Miracle-dz/UniFAR-FTUs huggingface dataset:
Murine De Novo Methyltransferase Dnmt3a Demonstrates Strand Asymmetry and Site Preference in the Methylation of DNA In Vitro

ABSTRACT CpG methylation is involved in a wide range of biological processes in vertebrates as well as in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA methyltransferase activity in mouse and human. It has been proposed that de novo methylation observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b methyltransferases, while Dntm1 is believed to be responsible for maintaining the established methylation patterns upon replication. Analysis of the sites methylated in vivo using the bisulfite genomic sequencing method confirms the previous finding that some regions of the plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However, the preferred targets of the enzyme cannot be determined due to the presence of other methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed. These analyses revealed that the two cDNA strands have distinctly different methylation patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most likely methylates one strand of DNA without concurrent methylation of the CpG site on the complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites more frequently than others, depending on the sequence context. Methylation of each DNA strand independently and with possible sequence preference is a novel feature among the known DNA methyltransferases.
Paradoxical enhancement of CD8 T cell‐dependent anti‐tumor protection despite reduced CD8 T cell responses with addition of a TLR9 agonist to a tumor vaccine

Generation of antigen‐specific CD8+ T cell responses is considered optimal for an effective immunotherapy against cancer. In this study, we provide a proof of principle that in vitro observed diminished CD8+ T cell response provided a strong in vivo tumor protection. Immunization with an adenovirus vaccine containing ovalbumin (OVA) gene (Ad5‐OVA) strongly induces antigen‐specific CD8+ T cell responses measured in vitro using various immunological assays. However, in an attempt to augment the antigenic CD8+ T cell response, coinjection of a TLR9 agonist CpG ODN with the viral vaccine unexpectedly reduced the CD8+ T cell responses measured in vitro but provided a remarkably enhanced tumor protection compared to the CD8+ T cell response generated by Ad5‐OVA vaccine alone. Interestingly, despite reduced ex vivo/in vitro CD8+ T cell responses following Ad5‐OVA+CpG immunization, immunodepletion studies revealed that the augmented anti‐tumor immunity was primarily dependent on CD8+ T cells. The magnitude and effector function of anti‐OVA CD8+ T cells remain low following primary and secondary antigenic challenge, presenting a dichotomy between in vitro CD8 T cell responses and in vivo anti‐tumor immunity. To examine the impact of CpG ODN, we observed that presence of CpG suppresses the CD8+ T cell proliferation both in vitro and in vivo. These data demonstrate that coadministration of adenovirus vaccine with a TLR9 agonist can generate potentially effective tumor‐reactive CD8+ T cells in vivo. In addition, the results indicate that widely used standard immune parameters may not predict the vaccine efficacy containing a TLR9 agonist as adjuvant. © 2007 Wiley‐Liss, Inc.
Nutrition support after total laryngectomy.

This study was performed to evaluate the influence of different nutrition supports (enteral vs parenteral) on nutritional status, postoperative complications, and length of hospitalization in patients undergoing total laryngectomy. Forty-eight patients were divided at random into two groups and received enteral nutrition support by percutaneous endoscopic gastrostomy with a casein and soy-based polymeric formula blended with a modular protein (group A) or a balanced formula in total parenteral nutrition given through a subclavian venous catheter (group B). The results show a satisfactory preservation of nutritional status after total laryngectomy and no significant differences in the nutritional parameters between groups fed enterally or parenterally; however, percutaneous endoscopic gastrostomy could avoid many problems related to enteral nutrition support for patients undergoing laryngectomy. This route of administration was well tolerated by all the patients and, moreover, the percutaneous endoscopic gastrostomy-related complications were clinically less significant than those associated with total parenteral nutrition; this fact could explain the longer hospitalization for group B (34 +/- 11 vs 26 +/- 11 days) (p < .05).
Novel FMCW radar system concept with adaptive compensation of phase errors

A new high-performance FMCW sensor system concept is presented. The approach is based on an adaptive signal processing scheme compensating phase errors caused by VCO phase noise as well as the non-linearity of the frequency modulation. The key component of the low-cost sensor is a SAW (surface acoustic wave) delay line representing a miniaturised high-precision radar reference path. A correction algorithm equalises the target signal according to the phase errors simultaneously measured with the reference path. Employing this method, an excellent range resolution as well as a high dynamic range and multi-target selectivlty is obtained, which has been experimentally demonstrated at millimetrewave frequencies.
Selective hypertrophy of the quadriceps musculature after 14 weeks of isokinetic and conventional resistance training

