Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic relationships and generic concepts in the red order Bangiales: challenges ahead

Wendy A. Nelson, Tracy J. Farr and Judy E.S. Broom. 2006. Phylogenetic relationships and generic concepts in the red order Bengiales: challenges ahead. Phycologia 45: 249–259. DOI: 10.2216/05-26.1 Over the past decade molecular sequence data and phylogenetic analyses have provided strong evidence that the order Bangiales is monophyletic, but that Porphyra and Bangia as currently understood are not. Previous research on the Bangiales has focused primarily on taxa from the North Pacific and North Atlantic. Recent exploration of Bangiales diversity in other regions, particularly the southern hemisphere, has revealed deep divergences in the order in phylogenetic analyses employing the slowly evolving 18S rRNA gene. The presence of high diversity in New Zealand raises the prospect that the southern hemisphere, and particularly eastern Gondwana, is not only a centre of diversity but a centre of origin for the Bangiales. Although the need for new generic concepts within this order is clear, it is our conclusion that approaches to revising the Bangiales based solely on regional approaches will not succeed: the completion of a modern and robust taxonomic revision of this order requires a global collaborative effort. Enhanced taxon sampling and verifiable application of names, based on vouchered specimens, will be essential for this to be achieved. The determination of phylogenetic relationships in the Bangiales has implications for the qua.gification of biodiversity. The number of taxa in the evolutionarily diverse Bangiales has been significantly underestimated, and the diversity in this group has been obscured by the recognition of only two genera. Based on the analyses completed to date, in a revised Bangiales there will be at least 10 genera, 5 of which are currently recognised (Bangia, Dione, Minerva, Pseudobangia and Porphyra), as well as further genera yet to be circumscribed. The majority of species currently placed in Porphyra, including species of commercial value, will not remain in Porphyra sensu stricto.
Phylogenetic Diversity of Trichoderma Strains and Their Antagonistic Potential against Soil-Borne Pathogens under Stress Conditions

Trichoderma species are known as excellent biocontrol agents against soil-borne pathogens that cause considerable crop losses. Eight strains of Trichoderma were isolated from five Egyptian regions. They identified based on translation elongation factor-1α (TEF1) sequencing as four different Trichoderma species: Trichoderma asperellum, Trichoderma harzianum, Trichoderma viride, and Trichoderma longibrachiatum. Optimal growth conditions (temperature and media), and the phosphate solubilization capability of Trichoderma strains were evaluated in vitro. Further, the ability of these strains to antagonize Fusarium solani, Macrophomina phaseolina, and Fusarium graminearum was also evaluated. The results revealed that Trichoderma harzianum (Th6) exhibited the highest antagonistic ability against F. solani, M. phaseolina and F. graminearum with inhibition rates of 71.42%, 72.97%, and 84.61%, respectively. Trichoderma viride (Tv8) exhibited the lowest antagonism against the same pathogens with inhibition rates of 50%, 64% and 69.23%, respectively. Simple-sequence repeats (SSRs) and random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic variability of the Trichoderma strains. The results revealed that of 45 RAPD amplified bands, 36 bands (80%) were polymorphic and of SSRs amplified 36 bands, 31 bands (86.11%) were polymorphic. The amplification of calmodulin and β-1,3-endoglucanase was noted at 500 bp and 230 bp, respectively. Data indicated that T. viride (Tv8) had the highest phosphate solubilization index (10.0 mm), while T. harzianum (Th6) had the lowest phosphate solubilization index (4.0 mm). In conclusion, T. harzianum (Th6) had the highest antagonistic activity in dual culture assay along with the growth rate; while T. viride (Tv8) had the highest phosphate solubilization activity. There are still gaps in obtaining new formulations, selecting potent Trichoderma strains to confirm disease control in planta. For improving Trichoderma recommendation in the organic agricultural system and sustaining the fertility of the soil, the field application of highly antagonistic biocontrol agents in different types of soil and plant species will be the first approach toward bio-pesticide treatments along with bio-fertilizer inoculation. Furthermore, secondary metabolites will be investigated for the most promising strains with the combination of different pathogens and application timing.
Neonate Galerucella calmariensis (Coleoptera: Chrysomelidae) Behavior on Purple Loosestrife (Lythrum salicaria) Contributes to Reduced Predation

