Miracle-dz/UniFAR-FTUs huggingface dataset:
Comprehensive genomic analysis of human cancer Comprehensive genomic profiling by NGS

Comprehensive genomic profiling using next-generation sequencing technologies provides insights into understanding the genomic architecture of human cancer. This new understanding of the cancer genome allows us to identify many more genomic alterations occurring within tumors than before, some of which could be potential therapeutic targets throughmolecular targeted agents. Currently, a large number of molecular targeted agents are being developed, and consequently, cancer treatment is rapidly shifting from empiric therapy employing cytotoxic anticancer drugs to genotypedirected therapy using molecular targeted agents. In current daily clinical practice, hotspot-based single-gene assays that detect RAS mutations in colorectal cancer or EGFR mutations in non-small cell lung cancer are widely used to identify variants. However, it is becoming evident that more comprehensive genomic analysis is crucial in identifying the patient population that may benefit from molecular targeted therapy and the accelerated development of novel drugs for early clinical trials. For these purposes, an increasing number of gene panel-based targeted sequencing is commercially available in clinical practice from sequencing companies. Despite several challenges in implementing this approach, comprehensive genomic profiling and identification of actionable mutations is likely to become one of the standard options in the management of cancer in the near future. The use of clinical sequencing has the potential to usher a new era in precision medicine for cancer diagnosis and treatment. In this review, we discuss the application of comprehensive genomic profiling using next-generation sequencing technologies in clinical oncology and address the current challenges for its implementation.
Replicating Brain’s Resting State Functional Connectivity Network Using a Multi-Factor Hub-Based Model

 Abstract — The brain’s functional connectivity while temporally non-stationary does express consistency at a macro spatial level. The study of stable resting state connectivity patterns hence provides opportunities for identification of diseases if such stability is severely perturbed. A mathematical model replicating the brain’s spatial connections will be useful for understanding brain’s representative geometry and complements the empirical model where it falls short. Empirical computations tend to involve large matrices and become infeasible with fine parcellation. However, the proposed analytical model has no such computational problems. To improve replicability, 92 subject data are obtained from two open sources. The proposed methodology, inspired by financial theory, uses multivariate regression to find relationships of every cortical region of interest (ROI) with some pre-identified hubs. These hubs acted as representatives for the entire cortical surface. A variance-covariance framework of all ROIs is then built based on these relationships to link up all the ROIs. The result is a high level of match between model and empirical correlations in the range of 0.59 to 0.66 after adjusting for sample size; an increase of almost forty percent. More significantly, the model framework provides an intuitive way to delineate between systemic drivers and idiosyncratic noise while reducing dimensions by more than 30 folds, hence, providing a way to conduct attribution analysis. Due to its analytical nature and simple structure, the model is useful as a standalone toolkit for network dependency analysis or as a module for other mathematical models.
BUT System Description for DIHARD Speech Diarization Challenge 2019

This paper describes the systems developed by the BUT team for the four tracks of the second DIHARD speech diarization challenge. For tracks 1 and 2 the systems were based on performing agglomerative hierarchical clustering (AHC) over x-vectors, followed by the Bayesian Hidden Markov Model (HMM) with eigenvoice priors applied at x-vector level followed by the same approach applied at frame level. For tracks 3 and 4, the systems were based on performing AHC using x-vectors extracted on all channels.
S 100 A 9 Interaction with TLR 4 Promotes Tumor Growth

