Miracle-dz/UniFAR-FTUs huggingface dataset:
The complete chloroplast genome sequence of Aphanamixis polystachya

Abstract The first complete chloroplast genome (cpDNA) sequence of Aphanamixis polystachya was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,236 bp in length, contains a large single-copy region (LSC) of 87,484 bp and a small single-copy region (SSC) of 18,670 bp, which were separated by a pair of inverted repeats (IR) regions of 27,040 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 37.6%, and the corresponding values of the LSC, SSC, and IR regions are 35.6%, 31.8%, and 42.8%, respectively. Further phylogenomic analysis showed that A. polystachya and Cipadessa cinerascens clustered in a clade in family Meliaceae.
Identification of conserved gene regulatory networks that integrate environmental sensing and growth in the root cambium

Cambium drives lateral growth of stems and roots, contributing to diverse plant growth forms. Root crop is one outstanding example of the cambium-driven growth. To understand its molecular basis, we used radish to generate a compendium of root tissue- and stage-specific transcriptomes from two contrasting inbred lines in root growth. Expression patterns of key cambium regulators and hormone signaling components were validated. Clustering and GO enrichment analyses of radish datasets followed by comparative analysis against the newly established Arabidopsis early cambium data revealed evolutionary conserved stress-response transcription factors that might intimately control the cambium. Indeed, in vivo network made of selected stress-response and cambium regulators indicated ERF-1 as a potential key checkpoint of cambial activities, explaining how the cambium-driven growth is altered in response to environmental changes. Together, this study provides rich information about dynamic gene expression changes along the cambium-driven root growth with future engineering schemes for crop yields.
A Priori Activation of Apoptosis Pathways of Tumor (AAAPT) technology: Development of targeted apoptosis initiators for cancer treatment

Cancer cells develop tactics to circumvent the interventions by desensitizing themselves to interventions. The principle routes of desensitization include a) activation of survival pathways (e.g. NF-kB, PARP) and b) downregulation of cell death pathways (e.g. CD95/CD95L). As a result, it requires high therapeutic dose to achieve tumor regression which, in turn damages normal cells through the collateral damaging effects. Methods are needed to sensitize the low and non-responsive resistant tumor cells including cancer stem cells (CSCs) in order to evoke a better response from the current treatments. Current treatments including chemotherapy can induce cell death only in bulk cancer cells sparing CSCs and cancer resistant cells (CRCs) which are shown to be responsible for high recurrence of disease and low patient survival. Here, we report several novel tumor targeted sensitizers derived from the natural Vitamin E analogue (AMP-001-003). The drug design is based on a novel concept “A priori activation of apoptosis pathways of tumor technology (AAAPT) which is designed to activate specific cell death pathways and inhibit survival pathways simultaneously. Our results indicate that AMP-001-003 sensitize various types of cancer cells including MDA-MB-231 (triple negative breast cancer), PC3 (prostate cancer) and A543 (ling cancer) cells resulting in reducing the IC-50 of doxorubicin in vitro. At higher dose, AMP-001 acts as an anti-tumor agent on its own. The synergy between AMP-001 and doxorubicin could pave a new pathway to use AMP-001 as a neoadjuvant to chemotherapy to achieve a better efficacy and reduced off-target toxicity by the current treatments. Summary Statement A Priori Activation of Apoptosis Pathways of Tumor often referred to as “AAAPT” is a novel targeted tumor sensitizing technology which synergizes with chemotherapy to enhance the treatment efficacy.
Physiological Parameters of Barley as Affected by Stripe Disease

Stripe disease of barley caused by Drechslera graminea (Rabenh.) Shoemaker is a widely distributed disease in many barley grown parts of the world, but it has assumed more importance with the introduction of some new high yielding varieties. The present investigations were undertaken during 2007-08 and 2008-09 crop seasons with a view of elicit information on effect of disease on physiological parameters particularly chlorophyll content, leaf area, photosynthesis, stomatal conductance and transpiration. Stripe infection resulted in reduction of all the physiological parameters at both the stages i.e. 35 days and 50 days after disease appearance.
Natural cryptic epigenetic variation in an embryonic gene regulatory network

