julilili42/papers huggingface dataset:
Peer Review #1 of "Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems (v0.2)"
2020-10-13

Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning.Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices.We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems.Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers.Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq).The R package 'picante' and FUNGuild were used to analyse fungal community composition and trophic mode, respectively.Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota ( 14) and to the Glomeromycota (1).Fungal communities from conventional farming sites are phylogenetically more related than expected by chance.Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU's abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised.The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming.Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices.Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive
Peer Review #2 of "Belowground fungal community diversity, composition and ecological functionality associated with winter wheat in conventional and organic agricultural systems (v0.2)"
2020-10-13

Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning.Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices.We investigated the diversity, composition and ecological functionality of fungal communities in roots of winter wheat (Triticum aestivum) growing in conventional and organic farming systems.Direct and nested polymerase chain reaction (PCR) amplifications spanning the internal transcribed spacer (ITS) region of the rDNA from pooled fine root samples were performed with two different sets of fungal specific primers.Fungal identification was carried out through similarity searches against validated reference sequences (RefSeq).The R package 'picante' and FUNGuild were used to analyse fungal community composition and trophic mode, respectively.Either by direct or cloning sequencing, 130 complete ITS sequences were clustered into 39 operational taxonomic units (OTUs) (25 singletons), belonging to the Ascomycota (24), the Basidiomycota ( 14) and to the Glomeromycota (1).Fungal communities from conventional farming sites are phylogenetically more related than expected by chance.Constrained ordination analysis identified total N, total S and Pcal that had a significant effect on the OTU's abundance and distribution, and a further correlation with the diversity of the co-occurring vegetation could be hypothesised.The functional predictions based on FUNGuild suggested that conventional farming increased the presence of plant pathogenic fungi compared with organic farming.Based on diversity, OTU distribution, nutrition mode and the significant phylogenetic clustering of fungal communities, this study shows that fungal communities differ across sampling sites, depending on agricultural practices.Although it is not fully clear which factors determine the fungal communities, our findings suggest that organic farming systems have a positive
Loss of the common immune coreceptor BAK1 leads to NLR-dependent cell death
2020-10-14

Significance BAK1 plays a key role in multiple PRR-triggered immune signaling pathways. Double mutants generated by BAK1 and its paralog BKK1 show spontaneous cell death, which is not seen in any known PRR mutants. We discovered that the ADR1 class of helper nucleotide-binding leucine-rich repeat proteins (NLRs) is required for the autoimmune responses of bak1 bkk1 . Knocking out three ADR1 s can significantly suppress the cell death of bak1-3 bkk1-1 , suggesting the autoimmune responses of bak1 bkk1 are caused by NLR activation. Furthermore, expression of HopB1, an effector derived from Pseudomonas syringae that cleaves activated BAK1 and its paralogs, leads to cell death similar to bak1 bkk1 , which requires ADR1 s. Our results indicate BAK1 and its paralogs serve as guardees for NLRs.
Building Continuous Time Crystals from Rare Events
2020-10-14

Symmetry-breaking dynamical phase transitions (DPTs) abound in the fluctuations of nonequilibrium systems. Here, we show that the spectral features of a particular class of DPTs exhibit the fingerprints of the recently discovered time-crystal phase of matter. Using Doob's transform as a tool, we provide a mechanism to build classical time-crystal generators from the rare event statistics of some driven diffusive systems. An analysis of the Doob's smart field in terms of the order parameter of the transition then leads to the time-crystal lattice gas (TCLG), a model of driven fluid subject to an external packing field, which presents a clear-cut steady-state phase transition to a time-crystalline phase characterized by a matter density wave, which breaks continuous time-translation symmetry and displays rigidity and long-range spatiotemporal order, as required for a time crystal. A hydrodynamic analysis of the TCLG transition uncovers striking similarities, but also key differences, with the Kuramoto synchronization transition. Possible experimental realizations of the TCLG in colloidal fluids are also discussed.
Pathophysiology-based subphenotyping of individuals at elevated risk for type 2 diabetes
2020-10-14

Abstract The state of intermediate hyperglycemia is indicative of elevated risk of developing type 2 diabetes 1 . However, the current definition of prediabetes neither reflects subphenotypes of pathophysiology of type 2 diabetes nor is it predictive of future metabolic trajectories. We used partitioning on variables derived from oral glucose tolerance tests, MRI measured body fat distribution, liver fat content, and genetic risk in a cohort of extensively phenotyped individuals who are at increased risk for type 2 diabetes 2,3 to identify six distinct clusters of subphenotypes. Three of the identified subphenotypes have increased glycemia (clusters 3, 5 and 6), but only individuals in clusters 5 and 3 have immanent diabetes risks. By contrast, those in cluster 6 have moderate risk of type 2 diabetes, but an increased risk of kidney disease and all-cause mortality. Findings were replicated in an independent cohort using simple anthropomorphic and glycemic constructs 4 . This proof-of-concept study demonstrates that pathophysiological heterogeneity exists before diagnosis of type 2 diabetes and highlights a group of individuals who have an increased risk of complications without rapid progression to overt type 2 diabetes.
Phylogenetic patterns and ontogenetic origins of limb length variation in ecologically diverse lacertine lizards
2020-10-14