By breeding TRAMP mice with S100A9 knock-out (S100A9) animals and scoring the appearance of palpable tumors we observed a delayed tumor growth in animals devoid of S100A9 expression. CD11b S100A9 expressing cells were not observed in normal prostate tissue from control C57BL/6 mice but were readily detected in TRAMP prostate tumors. Also, S100A9 expression was observed in association with CD68 macrophages in biopsies from human prostate tumors. Delayed growth of TRAMP tumors was also observed in mice lacking the S100A9 ligand TLR4. In the EL-4 lymphoma model tumor growth inhibition was observed in S100A9 and TLR4, but not in RAGE animals lacking an alternative S100A9 receptor. When expression of immune-regulating genes was analyzed using RT-PCR the only common change observed in mice lacking S100A9 and TLR4 was a down-regulation of TGFb expression in splenic CD11b cells. Lastly, treatment of mice with a small molecule (ABR-215050) that inhibits S100A9 binding to TLR4 inhibited EL4 tumor growth. Thus, S100A9 and TLR4 appear to be involved in promoting tumor growth in two different tumor models and pharmacological inhibition of S100A9-TLR4 interactions is a novel and promising target for anti-tumor therapies. Citation: Källberg E, Vogl T, Liberg D, Olsson A, Björk P, et al. (2012) S100A9 Interaction with TLR4 Promotes Tumor Growth. PLoS ONE 7(3): e34207. doi:10.1371/ journal.pone. 0034207 Editor: Irina V. Lebedeva, Enzo Life Sciences, Inc., United States of America Received September 14, 2011; Accepted February 28, 2012; Published March 28, 2012 Copyright: 2012 Källberg et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: TL, PW and AB are supported by grants from the Swedish Cancer Foundation and the Swedish Science Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation, or preparation of the manuscript. Competing Interests: The authors have read the journals policy and have the following conflicts: TL is a part time employee and DL, AO and PB are full time employees of Active Biotech that develops ABR-215050 for the treatment of prostate cancer. FI has a research grant from Active Biotech. This does not alter the authors’ adherence to all the PLoS ONE policies on sharing data and materials. * E-mail: tomas.leanderson@med.lu. se
Mycobacterium tuberculosis PE 9 protein has high activity binding peptides which inhibit target cell invasion Running title : PE 9 peptides inhibit human cell infection

PE/PPE proteins are involved in several processes during Mycobacterium tuberculosis (Mtb) infection of target cells; studying them is extremely interesting as they are the only ones from the Mycobacterium genus, they abound in pathogenic species such as Mtb and their function remains yet unknown. The PE9 protein (Rv1088) was characterised, the rv1088 gene was identified by PCR in Mtb complex strains and its expression and localisation on mycobacterial surface was confirmed by Western blot and immunoelectron microscopy. Bioinformatics tools were used for predicting PE9 protein structural aspects and experimental study involved the circular dichroism of synthetic peptides. The peptides were tested in binding assays involving U937 and A549 cells; two high activity binding peptides (HABPs) were found for both cell lines (392261 MSYMIATPAALTAAATDIDGI 21 and 39232125 YQRHFGTGGQPEFRQHSEHRR 144 ), one for U937 (39231104 YAGAGRRQRRRRSGDGQWRLRQ 124 ) and one for A549 (3923083 YGTGVFRRRRGRQTVTAAEHRA 103 ). HABP 39232 inhibited mycobacterial entry to A549 cells (~70%) and U937 cells (~50%), peptides 39226 and 39231 inhibited entry to U937 cells (~60% and 80%, respectively) and peptide 39230 inhibited entry to A549 cells (~60%). This emphasised HABPs’ functional importance in recognition between Mtb H37Rv and target cell receptors. These peptide sequences could be involved in invasion and were recognised by the host’s immune system, thereby highlighting their use when designing an efficient anti-tuberculosis multiantigenic vaccine.
Phytoremediation Potential of Three Species of Macrophytes for Nitrate in Contaminated Water

