Miracle-dz/UniFAR-FTUs huggingface dataset:
MHC-Independent Inhibitory Mechanism of Melanoma and NK Cells: A Novel Class I CD66a Interactions Between Human

NK cells are able to kill virus-infected and tumor cells via a panel of lysis receptors. Cells expressing class I MHC proteins are protected from lysis primarily due to the interactions of several families of NK receptors with both classical and nonclassical class I MHC proteins. In this study we show that a class I MHC-deﬁcient melanoma cell line (1106mel) is stained with several Ig-fused lysis receptors, suggesting the expression of the appropriate lysis ligands. Surprisingly, however, this melanoma line was not killed by CD16-negative NK clones. The lack of killing is shown to be the result of homotypic CD66a interactions between the melanoma line and the NK cells. Furthermore, 721.221 cells expressing the CD66a protein were protected from lysis by YTS cells and by NK cells expressing the CD66a protein. Redirected lysis experiments demonstrated that the strength of the inhibitory effect is cor-related with the levels of CD66a expression. Finally, the expression of CD66a protein was observed on NK cells derived from patients with malignant melanoma. These ﬁndings suggest the existence of a novel class I MHC-independent inhibitory mechanism of human NK cell cytotoxicity. This may be a mechanism that is used by some of the class I MHC-negative melanoma cells to evade attack by CD66a-positive NK cells. The Journal of Immunology, 2002, 168: 2803–2810. class I self
Soil Moisture Response to Spraying Big Sagebrush the Year of Treatment.

Livestock grazing is the dominant land usage on 145 million acres of sagebrush lands in the West. Numerous studies, substantiated by ranchers’ practical experiences, amply demonstrate that production by grasses at least doubles after chemical control of sagebrush. This practice is now one of the chief management techniques for improving rangeland production. Kearl’ estimates that 1.3 to 1.4 million acres of sagebrush range have been sprayed in Wyoming alone through 1970, and extensive areas have also been sprayed in other western states. Ecologic changes, other than herbaceous production, which accompany spraying have not received attention commensurate with their importance. Modification of the soil moisture regime is one such important change. After control, the moisture normally withdrawn by sagebrush becomes available for other on-site uses, or may ultimately enter a groundwater system and augment streamflow.
Descobertas associadas aos mecanismos de defesa antiviral baseados em silenciamento por RNA em Glycine max e Nicotiana Benthamiana

The main defense mechanism of plants facing a viral infection is based on the phenomenon called RNA interference (RNAi). Through the coordinated action of proteins such as Argonaut, Dicers, RNA dependent RNA polymerases and double-stranded RNAbinding proteins (DRBs), the viral RNA is recognized and cleaved to virus-derived interfering small RNAs (vsiRNAs). The vsiRNAs, coupled to a protein complex that induce the silencing, act on DNA or RNA viral sequences promoting cleavage, translational inhibition or methylation of their targets (for DNA viruses). This work described two studies that address new defense mechanisms based on RNAi in plants. In the first chapter of this thesis is described the integration of the cucumber mosaic virus (CMV) RNA1 in the genome of Glycine max. Through the analysis of deep sequencing libraries of messenger RNA, small RNAs and DNA from different cultivars and different soybean tissues it was possible to identified that the integration event involved two molecules of CMV RNA1, the RNA of a retrotransposon and the mRNA of an endogenous gene. In the locus where the integration occurred the two RNA1 sequences are in opposite directions. Small RNAs (sRNAs) from our libraries mostly aligned in the region of CMV RNA1 and are practically absent in other regions of the integrated sequence, strongly suggesting the formation of a hairpin where both CMV sequences hybridize. The presence of these CMV-derived sRNAs in all surveyed tissues suggests a probable antiviral function for the sequence that was integrated into soybeans. In the second chapter, the interaction between the DRB proteins and the Potato virus X (PVX) during viral infection in Nicotiana benthamiana is assessed by confocal microscopy. It is shown that the DRBs 2, 3 and 5 relocate from its original position and concentrated in structures called viral replication complexes during infection by PVX. This is an indication that these proteins can act in the early stages of plant defense against the virus. _________________________________________________________________________ Ph.D. Thesis, Graduate Program in Cell and Molecular Biology, Center for Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil. July, 2015.
Elucidating the precise interaction of reduced and oxidized states of Neuroglobin with Ubc12 and Cop9 using molecular mechanics studies

