Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene expression profiles and risk stratification in childhood acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) in children is a heterogeneous disease with a varied response to treatment. Despite overall survival rates approaching 75-80%, a significant fraction of patients still cannot be cured. Because of this heterogeneity, accurate assignment of patients to different risk groups at the earliest time possible is important in order to select the best strategy for each individual. Current risk stratification into standard(low-), intermediateor high-risk groups is based on molecular/cytogenetic markers (BCR-ABL and MLL-AF4 rearrangements) and the in vivo response to treatment. Chromosomal aberrations frequently involve non-random chromosomal translocations that produce novel gene fusions or lead to inappropriate expression of oncogenes. These genetic alterations have a clear impact on the patient’s prognosis as exemplified by the association of Philadelphia chromosome positive ALL with a poor outcome. Because of the significance of cytogenetic abnormalities such as t(9;22), t(1;19), t(12;21), and rearrangement of the MLL gene on chromosome 11q23, great efforts have been made recently to establish gene expression profiles that discriminate among these subtypes. Intriguingly, distinct expression profiles that can accurately predict cytogenetic subgroups have indeed been identified in these studies. A patient’s initial response to treatment, which can be monitored with molecular biology techniques, is one of the strongest indicators of subsequent prognosis. Polymerase chain reaction (PCR)-based analysis of minimal residual disease (MRD) can detect residual leukemic cells during induction therapy down to a level of one leukemic cell in 10 normal cells. Given the From the Departments of Oncology University Children’s Hospital Zurich,Switzerland (OT, FKN, BWS) Seminar for Statistics, Swiss Federal Institute of Technology (ETH) Zurich, Switzerland (MD, PB) Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany (GC, MSt, MSc).
Regional Mapping of the Coastal Zone with Airborne LIDAR

Abstract : Recent advancements in lidar sensors now allow for near-synoptic, regional-scale mapping of the coastal zone. One such sensor is the U.S. Army Corps of Engineers SHOALS (Scanning Hydrographic Operational Airborne Lidar Survey) system. SHOALS is unique in that it is the only lidar sensor, worldwide, that simultaneously collects bathymetry and adjacent topography. Because of SHOALS' high collection rate, data density, and system accuracy, it is now cost effective to quantify regional coastal geomorphology and to better engineer management solutions on a regional scale. This article presents the SHOALS survey collected in Hawaii and discusses the value of lidar mapping to the coastal zone management community. SHOALS uses a scanning, pulsing laser to deliver light at two frequencies: blue-green and infrared. While the infrared pulse provides a direct ranging of the water surface, the blue-green pulse penetrates the water column to provide direct ranging of the sea bottom. Two- or three-dimensional positioning of the SHOALS aircraft is from differential GPS or kinematic GPS, respectively. In addition to depth measurements, the SHOALS system simultaneously measures adjacent shoreline topography by directly ranging the terrain with its blue-green laser. The ability to map the entire coastal zone from the dry beach through the nearshore reveals linkages between nearshore and upland processes, such as the influence of changes in nearshore bathymetry on the shape of the shoreline. For regional coastal zone management surveys, SHOALS collects individual soundings every 8 meters and surveys at a rate of 400 soundings per second, or 25 sq km per hour. The accuracy of the soundings conforms to IHO Standards, or +/- 3 m in the horizontal and +/- 15 cm in the vertical.
Accelerating MPI Message Matching by a Data Clustering Strategy

Message Passing Interface (MPI) is one of the most popular parallel programming models for high-performance computing. In MPI, message matching operations are in the critical path of communication, which could adversely affect the application performance. MPI libraries typically use a linked list data structure to maintain early posted receives and unexpected messages for matching operations. However, they perform poorly at scale due to long message queue traversals. In this paper, we propose an MPI message matching mechanism based on K-means clustering that considers the behavior of the applications to categorize the communicating peers into clusters, and assign a dedicated queue to each cluster. The clustering is done based on the number of queue elements each communicating process adds to the posted receive or unexpected message queue at runtime. The proposed approach provides an opportunity to parallelize the search operation for different processes based on the application‘s message queue characteristic. The experimental study with real applications confirm that the proposed message matching approach reduces the number of queue traversals, the queue search time, and the application runtime.
Generation and maintenance of recirculations by Gulf Stream instabilities

