Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Water Deficit Stress on Seedling Biomass and Physio-Chemical Characteristics in Different Species of Wheat Possessing the D Genome

Wild relatives of wheat serve as an extraordinary source of variability for breeding programs due to their capabilities to respond to various environmental stresses. Here, we investigated some species possessing a D genome (T. aestivum, Ae. tauschii, Ae. crassa and Ae. cylindrica) in terms of relative water content (RWC), stomatal conductance (Gs), relative chlorophyll content, initial fluorescence (Fo), maximum quantum yield of PSII (Fv/Fm), maximum primary yield of PSII photochemistry (Fv/Fo), as well as shoot fresh and dry biomasses under control and water deficit conditions. Our results revealed that water deficit negatively affected all traits; shoot fresh weight, Gs and RWC showed the highest reduction compared to the control condition. Principal component analysis (PCA) identified two PCs that accounted for 53.36% of the total variation in the water deficit conditions. Correlation analysis and PCA-based biplots showed that stress tolerance index (STI) is significantly associated with Fv/Fm and Fv/Fo under water stress conditions, suggesting that these are the best parameters to evaluate when screening for tolerant samples at the seedling stage. We identified 19 accessions from Ae. crassa and one from Ae. tauschii as the most tolerant samples. In conclusion, Ae. crassa might provide an ideal genetic resource for drought-tolerant wheat breeds.
The Macrophage in Cystic Fibrosis

Name: Adam Wright Thesis Title: The Macrophage in Cystic Fibrosis Background: Cystic fibrosis (CF) is caused by absent/defective CF transmembrane conductance regulator protein (CFTR). CF is characterized by thick airway mucus, chronic infection and neutrophil inflammation leading to respiratory failure. I analysed airway macrophages (M<t>s) and their expression ofpattern recognition receptors (PRRs) in CF, since these cells are crucial to airway immune defence and they can orchestrate inflammation. I also performed transcript analysis of CF monocyte-derived M<t>s (MDMs). Methods: Sputum was induced in CF paediatric and adult cohorts. Phenotype and function of CF M<t> were determined by flow cytometry and compared to controls. Monocytes (>92° o purity) were grown in vitro to generate MDMs (n=15). Transcripts encoding the entire human genome were analysed (n=5) and expression of individual genes were confirmed by RT-PCR. Results: In classical CF (n=10) there was an increase in the proportion of monocyte-like small M<t>s (of total M<t» compared to controls (n=IO) (73 ± 18% and 16 ± 8%, respectively, p< 0.0001). In non-classical CF (n=4), with milder lung disease, small M<t>s increased to 31 ± 20% (p>0.05). PRRs were absent on small M<t>s from CF and control. In contrast, clear expression could be detected on large M<t>s from control but not CF. In line with this, CF small M<t>s showed a strongly reduced uptake of particles compared to controls. Microarray analysis of MDMs revealed aand ~-tryptase as being significantly higher under constitutive and stimulated conditions in CF compared to control. However, using RT -PCR, expression of aand ~-tryptase was similar between groups. Conclusions: The phenotype of small M<t>s in CF suggests that these cells are newly recruited monocytes from blood. Low expression of PRRs on these cells in CF and their reduced uptake indicates a reduced capacity to clear inhaled particles, which may contribute to further damage in CF. Further to this I was unable to confirm any transcript differences between CF and control MDMs due to mutant CFTR.
Evolución del gameto masculino de lagartos del género Tupinambis asociada al riesgo de competencia espermática.