Abstract Limb length is intrinsically linked to function and, ultimately, fitness. Thus, it can co-evolve with habitat structure, as exemplified by tropical lizards in highly heterogeneous environments. But does lizard limb length respond in a similar manner during adaptive diversification in temperate zones? Here, we examine variation in habitat preference and limb length in lacertine lizards from the Palaearctic. We tested the following three hypotheses: (1) species of the Lacertini tribe descended from a generalist ancestor and subsequently underwent habitat specialization; (2) specialized ecological roles are associated with relative limb length in extant species; and (3) interspecific differences in limb length emerge in embryonic development. Our comparisons supported an ancestral ‘rocky’ or ‘generalist’ habitat preference, and phenotype–habitat associations were particularly supported when examining size-adjusted forelimb length in 69 species that represented all known Lacertini genera. Moreover, we revealed an elevated interlimb ratio in high-vegetation species, which might be linked to climbing performance in species with relatively longer forelimbs. Furthermore, embryonic limb variation was detected solely against an Eremiadini outgroup species. Instead, hind limb length differences within Lacertini originated in post-hatching ontogeny. The mechanisms that modulate limb growth are likely to be limited in Lacertini, because adaptive morphological change might mirror historical contingency and the ecological context wherein this clade diversified.
Simulating phonological and semantic impairment of English tense inflection with linear discriminative learning
2020-10-14

Abstract This study applies the computational theory of the ‘discriminative lexicon’ ( Baayen, Chuang, and Blevins, 2019 ) to the modeling of the production of English verbs in aphasic speech. Under semantic impairment, speakers have been reported to have greater difficulties with irregular verbs, whereas speakers with phonological impairment are described as having greater problems with regulars. Joanisse and Seidenberg (1999) were able to model this dissociation, but only by adding noise to the semantic units of their model. We report two simulation studies in which topographically coherent regions of phonological and semantic networks were selectively damaged. Our model replicated the main findings, including the high variability in the consequences of brain lesions for speech production. Importantly, our model generated these results without having to lesion the semantic system more than the phonological system. The model’s success hinges on the use of a corpus-based distributional vector space for representing verbs’ meanings. Irregular verbs have denser semantic neighborhoods than do regular verbs ( Baayen and Moscoso del Prado Martín, 2005 ). In our model this renders irregular verbs more fragile under semantic impairment. These results provide further support for the central idea underlying the discriminative lexicon: that behavioral patterns can, to a considerable extent, be understood as emerging from the distributional properties of a language and basic principles of human learning.
Synthesis of Chiral Donor–Acceptor Dyes to Study Electron Transfer Across a Chiral Bridge
2020-10-14

Chiral organic dyes comprising a donor <b>(D)</b>, spacer <b>(S)</b>, primary acceptor <b>(A1)</b>, chiral bridge <b>(B(</b><i><b>S</b></i><b>))</b>, and final acceptor/radical <b>(A2)/(R)</b> have been synthesized and fully characterized. The goal behind this synthetic pursuit is to study whether the chiral dyes can impart a chiral-induced spin selectivity (CISS) spin-filtering effect during an intramolecular charge-transfer (CT) process. Additionally, appending a stable free radical (SFR) allows the study of how an unpaired spin influences the CT state. The dyes are reported to vary in the position of <b>(A1)</b> with respect to <b>(B(</b><i><b>S</b></i><b>))</b>. Two series of dyes have been synthesized: one series incorporates <b>(A1)</b> before <b>(B(</b><i><b>S</b></i><b>))</b> and the second series places <b>(A1)</b> after <b>(B(</b><i><b>S</b></i><b>))</b>. In the case where <b>(A1)</b> is before <b>(B(</b><i><b>S</b></i><b>))</b>, CT is observed between <b>(D)</b> and <b>(A1)</b>, but the CT state does not transverse over the chiral bridge to the final <b>(A2)/(R)</b> termini. However, when <b>(A1)</b> is placed after <b>(B(</b><i><b>S</b></i><b>))</b>, CT over or through the bridge occurs. Computations support the experimental data, which indicate that it is necessary to have <b>(A1)</b> located after <b>(B(</b><i><b>S</b></i><b>))</b> to achieve CT over the chiral bridge. Hence, the second set of dyes are optimal candidates to explore intramolecular CISS.
Arsen in Grundwasser und Reis — Ursachen und Konsequenzen
2020-10-14