Abstract Galerucella calmariensis L. has been widely released in North America to control Lythrum salicaria L. , an invasive Eurasian wetland perennial. Previous studies suggest that generalist predators such as Coleomegilla maculata (DeGeer) may affect establishment and spread of G. calmariensis. The objectives of this study were to determine the preferred feeding sites of neonate G. calmariensis, to quantify neonate survivorship on L. salicaria leaves and shoot tips, to assess the relationship between larval density and residence time in shoot tips, and to determine if larval density influences survivorship of larvae on L. salicaria in the presence/absence of predators. Neonate G. calmariensis exhibited a significant propensity to ascend L. salicaria stems and conceal themselves inside shoot tips, where 77% were located after 1 h. Neonate survival in the presence of C. maculata was higher in shoot tips (70%) than on leaves (7.1%). At low densities (one to two larvae per shoot tip), G. calmariensis fed inside shoot tips for a prolonged period of time with only 25–30% exiting the shoot tip by 126 h. At higher densities, larvae left shoot tips more rapidly with 50% (seven larvae per shoot tip) and 80% (16 larvae per shoot tip) exiting by 126 h. The number of larvae that fed externally on foliage, i.e., were exposed to potential predation, similarly increased with increasing larval density. In the presence of adult C. maculata, G. calmariensis survival was inversely density dependent. At low larval densities, larvae remained concealed in shoot tips longer and were protected from predation. However, at high densities, larvae left shoot tips resulting in greater mortality by predators. This study indicates that density-dependent predation of G. calmariensis may occur as sheltered feeding sites within shoot tips become a limiting resource. This would occur under high G. calmariensis density and require the concurrent presence of effective predators. Further studies are necessary to determine if these conditions occur in nature and are of sufficient magnitude to alter G. calmariensis establishment or spread as a biological control agent of L. salicaria.
A Naturalistic Study of Youth Referred to a Tertiary Care Facility for Acute Hypomanic or Manic Episode

Background: Bipolar Disorders (BD) in youth are a heterogeneous condition with different phenomenology, patterns of comorbidity and outcomes. Our aim was to explore the effects of gender; age at onset (prepubertal- vs. adolescent-onset) of BD; and elements associated with attention deficit hyperactivity disorder (ADHD) and Substance Use Disorder (SUD) comorbidities, severe suicidal ideation or attempts, and poorer response to pharmacological treatments. Method: 117 youth (69 males and 57 females, age range 7 to 18 years, mean age 14.5 ± 2.6 years) consecutively referred for (hypo)manic episodes according to the Diagnostic and Statistical Manual of Mental Disorders, 54th ed (DSM 5) were included. Results: Gender differences were not evident for any of the selected features. Prepubertal-onset BD was associated with higher rates of ADHD and externalizing disorders. SUD was higher in adolescent-onset BD and was associated with externalizing comorbidities and lower response to treatments. None of the selected measures differentiated patients with or without suicidality. At a 6-month follow up, 51.3% of the patients were responders to treatments, without difference between those receiving and not receiving a psychotherapy. Clinical severity at baseline and comorbidity with Conduct Disorder (CD) and SUD were associated with poorer response. Logistic regression indicated that baseline severity and number of externalizing disorders were associated with a poorer outcome. Conclusions: Disentangling broader clinical conditions in more specific phenotypes can help timely and focused preventative and therapeutic interventions.
Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population

Simple Summary The number of thoracic vertebrae (NTV) and number of vertebrae (NV) varies among pig breeds with a high correlation of about 0.8. It is important to discover variants associated with the NTV by considering the effect of the NV in pig. The results suggest that regulation variants on SSC7 might play crucial roles in the NTV and the FOS on SSC7 should be further studied as a critical candidate gene. In addition, BMPR1A was identified as a novel candidate gene affecting the NTV in pigs. Abstract The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.
Urinary and Serum N-acetyl B-Glucosaminidase as Biomarkers of Albuminuria in Patients with Type 2 Diabetes

Background: Diabetic nephropathy is a serious kidney-related complication of type 1 diabetes and type 2 diabetes. It is also called diabetic kidney disease. About 25% of people with diabetes eventually develop kidney disease. The enzyme N-Acetyl-? -glucosaminidase (NAG) (EC: 3.2.1.30) is one of lysosomal acid hydrolases enzyme present in many body tissues with a high molecular weight (~ 140 kDa). It breaks chemical bonds of glycoside and amino sugars which form structural components in many tissues. Different pieces of cells need to be degraded and disposed of, including the cell membrane. Method: By using ELISA kit, we measured urine and serum level of N-acetyl B-Glucosaminidase in 30 patients diabetes with Microalbuminuria: ACR: 30 mg/g with 30 healthy volunteers enlisted as normal controls. Result: Urine concentration of NAG in macro and micro- groups was comparable (13.23±1.04 ng/mL and 13.1±1.46 ng/mL, respectively) with no significant difference, while both groups showed highly significant difference compared with normo- group (5.15±2.11 ng/mL) On the other hand, serum concentration of NAG in normo- micro- and macroabluminuria was 1.2±0.3 ng/mL, 2.5±0.58 ng/mL and 3.2±0.77 ng/mL, respectively, with highly significant differences between the three groups. Conclusion: N-Acetyl-? -Glucosaminidase: the present study, diabetic nephropathy was associated with elevated urinary and serum NAG values compared to a control group. This increase in NAG was parallel to the severity of renal involvement with a characteristic increasing trend was observed among the study groups regarding albuminuria
Application of nanoemulsion technology for development of novel functional foods with essential oils encapsulation: A review

