Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutational Inactivation of the Nijmegen Breakage Syndrome Gene (NBS1) in Glioblastomas Is Associated With Multiple TP53 Mutations

Nijmegen breakage syndrome caused by NBS1 germline mutations is a rare autosomal recessive disease with clinical features that include microcephaly, increased radiosensitivity, and predisposition to cancer. NBS1 plays a key role in DNA double-strand break repair and the maintenance of genomic stability. We screened 87 glioblastomas for NBS1 mutations (all 16 exons). Single-strand conformation polymorphism followed by direct DNA sequencing revealed 12 NBS1 mutations (8 missense and 4 intronic mutations) in 9 (32%) of 28 primary (de novo) glioblastomas carrying 2 or more TP53 mutations. None of the NBS1 mutations has been previously reported as a germline mutation in Nijmegen breakage syndrome patients. NBS1 mutations were not detected in 19 primary glioblastomas with 1 TP53 mutation or in 21 primary glioblastomas without TP53 mutations. Secondary glioblastomas that developed through progression from low-grade or anaplastic astrocytoma had TP53 mutations in 16 (84%) of 19 cases, but none contained mutations of the NBS1 gene. These results suggest that multiple TP53 mutations in glioblastomas are due to deficient repair of DNA double-strand breaks caused by mutational inactivation of the NBS1 gene.
Increasing airline travel may facilitate co-circulation of multiple dengue virus serotypes in Asia

The incidence of dengue has grown dramatically in recent decades worldwide, especially in Southeast Asia and the Americas with substantial transmission in 2014–2015. Yet the mechanisms underlying the spatio-temporal circulation of dengue virus (DENV) serotypes at large geographical scales remain elusive. Here we investigate the co-circulation in Asia of DENV serotypes 1–3 from 1956 to 2015, using a statistical framework that jointly estimates migration history and quantifies potential predictors of viral spatial diffusion, including socio-economic, air transportation and maritime mobility data. We find that the spread of DENV-1, -2 and -3 lineages in Asia is significantly associated with air traffic. Our analyses suggest the network centrality of air traffic hubs such as Thailand and India contribute to seeding dengue epidemics, whilst China, Cambodia, Indonesia, and Singapore may establish viral diffusion links with multiple countries in Asia. Phylogeographic reconstructions help to explain how growing air transportation networks could influence the dynamics of DENV circulation.
Different Patterns of Epstein-Barr Virus Latency in Endemic Burkitt Lymphoma (BL) Lead to Distinct Variants within the BL-Associated Gene Expression Signature

ABSTRACT Epstein-Barr virus (EBV) is present in all cases of endemic Burkitt lymphoma (BL) but in few European/North American sporadic BLs. Gene expression arrays of sporadic tumors have defined a consensus BL profile within which tumors are classifiable as “molecular BL” (mBL). Where endemic BLs fall relative to this profile remains unclear, since they not only carry EBV but also display one of two different forms of virus latency. Here, we use early-passage BL cell lines from different tumors, and BL subclones from a single tumor, to compare EBV-negative cells with EBV-positive cells displaying either classical latency I EBV infection (where EBNA1 is the only EBV antigen expressed from the wild-type EBV genome) or Wp-restricted latency (where an EBNA2 gene-deleted virus genome broadens antigen expression to include the EBNA3A, -3B, and -3C proteins and BHRF1). Expression arrays show that both types of endemic BL fall within the mBL classification. However, while EBV-negative and latency I BLs show overlapping profiles, Wp-restricted BLs form a distinct subgroup, characterized by a detectable downregulation of the germinal center (GC)-associated marker Bcl6 and upregulation of genes marking early plasmacytoid differentiation, notably IRF4 and BLIMP1. Importantly, these same changes can be induced in EBV-negative or latency I BL cells by infection with an EBNA2-knockout virus. Thus, we infer that the distinct gene profile of Wp-restricted BLs does not reflect differences in the identity of the tumor progenitor cell per se but differences imposed on a common progenitor by broadened EBV gene expression.
The Standard Model of particle physics in other universes