Abstract The toxic metalloid arsenic (As) is present in the environment often associated with iron(III) oxide minerals. Arsenic can be mobilized into groundwater by iron(III)-reducing, and thus, mineral-dissolving bacteria. We investigate in situ natural organic matter and methane as electron donors fueling microbial iron(III) reduction, the removal of As by iron oxides in drinking water filters, and the effect of climate change on redox processes in the rice rhizosphere and on uptake of As into rice.
Metaphyseal anchoring short stem hip arthroplasty provides a more physiological load transfer: a comparative finite element analysis study
2020-10-14

Abstract Background: Short stem total hip arthroplasty (SHA) preserves femoral bone stock and is supposed to provide a more natural load transfer compared to standard stem total hip arthroplasty (THA). As comparative biomechanical reference data are rare we used a finite element analysis (FEA) approach to compare cortical load transfer after implantations of a metaphyseal anchoring short and standard stem in native biomechanical femora. Methods: The subject specific finite element models of biomechanical femora, one native and two with implanted metaphyseal anchoring SHA (Metha, B.Braun Aesculap) and standard THA (CLS, Zimmer-Biomet), were generated from computed tomography datasets. The loading configuration was performed with an axial force of 1400 N. Von Mises stress was used to investigate the change of cortical stress distribution. Results: Compared to the native femur, a considerable reduction of cortical stress was recorded after implantation of SHA and standard THA. The SHA showed less reduction proximally with a significant higher metaphyseal cortical stress compared to standard THA. Moreover, the highest peak stresses were observed metaphyseal for the SHA stem while for the standard THA high stress pattern was observed more distally. Conclusions: Both, short and standard THA, cause unloading of the proximal femur. However, the metaphyseal anchoring SHA features a clearly favorable pattern in terms of a lower reduction proximally and improved metaphyseal loading, while standard THA shows a higher proximal unloading and more distal load transfer. These load pattern implicate a reduced stress shielding proximally for metaphyseal anchoring SHA stems and might be able to translate in a better bone preservation.
Menopausal symptoms among Chinese peri- and postmenopausal women: a large prospective single-center cohort study
2020-10-15

Urogenital symptoms among midlife Chinese women are common, frequently also in combination with sexual dysfunction, although many do not often complain about these in the first place. Postmenopausal women presented more prevalent and severe menopausal symptoms. In contrast to Western countries, VMS are rare among our population. A multidisciplinary approach and use of hormonal and non-hormonal therapies should be considered for these women.
The Association Between Vulnerable/Grandiose Narcissism and Emotion Regulation
2020-10-15

Narcissism has been widely discussed in the context of career success and leadership. Besides several adaptive traits, narcissism has been characterized by difficulties in emotion regulation. However, despite its essential role in mental health, there is little research on emotion regulation processes in narcissism. Specifically, the investigation of not only the habitual use of specific regulation strategies but also the actual ability to regulate is needed due to diverging implications for treatment approaches. Thereby it is important to differentiate between vulnerable and grandiose narcissism as these two phenotypes might be related differently to regulation deficits. The aim of this study was to examine the association between grandiose and vulnerable narcissism and emotion regulation in healthy individuals (30f/30m) focusing on the strategy reappraisal. Additionally, potential sex effects have been explored. Narcissism was assessed using self-report measures and emotion regulation with self-report questionnaires as well as an experimental regulation task. During this task, participants were presented with pictures of sad/happy faces with the instruction to indicate their subjective emotions via button press. Depending on the condition, participants either indicated their natural response or applied cognitive control strategies to regulate their own subjective emotions. Results indicate no relationship between grandiose and vulnerable narcissism and emotion regulation ability, irrespective of sex. Individuals high on vulnerable narcissism use the maladaptive regulation strategy suppression more frequently than individuals with low expressions. Individuals high on grandiose narcissism, in contrast, seem to avoid the suppression of positive emotions and do not express negative emotions in an uncontrolled manner. Interestingly, while grandiose narcissism was not associated with depressive symptoms, vulnerable narcissism correlated positively with depressive symptoms and anhedonia. Findings of this study underline the need to differentiate between grandiose and vulnerable manifestations of narcissism. Against our expectation, narcissism was not related to emotion regulation performance. In line with previous research, grandiose narcissism seems less harmful for mental health, while vulnerable narcissism is associated with psychological problems and the use of rather maladaptive emotion regulation strategies, i.e., suppression. Future research should investigate the relationship between pathological narcissism and emotion regulation also by extending the scope to other relevant regulation strategies.
Emergence of racial/ethnic and socioeconomic differences in objectively measured sleep–wake patterns in early infancy: results of the Rise & SHINE study
2020-10-15