Abstract : This thesis studies the problems of generation and maintenance of recirculations by Gulf Stream instabilities. The problem of recirculation development is considered in a framework of a free spin down of the two-layer and the reduced-gravity, zonally symmetric, quasi-geostrophic jets. The strength of recirculations is examined as a function of the model's parameters. Linear eddy-mean flow interactions for strongly baroclinic basic flows and strongly nonlinear eddy-eddy and eddy-mean flow interaction for strongly barotropic flows are responsible for driving strongest recirculations. Low-frequency variability of the recirculations is studied in a framework of a colliding jets model with open boundary conditions and no wind forcing. When only the mechanism of barotropic instability is present, the model has two energy states. The high energy state is characterized by well-developed, spatially varying recirculations and by a pulsating eddy field. The low energy state is characterized by large meridional excursions in the jet separation point and by westward propagating meanders producing strong rings on the western wall. For physically relevant bottom friction values, the presence of baroclinic instability in the recirculation regions of the 2-layer model allows for a unique dynamical regime characterized by well-developed recirculations in both layers with weak low-frequency variability.
First documented record of barn swallow (Hirundo rustica) in the Antarctic

Here we report a photo−documented record of a barn swallow (Hirundo rustica) from the South Shetland Islands. We also review previous records of passerine vagrants in the Antarctic (south of the Antarctic Convergence Zone). This barn swallow is the first re− corded member of the Hirundinidae family on King George Island and is only the second passerine recorded in the South Shetland Islands. This sighting, along with previous records of austral negrito and austral trush represent the southernmost sightings of any passerine bird anywhere in the world.
The Risk Assessment Study of Potential Forest Fire in Idukki Wildlife Sanctuary using RS and GIS Techniques

In recent years, forest fires have become a major disaster in many countries of the world because of their impact on biodiversity, landscape, health, environment, ecology and economy. Forest fires are one of the major natural hazards occurring in the forests of the Western Ghats, a biodiversity hotspot in India. The present study aims to demarcate the risk zones of potential forest fire in Idukki Wildlife Sanctuary using integrated Remote Sensing (RS) and Geographic Information System (GIS) techniques. Every year, during March-May months, the forests in this area are affected by severe fires. In order to generate the fire risk zone map of the study area, a thematic study was carried out on each of the influencing factors viz. land cover type, slope, distance from settlement, distance from road, and elevation. A Fire Risk Index method was used to prepare the risk zone map. The area of the final map was grouped into five different categories of risk zones, viz. very low, low, moderate, high, and very high. Finally the risk zone map was validated with the fire incidence data for the last 10 years. Results of this study show that the most important factors which contribute to fire ignition are the human induced factors, also known as the anthropogenic factors. The resulting map of forest fire risk zone can be of great benefit for understanding the fire problem and will offer a more effective database for the preparation and control of forest fires.
Vitamin D and responses to inhaled fluticasone in severe chronic obstructive pulmonary disease