One of the fundamental adaptations observed with resistance training (RT) is muscle hypertrophy. Conventional and isokinetic machines provide different forms of mechanical stress, and it is possible that these two training modes could promote differing degrees of hypertrophic adaptations. There is a lack of data comparing the selective hypertrophy of the quadriceps musculature after training with a conventional knee extension machine versus an isokinetic machine. The purpose of this study was to evaluate the selective hypertrophy of the quadriceps musculature and knee extension maximal isometric torque after 14 weeks of conventional versus isokinetic RT. Thirty‐five men were assigned to three groups: control group and training groups (conventional and isokinetic) performed three sets of unilateral knee extensions per session with a progressive loading scheme twice a week. Prior to and following the intervention, maximal isometric knee extensor torque was measured using an isokinetic dynamometer, and muscle thickness (MT) of quadriceps femoris muscles was assessed via ultrasound. The results indicated non‐uniform changes in MT between the muscles that comprise the quadriceps femoris group. For the conventional group, significantly greater increases in rectus femoris thickness were evident versus all other quadriceps muscles (14%). For the isokinetic group, increases in RF thickness (11%) were significantly greater in comparison with the vastus intermedius only. Although the muscle thickness did not increase for all the quadriceps femoris muscles, the relative rectus femoris adaptation suggested a selective hypertrophy favouring this portion.
A new species of Hyphessobrycon (Characiformes, Characidae) from the upper Guaviare River, Orinoco River Basin, Colombia

Abstract Hyphessobrycon klausanni sp. n. is described from small drainages of the upper Guaviare River (Orinoco River Basin) in Colombia. It differs from all congeners by having a wide, conspicuous, dark lateral stripe extending from the anterior margin of the eye across the body and continued through the middle caudal-fin rays, and that covers (vertically) three or four horizontal scale rows. It also differs by having an orange-yellow stripe extending from the anterosuperior margin of the eye to the caudal peduncle above the lateral line in life. It differs from all other species of Hyphessobrycon that have a similar dark lateral stripe: H. cyanotaenia, H. loretoensis, H. melanostichos, H. nigricinctus, H. herbertaxelrodi, H. eschwartzae, H. montogoi, H. psittacus, H. metae, H. margitae, H. vanzolinii, and H. peruvianus in having only three or four pored scales in the lateral line, 21 to 24 lateral scales and six teeth in the inner premaxillary row. Hyphessobrycon klausanni differs from H. loretoensis in having seven to eight maxillary teeth (vs. three to four) and in having a longer caudal peduncle (12.4–17.0% SL vs. 4.6–8.0% SL). Additionally Hyphessobrycon klausanni can be distinguished from the other species of Hyphessobrycon with a dark lateral stripe from the Orinoco River Basin (H. metae and H. acaciae) in having two teeth in the outer premaxillary row (vs. three to four) and 10 branched pectoral–fin rays (vs. 11 to 12). It further differs from H. metae by the length of the snout (17.6–22.8% HL vs. 9.9–15.2% HL) and by the length of the caudal peduncle (12.4–17.0% SL vs. 7.3–11.8% SL).
Predictive Power of Google Search Volume on Stock Returns

We investigate whether search statistics from Google can be used to forecast stock returns over different time horizons. We use daily, weekly and quarterly Google searches, covering the period from 2010 to 2014. The results show a small, positive short-term relationship between daily searches and excess stock returns, a negative relationship between weekly searches and excess returns with subsequent reversal, while quarterly searches are positively related to excess returns without reversal. Next we examine a trading strategy based on our model. The trading strategy shows that there is economical value in including Google search statistics in forecasting models. Sammendrag Vi undersøker om søkestatistikk fra Google kan brukes til å predikere aksjeavkastning over ulike tidshorisonter. Vi bruker daglige, ukentlige og kvartalvise Googlesøk, fra perioden 2010 til 2014. Resultatene viser en liten, positiv kortsiktig sammenheng mellom daglige søk og meravkastning, en negativ sammenheng mellom ukentlige søk og meravkastning med påfølgende reversering, mens kvartalvise søk har en positiv sammenheng med meravkastning uten reversering. Videre vurderer vi en handelsstrategi basert på vår modell. Handelsstrategien viser at det er økonomisk verdi i å inkludere søkestatistikk fra Google i prognosemodeller. 8
Respiratory Inflammation Among Workers Exposed to Airborne Dust With Endotoxins in a Coffee Curing Factory

Objective: To study dust exposure and inflammatory reactions in the respiratory tract among coffee curing workers in Tanzania. Methods: A cross-sectional study was conducted in a Tanzanian coffee curing factory. Coffee workers (n = 15) were compared with unexposed controls (n = 18); all workers were nonsmokers. Exhaled nitric oxide was examined using an electrochemistry-based NIOX MINO device. Personal air samples were analyzed for total dust and endotoxins, using gravimetric analysis and the chromogenic Limulus amebocyte lysate endpoint assay, respectively. Results: Total dust levels ranged from 0.2 to 27.9 mg/m3, and endotoxin levels ranged from 42 to 75,083 endotoxin units/m3. Concentrations of exhaled nitric oxide, analyzed by linear regression and adjusted for age (&bgr; = 0.57; 95% confidence interval, 0.08 to 1.06; P = 0.02), was higher among coffee workers than among the control group. Conclusion: The results indicate a relationship between the coffee dust and signs of respiratory inflammation.
Perceptions of Health Among Immigrant Latino Adolescents From Mexico