Abstract Study Objectives To characterize objectively assessed sleep–wake patterns in infants at approximately 1 month and 6 months and examine the differences among infants with different racial/ethnic backgrounds and household socioeconomic status (SES). Methods Full-term healthy singletons wore an ankle-placed actigraph at approximately 1 month and 6 months and parents completed sleep diaries. Associations of racial/ethnic and socioeconomic indices with sleep outcomes were examined using multivariable analyses. Covariates included sex, birth weight for gestational age z-score, age at assessment, maternal education, household income, bed-sharing, and breastfeeding. Results The sample included 306 infants, of whom 51% were female, 42.5% non-Hispanic white, 32.7% Hispanic, 17.3% Asian, and 7.5% black. Between 1 month and 6 months, night sleep duration increased by 65.7 minutes (95% CI: 55.4, 76.0), night awakenings decreased by 2.2 episodes (2.0, 2.4), and daytime sleep duration decreased by 73.3 minutes (66.4, 80.2). Compared to change in night sleep duration over this development period for white infants (82.3 minutes [66.5, 98.0]), night sleep increased less for Hispanic (48.9 minutes [30.8, 66.9]) and black infants (31.6 minutes [−5.9, 69.1]). Night sleep duration also increased less for infants with lower maternal education and household income. Asian infants had more frequent night awakenings. Adjustment for maternal education and household income attenuated all observed day and night sleep duration differences other than in Asians, where persistently reduced nighttime sleep at 6 months was observed. Conclusions Racial/ethnic differences in sleep emerge in early infancy. Night and 24-hour sleep durations increase less in Hispanic and black infants compared to white infants, with differences largely explained by SES.
Inefficient resource allocation is associated with reduced alpha activity in parietal regions in individuals with Parkinson’s disease
2020-10-15

Abstract The brain's ability to act as an input filter and to suppress actions is crucial to navigate everyday life and impairments in these abilities affect quality of life substantially. Although Parkinson's disease (PD) is primarily known as a movement disorder, recent research has redefined it as a multisystem disorder affecting cognition, in particular inhibitory control and attentional resource allocation. Analysing the neural mechanisms underlying this cognitive deficit provides a better understanding of brain changes observed in patients affected by PD. Therefore, this study aimed to identify resource allocation to relevant and irrelevant stimuli in patients affected by PD. Besides neuropsychological tests, we employed electroencephalographic recordings during an auditory oddball paradigm in 13 patients suffering from idiopathic PD and 11 healthy controls (HC). Participants were instructed to ignore the standard stimulus and to respond as fast as possible to the rarely presented target tone. Event‐related potentials (ERP) and time‐frequency representations (TFR) were analyzed. Patients affected by PD showed faster response latencies to the task‐irrelevant standard tones, but slower response latencies to target tones compared to HC. This observation was prominent at frontal sites during later P3‐like processing stages. Reaction time, however, was prolonged in patients with PD, suggesting inefficient resource allocation. Additionally, TFR revealed reduced parietal alpha activity, which is associated with distractor suppression and functional inhibition in patients with PD compared to healthy controls. Thus, our results point towards inefficient resource allocation in patients with PD possibly driven by less functional inhibition through parietal alpha activity.
Rotating tensor-multiscalar black holes with two scalars
2020-10-15

We construct hairy black hole solutions in a particular set of\\ntensor-multi-scalar theories of gravity for which the target-space admits a\\nKilling vector field with periodic flow that is furthermore the generator of a\\none-parameter family of point transformations which leave the whole theory\\ninvariant. As for black holes with scalar hair in general relativity, these\\nmust be rotating objects as the scalarization arises from superradiant\\ninstability. We analyze the most fundamental rotating solutions (winding number\\n ) in five theories which differ from each other by the value of the Gauss\\ncurvature of the target-space. The domain of existence of these solutions is\\ninvestigated, as well as their hairyness, horizon area and deformation factor.\\n
Clinical Phenotype and Course of PDE6A-Associated Retinitis Pigmentosa Disease, Characterized in Preparation for a Gene Supplementation Trial
2020-10-15

Seventeen of the PDE6A variants found in these patients appeared to be novel. Regarding the clinical findings, disease was highly symmetrical between the right and left eyes and visual impairment was mild or moderate in 90% of patients, providing a window of opportunity for gene therapy.