Miracle-dz/UniFAR-FTUs huggingface dataset:
Probing mechanisms of transcription elongation through cell-to-cell variability of RNA polymerase

The process of transcription initiation and elongation are primary points of control in the regulation of gene expression. While biochemical studies have uncovered the mechanisms involved in controlling transcription at each step, how these mechanisms manifest in vivo at the level of individual genes is still unclear. Recent experimental advances have enabled single-cell measurements of RNAP molecules engaged in the process of transcribing a gene of interest. In this manuscript, we use Gillespie simulations to show that measurements of cell-to-cell variability of RNAP numbers and inter-polymerase distances can reveal the prevailing mode of regulation of a given gene. Mechanisms of regulation at each step, from initiation to elongation dynamics, produce qualitatively distinct signatures which can further be used to discern between them. Intriguingly, depending on the initiation kinetics, stochastic elongation can either enhance or suppress cell-to-cell variability at the RNAP level. To demonstrate the value of this framework, we analyze RNAP number distribution data for ribosomal genes in S. cerevisiae from three previously published studies and show that this approach provides crucial mechanistic insights into the transcriptional regulation of these genes. Author Summary The process of transcription comprises many distinct steps and understanding the regulation of each of these steps provides insight into how the levels of gene expression are controlled in the cell. In this manuscript, we use stochastic simulations to explore how regulation at the level of elongation and initiation together influences the distribution of actively transcribing RNAP on a gene. We find that each of these steps of regulation leaves a distinct imprint on the gene-to-gene variability of number of actively transcribing RNAP on the gene and their inter-RNAP distances. Using these results, we analyze recent experimental data of transcribing RNAP distributions and find that the perturbations in these studies primarily impact the transcription initiation dynamics of the genes.
A Framework of Evaluation Methodologies for Network Anomaly Detectors

Anomaly detection has been a field of intensive research over the last years. Along with that several works to evaluate anomaly detectors have been proposed. In this paper we argue four properties regarding ideal evaluation methodologies that cannot be answered by single current evaluation technique employed today. We therefore present an framework of an evaluation methodology that leverages traces from operational networks, simulation and emulation to satisfy the four properties.
Automatic semantic image annotation and retrieval

As the number of Web images is increasing at a rapid rate, searching them semantically presents a significant challenge. Many raw images are constantly uploaded with few meaningful direct annotations of semantic content, limiting their search and discovery. As definite relationships exist between the type of scenes and image acquisition parameters, image metadata and parametric dimensions, it is possible to determine from these the semantic content of images. By exploiting the judgment and expertise that has gone into the image-capture process, and through the use of decision trees and rule induction, we have established a set of rules which allows the semantic contents of images to be identified. When jointly applied with ontology-based and contextual-based expansion approaches, they are able to produce a new level of meaningful automatic image annotation, from which meaningful high-level semantic image searches are performed. The system is evaluated quantitatively using more than 100,000 Web images with 1,000,000 associated human tags outside the training database. Experimental results indicate that this approach is able to deliver highly competent performance, attaining good recall and precision rates of sometimes over 80%. This approach enables an advanced degree of semantic richness to be automatically associated with images which could previously only be performed manually.
Outcome of Concurrent Chemoradiotherapy and Radiotherapy Alone Following Induction Chemotherapy in Locally Advanced Squamous Cell Carcinoma of Head and Neck