BACKGROUD & OBJECTIVE: Neuroglobin is an oxygen binding globin protein highly expressed in neurons. It is an iron containing heme protein, that exist in both ferrous and ferric form. Recent studies have indicated its role as an endogenous neuroprotective molecule. It is proposed that neuroglobin undergoes post-translational modification by the process of neddylation and deneddylation. Hence in this study an attempt was made to investigate the mode and mechanism of interaction of ferrous and ferric forms of neuroglobin with Ubc12 and op9, proteins involved in regulation of neddylation and deneddylation respectively, utilizing molecular modelling calculations. METHODOLOGY: In this study, the mode of interactions of Ubc12 and Cop9 with the reduced (Fe 2+ ) and oxidized state (Fe 3+ ) of neuroglobin was carried out using ZDock. The top scoring poses for each complex were subjected to energy minimization using CHARMM Polar H force field in RDock to obtain the binding affinities. RESULTS: The binding affinities between of ferrous and ferric forms of neuroglobin with Ubc12 and Cop9 were calculated. CONCLUSION: Results obtained strongly indicate that both Ubc12 and Cop9 interacts with neuroglobin in regulation of neddylation and deneddylation process. Furthermore these results guided us in precisely designing experiments for biological evaluations.
Progress in enzyme inhibition based detection of pesticides

The previous few decades have seen the development of biosensors and their use in monitoring of pesticides in food and environmental samples. Although inhibition‐based biosensors have been subject of several recent research works, their performance characteristics greatly depend on the type of immobilization and the presence of interfering compounds in the samples. Moreover, sensitivity, detection limits, and rapidity of the response are few of the other major features that need to be investigated further if they are to become operationally user‐friendly. This review will highlight research carried out in the past on biosensors that are based on enzyme inhibition for determination of organophosphorus compounds and carbamate pesticides.
Detección molecular y análisis filogenético de Hepatozoon canis (Eucoccidiorida: Haemogregarinidae) en perros clínicamente sanos de Bahía Blanca (Buenos Aires)

Las enfermedades caninas causadas por protozoarios y transmitidas por garrapatas representan un importante problema en medicina veterinaria. El objetivo del estudio fue detectar molecularmente Hepatozoon spp. , Babesia spp. y Theileria spp. en perros clinicamente sanos de distintas regiones de Argentina y analizar la diversidad genetica de los hallazgos obtenidos. Se analizaron 163 muestras de ADN de sangre de perros (40 de Ciudad Autonoma de Buenos Aires; 33 de Bahia Blanca, Buenos Aires; 15 de Castelli, Chaco; 27 de Salsipuedes, Cordoba; 40 de Merlo, San Luis; y 8 de San Miguel, Corrientes). Mediante una PCR que amplifica un fragmento variable (460-540 pb) del gen ARNr 18S incluyendo la region V4 de los generos Hepatozoon , Babesia y Theileria , el 12,1 % (4/33) de los perros de Bahia Blanca (Buenos Aires) resultaron positivos. Las secuencias obtenidas se identificaron como Hepatozoon canis y resultaron filogeneticamente similares a hallazgos en Sudamerica y en el resto del mundo. El estudio de H. canis en Argentina mediante tecnicas moleculares de diagnostico junto con el analisis filogenetico resulta de suma importancia para conocer la situacion de este patogeno en el pais.
Dendritic processing of spontaneous neuronal sequences for one-shot learning

