More than a piece of cake: Noun classifier processing in primary progressive aphasia.

INTRODUCTION: Clinical understanding of primary progressive aphasia (PPA) has been primarily derived from Indo-European languages. Generalizing certain linguistic findings across languages is unfitting due to contrasting linguistic structures. While PPA patients showed noun classes impairments, Chinese languages lack noun classes. Instead, Chinese languages are classifier language, and how PPA patients manipulate classifiers is unknown. METHODS: We included 74 native Chinese speakers (22 controls, 52 PPA). For classifier production task, participants were asked to produce the classifiers of high-frequency items. In a classifier recognition task, participants were asked to choose the correct classifier. RESULTS: Both semantic variant (sv) PPA and logopenic variant (lv) PPA scored significantly lower in classifier production task. In classifier recognition task, lvPPA patients outperformed svPPA patients. The classifier production scores were correlated to cortical volume over left temporal and visual association cortices. DISCUSSION: This study highlights noun classifiers as linguistic markers to discriminate PPA syndromes in Chinese speakers. HIGHLIGHTS: Noun classifier processing varies in the different primary progressive aphasia (PPA) variants. Specifically, semantic variant PPA (svPPA) and logopenic variant PPA (lvPPA) patients showed significantly lower ability in producing specific classifiers. Compared to lvPPA, svPPA patients were less able to choose the accurate classifiers when presented with choices. In svPPA, classifier production score was positively correlated with gray matter volume over bilateral temporal and left visual association cortices in svPPA. Conversely, classifier production performance was correlated with volumetric changes over left ventral temporal and bilateral frontal regions in lvPPA. Comparable performance of mass and count classifier were noted in Chinese PPA patients, suggesting a common cognitive process between mass and count classifiers in Chinese languages.

Control of OsARF3a by OsKANADI1 contributes to lemma development in rice.

In rice (Oryza sativa), the lemma and palea protect the internal organs of the floret，provide nutrients for seed development, and determine grain size. We previously revealed that a trans-acting small interfering RNA targeting AUXIN RESPONSE FACTORS (tasiR-ARF) regulates lemma polarity establishment via post-transcriptional repression of AUXIN RESPONSE FACTORS (ARFs) in rice. TasiR-ARF formation requires RNA-DEPENDENT RNA POLYMERASE 6 (RDR6). However, the underlying molecular mechanism of the tasiR-ARF-ARF regulon in lemma development remains unclear. Here, by genetic screening for suppressors of the thermosensitive mutant osrdr6-1, we identified three suppressors, huifu 1 (hf1), hf9, and hf17. Mapping-by-sequencing revealed that HF1 encodes a MYB transcription factor belonging to the KANADI1 family. The hf1 mutation partially rescued the osrdr6-1 lemma defect but not the defect in tasiR-ARF levels. DNA affinity purification sequencing analysis identified 17 725 OsKANADI1-associated sites, most of which contain the SPBP-box binding motif (RGAATAWW) and are located in the promoter, protein-coding, intron, and intergenic regions. Moreover, we found that OsKANADI1 could directly bind to the intron of OsARF3a in vitro and in vivo and promote OsARF3a expression at the transcriptional level. In addition, hf9 and hf17 are intragenic suppressors containing mutations in OsRDR6 that partially rescue tasiR-ARF levels by restoring OsRDR6 protein levels. Collectively, our results demonstrate that OsKANADI1 and tasiR-ARFs synergistically maintain the proper expression of OsARF3a and thus contribute to rice lemma development.

Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice.

BACKGROUND: The sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma. RESULTS: In the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas. CONCLUSION: The regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.

The global asymptotical stability of pseudorabies model with age-structure.

In this paper, the dynamics of an infectious disease is studied by considering age-structured models; a stage structure and an age-structured epidemic model. The respective basic reproduction numbers for the proposed models are calculated, and the local analyses of the equilibria of the models are investigated by using the method of linearization. The global dynamics of the two models are analyzed by using the wave lemma and the Lyapunov function theory. This study establishes a solid theoretical framework and a rigorous mathematical formulation for the prevention and control of pseudorabies.

On the decomposition of WKL!!