Background: Patients with chronic obstructive pulmonary disease (COPD) demonstrate variable responses to inhaled corticosteroids (ICS). The factors contributing to this variability are not well understood. Data from patients with asthma have suggested that low 25-hydroxyvitamin D [25(OH)D] levels contribute to a lack of ICS response in asthma. The objective of this study was to determine whether serum levels of 25(OH)D were related to ICS responses in patients with COPD. Methods: A total of 60 exsmokers with severe COPD (mean forced expiratory volume in one second [FEV 1 ] 1.07 L, 36% of predicted) spent 4 weeks free of any ICS, followed by 4 weeks of ICS use (fluticasone propionate 500 µ g twice daily). Spirometry was performed prior to and after 4 weeks of ICS use. Blood 25(OH)D levels were measured prior to ICS use and examined for relationships to changes in FEV 1 following the 4 weeks of ICS use. Results: The mean 25(OH)D level was 23.3 ± 9.3 ng/mL. There was a high prevalence of vitamin D insufficiency (35%) and deficiency (40%). There was no relationship between baseline 25(OH)D and changes in FEV 1 following 4 weeks of ICS. Conclusion: Baseline 25(OH)D does not contribute to the variation in short-term FEV 1 responses to ICS in patients with severe COPD.
Factors influencing the transparency in Portuguese Local Government : an empirical study * *

Citizens is demanding access to public information as a way to have more control over governments. Been more transparent in the conduct of their activities and political responsibilities, has been the response from governments to such pressures. A response which aim to improve good governance. Transparency is about government decisions, increasing the effectiveness of government management and look for standards of ethics (Backstrand & Saward, 2004). It about the availability of information concerning government organizations that allows citizens and other external actors to monitor and assess internal work and performance of public organizations (Meijer, 2013; Grimmelikhuijsen & Welch, 2012). It is a mechanism used to improve good governance in public services (Piotrowski, 2007; Bauhr & Grimes, 2014) and increase the public’s ability to access government information (Roberts, 2006). Literature about transparency is largely based on the explanations of the agency theory (Zimmerman, 1977) and the legitimacy theory (Patten, 1992). Based on the postulates of both theories, the purpose of this paper is to analyses the main features that are affecting transparency in Portuguese municipalities. It aims to answer the following research questions: What has been the evolution in the level of transparency in Portuguese municipalities? What factors influenced Local Government transparency? Recent literature about local governments transparency claims that the disclosure of information may be conditioned by certain socioeconomic and political characteristics (Araujo & Tejedo-Romero, 2016; Cuadrado-Ballesteros, 2014). Since transparency problems are more frequent at local level, the construction of a transparency index for municipalities by a non-governmental Portuguese agency, the Transparency and Integrity Civic Association (TIAC), open the opportunity to test which factors influence municipal transparency. This paper contributes to the literature on transparency by empirically testing a theoretical framework that explains the factors influencing Local Government transparency in Portuguese municipalities. It examines empirical evidence from Portuguese municipalities for two reasons: first, (1) to analyse the evolution of the Transparency in Portuguese municipalities, (2) to analyse the factors which influenced municipal transparency. Few studies have been produced for the Portuguese case and this is a contribution to understand municipalities answers to the increasing demands for transparency from Portuguese civil society. The empirical framework focuses on the factors, which influences transparency, using panel data and hypothesizes two explanations for it: socioeconomic and political factors. Data is collected for all the Portuguese municipalities from official sources.
Economic Geography in R: Introduction to the EconGeo Package

The R statistical software is increasingly used to perform analysis on the spatial distribution of economic activities. It contains state-of-the-art statistical and graphical routines not yet available in other software such as SAS, Stata, or SPSS. R is also free and open-source. Many graduate students and researchers, however, find programming in R either too challenging or end up spending a lot of their precious time solving trivial programming tasks. This paper is a simple introduction on how to do economic geography in R using the EconGeo package (Balland, 2017). Users do not need extensive programming skills to use it. EconGeo allows to easily compute a series of indices commonly used in the fields of economic geography, economic complexity, and evolutionary economics to describe the location, distribution, spatial organization, structure, and complexity of economic activities. Functions include basic spatial indicators such as the location quotient, the Krugman specialization index, the Herfindahl or the Shannon entropy indices but also more advanced functions to compute different forms of normalized relatedness between economic activities or network-based measures of economic complexity. By opening and sharing the codes used to compute popular indicators of the spatial distribution of economic activities, one of the goals of this package is to make peer-reviewed empirical studies more reproducible by a large community of researchers.
Preventing Depression in Adults With Subthreshold Depression: Health-Economic Evaluation Alongside a Pragmatic Randomized Controlled Trial of a Web-Based Intervention

