bluuebunny/crossref_metadata_2025 huggingface dataset:
Distortion Effects in Equal Area Unit Maps
Authors: Schiewe Jochen
Published: February 2021

Maps that correctly represent the geographic size and shape of regions, taking into account scaling and generalization, have the disadvantage that small regions can easily be overlooked or not seen at all. Hence, for some map use tasks where small regions are of importance, alternative map types are needed. One option is the so-called equal area unit maps (EAUMs), where every enumeration unit has the same area size, possibly also the same basic shape such as squares or hexagons. The geometrical distortion of EAUMs, however, leads to a more difficult search for regions as well as a falsification of topological relationships and spatial patterns. To describe these distortions, a set of analytical measures is proposed. But it turns out that the expressiveness of these measures is rather limited. To better understand and to model the influence of distortions, two user studies were conducted. The study on the search in EAUMs (also with the aim of reconstruct the search strategies of the users) revealed how important it is to consider the local topology (e.g. corner or border positions of regions) during the generation process. With regard to pattern identification, it could be shown that EAUMs significantly increase the detection rate of local extreme values. On the other hand, global lateral gradients or geostatistical hot spots often get blurred or even lost. As a consequence, a task-oriented selection of map types and further developments are recommended.
Clinical Guidelines in the Management of Frozen Shoulder: An Update!
Authors: Pandey Vivek , Madi Sandesh
Published: February 2021

Among all the prevalent painful conditions of the shoulder, frozen shoulder remains one of the most debated and ill-understood conditions. It is a condition often associated with diabetes and thyroid dysfunction, and which should always be investigated in patients with a primary stiff shoulder. Though the duration of ‘traditional clinicopathological staging’ of frozen shoulder is not constant and varies with the intervention(s), the classification certainly helps the clinician in planning the treatment of frozen shoulder at various stages. Most patients respond very well to combination of conservative treatment resulting in gradual resolution of symptoms in 12–18 months. However, the most effective treatment in isolation is uncertain. Currently, resistant cases that do not respond to conservative treatment for 6–9 months could be offered surgical treatment as either arthroscopic capsular release or manipulation under anaesthesia. Though both invasive options are not clinically superior to another, but manipulation could result in unwarranted complications like fractures of humerus or rotator cuff tear.
Rewarding in International Law
Authors: van Aaken Anne , Simsek Betül
Published: February 2021

Why states comply with international law has long been at the forefront of international law and international relations scholarship. The compliance discussion has largely focused on negative incentives. We argue that there is another, undertheorized mechanism: rewarding. We provide a typology and illustrations of how rewards can be applied. Furthermore, we explore the rationale, potential, and limitations of rewarding, drawing on rationalist and psychological approaches. Both approaches provide ample justifications for making greater use of rewarding in international law.
Accounting for the Effects of Employment, Equity, and Risk Aversion in Cost–Benefit Analysis: An Application to an Adaptation Project
Authors: Markanday Ambika , Markandya Anil , de Murieta Elisa Sainz , Galarraga Ibon
Published: February 2021

This paper sets out to explore to what extent integrating employment effects, equity, and risk aversion within cost–benefit analysis (CBA) affect the economic appraisal of a climate change adaptation project designed to protect against flood risk in a region of Bilbao (Basque Country, Spain). Four CBAs are conducted: (i) a standard CBA; (ii) a standard CBA considering equity; (iii) a standard CBA considering equity and employment; and (iv) a standard CBA considering equity, employment and risk aversion. All CBAs are conducted using a time frame of 2014–2080 and considering a 100-year return period under a middle of the road emission scenario (RCP4.5). A sensitivity analysis is also undertaken. Results suggest that the economic efficiency of the adaptation investment is contingent on what types of considerations are included within CBA. Integrating elements of employment, equity and risk aversion can strengthen or weaken the case for action (leading to higher or lower net-present values) and (depending on the discount rate chosen) may even be the deciding factor for determining whether a particular action should be carried out or not (whether the net-present value is positive or negative).
Cognition in the first week after stroke: how does it relate to personal and instrumental activities of daily living at follow-up?
Authors: Buys Sarah , Gustafsson Louise , Gullo Hannah , Grimley Rohan , Summers Mathew , Campbell Alana
Published: February 2021

Background:

The Montreal Cognitive Assessment (MoCA) is routinely used during the early assessment of people after stroke to indicate cognitive effects and inform clinical decision-making.

Aim:

The purpose of this study was to examine the relationship between cognition in the first week post-stroke and personal and instrumental activities of daily skills at 1 month and 3 months post-stroke.

Method:

A prospective cohort study consecutively recruited people admitted to the acute stroke ward. Acute cognitive status was measured using the MoCA within 1 week post-stroke onset. Functional outcomes were measured using the Functional Independence Measure (FIM) and the Australian Modified Lawton’s Instrumental Activities of Daily Living Scale (Lawton’s) at 1 month and 3 months post-stroke.

Results:

Fifty participants with predominantly mild stroke (n = 47) and mean age of 69.8 achieved a mean MoCA score of 23.1. Controlling for age, the MoCA was associated with the overall FIM score at 1 month (P = 0.02). It was nearing significance for the Lawton’s at 1 month (P = 0.06) but was not associated with either outcome at 3 months. A score of less than 23 on the MoCA was indicative of lower scores on both outcomes.

