Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of the proto-oncogene ERG by microRNAs and the role of microRNAs in the distinct ETP-ALL subgroup of T-ALL

Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) has been identified as high-risk subgroup of acute Tlymphoblastic leukemia (T-ALL) with a high rate of FLT3-mutations in adults. To unravel the underlying pathomechanisms and the clinical course we assessed molecular alterations and clinical characteristics in a large cohort of ETP-ALL (n = 68) in comparison to non-ETP T-ALL adult patients. Interestingly, we found a high rate of FLT3-mutations in ETP-ALL samples (n = 24, 35%). Furthermore, FLT3 mutated ETP-ALL was characterized by a specific immunophenotype (CD2+/CD5-/CD13+/ CD33-), a distinct gene expression pattern (aberrant expression of IGFBP7, WT1, GATA3) and mutational status (absence of NOTCH1 mutations and a low frequency, 21%, of clonal TCR rearrangements). The observed low GATA3 expression and high WT1 expression in combination with lack of NOTCH1 mutations and a low rate of TCR rearrangements point to a leukemic transformation at the pluripotent prothymocyte stage in FLT3 mutated ETP-ALL. The clinical outcome in ETP-ALL patients was poor, but encouraging in those patients with allogeneic stem cell transplantation (3-year OS: 74%). To further explore the efficacy of targeted therapies, we demonstrate that T-ALL cell lines transfected with FLT3 expression constructs were particularly sensitive to tyrosine kinase inhibitors. In conclusion, FLT3mutated ETP-ALL defines a molecular distinct stem cell like leukemic subtype. These data warrant clinical studies with the implementation of FLT3 inhibitors in addition to early allogeneic stem cell transplantation for this high risk subgroup. Citation: Neumann M, Coskun E, Fransecky L, Mochmann LH, Bartram I, et al. (2013) FLT3 Mutations in Early T-Cell Precursor ALL Characterize a Stem Cell Like Leukemia and Imply the Clinical Use of Tyrosine Kinase Inhibitors. PLoS ONE 8(1): e53190. doi:10.1371/journal.pone. 0053190 Editor: Kristy L. Richards, University of North Carolina at Chapel Hill, United States of America Received July 25, 2012; Accepted November 29, 2012; Published January 24, 2013 Copyright: � 2013 Neumann 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: This study was supported by research funding from Berliner Krebsgesellschaft and Deutsche Krebshilfe to C.D. B. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: TKI258 was a kind gift from Novartis (Basel, Switzerland). There are no further patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials. * E-mail: claudia.baldus@charite.de
A deterministic, age-stratified, extended SEIRD model for investigating the effect of non-pharmaceutical interventions on SARS-CoV-2 spread in Belgium

As a response to a rapidly rising number of SARS-CoV-2 infections, the Belgian government imposed strict social contact restrictions on March 13th, 2020. After nearly two months, the curve was succesfully flattened and social restrictions were gradually released. Unfortunately, pharmaceutical interventions are not yet available so it is expected that preventing COVID-19 outbreaks will depend mostly on the successful implementation of non-pharmaceutical interventions, hence the need for well-informed models. In this study, we built a deterministic, continuous-time, age-stratified-SEIRD model with detailed hospital dynamics. Because the hospitalization data for Belgium have not been made public yet by the Belgian scientific institute of public health, we computed the hospitalization parameters based on data from 370 patients in two Ghent (Belgium) hospitals. The basic reproduction number during March 2020 was estimated as R0 = 2.83 and the model fits the hospitalization and ICU admission incidence under lockdown measures well. In spite of the release of social restrictions, hospitalizations have been steadily declining. We recomputed the basic reproduction number under lockdown release and found that it had to be as low as R0 = 0.73 to explain the endemic trend under the observed community mobility data. We further found that although the basic reproduction number in the population older than 70 years was smaller than one, this group compromises nearly half of the expected hospitalizations. This indicates that protection of the elderly may be the most efficient way to reduce strain on the public health care system in case of another SARS-CoV-2 outbreak.
Tritiated Water Induces Toxicity in Human Umbilical Vein Vascular Endothelial Cells via IL8

