Miracle-dz/UniFAR-FTUs huggingface dataset:
Tangent normalization for somatic copy-number inference in cancer genome analysis

MOTIVATION Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas (TCGA), the Broad Institute Genome Characterization Center developed the Tangent normalization method to generate copy-number profiles using data from single-nucleotide polymorphism (SNP) arrays and whole-exome sequencing (WES) technologies for over 10,000 pairs of tumors and matched normal samples. Here, we describe the Tangent method, which uses a unique linear combination of normal samples as a reference for each tumor sample, to subtract systematic errors that vary across samples. We also describe a modification of Tangent, called Pseudo-Tangent, which enables denoising through comparisons between tumor profiles when few normal samples are available. RESULTS Tangent normalization substantially increases signal-to-noise ratios (SNRs) compared to conventional normalization methods in both SNP array and WES analyses. Tangent and Pseudo-Tangent normalizations improve the SNR by reducing noise with minimal effect on signal and exceed the contribution of other steps in the analysis such as choice of segmentation algorithm. Tangent and Pseudo-Tangent are broadly applicable and enable more accurate inference of SCNAs from DNA sequencing and array data. AVAILABILITY Tangent is available at https://github.com/broadinstitute/tangent and as a Docker image (https://hub.docker.com/r/broadinstitute/tangent). Tangent is also the normalization method for the copy-number pipeline in Genome Analysis Toolkit 4 (GATK4). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
LcNAC13 Physically Interacts with LcR1MYB1 to Coregulate Anthocyanin Biosynthesis-Related Genes during Litchi Fruit Ripening

Anthocyanin accumulation is crucial for the development of quality for most fruit. The mechanism underlying the regulation of anthocyanin biosynthesis by transcription factors in litchi fruit remains largely unknown. In this study, we isolated one NAC (NAM, ATAF1/2 and CUC2) TF gene, LcNAC13. Expression of LcNAC13 was upregulated as ripening proceeded, followed by the accumulation of anthocyanins. Electrophoretic mobility shift assay (EMSA) and transient expression assay showed that LcNAC13 could negatively regulate the expression of anthocyanin biosynthesis-related genes, including LcCHS1/2, LcCHI, LcF3H, LcF3’H, LcDFR, and LcMYB1. Furthermore, LcR1MYB1, as one R1-MYB type MYB, was identified to physically interact with LcNAC13 and reverse the effect of LcNAC13. Taken together, these results suggested that LcNAC13 and LcR1MYB1 may act together to antagonistically regulate anthocyanin biosynthesis during litchi fruit ripening, which helps to provide new insights into the regulatory networks of anthocyanin biosynthesis.
Expanded potential for recombinant tri-segmented LCM viruses: 1 protein production, antibody production and in vivo assessment of 2 biological function of genes of interest

: 2 The recombinant engineering of tri-segmented LCMV to express two genes of interest 3 was recently reported. We used this technology to efficiently express GFP and the 4 immunoregulatory gene IL-10 in vitro, assess IL-10 function in vivo during viral 5 meningitis and generate specific, robust monoclonal antibody responses to IL-10 . 6 Tripartite viruses were attenuated in wildtype and TLR7-/- mice. However, IFNAR1-/- mice 7 sustained systemic viral replication when 2 nucleotide substitutions from a persistent 8 LCMV variant were present. These findings demonstrate the utility of tripartite LCMV in 9 vitro and in vivo to study genes in the context of a well-defined model system. 10 11 Infection of the mouse, the natural host, with the prototypic arenavirus lymphocytic 13 choriomeningitis virus (LCMV) has served as one of the most fruitful models for the investigation 14 of acute and persistent viral infections (6, 17). LCMV is a natural pathogen of rodents which 15 can replicate robustly both in vitro and in vivo. A major boon to the LCMV model is that two 16 similar genetic variants whose biology is dramatically different can be directly compared. This 17 difference in biological activity of the non-persistent LCMV Armstrong (Arm) and the persistent 18 LCMV Clone 13 (Cl13) is dependent on only 2 amino acid differences: Arm/Cl13, GP260 19 (glycoprotein) Phe/Leu, L1079 (polymerase) Gln/Lys. Arm is cleared within one week by the 20 host while Cl13 persists several months to potentially the life of the mouse (12, 23). This 21 difference in clearance is inversely correlated with the cytotoxic CD8+ T lymphocyte (CTL) 22 response against these two variants. Therefore, LCMV Arm infection is rapidly cleared in the 23 presence of a robust host CTL response. In contrast, LCMV Cl13 infection is persistent and 24 accompanied by a poorly functional CTL response (reviewed in (16)).
Reconstruction of Viscosity Maps in Ultrasound Shear Wave Elastography