Gene regulatory networks (GRNs) that direct animal embryogenesis must respond to varying environmental and physiological conditions to ensure robust construction of organ systems. While GRNs are evolutionarily modified by natural genomic variation, the roles of epigenetic processes in shaping plasticity of GRN architecture are not well-understood. The endoderm GRN in C. elegans is initiated by the maternally supplied SKN-1/Nrf2 bZIP transcription factor; however, the requirement for SKN-1 in endoderm specification varies widely among distinct C. elegans wild isolates owing to rapid developmental system drift driven by accumulation of cryptic genetic variants. We report here that heritable epigenetic factors that are stimulated by transient developmental diapause also underlie cryptic variation in the requirement for SKN-1 in endoderm development. This epigenetic memory is inherited from the maternal germline, apparently through a nuclear, rather than cytoplasmic, signal, resulting in a parent-of-origin effect (POE), in which the phenotype of the progeny resembles that of the maternal founder. The occurrence and persistence of POE varies between different parental pairs, perduring for at least ten generations in one pair. This long-perduring POE requires piwi-piRNA function and the germline nuclear RNAi pathway, as well as MET-2 and SET-32, which direct histone H3K9 trimethylation and drive heritable epigenetic modification. Such non-genetic cryptic variation between wild isolates may provide a resource of additional phenotypic diversity through which adaptation may facilitate evolutionary change and shape developmental regulatory systems.
Altered updating of bodily and spatial representations following tool-use in Complex Regional Pain Syndrome

Distorted representations of the body and peripersonal space are common in Complex Regional Pain Syndrome (CRPS), and might modulate its symptoms (e.g. asymmetric limb temperature). In pain-free people, such representations are malleable, and update when we interact with objects in our environment (e.g. during tool-use). Distortions are also common after immobilisation, but quickly normalise once movement is regained. We tested the hypothesis that people with CRPS have problems updating bodily and spatial representations, which contributes to the maintenance of their distorted representations by preventing normalization. We also explored spatially defined modulations of hand temperature asymmetries, and any influence of updating bodily and spatial representations on this effect. Thirty-six people with unilateral CRPS (18 upper limb, 18 lower limb) and 36 pain-free controls completed tool-use tasks considered to alter body and peripersonal space representations (measured using tactile distance judgements and a visuotactile crossmodal congruency task, respectively). We also tested how the arrangement (crossed, uncrossed) of the hands and tools affected hand temperature. In upper limb CRPS the non-affected arm representation updated normally, but the affected arm representation updated in the opposite to normal direction. A similar pattern was seen in lower limbs CRPS, although not significant. Furthermore, people with CRPS showed more pronounced updating of peripersonal space than the controls. We did not observe any modulation of hand temperature asymmetries by the arrangement of hands or tools. Our findings suggest enhanced malleability of bodily and spatial representations in CRPS, potentially implicating central mechanisms in the aetiology of this condition.
Identifying the best metrics to find the best quality clusters of genes from gene expression data

With the recent advancement of computing technique and data availability in the field of computational biology, it has been a great opportunity for the scientists to find the evolutionary relation among the living beings in terms of their genotypic and phenotypic attributes. Microarray, one of the efficient ways to store the expression level of genes in the living being, can be used to create groups from a set of genes based on their phenotypic information. This information plays an important role in pathway analysis, disease prediction, target identification in drug design and many other important functionalities and applications in biology. However, it has become a great challenge over time to select a particular distance metric to calculate the similarity between the genes. In this work, we have studied 16 possible combinations of metrics to find the groups of similar genes in terms of their expression level by building their phylogenetic relation and keeping the most related genes together. Moreover, we have validated our findings by evaluating the output of the same trials on different data sets. We have found that, for grouping the similar genes together by building a Phylogenetic Tree, Maximum Distance Metric and Average Linkage tends to give the best quality.
Geodina (Pezizomycetes: Wynneaceae) has a single widespread species in tropical America

Geodina salmonicolor is shown to be a synonym of G. guanacastensis, the type and only species of the genus. Comparisons of ITS rDNA sequences of a paratype and two recent collections of G. guanacastensis with published ITS sequences of G. salmonicolor, from the Dominican Republic, show that these are nearly identical. When G. salmonicolor was erected no sequences of the type species were available. Morphological comparisons supports the conspecificity. Details regarding the description of G. salmonicolor are pointed out. A four-gene phylogeny places Geodina and Wynnea as a supported sister group to the rest of the Sarcoscyphaceae. Species in these genera share morphological traits of cyanophobic spore markings, dark angular outer excipular cells that give rise to hairs and the origin of several apothecia from a common basal stalk. Their occurrence on soil rather than on wood or plant material distinguish them from other Sarcoscyphaceae. Based on morphology, phylogenic relationships and trophic interactions we erect a new family, Wynneaceae, for Geodina and Wynnea.
Formal String Instrument Training in a Class Setting Enhances Cognitive and Sensorimotor Development of Primary School Children