We aimed to determine the toxic effects of tritiated water (HTO) on 12 generations (T1-T12) of human umbilical vein vascular endothelial cells (HUVECs) and elucidate the underlying mechanisms. We evaluated cellular senescence, interleukin (IL) 8 concentrations, and angiogenesis using β-galactosidase staining, enzyme-linked immunosorbent assay, and in vitro assays, respectively. The adhesion properties of contaminated cells and differentially expressed genes were assessed using the xCELLigence RTCA SP system and gene chip analysis, respectively. We found that long-term exposure to low levels of HTO can reduce the adhesion of HUVECs to the cellular matrix as well as their angiogenic capacity, while increasing their permeability, senescence, and adhesion to monocytes. Interleukin 8 activated the p38 and Epidermal Growth Factor Receptor (EGFR) pathways in HTO-treated cells and hence was identified as a key candidate of biomarker. The present study clarified the toxicity of HTO in vascular endothelial cells and identified IL8 as a novel protective target with important theoretical and practical values.
Progress in the Ecological Genetics and Biodiversity of Freshwater Bacteria

ABSTRACT The field of microbial ecology has grown tremendously with the advent of novel molecular techniques, allowing the study of uncultured microbes in the environment, and producing a paradigm shift: now, rather than using bacteria cultures for evaluating cell-specific questions, researchers use RNA and DNA techniques to examine more broad-based ecological and evolutionary constructs such as biogeography and the long-debated biological species concept. Recent work has begun to relate bacteria functional genes to ecosystem processes and functioning, thereby enabling a better understanding of the interactive role of bacteria in different and often-changing environments. The field continues to mature and will most likely make substantial contributions in the future with additional efforts that include metagenomics and genomics. Here we review progress in the application of molecular techniques to study microbial communities in freshwater environments.
A method for screening diacetyl and acetoin‐producing bacteria on agar plates

A simple method for screening bacteria for diacetyl and acetoin production was developed. This method is based on the ability of diacetyl and acetoin to form a red insoluble complex with α‐naphthol in the presence of creatine. Addition of carboxymethyl‐cellulose containing calcium citrate in the medium allowed discrimination between citrate utilizing and non‐utilizing bacteria.
Factores pronósticos para pérdida de extremidad con trauma arterial periférico en un hospital de Colombia

Introduction : Vascular trauma is a low frequency event, with high morbidity and mortality that affects the young population; In general, it requires surgical management. It is associated with complications from surgical reintervention to amputation of the limb, influenced by trauma associated variables such as hospital care. Aim : Determine risk factors related to amputation, in patients with peripheral arterial trauma (TAP), treated at a Hospital of III level Huila-Colombia between 2014-2017. Materials and Method: Observational, retrospective analytical study with patients older than 13 years with TAP. Results: We included 79 patients with an incidence of 1.56%. 89% men, average age 28.5 years. The main comorbidity was 8.8% drug dependence. The MESS (Mangled extremity severity) average was of 5.27 points and a critical time of limb ischemia > to 6 hours in 38%. The greater commitment was of superior members, secondary to injuries by sharp weapon. The predominant lesion was arterial transection. The main postoperative complications were vessel thrombosis (21.5%) and amputation in 13.9%. Risk factors associated with amputation were determined by age > 20 years, hospital stay > 7 days, MESS > 7 points, and that they presented arterial thrombosis as a surgical complication and finally required surgical reoperation. Conclusions: Peripheral arterial trauma is a pathology with great socioeconomic impact and functional sequelae. It is necessary the timely attention with treatment of the variables related to poor prognosis, in order to decrease the morbidity and mortality rates.
Adoption of a Urologic Oncology Perioperative Surgical Home is Associated with Decreased Total Length of Stay: A Pilot Study.