Conclusions:

A low MoCA score within 1 week of stroke may indicate need for support or rehabilitation due to early impacts on personal activities of daily living, but is not associated with poor functional outcomes at 3 months.
Nonlinear and non-local analytical solution for Darcy–Forchheimer flow through a deformable porous inclusion within a semi-infinite elastic medium
Authors: Zhang Wei , Mehrabian Amin
Published: February 2021

Permeability is a nonlinear and non-local function of the intimate coupling between pore fluid flow and solid deformation in porous media. A class of related problems involves the effect of fluid injection or withdrawal on the transport properties of geomaterials. This paper presents an analytical solution for the nonlinear and non-local problem of fluid flow through a disk-shaped porous elastic inclusion below the free surface of an elastic half-space. The solution accounts for the following nonlinear mechanisms: (i) variations in the permeability coefficient due to the flow-induced deformation of the inclusion; (ii) the inertial losses of the pore fluid flow. The former and latter mechanisms are formulated using the Green's function for a dilatation centre in an elastic half-space and the Darcy–Forchheimer equation for fluid flow through porous media, respectively. An analytical perturbation solution to the considered problem is developed and validated against the numerical finite element solution to the same problem. The described nonlinear mechanisms are represented by two dimensionless parameter groups. The extreme values of these dimensionless groups govern the solution asymptotic behaviours mimicking the special-case solutions in which either mechanism is forced to vanish. The applied aspects of the solution are demonstrated through the wellbore performance index parameter that quantifies the subsurface rock ability to deliver the pore fluid toward or away from a wellbore in a porous reservoir. Unlike the linear models, the presented nonlinear solution captures the observed dependence of the performance index on the wellbore flow rate.
THE OPEN AND CLOPEN RAMSEY THEOREMS IN THE WEIHRAUCH LATTICE
Authors: MARCONE ALBERTO , VALENTI MANLIO
Published: February 2021

We investigate the uniform computational content of the open and clopen Ramsey theorems in the Weihrauch lattice. While they are known to be equivalent to
$\mathrm {ATR_0}$
from the point of view of reverse mathematics, there is not a canonical way to phrase them as multivalued functions. We identify eight different multivalued functions (five corresponding to the open Ramsey theorem and three corresponding to the clopen Ramsey theorem) and study their degree from the point of view of Weihrauch, strong Weihrauch, and arithmetic Weihrauch reducibility. In particular one of our functions turns out to be strictly stronger than any previously studied multivalued functions arising from statements around
$\mathrm {ATR}_0$
.
FINDING DESCENDING SEQUENCES THROUGH ILL-FOUNDED LINEAR ORDERS
Authors: GOH JUN LE , PAULY ARNO , VALENTI MANLIO
Published: February 2021

In this work we investigate the Weihrauch degree of the problem Decreasing Sequence (
$\mathsf {DS}$
) of finding an infinite descending sequence through a given ill-founded linear order, which is shared by the problem Bad Sequence (
$\mathsf {BS}$
) of finding a bad sequence through a given non-well quasi-order. We show that
$\mathsf {DS}$
, despite being hard to solve (it has computable inputs with no hyperarithmetic solution), is rather weak in terms of uniform computational strength. To make the latter precise, we introduce the notion of the deterministic part of a Weihrauch degree. We then generalize
$\mathsf {DS}$
and
$\mathsf {BS}$
by considering
$\boldsymbol {\Gamma }$
-presented orders, where
$\boldsymbol {\Gamma }$
is a Borel pointclass or
$\boldsymbol {\Delta }^1_1$
,
$\boldsymbol {\Sigma }^1_1$
,
$\boldsymbol {\Pi }^1_1$
. We study the obtained
$\mathsf {DS}$
-hierarchy and
$\mathsf {BS}$
-hierarchy of problems in comparison with the (effective) Baire hierarchy and show that they do not collapse at any finite level.
Decoupling of morphological disparity and taxonomic diversity during the end-Permian mass extinction
Authors: Wan Junyu , Foster William J. , Tian Li , Stubbs Thomas L. , Benton Michael J. , Qiu Xincheng , Yuan Aihua
Published: February 2021

An increasing number of unexpectedly diverse benthic communities are being reported from microbially precipitated carbonate facies in shallow-marine platform settings after the end-Permian mass extinction. Ostracoda, which was one of the most diverse and abundant metazoan groups during this interval, recorded its greatest diversity and abundance associated with these facies. Previous studies, however, focused mainly on taxonomic diversity and, therefore, left room for discussion of paleoecological significance. Here, we apply a morphometric method (semilandmarks) to investigate morphological variance through time to better understand the ecological consequences of the end-Permian mass extinction and to examine the hypothesis that microbial mats played a key role in ostracod survival. Our results show that taxonomic diversity and morphological disparity were decoupled during the end-Permian extinction and that morphological disparity declined rapidly at the onset of the end-Permian extinction, even though the high diversity of ostracods initially survived in some places. The decoupled changes in taxonomic diversity and morphological disparity suggest that the latter is a more robust proxy for understanding the ecological impact of the extinction event, and the low morphological disparity of ostracod faunas is a consequence of sustained environmental stress or a delayed post-Permian radiation. Furthermore, the similar morphological disparity of ostracods between microbialite and non-microbialite facies indicates that microbial mats most likely represent a taphonomic window rather than a biological refuge during the end-Permian extinction interval.
Feasible Arm Configurations and its Application for Human-Like Motion Control of S-R-S-Redundant Manipulators with Multiple Constraints
Authors: Xia Jing , Jiang Zai-nan , Zhang Ting
Published: February 2021