The demand for shelf-stable and nutritious food products is increasing day by day and consumers are ready to pay a higher price for such food products. Some artificial preservatives and antioxidant agents, such as butyrate hydroxanisole (BHA), tertiary butyl hydroquinone (TBHQ), and butyrate hydroxytoluene (BHT), have been widely used for food preservation, but these are harmful for human health and can cause DNA mutation and carcinogenesis. Now-a-days, the latest researches focus on compounds of natural origin as preservatives of novels that can help in the extension of food shelf life without harmful effects on human health. Spices and aromatic herbs with medicinal value have been traditionally applied in phytotherapy due to the presence of a variety of activities of their secondary biomolecules, particularly carminative, antiviral, antimicrobial, spasmolytic, hepatoprotective, anticarcinogenic, etc. Essential oils and extracts from these herbs have bio-preservation actions and a lot of research has been done for the use of these essential oils and extracts in the food sector. Essential oils are aromatic metabolites derived from plants, such as grasses, buds, flowers, leaves, roots, stems, bark, resins, and its secretions, which have excellent antioxidant and antimicrobial properties. Therefore, essential oils from these traditional herbs and spices have excellent potential in the food industries, but have some limitations in its direct incorporation. Due to their hydrophobic nature, they are unstable in aqueous medium, which poses more challenges for incorporating it into food due to the interaction of essential oil with protein and fat that may reduce its antioxidant and antimicrobial potential. In addition, strong taste with a high concentration for effective microbial inhibition would exceed organoleptic levels of acceptance. Therefore, one of the ways to overcome these deficiencies is to encapsulate essential oils before incorporating them into food matrices. Encapsulation provides isolation, penetration, protection, or controlled release of reactive substances from the surrounding matter. Nanoemulsion delivery systems are known to use a low concentration of essential oils to increase their functionality in food.
On the linear convergence of the general first order primal-dual algorithm

In this paper, we consider the general first order primal-dual algorithm, which covers several recent popular algorithms such as the one proposed in [Chambolle, A. and Pock T. , A first-order primal-dual algorithm for convex problems with applications to imaging, J. Math. Imaging Vis. , 40 (2011) 120-145] as a special case. Under suitable conditions, we prove its global convergence and analyze its linear rate of convergence. As compared to the results in the literature, we derive the corresponding results for the general case and under weaker conditions. Furthermore, the global linear rate of the linearized primal-dual algorithm is established in the same analytical framework.
Corrupted Image Modeling for Self-Supervised Visual Pre-Training

We introduce Corrupted Image Modeling (CIM) for self-supervised visual pre-training. CIM uses an auxiliary generator with a small trainable BEiT to corrupt the input image instead of using artificial [MASK] tokens, where some patches are randomly selected and replaced with plausible alternatives sampled from the BEiT output distribution. Given this corrupted image, an enhancer network learns to either recover all the original image pixels, or predict whether each visual token is replaced by a generator sample or not. The generator and the enhancer are simultaneously trained and synergistically updated. After pre-training, the enhancer can be used as a high-capacity visual encoder for downstream tasks. CIM is a general and flexible visual pre-training framework that is suitable for various network architectures. For the first time, CIM demonstrates that both ViT and CNN can learn rich visual representations using a unified, non-Siamese framework. Experimental results show that our approach achieves compelling results in vision benchmarks, such as ImageNet classification and ADE20K semantic segmentation.
MANA: Microarchitecting a Temporal Instruction Prefetcher