Change in viscoelastic properties of biological tissues may often be symptomatic of dysfunction that can be correlated with tissue pathology. Shear wave (SW) elastography is an imaging method mainly used to assess stiffness but with the potential to measure viscoelasticity of biological tissues. This can enable tissue characterization and, thus, can be used as a marker to improve the diagnosis of pathological lesions. In this study, a frequency-shift method-based framework is presented for the reconstruction of viscosity by analyzing the spectral properties of acoustic radiation force-induced SWs. The aim of this study was to investigate the feasibility of viscosity reconstruction maps in homogeneous as well as heterogeneous samples. Experiments were performed in four in vitro phantoms, two ex vivo porcine liver samples, two ex vivo fatty duck liver samples, and one in vivo fatty goose liver. Successful viscosity maps were reconstructed in homogeneous and heterogeneous phantoms with embedded mechanical inclusions having different geometries. Quantitative values of viscosity obtained for two porcine liver tissues, two fatty duck liver samples, and one goose fatty liver were (mean ± SD) 0.61 ± 0.21 and 0.52 ± 0.35, 1.28 ± 0.54 and 1.36 ± 0.73, and 1.67 ± 0.70 Pa.s, respectively.
Using a Network of Untrusted Computers for Secure Computing

—This paper deﬁnes a new problem in distributed computing: How to securely compute one’s own problem using a network of untrusted computers? A theoretic solution of the problem is also presented. All secret input data and a secret result are known only by the initiator of the computation. Other computers are used only to carry out the computation using their computer time and memory. The communication can be eavesdropped, and any of untrusted computers can arbitrarily tamper the computation, assuming that no cooperation between untrusted computers occurs. This problem is different from a well-known multiparty distributed computation problem. Here, only one party has all the secret data. The computation is carried out on untrusted computers. An untrusted computer has access to only a small part of secret. Provided no or only a few untrusted computers are cooperating, the secret – input data, and the result of the computation – is not revealed.
Epicuticular Wax Columns in Cultivated Brassica Species

Three different types of epicuticular wax columns were found in Brassica species with a chromosome number (n) ̄ 9: long columns (LC), short columns (SC) and netted columns (NC). LC were found in B. incana and B. rupestris. SC were found in B. illosa, B. macrocarpa, B. cretica, B. hilarionis and also in B. montana. B. insularis columns were intermediate. NC waxes were found in B. oleracea and its close allies B. alboglabra and B. bourgeaui. Samples of B. rapa (n ̄ 10) and B. nigra (n ̄ 8) examined did not show any wax columns but their amphidiploids with B. oleracea (B. napus and B. carinata, respectively) seemed to inherit the NC type of wax present in B. oleracea. # 1999 Annals of Botany Company
Stochastic Inequality Constrained Closed-loop Model Predictive Control: With Application To Chemical Process Operation

Dit proefschrift is goedgekeurd door de promotor: Services. Thank you all for a wonderful cooperation, it has been an exiting time and we can look back upon a fantastic experience! Summary The chemical process industries are forced by the ever increasing global market competition to improve their efficiency of operation. Because of the large investment needed to build new plants it is of great interest to change the way existing plants are operated. It is therefore desirable that a plant produces a wider variety of products or that it can be switched faster between different product specifications or operation modes. To meet the requirements of the market, research and development are a necessity to innovate products, production processes and operational strategies. In almost all cases, plant and process models of varying complexity play an important role in analysis of technological problems and synthesis of solutions. Models formalize the current status of our system knowledge, point out weaknesses during validation, direct new research, are good carriers of knowledge over large time spans and they alow multidisciplinary teamwork between engineers and scientists far beyond individual capabilities. Model predictive control (MPC) has proved to be a successful example of model use for improvement of process operation. Typically it provides the ability for multi-variable process control in which many process constraints can be included. The large number of technology vendors and successful implementations of MPC over the last twenty years points out that MPC has matured from an engineering point of view, however, the lack of predictability of the closed-loop behavior shows that it is far from theoretical maturity. The main structural limitation of MPC is that it is an open-loop predictive control method with the paradoxical property that neither future disturbances nor future measurements are considered. The implicit feedback derived from receding horizon control is typically hard to analyze and makes systematic tuning of inequality constrained MPC impossible without extensive simulation efforts. It is unknown how to choose controller parameters to influence the process sensitivity, which is a basic characteristic of any systematic feedback design method. Hence, there are no simple handles to design a predictive controller for desired closed-loop performance, to find optimal safeguarding from constraint violation or to construct optimal constraint pushing schemes. The reality of modern advanced process control, where inequality constraints and stochastic disturbances play a central role, points out that there is a fundamental need to reformulate the …
of amygdala-expressed genes associated with autism spectrum disorder.