This paper presents a general framework for human-like motion control of 7-DOF S-R-S-redundant manipulators. The new framework simultaneously accomplishes five objectives: Cartesian trajectory tracking, obstacle avoidance, joint limit avoidance, human-like movement, and a feasibility evaluation of the Cartesian trajectory.We exhaustively compute all feasible arm configurations. This allows for quick evaluations of the feasibility of the Cartesian trajectories. They are applied to inverse kinematics of the redundant manipulator to improve the capability to handle multiple constraints, and enable the manipulator to imitate human movements. The efficiency of the proposed framework is demonstrated by kinematic experiments with a humanoid robot.
Diversity of SARS-CoV-2 isolates driven by pressure and health index
Authors: Singh R. K. Sanayaima , Malik Md. Zubbair , Singh R. K. Brojen
Published: February 2021

One of the main concerns about the fast spreading coronavirus disease 2019 (Covid-19) pandemic is how to intervene. We analysed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) isolates data using the multifractal approach and found a rich in viral genome diversity, which could be one of the root causes of the fast Covid-19 pandemic and is strongly affected by pressure and health index of the hosts inhabited regions. The calculated mutation rate (mr) is observed to be maximum at a particular pressure, beyond which mr maintains diversity. Hurst exponent and fractal dimension are found to be optimal at a critical pressure (Pm), whereas, for P > Pm and P < Pm, we found rich genome diversity relating to complicated genome organisation and virulence of the virus. The values of these complexity measurement parameters are found to be increased linearly with health index values.
CHAIN COMPONENTS WITH THE STABLE SHADOWING PROPERTY FOR C1 VECTOR FIELDS
Authors: LEE MANSEOB , TIEN LE HUY
Published: February 2021

Let M be a closed n-dimensional smooth Riemannian manifold, and let X be a $C^1$-vector field of $M.$ Let $\gamma $ be a hyperbolic closed orbit of $X.$ In this paper, we show that X has the $C^1$-stably shadowing property on the chain component $C_X(\gamma )$ if and only if $C_X(\gamma )$ is the hyperbolic homoclinic class.
Neuromythen
Authors: Paridon Hiltraut
Published: February 2021

Zusammenfassung. Als „Neuromythen“ bezeichnet man Fehlvorstellungen über das Gehirn. In den letzten Jahrzehnten gab es in den Neurowissenschaften zahlreiche Erkenntnisse über dessen Funktionsweise, die das Thema „Lernen“ betreffen. In diesem Zusammenhang sind jedoch auch viele Mythen entstanden. Der folgende Beitrag beschreibt typische Mythen sowie ihre Verbreitung und zeigt deren Gefahren in pädagogischen Zusammenhängen auf. Hinweise zum Umgang mit neurowissenschaftlichen Erkenntnissen schließen den Beitrag ab.
Unterstützung chronisch Kranker im Umgang mit Medikamenten
Authors: Mattes Melanie , Mayer Hanna
Published: February 2021

Zusammenfassung. Umstellungen der Medikation im Zuge eines Krankenhausaufenthaltes sind bei chronisch kranken Menschen keine Seltenheit, die Information über den Umgang damit ist jedoch oft ungenügend. Basierend auf einem multiperspektivischen Ansatz zur Entwicklung komplexer Interventionen wurde ein Rahmen für ein Beratungskonzept für das Rudolfinerhaus (Wien) entwickelt, das sich am Verlauf des Krankenhausaufenthaltes sowie am Prozess des Medikamentenselbstmanagements orientiert.
Modeling Intra‐Caldera Resurgence Settings: Laboratory Experiments With Application to the Los Humeros Volcanic Complex (Mexico)
Authors: Bonini Marco , Maestrelli Daniele , Corti Giacomo , Del Ventisette Chiara , Moratti Giovanna , Carrasco‐Núñez Gerardo , Giordano Guido , Lucci Federico , Norini Gianluca , Piccardi Luigi , Urbani Stefano , Montanari Domenico
Published: February 2021

Scaled analogue models explored the role of different boundary conditions in intra‐caldera resurgence processes. Models investigated the role of magma intrusion depth (ID) (Series 1), asymmetric and symmetric caldera collapse (Series 2), as well as the presence of existing discontinuities in the pre‐volcanic substratum (Series 3) on the style of caldera resurgence. Experimental results indicate that different IDs resulted in different resurgence styles and structural patterns, which evolved from piston‐like resurgence, for deeper intrusions, to intra‐caldera resurgent domes for shallower intrusions. Asymmetric collapse was typically accompanied by a tilted roof block above the emptied analogue magma reservoir, while inherited faults influenced significantly the deformation pattern of piston‐like resurgence. Experiments simulate many of the principal characteristics of calderas. We compare our modeling results primarily to the Los Potreros caldera nested within the Los Humeros Volcanic Complex, where the largest Mexico's Quaternary eruption occurred and which hosts an important geothermal field (eastern Trans‐Mexican Volcanic Belt). A structural field survey was conducted to identify the kinematics of faults within the caldera and outside the volcanic edifice. The Los Potreros caldera shows a sub‐orthogonal fault pattern strikingly similar to that of models deformed with shallow ID. We interpret this correlation as an evidence of similarity in dynamic processes, whereby modeling results would indicate a scaled ID of ∼4.5 km. The Acoculco caldera complex, in Mexico, shows a fault pattern similar to the Los Potreros caldera, and geological information corroborates the attribution of renewed magmatic pressure to similar IDs.
Isotopic Constraint on the Sources and Biogeochemical Cycling of Nitrate in the Jiulong River Estuary
Authors: Wang Xin , Wu Xiaoyan , Chen Min , Cheng Hua , Chen Nengwang , Yang Weifeng , Cai Yihua
Published: February 2021