Background Psychological interventions for the prevention of depression might be a cost-effective way to reduce the burden associated with depressive disorders. Objective To evaluate the cost-effectiveness of a Web-based guided self-help intervention to prevent major depressive disorder (MDD) in people with subthreshold depression (sD). Methods A pragmatic randomized controlled trial was conducted with follow-up at 12 months. Participants were recruited from the general population via a large statutory health insurance company and an open access website. Participants were randomized to a Web-based guided self-help intervention (ie, cognitive-behavioral therapy and problem-solving therapy assisted by supervised graduate students or health care professionals) in addition to usual care or to usual care supplemented with Web-based psycho-education (enhanced usual care). Depression-free years (DFYs) were assessed by blinded diagnostic raters using the telephone-administered Structured Clinical Interview for DSM-IV Axis Disorders at 6- and 12-month follow-up, covering the period to the previous assessment. Costs were self-assessed through a questionnaire. Costs measured from a societal and health care perspective were related to DFYs and quality-adjusted life years (QALYs). Results In total, 406 participants were enrolled in the trial. The mean treatment duration was 5.84 (SD 4.37) weeks. On average, participants completed 4.93 of 6 sessions. Significantly more DFYs were gained in the intervention group (0.82 vs 0.70). Likewise, QALY health gains were in favor of the intervention, but only statistically significant when measured with the more sensitive SF-6D. The incremental per-participant costs were €136 (£116). Taking the health care perspective and assuming a willingness-to-pay of €20,000 (£17,000), the intervention’s likelihood of being cost-effective was 99% for gaining a DFY and 64% or 99% for gaining an EQ-5D or a SF-6D QALY. Conclusions Our study supports guidelines recommending Web-based treatment for sD and adds that this not only restores health in people with sD, but additionally reduces the risk of developing a MDD. Offering the intervention has an acceptable likelihood of being more cost-effective than enhanced usual care and could therefore reach community members on a wider scale. Trial registration German Clinical Trials Register: DRKS00004709; http://www.drks. de/DRKS00004709 (Archived by WebCite at http://www.webcitation.org/6kAZVUxy9)
Transesophageal Echocardiography in Cryptogenic Stroke and PFO : The Analysis of Putative High Risk Features from the Risk of Paradoxical Embolism ( RoPE ) Database

Benjamin Wessler, MD; David E. Thaler, MD, PhD; Robin Ruthazer, MPH; Christian Weimar, MD; Marco R. Di Tullio, MD; Mitchell S. V. Elkind, MD, MS; Shunichi Homma, MD; Jennifer S. Lutz, MS; Jean-Louis Mas, MD; Heinrich P. Mattle, MD; Bernhard Meier, MD; Krassen Nedeltchev, MD; Federica Papetti, MD; Emanuele Di Angelantonio, MD, MSc, PhD; Mark Reisman, MD; Joaquín Serena, MD, PhD; David M. Kent , MD, CM, MSc
Use of Passive Samplers to Evaluate Pharmaceutical Fate in Surface Waters