Background: Studies of individuals with autism spectrum disorder (ASD) have revealed a strong multigenic basis with the identification of hundreds of ASD susceptibility genes. ASD is characterized by social deficits and a range of other phenotypes, implicating complex genetics and involvement of a variety of brain regions. However, how mutations and mis-expression of select gene sets are associated with the behavioral components of ASD remains unknown. We reasoned that for genes to be associated with ASD core behaviors they must be: (1) expressed in brain regions relevant to ASD social behaviors and (2) expressed during the ASD susceptible window of brain development. Methods: Focusing on the amygdala, a brain region whose dysfunction has been highly implicated in the social component of ASD, we mined publicly available gene expression databases to identify ASD-susceptibility genes expressed during human and mouse amygdala development. We found that a large cohort of known ASD susceptibility genes is expressed in the developing human and mouse amygdala. We further performed analysis of single-nucleus RNA-seq (snRNA-seq) data from microdissected amygdala tissue from five ASD and five control human postmortem brains ranging in age from 4 to 20 years to elucidate cell type specificity of amygdala-expressed genes and their dysregulation in ASD. Results: Our analyses revealed that of the high-ranking ASD susceptibility genes, 80 are expressed in both human and mouse amygdala during fetal to early postnatal stages of development. Our human snRNA-seq analyses revealed cohorts of genes with altered expression in the ASD amygdala postnatally, especially within excitatory neurons, with dysregulated expression of seven genes predicted from our datamining pipeline. Limitations: We were limited by the ages for which we were able to obtain human tissue; therefore, the results from our datamining pipeline approach will require validation, to the extent possible, in human tissue from earlier developmental stages. Conclusions: Our pipeline narrows down the number of amygdala-expressed genes possibly involved in the social pathophysiology of ASD. Our human single-nucleus gene expression analyses revealed that ASD is characterized by changes in gene expression in specific cell types in the early postnatal amygdala.
White blood cell recognition via geometric features and naïve bays classifier

Blood assessments are of the maximum crucial and frequently asked medical examinations. A manual microscopic evaluation must be done while a blood pattern is suspicious of abnormality. This manual technique is tedious, time ingesting and subjective. Automating microscopic blood type is appropriate to assist the pathologists to hurry-up and induce the consequences accuracy. Segmentation is the primary and common step in computerized WBCs category. On this paper, have been presented a powerful method for automated WBCs nuclei segmentation. The technique is based on gray scale contrast enhancement and then using Otsu thresholding tech-nique to segment WBCs. There are four features have found to extract the data from the segmented image. These features are (Area, Perim-eter, diameter, Circularity. Then these data was classified using Naive Bayes classifier under weka program. The approach is examined on 260 blood pictures. The class overall performance is quantitatively evaluated at the take a look at set to be 97,1 %. This over-all performance is excessive in comparison to other related work done at the identical dataset.
Genetic Effects of LPIN1 Polymorphisms on Milk Production Traits in Dairy Cattle

Our initial RNA sequencing work identified that lipin 1 (LPIN1) was differentially expressed during dry period, early lactation, and peak of lactation in dairy cows, and it was enriched into the fat metabolic Gene Ontology (GO) terms and pathways, thus we considered LPIN1 as the candidate gene for milk production traits. In this study, we detected the polymorphisms of LPIN1 and verified their genetic effects on milk yield and composition in a Chinese Holstein cow population. We found seven SNPs by re-sequencing the entire coding region and partial flanking region of LPIN1, including one in 5′ flanking region, four in exons, and two in 3′ flanking region. Of these, four SNPs, c.637T > C, c.708A > G, c.1521C > T, and c.1555A > C, in the exons were predicted to result in the amino acid replacements. With the Haploview 4.2, we found that seven SNPs in LPIN1 formed two haplotype blocks (D′ = 0.98–1.00). Single-SNP association analyses showed that SNPs were significantly associated with milk yield, fat yield, fat percentage, or protein yield in the first or second lactation (p = < 0.0001–0.0457), and only g.86049389C > T was strongly associated with protein percentage in both lactations (p = 0.0144 and 0.0237). The haplotype-based association analyses showed that the two haplotype blocks were significantly associated with milk yield, fat yield, protein yield, or protein percentage (p = < 0.0001–0.0383). By quantitative real-time PCR (qRT-PCR), we found that LPIN1 had relatively high expression in mammary gland and liver tissues. Furthermore, we predicted three SNPs, c.637T > C, c.708A > G, and c.1521C > T, using SOPMA software, changing the LPIN1 protein structure that might be potential functional mutations. In summary, we demonstrated the significant genetic effects of LPIN1 on milk production traits, and the identified SNPs could serve as genetic markers for dairy breeding.
After Respiratory Syncytial Virus Challenge Virus G Glycoprotein-Induced Eosinophilia IL-13 Is Sufficient for Respiratory Syncytial