Nitrate concentrations and isotopic compositions (δ15N‐NO3− and δ18O‐NO3−) in the Jiulong River Estuary (JRE) were determined in 2014 to better understand the transformation and source contributions of nitrate. In contrast to nitrate concentrations, which generally followed a conservative binary mixing pattern, both δ15N‐NO3− and δ18O‐NO3− deviated significantly from the binary isotopic mixing lines during all sampling cruises, indicating a dynamic transformation of nitrate in the JRE. The deviation of nitrate isotopic signatures from conservative mixing lines as well as the slope of the regression between N and O isotopes (δ15N‐NO3− vs. δ18O‐NO3−) had significant seasonal variability, showing the seasonal shifting of the dominant nitrification and sedimentary denitrification in the JRE. Furthermore, the elevated nitrate concentrations and isotopic compositions in the lower JRE during the dry season, along with an isotope regression slope of 1.16, indicated a significant local input of nitrate. Nitrate source apportionment is carried out through the Stable Isotope Analyses in R model with the incorporation of nitrate isotopic fractionation factors for nitrification and denitrification in the JRE. The model results revealed that fertilizer is the largest nitrate source to the JRE, contributing 33%–55% of the nitrate throughout the sampling period. Manure is another major source and contributed 32%–39% of the nitrate to the JRE. Sewage nitrate contributions to the JRE were 7% during April and June but dramatically increased to 18% during the wet season, probably as a result of the rapid flushing of suburban and rural untreated domestic sewage into the river.
EOMES and IL-10 regulate antitumor activity of T regulatory type 1 CD4+ T cells in chronic lymphocytic leukemia
Authors: Roessner Philipp M. , Llaó Cid Laura , Lupar Ekaterina , Roider Tobias , Bordas Marie , Schifflers Christoph , Arseni Lavinia , Gaupel Ann-Christin , Kilpert Fabian , Krötschel Marit , Arnold Sebastian J. , Sellner Leopold , Colomer Dolors , Stilgenbauer Stephan , Dietrich Sascha , Lichter Peter , Izcue Ana , Seiffert Martina
Published: February 2021

The transcription factor eomesodermin (EOMES) promotes interleukin (IL)-10 expression in CD4+ T cells, which has been linked to immunosuppressive and cytotoxic activities. We detected cytotoxic, programmed cell death protein-1 (PD-1) and EOMES co-expressing CD4+ T cells in lymph nodes (LNs) of patients with chronic lymphocytic leukemia (CLL) or diffuse large B-cell lymphoma. Transcriptome and flow cytometry analyses revealed that EOMES does not only drive IL-10 expression, but rather controls a unique transcriptional signature in CD4+ T cells, that is enriched in genes typical for T regulatory type 1 (TR1) cells. The TR1 cell identity of these CD4+ T cells was supported by their expression of interferon gamma and IL-10, as well as inhibitory receptors including PD-1. TR1 cells with cytotoxic capacity accumulate also in Eµ-TCL1 mice that develop CLL-like disease. Whereas wild-type CD4+ T cells control TCL1 leukemia development after adoptive transfer in leukopenic Rag2−/− mice, EOMES-deficient CD4+ T cells failed to do so. We further show that TR1 cell-mediated control of TCL1 leukemia requires IL-10 receptor (IL-10R) signaling, as Il10rb-deficient CD4+ T cells showed impaired antileukemia activity. Altogether, our data demonstrate that EOMES is indispensable for the development of IL-10-expressing, cytotoxic TR1 cells, which accumulate in LNs of CLL patients and control TCL1 leukemia in mice in an IL-10R-dependent manner.
The positive effects of running exercise on hippocampal astrocytes in a rat model of depression
Authors: Li Yue , Luo Yanmin , Tang Jing , Liang Xin , Wang Jin , Xiao Qian , Zhu Peilin , Xiao Kai , Jiang Lin , Dou Xiaoyun , Huang Chunxia , Xie Yuhan , Tang Yong
Published: February 2021