Sexual dimorphism patterns provide an opportunity to increase our understanding of trait evolution. Because selective forces may vary throughout the reproductive period, measuring dimorphism seasonally may be an interesting approach. An increased male head size may be important in intersexual and intrasexual interactions. In Tupinambis lizards, a big head is attributed in part to a large adductor muscle mass. Competition for mating can differ in species with different sex ratio and different degrees of sexual size dimorphism. We examined sexual differences in mass of the pterygoideus muscle, its temporal variation throughout the reproductive period and the relationship between muscle and reproductive condition in Tupinambis merianae and T. rufescens. We characterized sexual size dimorphism and sex ratio in both species. Mature males had larger jaw muscles than mature females in both species, mainly during the reproductive season. The dimorphism in jaw muscle was due to an increase in muscle mass in sexually active males. Seasonal increases in muscle mass and variation between immature and mature individuals suggest that the jaw muscle might be a secondary sexual character. We propose that the pterygoideus muscle may act as a signal of reproductive condition of males because it is associated with testis size and sperm presence. The patterns of sexual dimorphism in jaw muscle in both species were similar; however, the comparison shows how sexual characters remain dimorphic in different competition contexts and in species with different degrees of body size dimorphism. Our results suggest that jaw muscle as sexual character could be influenced by interand intrasexual selective pressures.
Previous Aphid Infestation Induces Different Expression Profiles of Genes Associated with Hormone-Dependent Responses in Near-Isogenic Winter Wheat Lines

Abstract Hormone-dependent responses in host plants induced by herbivore infestation have species-specific effects. This study focused on determining the relative expression profiles of the genes associated with hormone-dependent pathways in two near-isogenic wheat lines when attacked by cereal aphids. Infestation with Rhopalosiphum padi Linnaeus (Hemiptera: Aphididae) and/or Sitobion avenae Fabricius (Hemiptera: Aphididae) significantly upregulated the expression of marker genes related to the salicylic acid (SA)- and jasmonic acid (JA)-dependent pathways in the tested lines. In the resistant line 35-E4, previous infestation with R. padi significantly increased the relative expression of plant pathogenesis-related protein 1 at all sampling times but did not have a significant effect on the expression of the phenylalanine ammonia-lyase (PAL) gene. In addition, the expression levels of the lipoxygenase (LOX) and allene oxide synthase (AOS) genes immediately increased after the aphid attack. In susceptible line 35-A20, infestation with either R. padi or S. avenae led to significantly increased expression levels of the AOS and PAL genes. Moreover, sequential aphid infestation induced higher expression of AOS compared with a single-species aphid infestation, whereas the expression of the PAL gene was antagonistically affected by sequential aphid infestation. Overall, these results showed that aphid infestation induced SA- and JA-dependent responses in host plants. However, the expression profiles of these genes in resistant and susceptible host lines were significantly different.
Gamma-protocadherin localization at the synapse corresponds to parameters of synaptic maturation

Clustered protocadherins (Pcdhs) are a large family of ~60 cadherin-like proteins (divided into the subclasses α, β, and γ) that compose a surface “barcode” in individual neurons. The code is generated through combinatorial expression via epigenetic regulation at a large gene cluster that encodes the molecules. During early neural development, Pcdhs were shown to mediate dendrite self-recognition and avoidance in some neuronal types through a still uncharacterized anti-adhesive mechanism. Pcdhs have also been postulated to participate in synaptogenesis and the specificity of connectivity. Some synaptic defects were noted in knockout animals including synaptic number and physiology but the role of these molecules in synaptic development is not understood. We have shown previously that Pcdh-γs are highly enriched in intracellular compartments located in dendrites and spines with less frequent localization at the synaptic membrane. We compared synapses that expressed endogenous Pcdh-γs versus those that did not for parameters of synaptic maturation including pre- and postsynaptic punctum size, postsynaptic perforations and spine morphology in mature cultured hippocampal neurons. We also performed serial section immuno-electron microscopy in intact hippocampal CA1 and measured synaptic size and perforation status of Pcdh-γ positive and negative synapses. At both the light and ultrastructural levels, synapses immunopositive for Pcdh-γs were found to be larger in diameter with more frequent perforations. Analysis of spines in cultured neurons revealed that mushroom spines were more frequently immunopositive for Pcdh-γs at their tips than thin spines. Taken together, these results suggest that Pcdh-γ function at the synapse may be related to synaptic maturation and stabilization.
The TALE Factors and Nuclear Factor Y Cooperate to Drive Transcription at Zygotic Genome Activation