Although well studied in settings of helminth infection and allergen sensitization, the combined contributions of IL-4 and IL-13 and their signaling pathways in models of viral pathogenesis have not been reported. Using a murine model of respiratory syncytial virus (RSV) infection, we evaluated the contribution of IL-13, alone and in conjunction with IL-4, during immunization with recombinant vaccinia virus expressing RSV G glycoprotein (vvGs) or with formalin-inactivated RSV (FI-RSV). We showed that both IL-4 and IL-13 activity must be inhibited to modulate G-speciﬁc responses resulting in severe RSV-induced disease. Inhibition of IL-4 or IL-13 activity alone had minimal impact on disease in vvGs-immunized mice. However, treatment of IL-4-deﬁcient mice with IL-13Ra during vvGs immunization reduced IL-5, IL-13, and eotaxin production and pulmonary eosinophilia after RSV challenge. In contrast, FI-RSV-induced immune responses were diminished when either IL-4 or IL-13 activity was blocked. After RSV challenge, these type 2 T cell responses were also diminished in vvGs-primed IL-4R (cid:1) -deﬁcient mice. Our data suggest that secreted vvGs uses mechanisms requiring signaling through the IL-4R (cid:1) -chain by either IL-4 or IL-13 for induction of eosinophilia and is the ﬁrst description of the relative contributions of IL-4, IL-13, and their receptors in viral pathogenesis. The Journal of Immunology, 2003, 170: 2037–2045.
Prevalence of depressive symptoms and its associated factors among healthy community‐dwelling older adults living in Australia and the United States

This study was conducted to estimate prevalence rates and factors associated with depressive symptoms indexed by the Centre for Epidemiological Studies‐Depression (CES‐D‐10) score in a large sample of community‐dwelling healthy older adults from Australia and the United States. Convergent and divergent validity of the CES‐D‐10 were also examined.
TRY – A Global Database of Plant Traits The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, inﬂuence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69000 out of the world’s 300000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A ﬁrst data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspeciﬁc), but signiﬁcant intraspeciﬁc variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than ﬁxed parameter values. The improved availability of plant trait data in the uniﬁed global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.
Response Of Wheat To Foliar Application Of Iron At Different Growth Stages

: The experiment was conducted in Agriculture filed of Lovely Professional University, Jalandhar with wheat variety viz. HD 3086 to know the effect of foliar application of iron on nitrogen uptake and its combined impact on growth and yield of wheat. The plot design was RCBD with three replications and eight treatments. T1: Control (without fertilizer), T2: Control (with RDF), T3: RDF+ FeSO4 + Urea (at flowering stage), T4: RDF + FeSO4 (at flowering stage), T5: RDF + FeSO4 + Urea (at milking stage), T6: RDF+ FeSO4 (at milking stage), T7: RDF+ FeSO4 + Urea (at pre-maturity), T8: RDF + FeSO4 (at pre-maturity). The observed parameters plant height, length of spike, number of tiller, effective number of tillers, test weight of grain, number of spike lets per spike, number of grain per spike were taken at regular interval of 60, 90 ,120 DAS. In case of yield parameter the maximum test weight was recorded in T3 (49.75) and minimum was in T3 (45.09). For harvest index maximum value was recorded in T3 (45.42) and minimum in T1 (43.49). According to result, better growth and yield parameter was observed in treatments T3 due to foliar spray of iron and urea. Iron acts as catalyst and regulate many enzymatic activities which helps in better growth and increase in the yield, whereas urea is a source of nitrogen and in plants growth nitrogen play very important role because it helps in the synthesis of chlorophyll and many other activities.
Methods of nutrition assessment in patients with head and neck cancer

The head and neck tumors constitute large and complex group. The incidence of malnutrition in patients with head and neck tumors averages from 65 to 75%. That gives them the third place behind the pancreas and stomach tumors. The correct assessment of nutrition helps to recognize the degree of malnutrition and has influence on nutrition care and therapy. The dietary interview, anthropometric methods, bioimpedance and labolatory tests are used in evaluation of nutritional state in various scale. The degree of malnutrition has an influence on number of complications and ex tends the period of hospitalization, thus the methods evaluating the nutrition are commonly used in clinical practice. The objective of this article is to introduce the readers to the methods of nutrition assessment in patients with head and neck cancer.