Running exercise has been shown to alleviate depressive symptoms, but the mechanism of its antidepressant effect is still unclear. Astrocytes are the predominant cell type in the brain and perform key functions vital to central nervous system (CNS) physiology. Mounting evidence suggests that changes in astrocyte number in the hippocampus are closely associated with depression. However, the effects of running exercise on astrocytes in the hippocampus of depression have not been investigated. Here, adult male rats were subjected to chronic unpredictable stress (CUS) for 5 weeks followed by treadmill running for 6 weeks. The sucrose preference test (SPT) was used to assess anhedonia of rats. Then, immunohistochemistry and modern stereological methods were used to precisely quantify the total number of glial fibrillary acidic protein (GFAP)+ astrocytes in each hippocampal subregion, and immunofluorescence was used to quantify the density of bromodeoxyuridine (BrdU)+ and GFAP+ cells in each hippocampal subregion. We found that running exercise alleviated CUS-induced deficit in sucrose preference and hippocampal volume decline, and that CUS intervention significantly reduced the number of GFAP+ cells and the density of BrdU+/GFAP+ cells in the hippocampal CA1 region and dentate gyrus (DG), while 6 weeks of running exercise reversed these decreases. These results further confirmed that running exercise alleviates depressive symptoms and protects hippocampal astrocytes in depressed rats. These findings suggested that the positive effects of running exercise on astrocytes and the generation of new astrocytes in the hippocampus might be important structural bases for the antidepressant effects of running exercise.
Trazodone effects on developing brain
Authors: Korade Zeljka , Allen Luke B. , Anderson Allison , Tallman Keri A. , Genaro-Mattos Thiago C. , Porter Ned A. , Mirnics Karoly
Published: February 2021

Trazodone (TRZ) is a commonly prescribed antidepressant with significant off-label use for insomnia. A recent drug screening revealed that TRZ interferes with sterol biosynthesis, causing elevated levels of sterol precursor 7-dehydrocholesterol (7-DHC). Recognizing the well-documented, disruptive effect of 7-DHC on brain development, we designed a study to analyze TRZ effects during pregnancy. Utilizing an in vivo model and human biomaterial, our studies were designed to also account for drug interactions with maternal or offspring Dhcr7 genotype. In a maternal exposure model, we found that TRZ treatment increased 7-DHC and decreased desmosterol levels in brain tissue in newborn pups. We also observed interactions between Dhcr7 mutations and maternal TRZ exposure, giving rise to the most elevated toxic oxysterols in brains of Dhcr7+/− pups with maternal TRZ exposure, independently of the maternal Dhcr7 genotype. Therefore, TRZ use during pregnancy might be a risk factor for in utero development of a neurodevelopmental disorder, especially when the unborn child is of DHCR7+/− genotype. The effects of TRZ on 7-DHC was corroborated in human serum samples. We analyzed sterols and TRZ levels in individuals with TRZ prescriptions and found that circulating TRZ levels correlated highly with 7-DHC. The abundance of off-label use and high prescription rates of TRZ might represent a risk for the development of DHCR7 heterozygous fetuses. Thus, TRZ use during pregnancy is potentially a serious public health concern.
Novel variants in the stem cell niche factor WNT2B define the disease phenotype as a congenital enteropathy with ocular dysgenesis
Authors: Zhang Yanjia Jason , Jimenez Lissette , Azova Svetlana , Kremen Jessica , Chan Yee-Ming , Elhusseiny Abdelrahman M. , Saeed Hajirah , Goldsmith Jeffrey , Al-Ibraheemi Alyaa , O’Connell Amy E. , Kovbasnjuk Olga , Rodan Lance , Agrawal Pankaj B. , Thiagarajah Jay R.
Published: February 2021

WNT2B is a member of the Wnt family, a group of signal transduction proteins involved in embryologic development and stem cell renewal and maintenance. We recently reported homozygous nonsense variants in WNT2B in three individuals with severe, neonatal-onset diarrhea, and intestinal failure. Here we present a fourth case, from a separate family, with neonatal diarrhea associated with novel compound heterozygous WNT2B variants. One of the two variants was a frameshift variant (c.423del [p.Phe141fs]), while the other was a missense change (c.722 G > A [p.G241D]) that we predict through homology modeling to be deleterious, disrupting post-translational acylation. This patient presented as a neonate with severe diet-induced (osmotic) diarrhea and growth failure resulting in dependence on parenteral nutrition. Her gastrointestinal histology revealed abnormal cellular architecture particularly in the stomach and colon, including oxyntic atrophy, abnormal distribution of enteroendocrine cells, and a paucity of colonic crypt glands. In addition to her gastrointestinal findings, she had bilateral corneal clouding and atypical genital development later identified as a testicular 46,XX difference/disorder of sexual development. Upon review of the previously reported cases, two others also had anterior segment ocular anomalies though none had atypical genital development. This growing case series suggests that variants in WNT2B are associated with an oculo-intestinal (and possibly gonadal) syndrome, due to the protein’s putative involvement in multiple developmental and stem cell maintenance pathways.
Single-cell mapping of focused ultrasound-transfected brain
Authors: Mathew A. S. , Gorick C. M. , Price R. J.
Published: February 2021