Purpose: This ethnographic study describes the health-related perceptions of immigrant Latino adolescents from Mexico. Method: Fourteen adolescents, purposively recruited from two non-health-based community settings, participated. Each was interviewed twice and completed a visual narrative project using disposable cameras. Audiotaped transcripts and photographs were inductively analyzed. Findings: Being healthy is holistically perceived by these adolescents and includes physical, mental, spiritual, social, and environmental factors. Pictures portrayed healthy and unhealthy influences and behaviors, including eating habits, exercise, self-care, relationships, garbage, and pollution. Personal responsibility was important in being healthy and in promoting one's health. Family was identified as an important source of health-related information. Implications: Nurses recognizing the holistic, comprehensive health-related perceptions of immigrant Latino adolescents can promote their health and design culturally and developmentally appropriate educational strategies and health interventions aimed at eliminating health disparities.
Osteochondral Allograft Transplantation in the Knee

The technique of osteochondral allograft (OCA) transplantation has been used to treat a wide spectrum of cartilage deficiencies in the knee. Its use has been supported by basic science and clinical studies that show it is a safe and effective treatment option. What sets fresh OCA transplantation apart from other cartilage procedures in the knee, is the ability to treat large defects with mature hyaline cartilage. Studies looking at transplantation of fresh OCAs in the general population have shown reliable pain relief and return to activities of daily living. Reports of cartilage injuries in athletes have risen over the years and more research is needed in evaluating the successfulness of OCA transplantation in the athletic population.
Location-based services provisioning using WSN

Ubiquitous computing has gained momentum over the last years with the expansion of mobile devices. One area of pervasive computing is context-aware systems which are applications designed to react to the constant changes in the environment. This paper presents a context aware platform that handles context acquiring, processing and service provisioning management. The platform alleviates the process of high level application development and sets a common ground for building context-aware applications and services. The context-based platform objective is to support mobile users with personalized services. It offers sophisticated mechanisms in matching the mobile user's preferences with services that are enabled at the visited location, and provides them in adaptive manner to the user. As a proof of concept, we present a case study on tourism where tourists are provided with services and information of interest based on their location and time. An application for e-tourism is deployed on top of the platform to assist tourists during their travels by providing them with context sensitive services. The user preferences, the current time, and the user current location are incorporated in the proactive formulation of suggestions on the tourist mobile devices about nearby points of interests (e.g. museums, restaurants….).
An Inline Core-Cladding Intermodal Interferometer Using a Photonic Crystal Fiber

We propose a simple all-fiber structure based on intermodal interference between a core and a cladding mode of an endlessly single-mode photonic crystal fiber (PCF) section sandwiched between a lead-in and lead-out SMF-28 fiber. We have measured the intermodal dispersion and the polarization-dependent loss (PDL) of the structure. The sensitivities to strain, pressure, and temperature and external refractive index are studied. The interferometer is compared to an interferometer based on LP01-LP02 SMF-28 fiber and to a PCF-based tapered LPG.
Lossless Adaptive Digital Audio Steganography

This paper presents a lossless adaptive digital audio steganographic technique based on reversible two and higher dimensional integer transform. The adaptive technique is used to choose the best blocks for embedding perceptually inaudible stego information, and to select the best block sizes to maximize the number of blocks/capacity. The stego information is embedded in the integer domain by bit manipulation. In addition, we intro- duce a capacity measure to select audio carriers that in- troduce minimum distortion after embedding. The above technique is also applicable to compression based audio formats, such as MPEG audio layer-3 (mp3).
DNA double-helix binds regulatory peptides similarly to transcription factors.

PROBLEM Gerontology observations show that ageing of organism is accompanied by the decrease of the chromatin activity and slowing down of the protein synthesis. Natural regulatory oligopeptides and their synthetic analogues take part in the activation of chromatin and normalise rate of the protein synthesis in cultured tissues. Regulatory peptides significantly enhance longevity. OBJECTIVES The objective of this work is to find a possible molecular mechanism by which the regulatory peptides influence the part of genetic system is responsible for initiation of protein synthesis in higher organisms. METHODS An interdisciplinary approach was used to address the problem. The work involved not only medical scientists and biologists, but also specialists in biopolymer chemistry, and mathematicians for statistical analysis of information interaction of amino acid and nucleotide sequences. CONCLUSIONS The structures and metrics of peptides and the DNA double-helix cause the recognition and complementary binding of a regulatory peptide with DNA functional groups at the interface of the major groove. We have used complementary binding model to find a possible base pair sequence ATTTTC for specific binding of synthetic tetrapeptide epitalon. This base pair block and its reverse complement were found repeatedly in the promoter region of telomerase. A comparison of statistical information content of peptides and oligonucleotide sequences shows that these two classes of biopolymers are information carriers and. exchange the information to initiate the gene transcription.
Fast In-Memory Transaction Processing Using RDMA and HTM