The purpose of this paper is to demonstrate how the mathematical objects and structures associated with the particle physics in other universes, can be inferred from the mathematical objects and structures associated with the particle physics in our own universe. As such, this paper is a continuation of the research programme announced in McCabe (2004), which implemented this idea in the case of cosmology. The paper begins with an introduction that outlines the structuralist doctrine which this research programme depends upon. Section 2 explains how free elementary particles in our universe correspond to irreducible representations of the double cover of the local space-time symmetry group, and relates the configuration representation to the momentum representation. The difficulties of treating elementary particles in curved space-time, and the Fock space second-quantization are also explained. Section 2.1 explores the particle physics of universes in which the local symmetry group is the entire Poincare group or the isochronous Poincare group. Section 2.2 considers free particles in universes with a different dimension or geometrical signature to our own. Section 3 introduces gauge fields, and, via Derdzinski's interaction bundle approach, explains how connections satisfying the Yang-Mills equations correspond to the irreducible representations for `gauge bosons'. To explore the possible gauge fields, section 3.1 explains the classification of principal G-bundles over 4-manifolds, and section 3.2 expounds the structure theorem of compact Lie groups. Section 3.3 summarises the consequences for classifying gauge fields in other universes, and section 3.4 infers the structures used to represent interacting particles in other universes. The paper concludes in Section 3.5 by explaining the standard model gauge groups and irreducible representations which define interacting particle multiplets, and specifies the possibilities for such multiplets in other universes.
Heritability of corticosterone response and changes in life history traits during selection in the zebra finch

Vertebrates respond to environmental stressors through the neuro‐endocrine stress response, which involves the production of glucocorticoids. We have selected independent, duplicate divergent lines of zebra finches for high, low and control corticosterone responses to a mild stressor. This experiment has shown that over the first four generations, the high lines have demonstrated a significant realized heritability of about 20%. However, the low lines have apparently not changed significantly from controls. This asymmetry in response is potentially because of the fact that all birds appear to be showing increased adaptation to the environment in which they are housed, with significant declines in corticosterone response in control lines as well as low lines. Despite the existence of two‐ to threefold difference in mean corticosterone titre between high and low lines, there were no observed differences in testosterone titre in adult male birds from the different groups. In addition, there were no consistent, significant differences between the lines in any of the life history variables measured – number of eggs laid per clutch, number of clutches or broods produced per pair, number of fledglings produced per breeding attempt, nor in any of egg, nestling and fledgling mortality. These results highlight the fact that the mechanisms that underlie variation in the avian physiological system can be modified to respond to differences between environments through selection. This adds an additional level of flexibility to the avian physiological system, which will allow it to respond to environmental circumstances.
Fast-multipole-method solutions of new potential integral equations

A recently introduced potential integral equations for stable analysis of low-frequency problems involving dense discretizations with respect to wavelength are solved by using the fast multipole method (FMM). Two different implementations of FMM based on multipoles and an approximate diagonalization employing scaled plane waves are developed and used for rigorous solutions of low-frequency problems. Numerical results on canonical problems demonstrate excellent stability and solution capabilities of both implementations.
Vertically scaled MOSFET gate stacks and junctions: How far are we likely to go?

The vertical scaling requirements for gate stacks and for shallow extension junctions are reviewed. For gate stacks, considerable progress has been made in optimizing oxide/nitride and oxynitride dielectrics to reduce boron penetration and dielectric leakage compared to pure SiO2 in order to allow sub-2-nm dielectrics. Several promising alternative material candidates exist for 1-nm equivalent oxide thickness (EOT)-for example, HfO2, ZrO2, and their silicates. Nevertheless, considerable challenges lie ahead if we are to achieve an EOT of less than 0.5 nm. If only a single molecular interface layer of oxide is needed to preserve high channel mobility, it seems likely that an EOT of 0.4-0.5 nm would represent the physical limit of dielectric scaling, but even then with a very high leakage (∼105 A/cm2). For junctions, the main challenge lies in providing low parasitic series resistance as depths are scaled in order to reduce short-channel effects. Because contacts are ultimately expected to dominate the parasitic resistance, low-barrier-height contacts and/or very heavily doped junctions will be required. While ion implantation and annealing processes can certainly be extended to meet the junction-depth and series-resistance requirements for additional generations, alternative low-temperature deposition processes that produce either metastably or extraordinarily activated, abruptly doped regions seem better suited to solve the contact resistance problem.
Kepler GPU accelerated recursive sorting using dynamic parallelism