Gene delivery via focused ultrasound (FUS) mediated blood-brain barrier (BBB) opening is a disruptive therapeutic modality. Unlocking its full potential will require an understanding of how FUS parameters (e.g., peak-negative pressure (PNP)) affect transfected cell populations. Following plasmid (mRuby) delivery across the BBB with 1 MHz FUS, we used single-cell RNA-sequencing to ascertain that distributions of transfected cell types were highly dependent on PNP. Cells of the BBB (i.e., endothelial cells, pericytes, and astrocytes) were enriched at 0.2 MPa PNP, while transfection of cells distal to the BBB (i.e., neurons, oligodendrocytes, and microglia) was augmented at 0.4 MPa PNP. PNP-dependent differential gene expression was observed for multiple cell types. Cell stress genes were upregulated proportional to PNP, independent of cell type. Our results underscore how FUS may be tuned to bias transfection toward specific brain cell types in vivo and predict how those cells will respond to transfection.
Hydrogen sulfide promotes flowering in heading Chinese cabbage by S-sulfhydration of BraFLCs
Authors: Ma Xiaoli , Zhang Liping , Pei Zhuoya , Zhang Linlin , Liu Zhiqiang , Liu Danmei , Hao Xuefeng , Jin Zhuping , Pei Yanxi
Published: February 2021

Heading Chinese cabbage (Brassica rapaL. syn.B.campestrisL. ssp.chinensisMakino var.pekinensis(Rupr.) J. Cao et Sh. Cao) is a cruciferousBrassicavegetable that has a triplicate genome, owing to an ancient genome duplication event. It is unclear whether the duplicated homologs have conserved or diversified functions. Hydrogen sulfide (H2S) is a plant gasotransmitter that plays important physiological roles in growth, development, and responses to environmental stresses. The modification of cysteines through S-sulfhydration is an important mechanism of H2S, which regulates protein functions. H2S promotes flowering inArabidopsisand heading Chinese cabbage. Here we investigated the molecular mechanisms of H2S used to promote flowering in the latter. Four, five, and fourBraFLC,BraSOC I, andBraFThomologs were identified in heading Chinese cabbage. Different BraFLC proteins were bound to different CArG boxes in the promoter regions of theBraSOC IandBraFThomologs, producing different binding patterns. Thus, there may be functionally diverseBraFLChomologs in heading Chinese cabbage. Exogenous H2S at 100 μmol L−1significantly promoted flowering by compensating for insufficient vernalization. BraFLC 1 and BraFLC 3 underwent S-sulfhydration by H2S, after which their abilities to bind mostBraSOC IorBraFTpromoter probes weakened or even disappeared. These changes in binding ability were consistent with the expression pattern of theBraFTandBraSOC Ihomologs in seedlings treated with H2S. These results indicated that H2S signaling regulates flowering time. In summary, H2S signaling promoted plant flowering by weakening or eliminating the binding abilities of BraFLCs to downstream promoters through S-sulfhydration.
Site-directed mutagenesis identified the key active site residues of alcohol acyltransferase PpAAT1 responsible for aroma biosynthesis in peach fruits
Authors: Song Zhi-Zhong , Peng Bin , Gu Zi-Xia , Tang Mei-Ling , Li Bei , Liang Mei-Xia , Wang Li-Min , Guo Xiao-Tong , Wang Jian-Ping , Sha Yu-Fen , Zhang Hong-Xia
Published: February 2021

The aroma of peach fruit is predominantly determined by the accumulation of γ-decalactone and ester compounds. A previous study showed that the biosynthesis of these aroma compounds in peach fruit is catalyzed by PpAAT1, an alcohol acyltransferase. In this work, we investigated the key active site residues responsible for γ-decalactone and ester biosynthesis. A total of 14 candidate amino acid residues possibly involved in internal esterification and 9 candidate amino acid residues possibly involved in esterification of PpAAT1 were assessed via site-directed mutagenesis. Analyses of the in vitro enzyme activities of PpAAT1 and its site-directed mutant proteins (PpAAT1-SMs) with different amino acid residue mutations as well as the contents of γ-decalactone in transgenic tobacco leaves and peach fruits transiently expressing PpAAT1 and PpAAT1-SMs revealed that site-directed mutation of H165 in the conserved HxxxD motif led to lost enzymatic activity of PpAAT1 in both internal esterification and its reactions, whereas mutation of the key amino acid residue D376 led to the total loss of γ-decalactone biosynthesis activity of PpAAT1. Mutations of 9 and 7 other amino acid residues also dramatically affected the enzymatic activity of PpAAT1 in the internal esterification and esterification reactions, respectively. Our findings provide a biochemical foundation for the mechanical biosynthesis of γ-decalactone and ester compounds catalyzed by PpAAT1 in peach fruits, which could be used to guide the molecular breeding of new peach species with more favorable aromas for consumers.
Fire blight QTL analysis in a multi-family apple population identifies a reduced-susceptibility allele in ‘Honeycrisp’
Authors: Kostick Sarah A. , Teh Soon Li , Norelli John L. , Vanderzande Stijn , Peace Cameron , Evans Kate M.
Published: February 2021

Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with ‘Honeycrisp’ being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. ‘Honeycrisp’ inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent ‘Frostbite’. The highly resistant IBP ‘Enterprise’ had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.
Functional conservation of the grapevine candidate gene INNER NO OUTER for ovule development and seed formation
Authors: di Rienzo Valentina , Imanifard Zahra , Mascio Isabella , Gasser Charles S. , Skinner Debra J. , Pierri Ciro Leonardo , Marini Martina , Fanelli Valentina , Sabetta Wilma , Montemurro Cinzia , Bellin Diana
Published: February 2021