DrTM is a fast in-memory transaction processing system that exploits advanced hardware features such as remote direct memory access (RDMA) and hardware transactional memory (HTM). To achieve high efficiency, it mostly offloads concurrency control such as tracking read/write accesses and conflict detection into HTM in a local machine and leverages the strong consistency between RDMA and HTM to ensure serializability among concurrent transactions across machines. To mitigate the high probability of HTM aborts for large transactions, we design and implement an optimized transaction chopping algorithm to decompose a set of large transactions into smaller pieces such that HTM is only required to protect each piece. We further build an efficient hash table for DrTM by leveraging HTM and RDMA to simplify the design and notably improve the performance. We describe how DrTM supports common database features like read-only transactions and logging for durability. Evaluation using typical OLTP workloads including TPC-C and SmallBank shows that DrTM has better single-node efficiency and scales well on a six-node cluster; it achieves greater than 1.51, 34 and 5.24, 138 million transactions per second for TPC-C and SmallBank on a single node and the cluster, respectively. Such numbers outperform a state-of-the-art single-node system (i.e., Silo) and a distributed transaction system (i.e., Calvin) by at least 1.9X and 29.6X for TPC-C.
An efficient error protection scheme for point based 3-D models over packet erasure network

In this paper, an efficient error protection scheme for the transmission of point based 3D model over packet erasure network is described. This scheme deals with the limitation in conventional 3D mesh model transmission where the quality of the reconstructed model is highly dependent on the lossless transmission of 3D connectivity information and the correct decoding of lower hierarchical layers of the Level of details (LOD) mesh for progressive reconstruction. The proposed scheme is particular well designed to provide connectivity and layer dependency free transmission of the static 3D model across network. Coupled with error protection technique for resilience towards packet loss during transmission, the proposed algorithm is effective in ensuring the graceful degradation of the decoded model both visually and objectively as shown from the experimental results.
Charging station selection optimization for plug-in electric vehicles: An oligopolistic game-theoretic framework

In this paper, we describe a framework for the selection of the best charging station when plug-in electric vehicles (PEV) need to recharge their batteries, while at the same time the power utilities, which own the charging stations (CS), optimize their revenue. We use two-way communication to transmit positioning information, which is a key factor so that the plug-in electric vehicles evaluate its required energy. Within this framework, we also describe a procedure that is implemented in a distributed manner and is based on a non-cooperative oligopoly game that makes use of differentiated products theory and conjectural variations to provide a Nash equilibrium in prices and quantities.
miRNA genetic alterations in human cancers

MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs, which negatively regulate gene expression in a sequence-specific manner via translational repression and/or mRNA degradation. Their discovery revealed a new and exciting aspect of post-transcriptional gene regulation that is universally involved in cellular homeostasis. Importantly, the advent of miRNAs added another level of complication in the already complex regulatory networks of the cell, undermining that RNA molecules in general, should be considered gene regulators of equal importance with proteins. Recently, the scientific community drew attention to the miRNA field for an additional reason: an increasing line of evidence indicated that miRNA genes are tightly connected with the process of tumorigenesis. Indeed, several miRNAs have already been demonstrated to behave as oncogenes or tumor suppressor genes in many types of cancer. Even though the underlying mechanisms by which miRNAs can destabilize the normal cellular processes, promoting cell transformation and tumor progression, are not well understood, genetic and epigenetic alterations most probably play a critical role. Significant technologic advances facilitated the profiling of the miRNA expression patterns in normal and cancer tissues and discovered an unexpected greater reliability of miRNA expression signatures in classifying cancer types than the respective signatures of protein-coding genes. Along with this extraordinary diagnostic potential, miRNAs have also proved their prognostic value in predicting clinical behaviors of cancer patients. The aim of this review is to describe miRNA expression and how its deregulation is involved in the pathophysiology of human cancers.
Spline-DCS for Forecasting Trade Volume in High-Frequency Finance

We develop the spline-DCS model and apply it to trade volume prediction, which remains a highly non-trivial task in high-frequency finance. Our application illustrates that the spline-DCS is computationally practical and captures salient empirical features of the data such as the heavy-tailed distribution and intra-day periodicity very well. We produce density forecasts of volume and compare the model's predictive performance with that of the state-of-the-art volume forecasting model, named the component-MEM, of Brownlees et al. (2011). The spline-DCS significantly outperforms the component-MEM in predicting intra-day volume proportions.