From the conceptual viewpoint, many mathematical propositions implicitly contain at least two kinds of principle. One is a logical principle such as the law-of-excluded-middle or De Morgan's law. Another is a function-existence principle. For both conceptual and practical reasons, it is an interesting enterprise to calibrate how amount of logical and function-existence principles are implicit in mathematical theorems and axioms. This is the topic of constructive reverse mathematics, which specifies necessary and sufficient axioms to prove each mathematical proposition constructively. In this paper, we decompose weak König's lemma with a uniqueness hypothesis [Formula: see text] by Moschovakis, into logical and function-existence principles in a recent framework of constructive reverse mathematics. This article is part of the theme issue 'Modern perspectives in Proof Theory'.

DEGENERATED LEMMA (DEL) regulates lemma development and affects rice grain yield.

In grass, the lemma is a unique floral organ structure that directly determines grain size and yield. Despite a great deal of research on grain enlargement caused by changes in glume cells, the importance of normal development of the glume for normal grain development has been poorly studied. In this study, we investigated a rice spikelet mutant, degenerated lemma (del), which developed florets with a slightly degenerated or rod-like lemma. More importantly, del also showed a significant reduction in grain length and width, seed setting rate, and 1000-grain weight, which led to a reduction in yield. The results indicate that the mutation of the DEL gene further affects rice grain yield. Map-based cloning shows a single-nucleotide substitution from T to A within Os01g0527600/DEL/OsRDR6, causing an amino acid mutation of Leu-34 to His-34 in the del mutant. Compared with the wild type, the expression of DEL in del was significantly reduced, which might be caused by single base substitution. In addition, the expression level of tasiR-ARF in del was lower than that of the wild type. RT-qPCR results show that the expression of some floral organ identity genes was changed, which indicates that the DEL gene regulates lemma development by modulating the expression of these genes. The present results suggest that the normal expression of DEL is necessary for the formation of lemma and the normal development of grain morphology and therefore has an important effect on the yield. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01297-6.

Information Inequalities via Submodularity and a Problem in Extremal Graph Theory.

The present paper offers, in its first part, a unified approach for the derivation of families of inequalities for set functions which satisfy sub/supermodularity properties. It applies this approach for the derivation of information inequalities with Shannon information measures. Connections of the considered approach to a generalized version of Shearer's lemma, and other related results in the literature are considered. Some of the derived information inequalities are new, and also known results (such as a generalized version of Han's inequality) are reproduced in a simple and unified way. In its second part, this paper applies the generalized Han's inequality to analyze a problem in extremal graph theory. This problem is motivated and analyzed from the perspective of information theory, and the analysis leads to generalized and refined bounds. The two parts of this paper are meant to be independently accessible to the reader.

A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice.

BACKGROUND: Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). RESULTS: A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. CONCLUSIONS: Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).

Spikelet movements, anther extrusion and pollen production in wheat cultivars with contrasting tendencies to cleistogamy.

BACKGROUND: Cleistogamic flowers are a main barrier in pollen dispersal for cross-pollination necessary in wheat hybrid breeding. The aim of our study was to gain new knowledge on the biology of wheat flowering, in particular on the differences between the cleisto- and chasmogamic forms which has certainly cognitive significance, but it can also be used in practice when seeking a female and male ideotypes for cross hybridization. RESULTS: We characterized the most significant features defining the flowering specificity in two wheat cultivars with contrasting tendency to cleistogamy: Piko (chasmogamous) and Dacanto (cleistogamous). In the field observations we assessed diurnal pattern of anther extrusion and anther extrusion capacity. For the first time we adapted the time lapse method for measuring kinetics of the spikelet movement and 3-D image correlation technique for the non-invasive measurements of potential deformations of the spikelet lemmas. We found that the two cultivars differ in the potential of pollen dispersion for-cross-pollination and in the spikelet kinetics. We also described some anatomical traits that can have potential functional role in floret opening. None of the cultivars showed any symptoms of lemma surface deformation. CONCLUSIONS: The cleistogamic and chasmogamic wheat cultivars differ significantly in the potential for pollen dispersion for cross-pollination, which is mainly related to anther extrusion capacity. Although none of these features differentiated the cultivars clearly, we assume, based on spikelet kinetics and the lack of lemmas surface deformation, that the water transport and turgor of cells is essential for the floret opening and anther extrusion in wheat. The search for parental ideotype should be supported by marker assisted selection, e.g. based of polymorphisms in genes related to aquaporin biosynthesis.