Three species of aquatic plants (Scirpus validus, Phragmites australis and Acorus calamus) were used as experimental materials to study their capacity to purify contaminated water and their effects on water pH and dissolved oxygen (DO). The water was contaminated with different concentrations of nitrate (5 mg/L, 15 mg/L and 25 mg/L). The results indicated that the concentration of nitrate, species of aquatic plant and their interaction significantly impacted denitrification (P = 0.00). Under the same concentrations, the three species of aquatic plants provided varying degrees of purification. Acorus calamus provided effective purification under all three concentrations of nitrate wastewater, with removal percentages of 87.73%, 83.80% and 86.72% for nitrate concentrations of 5 mg/L, 15 mg/L and 25 mg/L, respectively. In terms of the purification ability by unit fresh weight, Acorus calamus exhibited the worst purification capacity, whereas the capacities of Scirpus validus and Phragmites australis were higher. The purification capacity of Scirpus validus for the three concentrations was as follows: 0.08 mg/(L·g FW), 0.29 mg/(L·g FW), and 0.51 mg/(L·g FW). The capacity of Phragmites australis was 0.07 mg/(L·g FW), 0.25 mg/(L·g FW), and 0.53 mg/(L·g FW). The capacity of Acorus calamus was 0.04 mg/(L·g FW), 0.12 mg/(L·g FW), and 0.21 mg/(L·g FW). Under increased concentrations of nitrate, the three species of aquatic plants exhibited various degrees of increased purification capacity. Under the different concentrations of nitrate, the three species exhibited the same trends with respect to water pH and DO, increasing first and then falling. The pH remained at approximately 7.5, and the DO fell to 4.0 mg/L. A comprehensive analysis reveals that Acorus calamus provides excellent nitrate purification, although by unit fresh weight, both Scirpus validus and Phragmites australis provide superior purification capacity.
UV-TO-FIR ANALYSIS OF SPITZER/IRAC SOURCES IN THE EXTENDED GROTH STRIP. II. PHOTOMETRIC REDSHIFTS, STELLAR MASSES, AND STAR FORMATION RATES

Based on the ultraviolet to far-infrared photometry already compiled and presented in a companion paper (Paper I), we present a detailed spectral energy distribution (SED) analysis of nearly 80,000 IRAC 3.6 + 4.5 μm selected galaxies in the Extended Groth Strip. We estimate photometric redshifts, stellar masses, and star formation rates (SFRs) separately for each galaxy in this large sample. The catalog includes 76,936 sources with [3.6] ⩽ 23.75 (85% completeness level of the IRAC survey) over 0.48 deg2. The typical photometric redshift accuracy is Δz/(1 + z) = 0.034, with a catastrophic outlier fraction of just 2%. We quantify the systematics introduced by the use of different stellar population synthesis libraries and initial mass functions in the calculation of stellar masses. We find systematic offsets ranging from 0.1 to 0.4 dex, with a typical scatter of 0.3 dex. We also provide UV- and IR-based SFRs for all sample galaxies, based on several sets of dust emission templates and SFR indicators. We evaluate the systematic differences and goodness of the different SFR estimations using the deep FIDEL 70 μm data available in the Extended Groth Strip. Typical random uncertainties of the IR-bases SFRs are a factor of two, with non-negligible systematic effects at z ≳ 1.5 observed when only MIPS 24 μm data are available. All data products (SEDs, postage stamps from imaging data, and different estimations of the photometric redshifts, stellar masses, and SFRs of each galaxy) described in this and the companion paper are publicly available, and they can be accessed through our the Web interface utility Rainbow-navigator.
reparation , characterization of 99 mTc-folic acid / chitosan anostructure and their biodistribution study in quail

Chitosan (CS) of low molecular weight is prepared using -irradiation method in presence of H2O2 as oxidizing agent. The chemical treatment of folic acid (FA) with low molecular weight CS is carried out to prepare FACS complex based on the reaction between NH2 group of CS and –COOH group of FA. The structure and properties of FACS complex was characterized by FT-IR, 1H NMR, UV, SEM, TEM, DLS and XRD analyses. TEM and DLS results showed that FACS complex has nanostructure and the mean size of particles was unimodal with average diameters in the range of 165–252 nm. Radiolabeling of FACS complex (99mTc-FACS) was done with Technetium–99 m (99mTc). The optimum conditions of labeling were investigated. The labeling yield was 85% at pH = 6 and 30 min reaction time. The effect of time on the stability of 99mTc-FACS complex was studied and the results revealed that it is stable up to 6 h after adiolabeling iodistribution uail labeling. Biodistribution studies of 99mTc-FACS complex in Quail showed that it distributed to different organs mainly in blood, liver and kidney. The results revealed that the uptake of 99mTc-FACS in the sexual organs (ovary and ovarian) of female Quail was higher than that in the sexual organs (testes) of male Quail, so 99mTc-FACS could be used to differentiate between them. It also showed that FACS is consumed and more essential in female than that in male. © 2016 Elsevier B.V. All rights reserved.
Effect of increased dietary fiber on hoof lesions of loose housed sows