This randomized controlled trial shows for the first time that focused musical instrumental practice as compared to traditional sensitization to music provokes robust cognitive and sensorimotor transfer effects. Over the last two years of primary school (10-12-year-old children), sixty-nine children received biweekly musical instruction by professional musicians within the regular school curriculum. The intervention group learned to play string instruments, whereas the control group, peers in parallel classes, was sensitized to music via listening, theory, and some practice. Broad benefits manifested in the intervention group as compared to the control group for working memory, attention, processing speed, cognitive flexibility, matrix reasoning, sensorimotor hand function and bimanual coordination Apparently, learning to play a complex instrument in a dynamic group setting impacts development much stronger than classical sensitization to music. Our results therefore highlight the added value of intensive musical instrumental training in a group setting, encouraging general implementation in public primary schools, better preparing children for secondary school and for daily living activities. Highlights - Music practice produces multiple cognitive transfer effects in school children - Making music causes stronger cognitive benefits than sensitization to music - Music practice in a class setting improves executive functions and abstract thinking - Playing string instruments enhances fine manual dexterity and bimanual coordination
Enhanced Secretion of Biologically Active Murine Interleukin-12 by Lactococcus lactis

The novel signal peptide SLPmod was used for the secretion of murine interleukin-12 (mIL-12) by Lacto- coccus lactis . A >4-fold increase in secretion was observed when SLPmod was used instead of the Usp45-derived secretion signal. Oral delivery of this cytokine using the autoinducible host L. lactis FI5876 utilizing SLPmod resulted in a signiﬁcant increase in mIL-12 plasma levels in mice. Many heterologous proteins and peptides have been suc-cessfully expressed in Lactococcus lactis for different biotech-nological applications. Despite its lack of invasiveness, L. lactis is able to deliver heterologous antigens and cytokines to the systemic and mucosal immune system (11). Cytokine mucosal delivery is dependent upon its release into the mucosa when L. lactis cells are in contact with the mucosa-associated lymphoid tissue. The secretion of recombinant cytokines has generally involved fusion of the relevant protein to the signal peptide of the abundant Usp45 protein (1, 13, 14, 15); however, poor secretion efﬁciency of the large murine cytokine interleukin-12 (mIL-12) was observed (1,
Asthma update: recommendations for diagnosis, treatment and management

Asthma is a chronic inflammatory disorder of the airways associated with a high level of morbidity. In the UK, much of the responsibility for asthma management rests in primary care. Diagnosing asthma requires careful clinical history taking and support for the diagnosis, using spirometry and measures of peak expiratory flow rates. A stepwise approach should be used in the treatment of asthma. The main strategy for reducing the burden of asthma is a shift in emphasis from acute management to long-term care and supported self-management. Structured asthma reviews should be undertaken by competent professionals, using a patient-centred approach that enables self-management and addresses symptom control, inhaler technique and adherence.
LA SUAVIDAD DE LA CARNE: IMPLICACIONES FÍSICAS Y BIOQUÍMICAS ASOCIADAS AL MANEJO Y PROCESO AGROINDUSTRIAL 1

Meat tenderness: Physical and biochemical facts related to agricultural and industrial process. Nowadays, the problem of meat tenderness is of great concern among producers because this parameter has become the most important criteria upon which consumers judge meat quality. This problem is especially critical when it is also a proven fact that one of every four sensorial experiences of the consumer is unsatisfactory when eating meat. This paper overviews the main aspects determining meat tenderness such has structural and chemical composition of meat, muscular contraction, biochemical postmortem changes (rigor mortis and meant aging) and the general effects caused by industrial processing when cooking and freezing. General methods for improving meat tenderness and the biochemical activity of the calcium ion dependent papain like cisteine proteases (CALPAIN) are also reviewed.
Complete mitochondrial genome sequence and phylogenetic analysis of Anisarchus medius (Reinhardt, 1837)

Abstract Anisarchus medius (Reinhardt, 1837) has been identified as a target species for investigating the effects of climate change on population patterns in coastal Arctic ecosystems. The complete mitochondrial genome of the Anisarchus medius was first sequenced in this study. The mitochondrial genome was sequenced with 16,524 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. All the protein-coding genes employed ATG as the start codon except COI using GTG. Three stop codons were observed in the protein-coding genes, including TAA, TAG and T. In addition, phylogenetic tree can provide further genetic analysis for this important species.
A study of tunable optical filters based on micro-ring structures