INTRODUCTION Urologists partnered with anesthesiologists to implement a model of perioperative and postoperative care known as the multidisciplinary perioperative surgical home in order to improve the quality and efficiency of care. We describe early outcomes associated with implementation of the perioperative surgical home. METHODS Retrospective chart review was performed of patients at a single institution undergoing radical prostatectomy, radical cystectomy, partial nephrectomy and radical nephrectomy from January 2014 to March 2016. Outcomes measured were length of stay and 30-day reoperation, readmission, unexpected intensive care unit admission and mortality rates. Statistical analysis was performed using the independent samples Mann-Whitney U test and Fisher exact test with p <0.05 considered significant. Univariate and multivariate analyses were performed to determine whether implementation of the perioperative surgical home was associated with improved outcomes. RESULTS Length of hospital stay decreased from 4.79 to 3.19 days and 30-day complication rate decreased from 15.3% to 5.7% after implementation of the perioperative surgical home (p <0.01 for both). There was no change in the 30-day readmission rate. On multivariate analysis surgery occurring after perioperative surgical home implementation was associated with decreased length of stay (p = 0.008). The direct cost savings resulting from this length of stay reduction totaled $1,245,585 for the study period. CONCLUSIONS The adoption of a perioperative surgical home is associated with a significantly decreased postoperative hospital stay and 30-day complication rate for urologic oncology cases.
Prospective motor control on tabletops: planning grasp for multitouch interaction

Substantial amount of research in Psychology has studied how people manipulate objects in the physical world. This work has unveiled that people show strong signs of prospective motor planning, i.e., they choose initial grasps that avoid uncomfortable end postures and facilitate object manipulation. Interactive tabletops allow their users great flexibility in the manipulation of virtual objects but to our knowledge previous work has never examined whether prospective motor control takes place in this context. To test this, we ran three experiments. We systematically studied how users adapt their grasp when asked to translate and rotate virtual objects on a multitouch tabletop. Our results demonstrate that target position and orientation significantly affect the orientation of finger placement on the object. We analyze our results in the light of the most recent model of planning for manipulating physical objects and identify their implications for the design of tabletop interfaces. \
Distances at which jumping spiders (Araneae: Salticidae) distinguish between prey and conspecific rivals

Distances at which jumping spiders (Salticidae) use optical cues to distinguish between prey insects and conspecific rivals were investigated using adult males of 37 species. During tests, salticids walked up a ramp toward a mirror or toward an insect enclosed in a transparent petri dish. All species directed threat displays toward their own mirror images and the displays were comparable to each species' typical behaviour during male–male interactions. The salticids never displayed in tests with insects at the top of the ramp. The virtual distances at which the spiders displayed are interpreted as an indication of the distances at which each species can distinguish rivals from prey. Representative species were from the subfamilies Lyssomaninae, Spartaeinae and Salticinae. Discrimination distances relate well to the foveal layer I receptor mosaics of the anterior median eyes for the three subfamilies. Compared with the salticines, the lyssomanines and, except for Portia, the spartaeines tended to have shorter discrimination distances. Portia spp. had discrimination distances comparable to the longest recorded for the salticines. The longest discrimination distances found were for the salticine Mogrus neglectus (max. 320 mm or 42 body lengths) and for the spartaeine Portia fimbriata (280 mm or 47 body lengths).
Innovative procedures to evaluate corn silage for milk yield

Riassunto Procedure innovative di valutazione del silomais per la produzione di latte. Su 58 campioni di silomais sono stati misurati i principali costituenti chimici e la degradabilità ruminale in vitro dell’NDF (NDFd) per stimare il contenuto in energia netta di lattazione (ENl) e la potenziale produzione di latte utilizzando un modello di previsione dell’ingestione basato sul contenuto e la degradabiità dell’NDF. La NDFd è risultata pari a 51±5% e la variabilità dei valori calcolati di ENl va ascritta per il 50-60% alle variazioni di NDFd e al 30-40% alle diverse frazioni dei carboidrati. Le differenze in produzione di latte (19%) sono in prevalenza attribuibili alla variabilità dell’NDFd (dal 55 al 61%). L’elevato contributo dell’NDFd alle variabilità suggerisce una verifica in vivo dei range di variazione ottenibili in vitro.
Inventory of Intertidal Marine Habitats, Boston Harbor Islands National Park Area

