate and net FDI inflows in Mauritius
Authors: Babubudjnauth Ashok , Seetanah Boopendra
Published: November 2019

Purpose

The purpose of this paper is to find out the impact of real exchange rate on foreign direct investment (FDI) in Mauritius.

Design/methodology/approach

Autoregressive distributed lag time series methodology is used.

Findings

Real exchange rate depreciation enhances inflows of FDI in both the short and long run.

Originality/value

The research is original, and data used are from official sources.
Firm productivity in Sub-Saharan Africa: how relevant is quality of tax administration?
Authors: Kamasa Kofi , Adu George , Oteng-Abayie Eric Fosu
Published: November 2019

Purpose

The purpose of this paper is to find the effect of quality of tax administration on firm productivity in Sub-Saharan Africa (SSA). Also, the paper investigates whether the effect of quality of tax administration on firm productivity varies with respect to firms of different ages and sizes.

Design/methodology/approach

The paper uses the World Bank Enterprise Survey data for 6,718 firms across 40 countries in SSA. By employing the least square method, the estimations are robust since country and industry heterogeneity are controlled, as well as other covariates that affect firm productivity such as capital, technology, business environment, infrastructure and firm characteristics.

Findings

Results of the paper reveal that productivity of firms reduces with poor quality of tax administration. With positive and significant interaction term coefficient between smaller firms and quality of tax administration, the findings also reveal that smaller firms do benefit in the presence of poor quality of tax administration than larger firms.

Originality/value

The study contributes to policy by providing empirical evidence on the impact that quality of tax administration has on firm productivity. Empirically, the paper is also the first to assess the effect of tax administration quality on firm productivity with sole emphasis on SSA (to the best of the authors’ knowledge after review of literature). The paper suggests reforms and improvement in tax administration so as to reduce compliance burden and improve productivity.
Scripting the experience of mathematics teaching
Authors: Biza Irene , Nardi Elena
Published: November 2019

Purpose

The purpose of this paper is to propose and evaluate a proactive reflective activity for mathematics student teachers in which they consider mathematical content and its teaching in highly specific classroom situations.

Design/methodology/approach

The study was conducted in context of a mathematics Initial Teacher Education programme in the UK. Participants were invited from the whole cohort of student teachers to identify, script and reflect upon critical classroom incidents. In total, 12 such scripts were produced and then discussed by 17 student teachers in group and plenary sessions. Discussions were audio-recorded. Scripts and discussions were analysed according to four characteristics: consistency between stated pedagogical priorities and intended practices; specificity of the reflection to the classroom situation reported in the scripts; reification of pedagogical discourse; and, reification of mathematical discourse.

Findings

In the results, the authors exemplify student teachers’ insights that emerged from the analysis of the scripts through the typology of the four characteristics, and the authors observe that the student teachers’ insights mirror the complexity and richness of the mathematics classrooms they face. The authors’ examples and their evaluation through the aforementioned typology of the four characteristics illustrate the potency of student teachers’ participation in producing, and reflecting upon, individually and collectively, critical incidents of their inaugural experiences in the classroom.

Practical implications

As these activities take placein the context of teacher education, professional development or developmental research environments, an additional challenge is to generate robust and informative evaluation of teachers’ engagement with reflection and research on their practice. This study takes on this challenge in the context of a mathematics teacher education programme in the UK: the authors propose and evaluate a proactive reflective activity for mathematics student teachers in which they consider mathematical content and its teaching in highly specific classroom situations.

Originality/value

The examples and their evaluation through the typology of four characteristics illustrate the potency of student teachers’ participation in producing, and reflecting upon, individually and collectively, critical incidents of their inaugural experiences in the classroom.