A tunable optical filter based on micro-ring structure is studied in the paper. The normalized energy expression is derived at the output port of the filter. Some factors, such as losses and coupling coefficient, are given to valuate the performance of the filter. The change of waveguide's effective refractive index is calculated to implement the tuning characteristics of the filter. The influence of refractive index's change on the free spectrum range (FSR) and the full width at half maximum (FWHM) of the filter is small, so the tuning method of changing refraction index is feasible. Structures using electrode thermal pad and p-i-n respectively are brought forwards to realize the tuning characteristics of the filter.
Next Generation Sequencing for Measurable Residual Disease Detection in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is the most common form of acute leukemia and generally associated with a poor prognosis. For both children and adults, the treatment is based on chemotherapy. Allogeneic hematopoietic stem cell transplant (alloHCT) is reserved for patients with intermediate or high risk of relapse, due to its associated risks. The initial response to treatment is a very important prognostic factor. The response is determined by the amount of residual leukemic cells in the bone marrow during treatment – measurable residual disease (MRD). The methods currently used for MRD analysis have drawbacks in terms of sensitivity and/or applicability. The work included in this thesis focused on the development, validation and investigation of the clinical applicability of a next generation sequencing based strategy for MRD analysis. The strategy was based on identification of leukemiaspecific mutations, present at diagnosis and suitable for MRD, using exome sequencing. These mutations were subsequently quantified in follow-up samples using an amplicon based sequencing method, targeted deep sequencing. The study samples comprised of blood and bone marrow collected at diagnosis, during followup, and at relapse from adults and children with AML. As proof-of-principle, we showed in paper I that exome-sequencing could be used for identification of leukemia-specific mutations at diagnosis and that targeted deep sequencing of these mutations in follow-up samples could be used for patient-tailored MRD analysis. Paper II showed that targeted deep sequencing of single nucleotide variations (SNVs) for patient-tailored MRD analysis was accurate with good reproducibility and sensitivity meeting the consensus criterion for molecular MRD analysis (<0.1% leukemic cells). Paper III showed that measurable levels of recurrent NPM1 insertions after alloHCT, analyzed with targeted deep sequencing were associated with higher risk of relapse and worse overall survival as compared to non-detectable levels. Paper IV showed that targeted deep sequencing of SNVs for patient-tailored MRD analysis in peripheral blood could detect increasing mutation burden before hematological relapse in children. In conclusion, the results show that targeted deep sequencing of leukemia-specific mutations is an applicable tool for MRD analysis, enabling molecular surveillance for virtually all AML patients. The method could provide better support for treatment decisions and thereby chances for improved prognosis in AML.
Morphometry and burst swimming in six continental fish species from Costa Rica

Introduction: Current research of fish locomotion is focused on creating better underwater vehicles and how environmental stress factors modify swimming. Objective: To study the relation of morphometric characteristics with burst swimming in six representative species of continental fishes from Costa Rica. Methods: We measured total length, standard length, height and area of the tail of 38 individuals from six species. We used a Kruskall-Wallis test and a Boxplot graphic to compare species; and a PCA test to identify body variables that influence swimming. A Non-Metric Dimensional Scaling (NMDS) test was done for species and position in the water column. Results: The fastest swimming corresponded to A. nigrofasciata (9,29cm/s), while S. salvini (1,65cm/s) was the slowest. Burst swimming speed is influenced by body size and tail type, and differed with position in the water column, being surface species the fastest. Conclusions: Morphological and ecological characteristics determine differences in burst swim.
Pulmonary rehabilitation in patients with chronic obstructive pulmonary disease

All patients with chronic obstructive pulmonary disease(COPD) may benefit from exercise training as a result of ameliorated dyspnea,improved exercise tolerance and increased health-associated quality of life.This has enabled an ex-tended application from steady state COPD to acute exacerbation.Pulmonary rehabilitation(PR) program encompasses as-sessment,exercise training,education,nutritional intervention and psychosocial support,where exercise training is most criti-cal.PR program based on local conditions is preferable,and family-based activity or exercising in a sustainable fashion is to be encouraged.The knowledge and skills of PR should be popularized among general practitioners on the basis of communi-ties.It should also be our nationwide strategy to promote PR program via integration of traditional Chinese medicine and western medicine.
Influences of ecology and climate on the distribution of restricted, rupicolous reptiles in a biodiverse hotspot

ABSTRACT Understanding the role of climatic and ecological factors in limiting species to their distributions is becoming ever more important in a world where anthropogenic activities are increasingly threatening species persistence. Species with restricted distributions are often poorly known even though they may be most vulnerable to extinction. We investigated the influences of climate and ecology on the distribution of five understudied, endemic, rupicolous reptiles from the Soutpansberg Mountains in South Africa. Using Maxent, we developed ecological niche models that were used to provide baseline insights into the factors delimiting these species distributions. Results indicated that most species were limited by climatic factors, with the average temperature of the coolest quarter having the most influence on the majority of the species, where they were limited to areas with cooler temperatures. This suggests that they may be negatively affected by climate change in the future. Distribution maps revealed that there were no strong interspecific interactions influencing the distributions between the species investigated and identified potential new localities for two species. There was high endemic richness located in the western Soutpansberg and this is likely to have been driven by past climatic and erosion events. Overall this study highlighted that performing environmental niche models on understudied species can provide essential, baseline information on which to drive future research.