Abstract The intertidal zone of the 34 islands that are the Boston Harbor Islands national park area encompasses over half of the total park area, thereby representing a significant natural resource. The purpose of this study was to inventory the intertidal zone by classifying and mapping all habitats and compiling species lists for major taxonomic groups. The Boston Harbor Intertidal Classification System was developed for mapping substrate and biotic assemblage types—a system specific to the local area, but capable of application throughout the Gulf of Maine. Intertidal habitats were mapped from GPS-based field delineations. Mixed coarse, consisting of rocks, boulders, cobbles, gravel, shell, and sand, was by far the most common substrate type; however, the islands were variable with a total of 13 discrete substrate types mapped, ranging from bedrock and boulders to mud. The outer islands (e.g., Outer and Little Brewster) were dominated by rocky substrate, while islands close to the mainland (e.g., Thompson, Slate) had high percentages of fine sediments. Of the 31 biotic assemblages mapped, Mytilus edulis (blue mussel) reef was the dominant assemblage on many of the middle and Hingham Bay islands, while the outer islands had assemblages common to the more exposed rocky substrates. The species inventory recorded 95 species of invertebrates, 70 marine algae, and 15 vascular plants. The information generated from this inventory will provide a foundation for natural resource management decisions, design of a long-term intertidal monitoring program, and identification of research needs.
Intraspecific variation in avian pectoral muscle mass: constraints on maintaining manoeuvrability with increasing body mass

1. Within a single year, long-distance migrants undergo a minimum of four cycles of fuel storage and depletion because their migrations have at least one stopover. Each cycle includes an almost twofold change in body mass (m(b)). Pervasive predation threats beg the question whether escape flight abilities keep up with such large changes in m(b). 2. We derive aerodynamic predictions how pectoral muscle mass (m(pm)) should change with m(b) to maintain constant relative flight power. 3. We tested these predictions with data on red knot Calidris canutus, a long-distance migrating wader that breeds in arctic tundra and winters in temperate and tropical coastal areas. We focused on the subspecies C. c. islandica. 4. m(pm) varied with m(b) in a piecewise manner. In islandica knots with m(b) 148 g) the slope was significantly lower (0.63), yielding a m(pm) 0.81 times lower than predicted at pre-departure weights (210 g). 5. Manoeuvrability tests showed that above 160 g, knots were increasingly unable to make a 90 degrees angle turn. This is consistent with m(pm) being increasingly smaller than predicted. 6. Relatively low m(pm) enables savings on mass and hence flight costs, and savings on overall energy expenditure. We predict that reduced escape flight ability at high m(b) will be compensated by behavioural strategies to minimize predation risk.
Estimating variance effect of QTL: an important prospect to increase the resolution power of interval mapping

Summary Equal variances within quantitative trait locus (QTL) groups in the segregating population are a usual simplifying assumption in QTL mapping. The objective of this paper is to demonstrate the advantages of taking into account potential variance effect of QTLs within the framework of standard interval mapping approach. Using backcross case as an example, we show that the resolution power of the analysis may be increased in the presence of variance effect, if the latter is allowed for in the model. For a putative QTL (say, A/a) one can compare two situations, (0 °la = <T L = a l an< 3 (ii) o"L + °"aa-It w as found that, if the variance effect of A/a is large enough, then in spite of the necessity to evaluate an increased number of parameters, the more correctly specified model provides an increase in the resolution power, as compared to the situation (i). This is not unexpected, if either <r 2a or o-aa in (ii) is lower than <j\ from (i). But our conclusion holds even if <r 2 a > cr 2 ^ = <j\ or <r aa > <T\ a = a\. These advantages are illustrated on sweet corn data (F 3 families of F 2 genotypes). In particular, the log-likelihood test statistics and the parameter estimates obtained for a QT locus in the distal region of chromosome 2 show that the allele enhancing the trait is recessive over the opposite allele simultaneously for the mean value and variance.
Optimal Scheduling with Automatic Power Generation of multi area power system by Fuzzy based PID Controller