L1 instruction (L1-I) cache misses are a source of performance bottleneck. While many instruction prefetchers have been proposed over the years, most of them leave a considerable potential uncovered. In 2011, Proactive Instruction Fetch (PIF) showed that a hardware prefetcher could effectively eliminate all instruction-cache misses. However, its enormous storage cost makes it an impractical solution. Consequently, reducing the storage cost was the main research focus in instruction prefetching in the past decade. Several instruction prefetchers, including RDIP and Shotgun, were proposed to offer PIF-level performance with significantly lower storage overhead. However, our findings show that there is a considerable performance gap between these proposals and PIF. While these proposals use different mechanisms for instruction prefetching, the performance gap is mainly not because of the mechanism, and instead, is due to not having sufficient storage. In this paper, we make the case that the key to designing a powerful and cost-effective instruction prefetcher is choosing a metadata record and microarchitecting the prefetcher to minimize the storage. We propose MANA, which offers PIF-level performance with 15.7× lower storage cost. MANA outperforms RDIP and Shotgun by 12.5 and 29%, respectively. We also evaluate a version of MANA with no storage overhead and show that it offers 98% of the peak performance benefits.
Reduction of GC 3 TA Transversion Mutation by Overexpression of MutS in Escherichia coli K-12

Overexpression of the MutS repair protein signiﬁcantly decreased the rate of lacZ GC 3 TA transversion mutation in stationary-phase and exponentially growing bacteria and in mutY and mutM mutants, which accumulate mismatches between 8-oxoguanine (8-oxoG) and adenine residues in DNA. Conversely, GC 3 TA transversion increased in mutL or mutS mutants in stationary phase. In contrast, overexpression of MutS did not appreciably reduce lacZ AT 3 CG transversion mutation in a mutT mutant. These results suggest that MutS-dependent repair can correct 8-oxoG:A mismatches in Escherichia coli cells but may not be able to compete with mutation ﬁxation by MutY in mutT mutants. The MutS homodimer binds to mismatched bases, small bulge loops, and damaged bases as an initial step in methyl-directed DNA mismatch repair in Escherichia coli (2, 4, 7, 22, 26, 27, 29, 30, 34). MutS is also thought to play roles in methyl- independent repair pathways, such as very-short-patch repair (18). The amount of MutS is strongly down regulated as E. coli cells enter stationary phase (9, 31). This regulation is partly mediated at the level of mRNA stability by the RNA chaper-one protein Hfq, which acts to destabilize the mutS transcript (31). Down regulation of the amount of MutS in stationary- phase cells may help to coordinate repair capacity with decreased DNA replication (9, 31). In addition, decreased amounts of MutS could contribute to increased mutagenesis or homeologous
TR Phosphorylation & Nuclear Import

The thyroid hormone receptor a (TRa) is a transcription factor, which can activate or repress gene expression in response to thyroid hormone. In addition, some of its actions, including DNA binding and transcriptional activation, are thought to be regulated by phosphorylation. Results presented here, using Xenopus oocyte micro injection assays, demonstrate that a phosphorylated form of TRa is present in the oocyte nucleus, whereas unphosphorylated TRa remains cytoplasmic. Changes in the phosphorylation state of TRa occur rapidly in Xenopus oocytes and point to the possibility that phosphorylation occurs in the nucleus. Furthermore, increasing the overall phosphorylation state of the oocyte leads to enhanced nuclear retention of TRa, suggesting that phosphorylation may have an important role in regulating nuclear localization of TRa. However, serine 12, a well-characterized casein kinase II phosphorylation site, is not necessary for this enhanced nuclear retention, nor is this site necessary for nuclear import. Taken together, these data provide evidence that phosphorylation of one or more sites other than serine 1 2 , while not directly involved in nuclear import, play an important role in regulating nuclear retention of TRa. These findings provide a foundation for future studies on the role of phosphorylation in the regulation of TRa. TR PHOSPHORYLATION & NUCLEAR IMPORT Introduction The thyroid hormone receptor (TR), like other members of the nuclear receptor superfamily, is a transcription factor that activates or inhibits the expression of target genes in response to ligand. These transcription factors play a vital role in the normal development and maintenance of homeostasis in many organisms. Mutant alleles of members of this family have also been linked to a variety of diseases including various forms of cancer and resistance to thyroid hormone. In recent years, phosphorylation of transcription factors such as TR has been shown to be an important regulatory factor in many systems. Along with tremendous advances in our understanding of TR phosphorylation, there has also been a great deal of confusion in the literature, as well as a host of new questions to be answered. This thesis will address the importance of phosphorylation in the nuclear localization of TR. The following introduction will review what is currently known about the thyroid hormone and how TR mediates its functions. What is known about the structure of TR, its subcellular trafficking, and how it acts on target genes will be addressed. Thyroid hormone production and regulation Two of the most important hormones in the body are triiodothyronine (T3 ) and tetraiodothyronine (T4 ), collectively known as the thyroid hormones. T3 is the physiologically active form; T4 is converted to T3 at the target tissue. A tight endocrine pathway regulates thyroid hormone release (Fig. 1). Regulation begins in the brain,