This paper focuses on the performance gain obtained on the Kepler graphics processing units (GPUs) for multi‐key quicksort. Because multi‐key quicksort is a recursive‐based algorithm, many of the researchers have found it tedious to parallelize the algorithm on the multi and many core architectures. A survey of the state‐of‐the‐art string sorting algorithms and a robust insight of the Kepler GPU architecture gave rise to an intriguing research idea of matching the template of multi‐key quicksort with the dynamic parallelism feature offered by the Kepler‐based GPU's. The CPU parallel implementation has an improvement of 33 to 50% and 62 to 75 improvement when compared with 8‐bit and 16‐bit parallel most significant digit radix sort, respectively. The GPU implementation of multi‐key quicksort gives 6× to 18× speed up compared with the CPU parallel implementation of parallel multi‐key quicksort. The GPU implementation of multi‐key quicksort achieves 1.5× to 3× speed up when compared with the GPU implementation of string sorting algorithm using singleton elements in the literature. Copyright © 2016 John Wiley & Sons, Ltd.
OPENRP: a reputation middleware for opportunistic crowd computing

The concepts of wisdom of crowd and collective intelligence have been utilized by mobile application developers to achieve large-scale distributed computation, known as crowd computing. The profitability of this method heavily depends on users' social interactions and their willingness to share resources. Thus, different crowd computing applications need to adopt mechanisms that motivate peers to collaborate and defray the costs of participating ones who share their resources. In this article, we propose OPENRP, a novel, lightweight, and scalable system middleware that provides a unified interface to crowd computing and opportunistic networking applications. When an application wants to perform a device-to-device task, it delegates the task to the middleware, which takes care of choosing the best peers with whom to collaborate and sending the task to these peers. OPENRP evaluates and updates the reputation of participating peers based on their mutual opportunistic interactions. To show the benefits of the middleware, we simulated the behavior of two representative crowdsourcing applications: message forwarding and task offloading. Through extensive simulations on real human mobility traces, we show that the traffic generated by the applications is lower compared to two benchmark strategies. As a consequence, we show that when using our middleware, the energy consumed by the nodes is reduced. Finally, we show that when dividing the nodes into selfish and altruistic, the reputation scores of the altruistic peers increase with time, while those of the selfish ones decrease.
Magnetresonanztomografie unter besonderer Berücksichtigung entzündlicher Knochenerkrankungen

Zusammenfassung Bei Kindern, die Schmerzen im Muskel- und Skelettapparat beklagen, ist eine große Bandbreite von Differenzialdiagnosen zu beachten. Abgesehen von einer Arthritis muss eine chronische Entzündung der Sehnen, des Periosts, der Knochen, der Muskeln und sogar der Haut berücksichtigt werden. Besonders wichtig ist die Differenzialdiagnose zu onkologischen und metabolischen Erkrankungen sowie Traumata. Noch vor zehn Jahren war die Technetium-Knochenszintigrafie das einzige Mittel, um einen Überblick über das gesamte Skelett innerhalb eines überschaubaren diagnostischen Zeitrahmens zu erhalten. In den vergangenen Jahren jedoch wurde die Ganzkörpermagnetresonanztomografie etabliert, die es dem/der pädiatrischen Radiologen/in rasch ermöglicht, Strukturveränderungen nicht nur im Knochen, sondern auch in allen Strukturen des muskuloskelettalen Systems abzubilden. Die vorliegende Arbeit gibt einen Einblick in die Differenzialdiagnose, indem sie besondere Erkrankungsbilder beschreibt. Die Relevanz der Magnetresonanztomografie in Verbindung mit anderer pädiatrisch-radiologischer Bildgebung wird erörtert.
Requirements and design of an integrated European environmental information communication system, (IEEICS)