This research study especially addresses over optimal scheduling of thermal based multi area power system in concern to the automatic power generation control. The work has employed a Fuzzy rule base PID controller to make required control actions in the system. The dynamic load nature in electrical market creates huge abnormal situations in the power system. These abnormal situations especially put adverse effects over system frequency and voltage of the power system. This study makes an objective to maintain nominal frequency and voltage of the system irrespective of the dynamics in applied load. The suggested Fuzzy PID controller takes up all the control actions to put stability on system performance. Further, a novel ant lion optimization (ALO) is proposed to produce optimal parameters of the suggested Fuzzy PID controller under different loadings. The performance of the proposed Fuzzy PID controller has been compared over PID controller to justify the superiority. Finally, in technique level the performance of the proposed ALO technique has been compared over standard PSO technique to optimal design the suggested Fuzzy PID controller.
SURFACE: detecting convergent evolution from comparative data by fitting Ornstein‐Uhlenbeck models with stepwise Akaike Information Criterion

We present a method, ‘SURFACE’, that uses the Ornstein‐Uhlenbeck stabilizing selection model to identify cases of convergent evolution using only continuous phenotypic characters and a phylogenetic tree. SURFACE uses stepwise Akaike Information Criterion first to locate regime shifts on a tree, then to identify whether shifts are towards convergent regimes. Simulations can be used to test the hypothesis that a clade contains more convergence than expected by chance. We demonstrate the method with an application to Hawaiian Tetragnatha spiders, and present numerical simulations showing that the method has desirable statistical properties given data for multiple traits. The r package surface is available as open source software from the Comprehensive R Archive Network.
Speech driven talking head from estimated articulatory features

In this paper, we present a talking head in which the lips and head motion are controlled using articulatory movements estimated from speech. A phone-size HMM-based inversion mapping is employed and trained in a semi-supervised fashion. The advantage of the use of articulatory features is that they can drive the lips motions and they have a close link with head movements. Speech inversion normally requires the training data recorded with electromagnetic articulograph (EMA), which restricts the naturalness of head movements. The present study considers a more realistic recording condition where the training data for the target speaker are recorded with a usual motion capture system rather than EMA. Different temporal clustering techniques are investigated for HMM-based mapping as well as a GMM-based frame-wise mapping as a baseline system. Objective and subjective experiments show that the synthesised motions are more natural using an HMM system than a GMM one, and estimated EMA features outperform prosodic features.
Testing the phylogenetic position of Cambrian pancrustacean larval fossils by coding ontogenetic stages

The study of ontogeny as an integral part of understanding the pattern of evolution dates back over 200 years, but only recently have ontogenetic data been explicitly incorporated into phylogenetic analyses. Pancrustaceans undergo radical ontogenetic changes. The spectacular upper Cambrian “Orsten” fauna preserves phosphatized fossil larvae, including putative crown‐group pancrustaceans with amazingly complete developmental sequences. The putative presence and nature of adult stages remains a source of debate, causing spurious placements in a traditional morphological analysis. We introduce a new coding method where each semaphoront (discrete larval or adult stage) is considered an operational taxonomic unit. This avoids a priori assumptions of heterochrony. Characters and their states are defined to identify changes in morphology throughout ontogeny. Phylogenetic analyses of semaphoronts produced possible relationships of each Orsten fossil to the crown‐group clade expected from morphology shared with extant larvae. Bredocaris is a member of the stem lineage of Thecostraca or (Thecostraca + Copepoda), and Yicaris and Rehbachiella are probably members of the stem lineage of Cephalocarida. These placements rely directly on comparisons between extant and fossil larval character states. The position of Phosphatocopina remains unresolved. This method may have broader applications to other phylogenetic problems which may rely on ontogenetically variable homology statements.