Spontaneous firing sequences colloquially called “preplay” are fundamental features of hippocampal network physiology. Preplay sequences have been hypothesized to participate in hippocampal learning and memory, but such functional roles and their potential cellular mechanisms remain unexplored. Here, we report a computational model based on the functional propagation of preplay sequences in the CA3 neuronal network. The model instantiates two synaptic pathways in CA3 neurons, one for proximal dendrite-somatic interactions to generate intrinsic preplay sequences and the other for distal dendritic processing of extrinsic sensory signals. The core dendritic computation is the maximization of matching between patterned activities in the two compartments through nonlinear spike generation. The model performs robust one-shot learning with long-term stability and independence that are modulated by the plasticity of dendrite-targeted inhibition. This model demonstrates that learning models combined with dendritic computations can enable preplay sequences to act as templates for rapid and stable memory formation.
Hypereosinophilic Syndrome Associated with the Onset of Rheumatoid Arthritis: A Case Report

Received:September 6, 2016, Revised:(1st) November 21, 2016, (2nd) November 28, 2016, Accepted:December 14, 2016 Corresponding to:Wan-Hee Yoo, Division of Rheumatology, Department of Internal Medicine, Chonbuk National University Medical School and Research Institute of Clinical Medicine of Chonbuk National University Hospital, 20 Geonji-ro, Deokjin-gu, Jeonju 54907, Korea. E-mail:ywhim@jbnu.ac. kr Copyright c 2017 by The Korean College of Rheumatology. All rights reserved. This is a Open Access article, which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited. Case Report pISSN: 2093-940X, eISSN: 2233-4718 Journal of Rheumatic Diseases Vol. 24, No. 3, June, 2017 https://doi.org/10.4078/jrd.2017. 24.3. 165
Planktonic diatoms and their environment in the lower Neretva River estuary (Eastern Adriatic Sea, NE Mediterranean)

The seasonal distribution of planktonic diatoms was investigated at one station in the lower Neretva River estuary (Middle Adriatic) at monthly intervals from April 1999 to April 2000. According to the TRIX trophic index, the lower estuary is mesotrophic. Ninety-six diatom taxa within 51 genera were identified. Of these, 32 occurred in at least 10 % of all samples and 12 rare taxa occurred in ≤ 1 % of samples. Nine, mostly rare, taxa were only found in brackish layer, and 27 taxa were exclusively presented in marine layer. Anosim analysis revealed that no significant difference occurred between these two layers in terms of diatom taxa abundances. The continuous presence of some benthic taxa, underlines the importance of wind-induced sediment resuspension, currents and tides. Unidentified phytoflagellates (55.68 – 99.60 %) and diatoms (0.20 – 42.10 %) represented the major proportion of total phytoplankton abundance. The diatom community of marine origin varied over five orders of magnitude (30 –1.2 × 10*6* cells L–1) and showed three peaks throughout the year: April 1999 (1.2 × 10*6* cells L–1), August 1999 (7.9 × 10*6* cells L–1), and October 1999 (1.3 × 10*6* cells L–1), while the lowest abundance was observed in November 1999. The most abundant diatoms (exceeding 10*5* cells L–1) were Nitzschia longissima, Leptocylindrus minimus, Skeletonema marinoi, and Thalassiosira sp. N. longissima (max. 7.9 × 10*6* cells L–1) dominated the highest peak (August 1999) and represented the 98.08 % and 29.26 %, respectively, of total diatom and phytoplankton abundance. Canonical Correspondence Analysis (CCA) showed that temperature, salinity and TIN were the main factors influencing diatom community structure in the estuary. No relationship was noted between the monthly distribution of diatom abundances, water column transparency, and microzooplankton abundance. A main feature of the diatom assemblages was the dominance of more than one species during the blooms. This, likely, is owed to the frequent and rapid environmental changes typical of this dynamic estuarine ecosystem.
Use of Neem (Azadirachta indica A. Juss) Oil in The Control of Musca domestica L.(Diptera:Muscidae) in Poultry Breeding Farms.