Seedlessness represents a highly appreciated trait in table grapes. Based on an interesting case of seedless fruit production described in the crop speciesAnnona squamosa, we focused on theVitis vinifera INNER NO OUTER (INO)gene as a candidate. This gene encodes a transcription factor belonging to theYABBYfamily involved in the determination of abaxial identity in several organs. InArabidopsis thaliana, this gene was shown to be essential for the formation and asymmetric growth of the ovule outer integument and its mutation leads to a phenotypic defect of ovules and failure in seed formation. In this study, we identified in silico theV. viniferaorthologue and investigated its phylogenetic relationship toINOgenes from other species and its expression in different organs in seeded and seedless varieties. Applying cross-species complementation, we have tested its functionality in the Arabidopsisino-1 mutant. We show that theV. viniferaINO successfully rescues the ovule outer integument growth and seeds set and also partially complements the outer integument asymmetric growth in the Arabidopsis mutant, differently from orthologues from other species. These data demonstrate that VviINO retains similar activity and protein targets in grapevine as in Arabidopsis. Potential implications for grapevine breeding are discussed.
Isolation and comparative proteomic analysis of mitochondria from the pulp of ripening citrus fruit
Authors: Li Xin , Chai Yingfang , Yang Hongbin , Tian Zhen , Li Chengyang , Xu Rangwei , Shi Chunmei , Zhu Feng , Zeng Yunliu , Deng Xiuxin , Wang Pengwei , Cheng Yunjiang
Published: February 2021

Mitochondria are crucial for the production of primary and secondary metabolites, which largely determine the quality of fruit. However, a method for isolating high-quality mitochondria is currently not available in citrus fruit, preventing high-throughput characterization of mitochondrial functions. Here, based on differential and discontinuous Percoll density gradient centrifugation, we devised a universal protocol for isolating mitochondria from the pulp of four major citrus species, including satsuma mandarin, ponkan mandarin, sweet orange, and pummelo. Western blot analysis and microscopy confirmed the high purity and intactness of the isolated mitochondria. By using this protocol coupled with a label-free proteomic approach, a total of 3353 nonredundant proteins were identified. Comparison of the four mitochondrial proteomes revealed that the proteins commonly detected in all proteomes participate in several typical metabolic pathways (such as tricarboxylic acid cycle, pyruvate metabolism, and oxidative phosphorylation) and pathways closely related to fruit quality (such as γ-aminobutyric acid (GABA) shunt, ascorbate metabolism, and biosynthesis of secondary metabolites). In addition, differentially abundant proteins (DAPs) between different types of species were also identified; these were found to be mainly involved in fatty acid and amino acid metabolism and were further confirmed to be localized to the mitochondria by subcellular localization analysis. In summary, the proposed protocol for the isolation of highly pure mitochondria from different citrus fruits may be used to obtain high-coverage mitochondrial proteomes, which can help to establish the association between mitochondrial metabolism and fruit storability or quality characteristics of different species and lay the foundation for discovering novel functions of mitochondria in plants.
Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance
Authors: Cantillon Daire , Wroblewska Justyna , Cooper Ian , Newport Melanie J. , Waddell Simon J.
Published: February 2021

Mycobacteria naturally grow as corded biofilms in liquid media without detergent. Such detergent-free biofilm phenotypes may reflect the growth pattern of bacilli in tuberculous lung lesions. New strategies are required to treat tuberculosis, which is responsible for more deaths each year than any other bacterial disease. The lengthy 6-month regimen for drug-sensitive tuberculosis is necessary to remove antimicrobial drug tolerant populations of bacilli that persist through drug therapy. The role of biofilm-like growth in the generation of these sub-populations remains poorly understood despite the hypothesised clinical significance and mounting evidence of biofilms in pathogenesis. We adapt a three-dimensional Rotary Cell Culture System to model M. bovis BCG biofilm growth in low-shear detergent-free liquid suspension. Importantly, biofilms form without attachment to artificial surfaces and without severe nutrient starvation or environmental stress. Biofilm-derived planktonic bacilli are tolerant to isoniazid and streptomycin, but not rifampicin. This phenotypic drug tolerance is lost after passage in drug-free media. Transcriptional profiling reveals induction of cell surface regulators, sigE and BCG_0559c alongside the ESX-5 secretion apparatus in these low-shear liquid-suspension biofilms. This study engineers and characterises mycobacteria grown as a suspended biofilm, illuminating new drug discovery pathways for this deadly disease.
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes
Authors: Peng Xuefeng , Wilken St. Elmo , Lankiewicz Thomas S. , Gilmore Sean P. , Brown Jennifer L. , Henske John K. , Swift Candice L. , Salamov Asaf , Barry Kerrie , Grigoriev Igor V. , Theodorou Michael K. , Valentine David L. , O’Malley Michelle A.
Published: February 2021