A Generalized Information-Theoretic Approach for Bounding the Number of Independent Sets in Bipartite Graphs.

This paper studies the problem of upper bounding the number of independent sets in a graph, expressed in terms of its degree distribution. For bipartite regular graphs, Kahn (2001) established a tight upper bound using an information-theoretic approach, and he also conjectured an upper bound for general graphs. His conjectured bound was recently proved by Sah et al. (2019), using different techniques not involving information theory. The main contribution of this work is the extension of Kahn's information-theoretic proof technique to handle irregular bipartite graphs. In particular, when the bipartite graph is regular on one side, but may be irregular on the other, the extended entropy-based proof technique yields the same bound as was conjectured by Kahn (2001) and proved by Sah et al. (2019).

On the Achievable Rate Region of the K-Receiver Broadcast Channels via Exhaustive Message Splitting.

This paper focuses on K-receiver discrete-time memoryless broadcast channels (DM-BCs) with private messages, where the transmitter wishes to convey K private messages to K receivers. A general inner bound on the capacity region is proposed based on an exhaustive message splitting and a K-level modified Marton's coding. The key idea is to split every message into ∑j=1KKj-1 submessages each corresponding to a set of users who are assigned to recover them, and then send these submessages via codewords chosen from a K-level structure codebooks. To guarantee the joint typicality among all transmitted codewords, a sufficient condition on the subcodebooks' sizes is derived through a newly establishing hierarchical covering lemma, which extends the 2-level multivariate covering lemma to the K-level case with more intricate dependences. As the number of auxiliary random variables and rate conditions both increase exponentially with K, the standard Fourier-Motzkin elimination procedure becomes infeasible when K is large. To tackle this problem, we obtain a closed form of achievable rate region with a special observation of disjoint unions of sets that constitute the power set of {1,⋯,K}. The proposed achievable rate region allows arbitrary input probability mass functions and improves over previously known achievable (closed form) rate regions for K-receiver (K≥3) BCs.

Du Bois-Reymond Type Lemma and Its Application to Dirichlet Problem with the p(t)-Laplacian on a Bounded Time Scale.

This paper is devoted to study the existence of solutions and their regularity in the p(t)-Laplacian Dirichlet problem on a bounded time scale. First, we prove a lemma of du Bois-Reymond type in time-scale settings. Then, using direct variational methods and the mountain pass methodology, we present several sufficient conditions for the existence of solutions to the Dirichlet problem.

Linear Programming from Fibonacci to Farkas.

At the beginning of the 13th century Fibonacci described the rules for making mixtures of all kinds, using the Hindu-Arabic system of arithmetic. His work was repeated in the early printed books of arithmetic, many of which contained chapters on 'alligation', as the subject became known. But the rules were expressed in words, so the subject often appeared difficult, and occasionally mysterious. Some clarity began to appear when Thomas Harriot introduced a modern form of algebraic notation around 1600, and he was almost certainly the first to express the basic rule of alligation in algebraic terms. Thus a link was forged with the work on Diophantine problems that occupied mathematicians like John Pell and John Kersey in the 17th century. Joseph Fourier's work on mechanics led him to suggest a procedure for handling linear inequalities based on a combination of logic and algebra; he also introduced the idea of describing the set of feasible solutions geometrically. In 1898, inspired by Fourier's work, Gyula Farkas proved a fundamental theorem about systems of linear inequalities. This topic eventually found many applications, and it became known as Linear Programming. The theorem of Farkas also plays a significant role in Game Theory.

Cloning of long sterile lemma (lsl2), a single recessive gene that regulates spike germination in rice (Oryza sativa L.).