Department of Biotechnology, Genetic and Cell Biology – State University of Maringá, Maringá, Paraná, CEP, 87020-900, Brazil Laboratory of Insects, Department of Morphology, Bioscience Institute,UNESP, São Paulo, State University, Botucatu, SP, CEP, 18618-970, Brazil *Corresponding author's Email: helconte@gmail.com Received: 12 Nov. 2015 Accepted: 15 Dec. 2015 ABSTRACT Pest infestation, in general such as flies, is a problem faced by poultry workers in poultry breeding farms. Control of these populations is desirable, due to the damage they cause and, most times, it is done through chemical management, with insecticide application. Musca domestica is one of the species with the greatest ability to develop resistance to insecticides, and the digestive system, especially the midgut, is one of the most vulnerable organs to structural alteration, because in it there is production of digestive enzymes and absorption of nutrients. Damage caused by use of synthetic insecticides reactivated studies with bioinsecticides for being one of the most selective options in pest control. Furthermore, they do not cause environmental alterations such as food, soil, water poisoning and they are practically nontoxic to mammals. Among vegetable species with insecticidal activities that have been used a lot, we have neem, subtropical plant that shows low residual power and lower risk of intoxication for mammals and poultry. Thus the objectives that guided this work, was the observation of morphological alteration in M. domestica larvae and malformation of pupae after the use of neem, powder and emulsifiable oil at different concentrations (0,5%, 1%, 1,5%) were tested. Following, after the applications, the midgut of flies in larval stage was isolated, processed and analyzed under light microscopy, scanning and transmission electron microscopy. As in most dipterous, the cell types found were columnar cells and regenerative cells, which showed alterations such as: coalescing vacuoles, intercellular spaces, formation of cytoplasmic protrusions, broken microvilli, rough endoplasmic reticulum and dilated mitochondria. The statistical analysis registered for pupa malformation showed significant results in comparison to control, but there was no difference among treatments. The different concentrations of neem oil contributed in altering morphological and ultrastructurally the midgut in M. domestica larvae, interrupting its development. These results showed that in poultry breeding farms, neem oil can be a pratical alternative to the control of M. domestica.
Analyses of anthocyanidins and anthocyanins in flower petals of Lychnis senno and its related species (Caryophyllaceae)

Lychnis senno Siebold et Zucc. , generally called 'Senno' in Japan, is a species belonging to Caryophyllaceae and native to China. Although this species had widely been cultivated in the Muromachi and the Edo eras in Japan, it is recently on the way of extinction, and we can hardly see it as a garden plant. From 1996 onward, several strains of L. senno were found in Chugoku and Kyushu districts, Japan, and they were introduced to the Botanic Gardens of Toyama as research materials (Godo et al., 2000, 2004). Flower color of L. senno is characteristic bright crimson (Godo et al., 2004), and this attractive trait is desired to be introduced via sexual or somatic hybridization into related species. In order to carry out systematic breeding for flower color alteration, analysis of the pigment composition in flower petals is one of the prerequisites. In the present study, therefore, we analyzed anthocyanidins and anthocyanins by HPLC in flower petals of L. senno and its related species.
Molecular mechanisms of cellular transport and resistance of platinum anti-cancer drugs

The acquired resistance and reversal of resistance of Pt drugs has been examined using an extensive review of the literature and molecular orbital computations. The cellular uptake of Pt drugs is fastest for neutral species, with high lipophilicity, since their desolvation penalties for crossing the cell membrane are lowest. Pt resistant cell lines generally have lower levels of drug uptake, indicating this is a dominant first order cause of cellular resistance. Resistance can be caused by complexation of charged Pt species to phosphatidylserine (PS) headgroups, or by Pt complexation to the inner terminii of the trans-membrane pore of the hCtr1 transporter. Drugs that are known to reverse induced Pt resistance can decomplex the Pt-PS or Pt-hCtr1 complexes, restoring normal PS or hCtr1 functions. Objectives Resistance to Pt drugs: to examine mechanisms involved in acquired resistance, particularly the cellular accumulation mechanisms: (a) passive diffusion, active transport including copper transporters, organic cation transporters; (b) active efflux and intracellular reductive processes Reversal of platinum resistance: to develop predictive criteria for drugs that can reverse acquired resistance.
Pollen grain flavonoid studies of four Iranian Trifolium (Leguminosae) taxa as future honey biomarkers