The TALE factors, comprising the pbx and prep/meis gene families, are transcription factors (TFs) vital to the proper formation of anterior anatomical structures during embryonic development. Although best understood as essential cofactors for tissue-specific TFs such as the hox genes during segmentation, the TALE factors also form complexes with nuclear factor Y (NFY) in the early zygote. In zebrafish, Pbx4, Prep1, and NFY are maternally deposited and can access their DNA binding sites in compact chromatin. Our results suggest that TALE/NFY complexes have a unique role in early embryonic development which is distinct from each factor’s independent functions at later stages. To characterize these TALE/NFY complexes, we employed highthroughput transcriptomic and genomic techniques in zebrafish embryos. Using dominant negatives to disrupt the function of each factor, we find that they display similar, but not identical, loss-of-function phenotypes and co-regulate genes involved in transcription regulation and embryonic development. Independently, the TALE factors regulate homeobox genes and NFY governs cilia-related genes. ChIP-seq analysis at zygotic genome activation reveals that the TALE factors occupy DECA sites adjacent to CCAAT boxes near genes expressed early in development and involved with transcription regulation. Finally, DNA elements containing TALE and NFY binding sites drive reporter gene expression in transgenic zebrafish, and disruption of TALE/NFY binding via
Ecological impacts of invasive carp in Australian dryland rivers

Invasive carp are widely reported to harm ecosystems. In Australia, carp are a serious pest and, consequently, investigations of biocontrol options are under way. Best practice biocontrol requires cost/risk:benefit evaluation. To assist this, the impacts of carp on aquatic ecosystems have been summarized. To aid the evaluation of benefits, general predictions were tested by comparing dryland river ecosystems with and without carp, and ecosystem responses to a gradient in local carp density. Expectations were that in the presence of carp, and with increasing density, there would be increasing turbidity, decreasing densities of macrophytes and macroinvertebrates, and associated changes in assemblage composition, resulting in decreasing native fish density. Not all expected responses were found, indicating that the general understanding of carp impact requires modification for dryland rivers. Notably, carp did not increase turbidity or reduce macroinvertebrate density or composition, probably because of key attributes of dryland rivers. In contrast, there were large impacts on native fish biomass, not from the mechanisms expected, but from food resource monopolization by carp. Macrophyte occurrence was reduced, but macrophytes are naturally rare in these rivers. It is likely that the extirpation of an endangered river snail resulted from carp predation. Impacts on native fish may be reversible by carp control, but reversal of impacts on the snail may require carp elimination and snail reintroduction. Modelling is necessary to predict the probability of beneficial versus undesirable outcomes from carp control, and complementary measures to control other stressors may be needed. Benefits of carp control on dryland river ecosystems are fewer than generally predicted. This reinforces the point that ecological understanding cannot always be transferred between diverse settings and highlights the need to understand system characteristics relevant to causal impact pathways when applying generic carp impact models to specific settings. This has global relevance to future carp control efforts.
Immunoinformatics Prediction of Epitope Based Peptide Vaccine Against Mycobacterium Tuberculosis PPE65 family Protein

Introduction Tuberculosis (TB) is a serious disease with varying rates of mortality and morbidity among infected individuals which estimates for approximately two million deaths/year. The number of deaths could increase by 60% if left untreated. It mainly affects immune-compromised individuals and people of third world, due to poverty, low health standards, and inadequate medical care. It has varying range of manifestations that is affected by the host immune system response, the strain causing the infection, its virulence, and transmissibility. Materials and methods A total of 1750 Mycobacterium Tuberculosis PPE65 family protein strains were retrieved from National Center for Biotechnology Information (NCBI) database on March 2019 and several tools were used for the analysis of the T- and B-cell peptides and homology modelling. Results and conclusion Four strong epitope candidates had been predicted in this study for having good binding affinity to HLA alleles, good global population coverage percentages. These peptides are YAGPGSGPM, AELDASVAM, GRAFNNFAAPRYGFK and a single B-cell peptide YAGP. This study uses immunoinformatics approach for the design of peptide based vaccines for M. tuberculosis. Peptide based vaccines are safer, more stable and less hazardous/allergenic when compared to conventional vaccines. In addition, peptide vaccines are less labouring, time consuming and cost efficient. The only weakness is the need to introduce an adjuvant to increase immunogenic stimulation of the vaccine recipient.
Endogenous esterases of Clostridium thermocellum are identified and disrupted for enhanced isobutyl acetate production from cellulose