Non-operative treatment strategies like radiotherapy and chemotherapy are practiced widely nowadays for the treatment of locally advanced squamous cell carcinoma of head and neck origin. Aim of this study was to compare the response of induction chemotherapy followed by radiotherapy alone with induction chemotherapy followed by concurrent chemoradiotherapy in terms of treatment response and toxicities. A quasi-experimental study was carried out in the Department of Radiation Oncology, National Institute of Cancer Research and Hospital (NICR&H), Dhaka; Department of Radiotherapy, Dhaka Medical College Hospital (DMCH), Dhaka and Department of Oncology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka during the period of January, 2014 to December, 2014. Induction chemotherapy by Cisplatin and 5-Fluorouracil was given to all the patients of Arm A and Arm B. Cisplatin was given concurrently during Radiotherapy weekly in case of Arm A. Arm B received radiotherapy alone. The patients were evaluated from the beginning of the treatment up to six months following the completion of treatment. In this study, male to female ratio was 4:1 and mean age of patients were 54.7±9.1 and 56.6±7.9 in Arm A and Arm B respectively. At final follow-up, complete response was seen in 27 (53.3%) patients of Arm A and Arm B respectively. Response rate was significant (p <0.05) for both the Arms. Acute toxicities observed during induction chemotherapy were almost equal in both the Arms, but during radiotherapy, Arm A had more toxicity though it was statistically insignificant. Induction chemotherapy followed by concurrent chemoradiotherapy is more effective than induction chemotherapy followed by radiotherapy alone in loco-regional control of locally advanced squamous cell carcinoma of head and neck origin.
Globalisation and health: action now!

There is a growing concern about the effects of globalisation on health. Different positions for and against globalisation are arising in the public health community world wide as they are in the different political persuasions in our societies. The JECH offers to its readers a debate on this topic with participation of Frances Baum, Ron Labonte, Douglas Bettcher, Heather Wipfli, and Kelley Lee. Irrespective of the positions of the different persuasions for and against globalisation, there is a growing body …
Utilización del Anacardium occidentale como nutracéutico en dietas hipoproteicas para gallinas ponedoras

Para evaluar la utilizacion del Anacardium occidentale como nutraceutico en dietas hipoproteicas para gallinas ponedoras, se utilizaron 160 gallinas White Leghorn (Hibrido L-33) de 30 semanas de edad, en pleno pico de puesta, durante 91 d. Se aplico un diseno totalmente aleatorizado, con cuatro tratamientos de polvo de hojas y retonos de Anacardium occidentale (0; 0.5; 1.0 y 1.5 %) como aditivo nutraceutico. No se evidencio morbilidad y mortalidad con la inclusion de este polvo en las dietas. La adicion de hasta 1.5 % de polvo de Anacardium occidentale incremento la produccion (75.50 a 80.00 %), el peso del huevo (61.20 a 62.37 g), la altura de la clara densa (6.72 a 7.78 mm), el grosor (0.36 a 0.41 mm) y la superficie de la cascara (75.90 a 78.24 cm2). La intensidad del color de la yema (10) se marco para la adicion de 0.5 % del polvo. La adicion de este polvo medicinal no disminuyo la calidad sensorial del albumen y la yema del huevo. No hubo afectaciones en el examen hematologico de las gallinas a las 30 y 43 semanas. Sin embargo, las dietas hipoproteicas incidieron en las proteinas totales del plasma (44.70 a 47.00 g/L). Se recomienda la utilizacion de 1.5 % de polvo de hojas y retonos de Anacardium occidentale en dietas hipoproteicas para gallinas ponedoras, con el proposito de incrementar la produccion y calidad del huevo, sin afectar su calidad sensorial, ni los indicadores de salud de las aves.
CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies

Motivation Although genome-wide association studies (GWAS) have deepened our understanding of the genetic architecture of complex traits, the mechanistic links that underlie how genetic variants cause complex traits remains elusive. To advance our understanding of the underlying mechanistic links, various consortia have collected a vast volume of genomic data that enable us to investigate the role that genetic variants play in gene expression regulation. Recently, a collaborative mixed model (CoMM) [42] was proposed to jointly interrogate genome on complex traits by integrating both the GWAS dataset and the expression quantitative trait loci (eQTL) dataset. Although CoMM is a powerful approach that leverages regulatory information while accounting for the uncertainty in using an eQTL dataset, it requires individual-level GWAS data and cannot fully make use of widely available GWAS summary statistics. Therefore, statistically efficient methods that leverages transcriptome information using only summary statistics information from GWAS data are required. Results In this study, we propose a novel probabilistic model, CoMM-S2, to examine the mechanistic role that genetic variants play, by using only GWAS summary statistics instead of individual-level GWAS data. Similar to CoMM which uses individual-level GWAS data, CoMM-S2 combines two models: the first model examines the relationship between gene expression and genotype, while the second model examines the relationship between the phenotype and the predicted gene expression from the first model. Distinct from CoMM, CoMM-S2 requires only GWAS summary statistics. Using both simulation studies and real data analysis, we demonstrate that even though CoMM-S2 utilizes GWAS summary statistics, it has comparable performance as CoMM, which uses individual-level GWAS data. Contact jin.liu@duke-nus.edu. sg Availability and implementation The implement of CoMM-S2 is included in the CoMM package that can be downloaded from https://github.com/gordonliu8100822/CoMM https://github.com/gordonliu8100822/CoMM. Supplementary information Supplementary data are available at Bioinformatics online.
DESIGN AND IMPLEMENTATION OF DEADLOCK CONTROL FOR AUTOMATED MANUFACTURING SYSTEMS