Pollen flavonoid studies provide useful information for evaluation of the nutritional and medicinal quality of natural honeys. In this study, pollen flavonoids of four Iranian Trifolium taxa are reported for the first time. Results have shown that all four studied taxa contain rutin, flavonoid sulphates, flavone C and C-/O-glycosides in their pollen. Morin is reported for the first time in the pollen of all studied taxa, with the exception of T. tumens. Apigenin, kaempferol, loteulin, myricetin, tricin, and vitexin were absent in the pollen of all studied species, but the pollen of T. fragiferum had quercetin. Flower pollen flavonoids are identical to those of the corresponding bee pollen confirming their use as chemical marker so important in ecology, pollination, honey qualification and preventing its adulteration.
Structural and Functional Studies of the β2-Sliding Clamp from Pathogenic Bacteria

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Redesigning chromosomes to optimize conformation capture (Hi-C) assays

In all chromosome conformation capture based experiments the accuracy with which contacts are detected varies considerably because of the uneven distribution of restriction sites along genomes. Here, we redesigned and reassembled in yeast a 145kb region with regularly spaced restriction sites for various enzymes. Thanks to this design, we enhanced the signal to noise ratio and improved the visibility of the entire region as well as our understanding of Hi-C data, while opening new perspectives to future studies.
Facts and misconceptions on the Palaearctic existence of the striped ground squirrel

Abstract The striped ground squirrel has a wide distribution in the Ethiopian region but is restricted to a small isolated area in Palaearctic Africa. This fragment was first recorded in the late 1940s in the Souss Valley (Morocco), however, not a single new observation has been published in the following decades. In September 2016 we surveyed the Souss Valley and found squirrels at 43 sites within the triangle between Agadir–Taroudant–Tiznit. Occupied sites were not distributed at random but occurred between an altitude of 45–254 m and on a substrate with coarse texture containing >65% sand. The vast majority of the sites with squirrels (69%) were classified as suburban, cultivated or both. Habitat suitability was estimated by applying geographically weighted logistic regression analysis. The influence of local predictor variables varied across the study area indicating the heterogeneous effects on the determination of the occurrence of the species. The modelled highly suitable habitat area for the striped ground squirrel in Morocco covers almost 690 km2 and only marginally overlaps the range for the species reported in the literature.
Probabilistic Programming with CuPPL

Probabilistic Programming Languages (PPLs) are a powerful tool in machine learning, allowing highly expressive generative models to be expressed succinctly. They couple complex inference algorithms, implemented by the language, with an expressive modelling language that allows a user to implement any computable function as the generative model. Such languages are usually implemented on top of existing high level programming languages and do not make use of hardware accelerators. PPLs that do make use of accelerators exist, but restrict the expressivity of the language in order to do so. In this paper, we present a language and toolchain that generates highly efficient code for both CPUs and GPUs. The language is functional in style, and the tool chain is built on top of LLVM. Our implementation uses de-limited continuations on CPU to perform inference, and custom CUDA codes on GPU. We obtain significant speed ups across a suite of PPL workloads, compared to other state of the art approaches on CPU. Furthermore, our compiler can also generate efficient code that runs on CUDA GPUs.
Decentralized Multi-Agent Pursuit Using Deep Reinforcement Learning

Pursuit-evasion is the problem of capturing mobile targets with one or more pursuers. We use deep reinforcement learning for pursuing an omnidirectional target with multiple, homogeneous agents that are subject to unicycle kinematic constraints. We use shared experience to train a policy for a given number of pursuers, executed independently by each agent at run-time. The training uses curriculum learning, a sweeping-angle ordering to locally represent neighboring agents, and a reward structure that encourages a good formation and combines individual and group rewards. Simulated experiments with a reactive evader and up to eight pursuers show that our learning-based approach outperforms recent reinforcement learning techniques as well as non-holonomic adaptations of classical algorithms. The learned policy is successfully transferred to the real-world in a proof-of-concept demonstration with three motion-constrained pursuer drones.