Medium chain esters are potential drop-in biofuels and versatile chemicals. Currently, these esters are largely produced by the conventional chemical process that uses harsh operating conditions and requires high energy input. Alternatively, the microbial conversion route has recently emerged as a promising platform for sustainable and renewable ester production. The ester biosynthesis pathways can utilize either esterases/lipases or alcohol acyltransferase (AAT), but the AAT-dependent pathway is more thermodynamically favorable in aqueous fermentation environment. Even though cellulolytic thermophiles such as Clostridium thermocellum harboring the engineered AAT-dependent pathway can directly convert lignocellulosic biomass into esters, the production is currently not efficient and requires optimization. One potential bottleneck is the ester degradation caused by the endogenous carbohydrate esterases (CEs) whose functional roles are poorly understood. In this study, we developed a simple, high-throughput colorimetric assay to screen the endogenous esterases of C. thermocellum responsible for ester hydrolysis. We identified, characterized, and disrupted two critical endogenous esterases that significantly contributes to isobutyl acetate degradation in C. thermocellum. We demonstrated that not only did the engineered esterase-deficient strain alleviate ester hydrolysis but also helped improve isobutyl acetate production while not affecting its robust metabolism for effective cellulose assimilation. IMPORTANCE Carbohydrate esterases (CEs) are important enzymes in the deconstruction of lignocellulosic biomass by the cellulolytic thermophile C. thermocellum, yet some are potential ester degraders in a microbial ester production system. Currently, the functional roles of CEs for hydrolyzing medium chain esters and negatively affecting the ester microbial biosynthesis are not well understood. This study discovered novel CEs responsible for isobutyl acetate degradation in C. thermocellum and hence identified one of the critical bottlenecks for direct conversion of lignocellulosic biomass into esters.
Perfil imuno-histoqumico de carcinomas mamrios invasores em homens

O câncer de mama em homens e uma doenca incomum. A cada 150 casos de câncer de mama e esperada a ocorrencia de apenas um no sexo masculino. Devido a baixa incidencia desta neoplasia, grande parte do seu conhecimento e oriunda do carcinoma de mama no sexo feminino, cujos parâmetros diagnosticos, prognosticos e terapeuticos sao bem estabelecidos na literatura. Entretanto, a distribuicao dos fenotipos moleculares dos carcinomas da mama masculina e pouco conhecida. Pela analise de dados clinicos e imuno-histoquimicos estudamos os diferentes perfis de uma amostra de 20 casos de tumores invasores de mama em homens. Utilizamos um painel de cinco anticorpos composto por receptor de estrogenio, citoqueratinas 5/6, citoqueratinas 8/18, HER-1 e HER-2. Dos 20 casos examinados, 19 eram carcinomas do tipo ductal nao-especial (95%) e um do tipo lobular (5%). A maioria dos casos foi composta por mastectomias (65%), sendo a media de tamanho das neoplasias de 2,8 cm e o grau histologico mais frequente o II (60%). Do total, 86,6% dos casos apresentaram metastases linfonodais. O numero medio de linfonodos comprometidos foi de 5,2 nas amostras com axila positiva. Foram determinados 14 tumores (70%) correspondentes ao fenotipo RE+/luminal, dois (10%) do tipo indeterminado, um unico tumor (5%) do fenotipo Basal, e tres de mama (15%) correspondendo ao fenotipo HER2-positivo. A imunofenotipagem dos carcinomas de mama no sexo masculino permite tracar paralelos com os tumores de mama feminina, possibilitando a elucidacao de fatores intrinsecos a doenca em cada um dos sexos.
Cross-Modal Contrastive Learning for Robust Reasoning in VQA