Petri nets are robust mathematical tools for the modelling, handling, and control of deadlock problems in automated manufacturing systems (AMSs). Several methods have been proposed to prevent deadlocks in AMSs. However, it is important to convert the controlled system represented by Petri nets into the program of a programmable logic controller (PLC) for the implementation of automation tasks. This study proposes a methodology based on Petri nets for deadlock prevention, and generates PLC codes for an AMS. In the suggested methodology, a Petri net model of an uncontrolled system is built, and the controlled Petri net model is developed using a deadlock-prevention method. The controlled Petri net model is then transformed into an automation-controlled Petri net model, which is further converted into a controlled token-passing logic model. The controlled token- passing logic model is utilised to generate the ladder diagrams for the AMS under consideration. The proposed methodology was tested using a real-world AMS at King Saud University labs. It provides an effective method for PLC implementation from a controlled system model represented by Petri nets.
Cellular and molecular analysis of extracellular matrix induced signalling cues on the differentiation of oligodendrocytes

Oligodendrocyten sind die myelinbildenden Zellen des zentralen Nervensystems und unabdingbar fur schnelle Reizweiterleitung, da das Myelin die elektrische Isolierung der Nervenfasern darstellt. Die Differenzierung von Oligodendrocyten erfolgt schrittweise von simplen Vorlauferzellen, uber unreife Pro-Oligodendrocyten bis hin zu terminal differenzierten Oligodendrocyten. Im Rahmen meiner Promotion habe ich mich mit dem Einfluss extrazellularer Matrixmolekule auf das Differenzierungsverhalten von Oligodendrocyten befasst. Ich konnte zeigen, dass definierte Komponenten der extrazellularen Matrix Oligodendrocytendifferenzierung unterschiedlich beeinflussen, da die Differenzierung, abhangig von der Zusammensetzung der Matrix, gehemmt oder gefordert wurde. Weiterhin ist es gelungen, am Beispiel des Tenascin C Molekuls die ausgelosten Signalkaskaden aufzuklaren die zur Beeinflussung der Differenzierung von Oligodendrocyten fuhren.
A New Periacetabular Osteotomy for the Treatment of Hip Dysplasias

The Bernese periacetabular osteotomy described by Ganz et al restores the position and acetabular coverage of the dysplastic hip to nearly normal, but it has several disadvantages due to the asphericity of the osteotomy surfaces. Because this osteotomy is a series of straight cuts, incongruity at the site of the osteotomy and anterior displacement of the hip joint may occur in patients who need an extensive acetabular reorientation. We designed a curved periacetabluar osteotomy to improve these drawbacks.The direct anterior approach described by Murphy et al is used with the patient supine. The triple osteotomy is done with a specially curved osteotome, designed to approximately correspond to the circumferential curvature of the acetabulum. Except for the use of the osteotome, an incomplete cut of the ischium and a complete cut of the pubis are performed in the similr manner as those of the Bernese periacetabular osteotomy. The first step in osteotomy of the ilium is to score the inner table of the pelvis with a power drill. A C-shaped osteotomy line is started proximal to the anteroinferior iliac spine and ended in the distal part of the quadriilateral surface. The actual osteotomy along the scored line is done with the osteotome being directed proximally in the supraacetabular portion, posteriorly in the proximal part of the quadrilateral surface, and distally in the distal part of the quadrilateral surface. Then, the acetabular fragment can be redirected and is fixed with two or three screws. The posterior column of the acetabulum is kept intact. The results of the first 24 hips in 24 patients were prospectively studied with a minimum of 6-month follow-up. All hips had residual hip dysplasias. At operation, the osteotomized acetabular fragment was rotated without difficulty and was medialized as necessary. The averge lateral center-edge angle was 6 degrees preoperatively, compared with 29 degrees postoperatively. The average anterior center-edge angle was 8 degrees preoperatively, compared with 26 degrees postoperatively. Bone union and relief of pain were obtained in all hips.
TRUST -BASED APPROACH IN WIRELESS SENSOR NETWORKS USING AN AGENT TO EACH CLUSTER