BACKGROUND: Rice is a typical monocotyledonous plant and an important cereal crop. The structural units of rice flowers are spikelets and florets, and floral organ development and spike germination affect rice reproduction and yield. RESULTS: In this study, we identified a novel long sterile lemma (lsl2) mutant from an EMS population. First, we mapped the lsl2 gene between the markers Indel7-22 and Indel7-27, which encompasses a 25-kb region. The rice genome annotation indicated the presence of four candidate genes in this region. Through gene prediction and cDNA sequencing, we confirmed that the target gene in the lsl2 mutant is allelic to LONG STERILE LEMMA1 (G1)/ELONGATED EMPTY GLUME (ELE), hereafter referred to as lsl2. Further analysis of the lsl2 and LSL2 proteins showed a one-amino-acid change, namely, the mutation of serine (Ser) 79 to proline (Pro) in lsl2 compared with LSL2, and this mutation might change the function of the protein. Knockout experiments showed that the lsl2 gene is responsible for the long sterile lemma phenotype. The lsl2 gene might reduce the damage induced by spike germination by decreasing the seed germination rate, but other agronomic traits of rice were not changed in the lsl2 mutant. Taken together, our results demonstrate that the lsl2 gene will have specific application prospects in future rice breeding. CONCLUSIONS: The lsl2 gene is responsible for the long sterile lemma phenotype and might reduce the damage induced by spike germination by decreasing the seed germination rate.

Postselection Inference in Structural Equation Modeling.

Most statistical inference methods were established under the assumption that the fitted model is known in advance. In practice, however, researchers often obtain their final model by some data-driven selection process. The selection process makes the finally fitted model random, and it also influences the sampling distribution of the estimator. Therefore, implementing naive inference methods may result in wrong conclusions-which is probably a prime source of the reproducibility crisis in psychological science. The present study accommodates three valid state-of-the-art postselection inference methods for structural equation modeling (SEM) from the statistical literature: data splitting (DS), postselection inference (PoSI), and the polyhedral (PH) method. A simulation is conducted to compare the three methods with the commonly used naive procedure under selection events made by L1-penalized SEM. The results show that the naive method often yields incorrect inference, and that the valid methods control the coverage rate in most cases with their own pros and cons. Real world data examples show the practical use of the valid inference methods.

Long paths and connectivity in 1-independent random graphs.

A probability measure µ on the subsets of the edge set of a graph G is a 1-independent probability measure (1-ipm) on G if events determined by edge sets that are at graph distance at least 1 apart in G are independent. Given a 1-ipm µ , denote by G µ the associated random graph model. Let ℳ 1 , ⩾ p ( G ) denote the collection of 1-ipms µ on G for which each edge is included in G µ with probability at least p. For G = Z 2 , Balister and Bollobás asked for the value of the least p ⋆ such that for all p > p ⋆ and all µ ∈ ℳ 1 , ⩾ p ( G ) , G µ almost surely contains an infinite component. In this paper, we significantly improve previous lower bounds on p ⋆. We also determine the 1-independent critical probability for the emergence of long paths on the line and ladder lattices. Finally, for finite graphs G we study f 1, G (p), the infimum over all µ ∈ ℳ 1 , ⩾ p ( G ) of the probability that G µ is connected. We determine f 1, G (p) exactly when G is a path, a complete graph and a cycle of length at most 5.

Composite Tests under Corrupted Data.

This paper focuses on test procedures under corrupted data. We assume that the observations Z i are mismeasured, due to the presence of measurement errors. Thus, instead of Z i for i = 1 , … , n, we observe X i = Z i + δ V i, with an unknown parameter δ and an unobservable random variable V i. It is assumed that the random variables Z i are i.i.d., as are the X i and the V i. The test procedure aims at deciding between two simple hyptheses pertaining to the density of the variable Z i, namely f 0 and g 0. In this setting, the density of the V i is supposed to be known. The procedure which we propose aggregates likelihood ratios for a collection of values of δ. A new definition of least-favorable hypotheses for the aggregate family of tests is presented, and a relation with the Kullback-Leibler divergence between the sets f δ δ and g δ δ is presented. Finite-sample lower bounds for the power of these tests are presented, both through analytical inequalities and through simulation under the least-favorable hypotheses. Since no optimality holds for the aggregation of likelihood ratio tests, a similar procedure is proposed, replacing the individual likelihood ratio by some divergence based test statistics. It is shown and discussed that the resulting aggregated test may perform better than the aggregate likelihood ratio procedure.

On the predictive validity of various corpus-based frequency norms in L2 English lexical processing.