Loose dry sow housing became mandatory in the European Union from January 2013 onwards. One of the major causes of injuries to sows’ hooves and associated lameness is fighting on concrete/slatted flooring at grouping. Previous studies observed that in sows submitted to feed restriction, feed supplemented with dietary fiber reduced the time spent in the standing position and increased the time spent in the lying position. Therefore, we investigated the effect of increased levels of dietary fiber (7.2-7.5% crude fiber/kg dry matter) on the severity of hoof lesions of group housed sows in three Greek swine herds. The feet of 596 sows were initially examined for lesions upon their entry to the lactation facilities. Lesions scored included hoof hyperkeratinization, erosions or cracks and toe and dew claws overgrowths. When exiting the farrowing facilities they were offered recipes with increased dietary fiber throughout one or two subsequent gestations. Thirty-eight percent were re-examined for feet lesions during the first and sixty-two percent during the second lactation after initial examination. The proportion of sows with at least one lesion on any foot, at first scoring, was more than 95% in all herds. The most frequently and severely affected sites were the heel and the elongated toes and dew claws. The increased dietary fiber had no effect on lesion severity on any of the hoof sites considered.
UK Laterality : Asymmetries of Body , Brain and Cognition

Right–left discrimination is related to the right hemisphere Tibor Auer a , Attila Schwarcz a , Mihály Aradi a , Zsuzsa Kalmár a , Clay Pendleton b , Imre Janszky c d , Réka A. Horváth e , Csaba Szalay e , Tamás Dóczi e , Sámuel Komoly e & József Janszky MD PhD e a University of Pécs, Pécs, Hungary b Louisiana State University, Shreveport, LA, USA c Karolinska Institute, Stockholm, Sweden d Semmelweis University, Budapest, Hungary e University of Pécs, Pécs, Hungary Version of record first published: 22 Aug 2008.
Substance Dependence as a Neurological Disorder

Traditionally, explanations of drug addiction adhered to a moralistic perspective. This perception, still held by many individuals and policy makers, suggests addiction is a problem to be addressed through the criminal justice system (Brown, 2011; Leshner, 1997). However, this approach has yielded little success in addressing the problem (Lee et al., 2010) and may serve to stigmatize addicts and act as a barrier to initiating treatment (Brown, 2011). Moreover, early theories of addiction grounded in learning theory have proven insufficient in explaining several key aspects of addictive behaviour (Robinson & Berridge, 1993). More recently, addiction has been viewed as disease which is characterized as a chronic relapsing disorder in which behavior is marked by a compulsion to seek and take drugs, a loss of control in limiting intake, and the emergence of a negative emotional state upon withdrawal (Koob & Le Moal, 1997). With recent advances in neuroscience and more widespread adoption of the disease model of addiction, current theories have shifted their emphasis to explaining addiction as a brain disease, subserved by varying degrees of cellular, molecular and neurocircuitry dysfunction (Koob & Le Moal, 1997; Volkow et al., 2011).
Climate response to externally mixed black carbon as a function of altitude

The climate response to the presence of black carbon (BC) aerosol at a given altitude in the atmosphere is investigated using a global circulation model. The vertical dependence of the efficiency with which BC exerts radiative forcing (RF) through the direct aerosol effect has previously been extensively studied. Here we use the Community Atmosphere Model version 4 atmospheric component of the National Center for Atmospheric Research Community Earth System model version 1.03 to calculate the three‐dimensional response to a BC layer inserted at various altitudes. Simulations have been performed both for fixed sea surface temperatures and using a slab ocean setup to include the surface temperature response. We investigate the vertical profiles of RF exerted per gram of externally mixed BC due to both the direct and semidirect aerosol effects. Associated changes in cloud cover, relative humidity, and precipitation are discussed. The precipitation response to BC is decomposed into a fast, stability‐related change and a slow, temperature‐driven component. We find that while the efficiency of BC to exert positive RF due to the direct effect strengthens with altitude, as in previous studies, it is strongly offset by a negative semidirect effect. The net radiative perturbation of BC at top of atmosphere is found to be positive everywhere below the tropopause and negative above. The global, annual mean precipitation response to BC, after equilibration of a slab ocean, is found to be positive between the surface and 900 hPa but negative at all other altitudes.
Firm Heterogeneity and Acquisition Incentives