Detection of malicious node in the neighborhood with minimal infrastructure and computations is a requirement. The existing models require more computation, storage, and complex security calculations. These models are inefficient in wireless sensor networks due to their resource limitations. Therefore, an agent-based approach that maintains the node’s current status is proposed in this research. In agent-based approach detection is possible through maintaining the ratings of each node. The ratings of a node will be done through the ratio of packet forwarded by packets received. Further, the ratings can be done using the E-commerce models. In E-commerce models, each node votes the successive node depending upon the ratio of packet forwarded by packets received. The update ratings will be done through Sporas formula or Molina’s formula or with a combination of both models. Further, the proposed agent-based framework uses reputation of a node through neighbouring nodes as part of trust calculation. The simulations were presented to calculate the trust of a node.
An Annual basal area growth model with multiplicative climate modifier fitted to longitudinal data for shortleaf pine

Understanding climatic influences on annual basal area growth (ABAG) rates of individual trees is necessary to predict future stand dynamics. We fitted nonlinear ABAG models for shortleaf pine (Pinus echinata Mill.) with climate variables linearly added to the arguments of logistic and exponential multiplicative functions of climate variables as climate modifiers to incorporate 14 growing seasons and 30 month-specific climate variables including standardized precipitation index. Data were collected from permanently established plots in Arkansas and Oklahoma. Six re-measurement events collected between 1985 and 2014 provided five growth periods (GPs) and ABAG models were fitted using a mixed-effects approach. Model performance was evaluated using likelihood ratio tests and fit statistics. Climate variables from GPs expressed as deviations from long-term means that performed better than other candidate variables included (1) month-specific: June mean maximum air temperature (°C) (DTMAX6), and September precipitation (mm) (DPPT9); and (2) growing seasons: mean maximum air temperature (°C) (DGTMAX) and precipitation (mm) (DGPPT). ABAG models fitted with multiplicative climate modifiers provided improved growth predictions compared with models fitted with climate variables linearly added to the argument of a logistic function. There was positive correlation with DGTMAX and negative correlation with DMPPT. In addition, 1°C increase in mean maximum temperature had a greater cumulative effect on ABAG rates of young versus old trees. Fitting ABAG models with climate modifiers are useful for assessing variations in productivity due to climate change in the future.
St. Stephen's Hospital Hervey Bay: Study of Developing a Digital Hospital

St Stephen’s Hospital in Hervey Bay, Queensland, Australia, is a new 96 bed state of the art digital hospital that opened on a greenfield site on 13 October 2014. The eHealth project was responsible for providing a fully integrated electronic medical record. The authors explore the unique challenges presented by the project and the solutions deployed. Key components related to the success of the project are identified. The results of the intense two and half year project timeline culminated in a successful go-live and certification as the first hospital in Australia to achieve Stage 6 HIMSS designation.
Germinability of Seed Reserves in a Big Sagebrush Community

We investigated seasonal variation in germinability of seed reserves in a degraded big sagebrush (Artemisia tridentata Nutt.) community. A bioassay was employed to determine germinability. There were many more germinable seeds and seedling establishment was greater under the shrub canopies than in the interspace. Caryopses of downy brome (Bromus tectorum L.) were the most abundant of any species in the litter where most of the seeds were located. Seasonal germinability of downy brome caryopses depends on the environment of the seedbed when the samples were collected and on the incidence of environmentally-induced dormancy or on loss of dormancy.
Pier Luigi Nervi: Architecture as Challenge