The needs for various forms of information systems relating to the European environment and ecosystem are reviewed, and limitations indicated. Existing information systems are reviewed and compared in terms of aims and functionalities. We consider TWO technical challenges involved in attempting to develop an IEEICS. First, there is the challenge of developing an Internet-based communication system which allows fluent access to information stored in a range of distributed databases. Some of the currently available solutions are considered, i.e. Web service federations. The second main challenge arises from the fact that there is general intra-national heterogeneity in the definitions adopted, and the measurement systems used throughout the nations of Europe. Integrated strategies are needed.
GAINING COMPETITIVE ADVANTAGE USING EFFECTIVE SUPPLY CHAIN MANAGEMENT

With supply chains becoming more elongated as they become more global, the pace of demand changes increasing and product lifecycles shrinking, the responsiveness of a company’s supply and fulfillment networks to change is becoming a more substantial determinant of company success. As such, companies must view their supply networks as a competitive weapon that can not only deliver low costs but impact top-line growth through superior responsiveness and best-in-class customer service. If these and other similar strategies as will be described in this write-up are available for only one company at the markets, this company has competitive advantage over its competitors (Barney, 1991; ketchen, 2004; Rungtusanatham et al., 2003). Another way to gain competitive advantage is to optimize one or several activities. However, a consideration has to be taken so that optimization does not end in optimizing one function at the expense of the others (Lumsden, 1998; Porter, 1985).
Architecture of a Consumer Lab-on-Chip for Pharmacogenomics

This paper presents the architecture of the electronic detection and data processing (analysis) part, of a lab-on-chip (LoC) device. The LoC consists of a microfluidics part for the sample preparation and hybridization, a micro-system part including the sensors for the hybridization electronic detection and finally a processing part for the data analysis and the consumer interface for results presentation. Consumers will use such LoCs for identifying the appropriate cluster of a pharmacogenomic medicine based on the gene analysis results and optimize the effectiveness of the drug or determine whether they belong to a group of patients who would suffer severe side effects.
Achilles Tendon Disorders in Athletes

Achilles tendon disorders are among the more common maladies seen by sports medicine physicians. Understanding the anatomy and biomechanics of the Achilles tendon and contiguous structures is essential to the diagnosis and treatment of Achilles tendon overuse injuries. Posterior heel pain is multifactorial and includes paratenonitis, tendinosis, tendinosis with partial rupture, insertional tendinitis, retrocalcaneal bursitis, and subcutaneous tendo-Achillis bursitis. Each of these entities is distinct, but they often occur in combination. Although most cases of this disorder are successfully treated nonoperatively, a small subgroup of recalcitrant cases may benefit from surgical intervention. Complete ruptures in active, athletic persons should be treated operatively in most cases and result in predictably good outcomes. There may be some cases that escape early recognition and require a reconstructive procedure to salvage a potentially severe functional deficit.
Clinical Study on Lobaplatin Combined with 5-Fu and Concurrent Radiotherapy in Treating Patients with Inoperable Esophageal Cancer.

OBJECTIVE To investigate short- and long-term treatment effects and side reactions of lobaplatin plus 5-Fu combined and concurrent radiotherapy in treating patients with inoperable middle-advanced stage esophageal cancer. METHODS Sixty patients with middle-advanced stage esophageal squamous cell cancer were retrospectively analyzed. All patients were administered lobaplatin (50 mg intravenously) for 2 h on day 1, and 5-Fu (500 mg/m2) injected intravenously from day 1 to 5 for 1 cycle, in an interval of 21 days for totally 4 cycles. At the same time, late-course accelerated hyperfractionated three-dimensional conformal radiotherapy was performed. Patients were firstly treated with conventional fractionated irradiation (1.8 Gy/d, 5 times/week, a total of 23 treatments, and DT41.4 Gy), and then treated with accelerated hyperfractionated irradiation (1.5 Gy, 2 times/d, a total of 27 Gy in 9 days, an entire course of 6-7 weeks, and DT 68.4 Gy). RESULTS All patients completed treatment, including 10 complete response (CR), 41 partial response (PR), 7 stable disease (SD), and 2 progressive disease (PD). The total effective rate was 85.0% (51/60). Thirty-nine patients had an increased KPS score. One-, 2-, and 3-year survival rates were 85.3%, 57.5%, and 41.7%, respectively. The median survival time was 27 months. The adverse reactions included myelosuppression, which was mainly degreeI and II. The occurrence rate of radiation esophagitis was 17.5%. No significant hepatic or renal toxicity was observed. CONCLUSION Lobaplatin plus 5-Fu combined with concurrent radiotherapy is safe and effective in treating patients with middle-advanced stage esophageal cancer. However, this result warrants further evaluation by randomized clinical studies.
Organ Accumulation in Mice After Inhalation of Single or Mixed Essential Oil Compounds