Multi-modal reasoning in visual question answering (VQA) has witnessed rapid progress recently. However, most reasoning models heavily rely on shortcuts learned from training data, which prevents their usage in challenging real-world scenarios. In this paper, we propose a simple but effective cross-modal contrastive learning strategy to get rid of the shortcut reasoning caused by imbalanced annotations and improve the overall performance. Different from existing contrastive learning with complex negative categories on coarse (Image, Question, Answer) triplet level, we leverage the correspondences between the language and image modalities to perform finer-grained cross-modal contrastive learning. We treat each Question-Answer (QA) pair as a whole, and differentiate between images that conform with it and those against it. To alleviate the issue of sampling bias, we further build connected graphs among images. For each positive pair, we regard the images from different graphs as negative samples and deduct the version of multi-positive contrastive learning. To our best knowledge, it is the first paper that reveals a general contrastive learning strategy without delicate hand-craft rules can contribute to robust VQA reasoning. Experiments on several mainstream VQA datasets demonstrate our superiority compared to the state of the arts. Code is available at \url{https://github.com/qizhust/cmcl_vqa_pl}.
Additional Results and Extensions for the paper "Probabilistic bounds on the k-Traveling Salesman Problem and the Traveling Repairman Problem"

This technical report provides additional results for the main paper ``Probabilistic bounds on the $k-$Traveling Salesman Problem ($k-$TSP) and the Traveling Repairman Problem (TRP)''. For the $k-$TSP, we extend the probabilistic bounds derived in the main paper to the case of distributions with general densities. For the TRP, we propose a utility-based notion of fairness and derive constant-factor probabilistic bounds for this objective, thus extending the TRP bounds from the main paper to non-linear utilities.
Uncovering the Genetic Architecture of Fruiting Efficiency in Bread Wheat: A Viable Alternative to Increase Yield Potential

To meet the estimated future increase in wheat (Triticum aestivum L.) demand, exploring and dissecting the genetic basis of yield-related traits play a crucial role in wheat yield improvement. In this study, we evaluated 12 grain yield-related traits including fruiting efficiency (FE) in a wheat panel through genome-wide association mapping (GWAS) approach. The panel displayed large phenotypic variation for all the measured traits, FE was positively associated with grain number per spike but not related to thousand kernel weight. Interestingly, FE was mostly explained by grain number per fertile spikelet (GFS), whereas the latter was determined by spikelet weight (SW). The GWAS identified 44 significant marker-trait associations (MTAs) across almost the entire wheat genome linked to the 12 yield-related traits, including four MTAs on chromosomes 2A, 2D, 4D, and 5A associated with FE. Several significant markers were identified in genomic regions previously reported, whereas others appeared to be potentially novel loci. Particularly, the co-location of significant markers for yield-related traits with major genes underlying plant development showed pleiotropic effects and the key role of these genes in modulating agronomic traits. The markers linked to FE, GFS, and SW are promising, especially considering that due to the destructive phenotypic determination, their improvement in early breeding generations can only be made by marker-assisted selection. Taken together, these findings are encouraging and suggest the potential value of FE and associated traits as possible selection criteria to increase yield potential in wheat breeding programs.
Characterization of the complete mitochondrial genome of Squalus brevirostris (Squaliformes, Squalidae)

Abstract The complete mitochondrial genome sequence of Squalus brevirostri was determined using next-generation sequencing. The whole circular genome is 16,734 bp in length. It contains 37 genes including13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA genes (tRNA), and a control region (D-Loop). The overall nucleotide composition is A: 30.38%, T: 30.73%, G: 24.61%, and C: 14.27%, with an A + T content of 61.11%. The phylogenetic analysis suggested that S. brevirostris was closely related to Squalus montalbani.
Characterization and transcriptional analysis of one carbonic anhydrase gene in the green‐tide‐forming alga Ulva prolifera (Ulvophyceae, Chlorophyta)

Ulva prolifera is a green‐tide‐forming macroalga dominating the green tides in the Yellow Sea from 2007 to 2019. The exponential growth of U. prolifera, and the correlating accumulation of biomass, rely heavily on its carbon fixation capability. Despite the importance of carbon fixation in algal growth, to date none of the genes involved in carbon fixation have undergone molecular characterization in U. prolifera. This study used Rapid Amplification of cDNA Ends (RACE) to characterize one full‐length carbonic anhydrase (CA) gene of U. prolifera (UpαCA1). An activity assay showed that UpαCA1 was an active CA. Real‐time quantitative PCR results showed that temperature, irradiance, salinity and pH could influence the transcriptional level of UpαCA1, indicating that UpαCA1 was sensitive to varying environmental factors. The results of this study provided further insights into our understanding of the influence of environmental factors on carbon fixation in U. prolifera and its subsequent role in the formation of green tides.