This paper presents a tractable model of acquisitions with heterogeneous firms. Acquisitions improve aggregate productivity by transferring productive assets from the least efficient firms to more efficient firms. However, these acquiring firms are in a mid-range of productivity, whether acquiring at home or abroad. This result is a function of a variable-elasticity demand framework, and highlights the sensitivity of investment decisions to model preliminaries. In linking the model to a Q-Theory of investment, a corollary of this result is that a firm’s average-Q is a poor proxy for marginal-Q, especially for the highest productivity firms. The predictions of the model are tested using a 25-year sample of firms from the Compustat database. To account for productivity, a measure of average Q is constructed which controls for serial correlation in Q values. By accounting for serial correlation, average-Q is positively related to firm size (sales). Using this measure, and by harnessing nonparametric techniques, I find precise evidence that mid-productivity (mid-Q) firms are the most likely to acquire another firm.
Importance of predation by groundfish, marine mammals and birds on walleye pollock Theragra chaicogramma and Pacific herring Clupea pallasi in the eastern Bering Sea

Consumption of walleye pollock Theragra chalcogramma and Pacific herring Clupea pallasi by groundfish predators in the eastern Bering Sea was quantified and described using data obtained in 1985-88. Groundfish predators considered here include walleye pollock Theragra chalcogramma; Pacific cod Gadus macrocephalus; yellowfin sole Pleuronectes asper; flathead sole Hippoglossoides elassodon; rock sole Pleuronectes bilineatus; Alaska plaice Pleuronectes quadrituberculatus; arrowtooth flounder Atheresthes stornias; and Greenland turbot Reinhardtius hippoglossoides. Marine mammal and bird consumption of pollock and herring was estimated for 1985 and compared with groundfish consumption. Groundfish predation on pollock during this time period was dominated by cannibalism on age-0 pollock by adult pollock. The highest predation rate occurred in 1985 when the largest pollock year class, as assessed at age 1, during the time period was produced. Predation mortality estimates by age on the 1985 year class were higher than adjacent year classes. Apparently, predators responded to the increased abundance of the 1985 pollock year class by switching to predation on that year class. The impact of this predation appeared to dampen the size of the 1985 year class at age 3 relative to other adjacent year classes. Marine mammal and bird predation on pollock was small relative to pollock cannibalism. However, marine mammal predation on older pollock was more important, almost doubling the estimated predation mortality rate of age-2 fish. Herring consumption by groundfish predators tended to be sporadic in time and space and may have depended on encounter rates of herring schools rather than overall biomass. Pacific cod was the most consistent groundfish predator on herring. There was no apparent relationship between biomass of herring consumed by groundfish predators and cohort analysis estimates of herring biomass in a given year, suggesting no density-dependent predator response. Marine mammal and bird predation on herring was approximately the same as that by groundfish in terms of weight and about half in terms of numbers. Total predation removals of herring were not large relative to exploitable stock size, indicating that predation of juvenile herring, at least during summer periods typically sampled, was not an important source of herring mortality.
Cutting patterns of membrane structures

Membrane structures are very lightweight and highly optimized structures. Due to the constant stress state, strength of materials is used optimally. In order to prevent the occurrence of large deformations even for small external loads, membrane structures are designed as a double curved surfaces and are stabilized by applying prestress. Minimal surfaces has zero mean curvature and the basic advantage is that the stress at all points and directions is equal and there are no extreme stresses anywhere on the surface. Also have minimal area for the given contour, so the weight and amount of material is reduced to minimum, which make them suitable for application in architecture. Practical realization involve process of cutting pattern generation, which divide surfaces in parts that are developable surfaces. When patterns are assembled and prestressed they provide three-dimensional surface. Ideally, the cutting lines should follow the geodesics lines. We use geodesics as the shortest path between two points on a surface. In the article we give method for finding shortest paths on polygonal representations of surfaces follows continual Dijkstra paradigm which, on some conditions, can give improved accuracy on a computer despite the restriction of available memory and execution time.