Some of his most important and iconic works were realized in Italy and Europe: the Exhibition Halls and the Palazzo del Lavoro in Turin, the stadium in Florence and the Sport Palaces for the Olympic Games of 1960 in Rome, the UNESCO Headquarters in Paris (with Macel Breuer and Bernard Zehrfuss), to quote just a few. An important group of his works is located in North America, the most famous being St. Mary Cathedral in San Francisco (with Pietro Belluschi), George Washington Bus Terminal in New York City, Scope Cultural and Convention Center in Norfolk, VA, Victoria Square Tower in Montreal and the Italian Embassy in Brasilia.
Patología vestibular y su asociación con enfermedades metabólicas v estibular pathology and its association with metabolic disease

aBsTRacT Introduction: There have been reports of vertigo and/or hypoacusia associated with metabolic diseases, specially metabolic syndrome (MS). Aim: To evaluate association between vertigo and metabolic disorders. Material and method: Study between October 2011 and March 2012 of patients consulting for vertigo in the otolaryngology-head and neck surgery service in Hospital Sotero del Rio. All patients recruited filled an epidemiological survey, a VIII nerve testing was performed, blood pressure, waist circumference, weight and height were measured. Serum glucose and lipid profile were indicated. Data obtained was compared to that presented in a national health survey. Results: Data of N =31 patients of an average age of 59,4 years old. A 70% preva-lence of MS was found. Blood pressure, waist circumference and body mass index, total colesterol, LDL and triglycerides were higher in vertigo patients. In the VIII nerve test, 35,8% of patients had a vestibular alteration and 38,7% had an audiogram alteration. Only DM2 showed statistical association with bilateral sensoneural hearing loss.
La lingüística textual en los trabajos de investigación producidos por alumnado universitario: Enseñanza en las planificaciones de aula y los libros de texto

This research project revolves around the properties of text linguistics under a qualitative approach. The author analyzed drafts of a research paper by two university students as well as lesson plans and textbooks of high school Spanish Language and Literature courses and lesson plans of courses from the Licentiate degree in Education. According to the information from the drafts, students struggle with coherence and cohesion in writing; however, they succeed in choosing the correct language for the type of writing. Difficulties are most likely due to fact that this topic is not included in secondary education plans and is not commonly addressed in textbooks or university classes. In conclusion, teachers should include the properties of text linguistics in their lesson plans in order to help students overcome these difficulties.
Using Design Fiction to Inform Shape-Changing Interface Design and Use

Abstract Shape-changing interfaces are tangible, physically dynamic devices which enable user-experience beyond 2D screens. Within Human Computer Interaction, researchers are developing these from low-resolution, low-fidelity prototypes, toward a vision of a truly malleable world. The main focus is in producing and testing hardware, and basic user interactions, which leaves the question unanswered: what are shape-changing interfaces good for? In response, we propose the use of design fiction to investigate potential applications for this technology: to create and analyse artifacts relating to future use-scenarios for shape-change. Whilst research within shape-change often proposes future use-cases for prototypes during discussion, they are seldom in a form that presents them as everyday artifacts. Here, we present and discuss a printed game-play instruction manual for a truly high resolution shape-changing game entitled First Hand, which aims to draw parallels between current gaming practices and the tangible nature of shape-changing interfaces.
Avaliação da resistência à fratura de resinas compostas submetidas ao envelhecimento artificial acelerado

Objetivo: O objetivo deste trabalho foi avaliar a influencia do envelhecimento artificial acelerado na resistencia a compressao de resinas compostas. Metodologia: Foram avaliadas cinco marcas comerciais de resinas compostas: Z250®, 4Seasons®, P60®, Z100® e Charisma®. Para cada resina foram obtidos 16 corpos de prova, divididos em dois grupos de oito, sendo um grupo submetido ao sistema envelhecimento acelerado para nao metalicos C-UV e o outro, a analise de resistencia a compressao 24 horas apos sua obtencao. Posteriormente, os corpos de prova envelhecidos foram submetidos ao ensaio de compressao. As medias das leituras de resistencia a compressao de cada corpo de prova foram submetidas ao teste Kolmogorov-Smirnov (p > 0,05), Anova e teste de Tukey (p