Emerging contaminants have been of importance in recent water research. Wastewater treatment plants (WWTPs) have proved ineffective at handling present-day antibiotic loads from hospital and municipal sources. Kolpin et al. (2002) performed a study that identified pharmaceuticals in numerous waters downstream from effluent discharge. Though present in trace levels, concern has been raised regarding pharmaceutical persistence in natural environments. In the present study, uptake rates were quantified in the laboratory for 25 pharmaceutical compounds using Polar Organic Chemical Integrative Samplers (POCIS). Twenty new uptake rates were determined for compounds that have no previously reported literature values. POCIS was also used to evaluate the fate of polar organic contaminants in Nebraska surface waters impacted by WWTP effluent. Select pharmaceuticals were observed to persist for at least 1300 m downstream. Carbamazepine and DEET showed persistence and the highest average concentrations of 110 and 60 ng/L, respectively. Decay rates were determined for 25 pharmaceuticals in receiving waters. Pharmaceutical loading rates were calculated for each compound using the average in-stream concentration and volumetric flow rate. Acknowledgements I would like to thank my adviser Dr. Shannon Bartelt-Hunt for doing an excellent job at supervising and directing this project. During times of frustration and misdirection, she provided advice that allowed me to circumvent problems along the path to completion. At the beginning of the paper I was a bit overwhelmed at the task before me, but as I finalized corrections suggested by my committee, I have acquired a new found appreciation for option I MS students and research as a whole. Preparation and defense of my research has been time-consuming, but a very satisfying experience, nonetheless. Dr. Daniel Snow also played a pivotal role in the completion of this work. He accompanied me to field, rubber waders and all, to deploy passive samplers in the effluent streams at both sites. The Hastings drainage canal was memorable due to stream turbidity, smell, and " sinking " sediment substance located at bottom of the ditch. Dr. Snow and Teyona Damon at the Water Science Laboratory were responsible for carrying out the analytical methods and recovery of pharmaceuticals from samplers. The data recovered was an essential part of accomplishing objectives set forth during research. Dr. Tian Zhang provided suggestions that made this thesis a lot more concise. After his editorial comments, I believe the average student with little to no prior knowledge 3 4 of emerging contaminants could read …
The Giant Mascot Ni-Cu-PGE Deposit, British Columbia: Mineralized Conduits in a Convergent Margin Tectonic Setting

The Giant Mascot Ni-Cu-PGE deposit is the only past-producing nickel mine (1958–1974) in the Canadian Cordillera of British Columbia, Canada, with ~4.2 Mt of ore grading 0.77% Ni and 0.34% Cu (Ni/Cu = 2.3). The deposit is part of an emerging class of convergent margin Ni-Cu-PGE sulfide deposits where the host rocks are characterized by abundant orthopyroxene and magmatic hornblende. The Giant Mascot intrusion is a crudely elliptical, 3- × 2-km plug composed of ultramafic arc cumulates (olivine-orthopyroxene, hornblende-clinopyroxene) that intruded the Late Cretaceous Spuzzum dioritic pluton. The ores are contained within subvertical pipe-like, lensoid, and tabular bodies ( n = 28), interpreted to represent mineralized conduits and consist of pyrrhotite, pentlandite (+argentopentlandite), chalcopyrite, minor pyrite, troilite, and Pt-Pd-Ni bismuthotellurides. The sulfides have moderate tenors (3–14 wt % Ni, 0.1–17.1 wt % Cu, 84 ppb to 5 ppm total PGE), and variations in PGE concentrations distinguish two geographic mineralized zones (western and eastern). Sulfur isotopes for sulfides span a restricted range of δ 34 S values (−3.4 to −1.3‰) and overlap with analyses from locally pyritiferous Settler schist (−5.4 to −1.2‰). Olivine chemistry reveals a wide range of both Fo (80–89 mol %) and Ni contents (336–3,859 ppm) and provides evidence that Ni contents of olivine were locally upgraded during equilibration with sulfide liquid. Sulfide saturation in the Giant Mascot parental magma(s) was triggered in response to (1) reduction of an oxidized, mantle-derived arc magma, producing ores that formed at an oxidation state of ~ ΔQFM +1; (2) addition of external sulfur and silica by assimilation of Settler schist and Spuzzum diorites; and (3) fractional crystallization of olivine ± orthopyroxene. The presence of high-tenor sulfides in the Giant Mascot deposit indicates that orthomagmatic Ni-Cu-PGE deposits in convergent margin tectonic settings may be of significance to future global exploration.