The predictive validity of various corpus-based frequency norms in first-language lexical processing has been intensively investigated in previous research, but less attention has been paid to this issue in second-language (L2) processing. To bridge the gap, in the present study we took English as a case in point and compared the predictive power of a large set of corpus-based frequency norms for the performance of an L2 English visual lexical decision task (LDT). Our results showed that, in general, the frequency norms from SUBTLEX-US and WorldLex-Blog tended to predict L2 performance better in reaction times, whereas the frequency norms from corpora with a mixture of written and spoken genres (CELEX, WorldLex-Blog, BNC, ANC, and COCA) tended to predict L2 accuracy better. Although replicated in both low- and high-proficiency L2 English learners, these patterns were not exactly the same as those found in LDT data from native English speakers. In addition, we only observed some limited advantages of the lemma frequency and contextual diversity measures over the wordform frequency measure in predicting L2 lexical processing. The results of the present study, especially the detailed comparisons among the different corpora, provide methodological implications for future L2 lexical research.

Metabolic pathways and genes identified by RNA-seq analysis of barley near-isogenic lines differing by allelic state of the Black lemma and pericarp (Blp) gene.

BACKGROUND: Some plant species have 'melanin-like' black seed pigmentation. However, the chemical and genetic nature of this 'melanin-like' black pigment have not yet been fully explored due to its complex structure and ability to withstand almost all solvents. Nevertheless, identification of genetic networks participating in trait formation is key to understanding metabolic processes involved in the expression of 'melanin-like' black seed pigmentation. The aim of the current study was to identify differentially expressed genes (DEGs) in barley near-isogenic lines (NILs) differing by allelic state of the Blp (black lemma and pericarp) locus. RESULTS: RNA-seq analysis of six libraries (three replicates for each line) was performed. A total of 957 genome fragments had statistically significant changes in expression levels between lines BLP and BW, with 632 fragments having increased expression levels in line BLP and 325 genome fragments having decreased expression. Among identified DEGs, 191 genes were recognized as participating in known pathways. Among these were metabolic pathways including 'suberin monomer biosynthesis', 'diterpene phytoalexins precursors biosynthesis', 'cutin biosynthesis', 'cuticular wax biosynthesis', and 'phenylpropanoid biosynthesis, initial reactions'. Differential expression was confirmed by real-time PCR analysis of selected genes. CONCLUSIONS: Metabolic pathways and genes presumably associated with black lemma and pericarp colour as well as Blp-associated resistance to oxidative stress and pathogens, were revealed. We suggest that the black pigmentation of lemmas and pericarps is related to increased level of phenolic compounds and their oxidation. The effect of functional Blp on the synthesis of ferulic acid and other phenolic compounds can explain the increased antioxidant capacity and biotic and abiotic stress tolerance of black-grained cereals. Their drought tolerance and resistance to diseases affecting the spike may also be related to cuticular wax biosynthesis. In addition, upregulated synthesis of phytoalexins, suberin and universal stress protein (USP) in lemmas and pericarps of the Blp carriers may contribute to their increased disease resistance. Further description of the DEGs haplotypes and study of their association with physiological characteristics may be useful for future application in barley pre-breeding.

The fifth leaf and spike organs of barley (Hordeum vulgare L.) display different physiological and metabolic responses to drought stress.

BACKGROUND: Photosynthetic organs of the cereal spike (ear) provide assimilate for grain filling, but their response to drought is poorly understood. In this study, we characterized the drought response of individual organs of the barley spike (awn, lemma, and palea) and compared them with a vegetative organ (fifth leaf). Understanding differences in physiological and metabolic responses between the leaf and spike organs during drought can help us develop high yielding cultivars for environments where terminal drought is prevalent. RESULTS: We exposed barley plants to drought by withholding water for 4 days at the grain filling stage and compared changes in: (1) relative water content (RWC), (2) osmotic potential (Ψs), (3) osmotic adjustment (OA), (4) gas exchange, and (5) metabolite content between organs. Drought reduced RWC and Ψs in all four organs, but the decrease in RWC was greater and there was a smaller change in Ψs in the fifth leaf than the spike organs. We detected evidence of OA in the awn, lemma, and palea, but not in the fifth leaf. Rates of gas exchange declined more rapidly in the fifth leaf than awn during drought. We identified 18 metabolites but, only ten metabolites accumulated significantly during drought in one or more organs. Among these, proline accumulated in all organs during drought while accumulation of the other metabolites varied between organs. This may suggest that each organ in the same plant uses a different set of osmolytes for drought resistance. CONCLUSIONS: Our results suggest that photosynthetic organs of the barley spike maintain higher water content, greater osmotic adjustment, and higher rates of gas exchange than the leaf during drought.