The herbivore digestive tract is home to a complex community of anaerobic microbes that work together to break down lignocellulose. These microbiota are an untapped resource of strains, pathways and enzymes that could be applied to convert plant waste into sugar substrates for green biotechnology. We carried out more than 400 parallel enrichment experiments from goat faeces to determine how substrate and antibiotic selection influence membership, activity, stability and chemical productivity of herbivore gut communities. We assembled 719 high-quality metagenome-assembled genomes (MAGs) that are unique at the species level. More than 90% of these MAGs are from previously unidentified herbivore gut microorganisms. Microbial consortia dominated by anaerobic fungi outperformed bacterially dominated consortia in terms of both methane production and extent of cellulose degradation, which indicates that fungi have an important role in methane release. Metabolic pathway reconstructions from MAGs of 737 bacteria, archaea and fungi suggest that cross-domain partnerships between fungi and methanogens enabled production of acetate, formate and methane, whereas bacterially dominated consortia mainly produced short-chain fatty acids, including propionate and butyrate. Analyses of carbohydrate-active enzyme domains present in each anaerobic consortium suggest that anaerobic bacteria and fungi employ mostly complementary hydrolytic strategies. The division of labour among herbivore anaerobes to degrade plant biomass could be harnessed for industrial bioprocessing.
Synthesis of multi-organo-functionalized fibrous silica KCC-1 for highly efficient adsorption of acid fuchsine and acid orange II from aqueous solution
Authors: Soltani Roozbeh , Pelalak Rasool , Pishnamazi Mahboubeh , Marjani Azam , Albadarin Ahmad B. , Sarkar Shaheen M. , Shirazian Saeed
Published: February 2021

Multi-functionalized fibrous silica KCC-1 (MF-KCC-1) bearing amine, tetrasulfide, and thiol groups was synthesized via a post-functionalization method and fully characterized by several methods such as FTIR, FESEM, EDX-Mapping, TEM, and N2 adsorption–desorption techniques. Due to abundant surface functional groups, accessible active adsorption sites, high surface area (572 m2 g−1), large pore volume (0.98 cm3 g−1), and unique fibrous structure, mesoporous MF-KCC-1 was used as a potential adsorbent for the uptake of acid fuchsine (AF) and acid orange II (AO) from water. Different adsorption factors such as pH of the dye solution, the amount of adsorbent, initial dye concentration, and contact time, affecting the uptake process were optimized and isotherm and kinetic studies were conducted to find the possible mechanism involved in the process. For both AF and AO dyes, the Langmuir isotherm model and the PFO kinetic model show the most agreement with the experimental data. According to the Langmuir isotherm, the calculated maximum adsorption capacity for AF and AO were found to be 574.5 mg g−1 and 605.9 mg g−1, respectively, surpassing most adsorption capacities reported until now which is indicative of the high potential of mesoporous MF-KCC-1 as an adsorbent for removal applications.
Context-dependent extinction learning emerging from raw sensory inputs: a reinforcement learning approach
Authors: Walther Thomas , Diekmann Nicolas , Vijayabaskaran Sandhiya , Donoso José R. , Manahan-Vaughan Denise , Wiskott Laurenz , Cheng Sen
Published: February 2021

The context-dependence of extinction learning has been well studied and requires the hippocampus. However, the underlying neural mechanisms are still poorly understood. Using memory-driven reinforcement learning and deep neural networks, we developed a model that learns to navigate autonomously in biologically realistic virtual reality environments based on raw camera inputs alone. Neither is context represented explicitly in our model, nor is context change signaled. We find that memory-intact agents learn distinct context representations, and develop ABA renewal, whereas memory-impaired agents do not. These findings reproduce the behavior of control and hippocampal animals, respectively. We therefore propose that the role of the hippocampus in the context-dependence of extinction learning might stem from its function in episodic-like memory and not in context-representation per se. We conclude that context-dependence can emerge from raw visual inputs.
Genetic variants of small airways and interstitial pulmonary disease in children
Authors: Alsamri Mohammed T. , Alabdouli Amnah , Alkalbani Alia M. , Iram Durdana , Tawil Mohamed I. , Antony Priya , Vijayan Ranjit , Souid Abdul-Kader
Published: February 2021

Genetic variants of small airways and interstitial pulmonary disease have not been comprehensively studied. This cluster of respiratory disorders usually manifests from early infancy (‘lung disease in utero’). In this study, 24 variants linked to these entities are described. The variants involved two genes associated with surfactant metabolism dysfunction (ABCA3 and CSF2RB), two with pulmonary fibrosis (MUC5B and SFTP), one with bronchiectasis (SCNN1B), and one with alpha-1-antitrypsin deficiency (SERPINA1). A nonsense variant, MUC5B:c.16861G > T, p.Glu5621*, was found in homozygous state in two siblings with severe respiratory disease from birth. One of the siblings also had heterozygous SFTPA1:c.675C > G, p.Asn225Lys, which resulted in a more severe respiratory disease. The sibling with only the homozygous MUC5B variant had lung biopsy, which showed alveolar simplification, interstitial fibrosis, intra-alveolar lipid-laden macrophages, and foci of foreign body giant cell reaction in distal airspaces. Two missense variants, MUC5B:c.14936 T > C, p.Ile4979Thr (rs201287218) and MUC5B:c.16738G > A, p.Gly5580Arg (rs776709402), were also found in compound heterozygous state in two siblings with severe respiratory disease from birth. Overall, the results emphasize the need for genetic studies for patients with complex respiratory problems. Identifying pathogenic variants, such as those presented here, assists in effective family counseling aimed at genetic prevention. In addition, results of genetic studies improve the clinical care and provide opportunities for participating in clinical trials, such as those involving molecularly-targeted therapies.