Essential oils are composed of multiple components. It is thought that the effect of essential oils is due to specific component ratios, which may differ from the original ratio when the essential oil is absorbed. However, very little detailed research exists in this area. We studied the distribution of essential oil components after inhalation of single and mixed components in mice. This research was done using four main components of Alpinia zerumbet (Pers.) B. L. Burtt. and R. M. Sm. : α‐pinene, p‐cymene, 1,8‐cineole, and limonene. After inhalation of single or mixed components for 90 min, component levels in the brain and liver of mice were measured. The results indicated that the amount of α‐pinene in the brain and liver was twofold greater after mixed‐component inhalation than that after single‐component inhalation. In a comparison of the components of the mixed inhalation, the ratio of α‐pinene increased to about three times that of 1,8‐cineole. It is thought that the absorption via the nasal mucus greatly influences this phenomenon. The results of this investigation of the bodily distribution of essential oil volatile components may provide clues for elucidating their action. Copyright © 2012 John Wiley & Sons, Ltd.
Índice de vulnerabilidad de la población en situación de discapacidad en Medellín

Objetivo Construir un indice de vulnerabilidad para la poblacion de Medellin en situacion de discapacidad en el 2008, con el fin de determinar los aspectos que disminuyen las oportunidades de hacer uso de sus activos materiales e inmateriales, deteriorando por ende la calidad de vida de esta poblacion. Metodos Estudio descriptivo transversal, con fuente de informacion secundaria de personas con algun tipo de limitacion registrada en la Encuesta de Calidad de Vida 2008. En la construccion del indice se agruparon las variables en los componentes fisico, humano, social, se corrieron modelos de analisis de componentes principales para determinar los grados de vulnerabilidad, los cuales se definieron segun numero de factores negativos identificados, quedando la categoria alta (4 o 5), mediana (2 o 3), y baja (1 o ninguno). Con esta clasificacion, se identificaron relaciones no causales con las variables demograficas, a traves de las pruebas de Mann-Whitney, Chi-cuadrado y Kruskal-Wallis, con nivel de significacion estadistica del 5,0 %;y medidas epidemiologicas, como razon de oportunidad e intervalo de confianza, se calcularon medidas ajustadas a traves de regresion logistica multinomial. Resultados El grado de vulnerabilidad media predomino en las personas en situacion de discapacidad de Medellin con el 60,3 %, seguido de la poblacion con baja vulnerabilidad (28,7 %) y con alta vulnerabilidad se encontro el 11,0 %. Conclusiones El indice de vulnerabilidad que se propone, clasifica las comunas de la ciudad segun vulnerabilidad alta, media o baja, apoyado en el uso de tecnicas estadisticas y de ubicacion espacial.
The isolation, properties, and enzymic breakdown of linamarin from cassava.

A new method for the isolation of linamarin from Cassava is described. Using the pure glucoside, its properties and assay were investigated and a number of modifications to the previous assay procedure were introduced. The paper chromatography of the glucoside and means of detecting it on chromatograms are described. A procedure for preparing and assaying a crude preparation of linamarase is given. The variation in activity with pH, the stability of the enzyme, and its inhibition by buffers and by (1·5)-gluconolactone are described. A suggestion is made as to the role of linamarin and linamarase in the plant.