Miracle-dz/UniFAR-FTUs huggingface dataset:
Causes and consequences of microsatellite instability in endometrial carcinoma.

Genetic instability of microsatellite repeat sequences [microsatellite instability (MI)] is commonly seen in tumors associated with the hereditary nonpolyposis colorectal cancer syndrome and is a result of inactivating mutations in any of several genes involved in a particular pathway of DNA mismatch repair. Sporadic (i.e., nonhereditary) manifestations of several tumor types, including colorectal, gastric, and endometrial carcinomas, also exhibit MI in a significant fraction of cases. Many MI+ sporadic colorectal carcinomas are associated with somatic mutations of mismatch repair genes, and several genes with coding region microsatellites are frequently mutated as a result in these cancers. The molecular causes and consequences of MI in sporadic endometrial carcinomas remain obscure, however. The aims of this study were: (a) to identify a series of sporadic endometrial carcinomas with clear evidence of MI; (b) to determine the extent to which somatic alterations in mismatch repair genes are associated with this MI; and (c) to establish whether the genes containing coding region microsatellite repeats that are known to be disrupted in MI+ gastrointestinal cancers are also disrupted in MI+ endometrial carcinomas. Matched pairs of normal and tumor DNA from 57 consecutive cases of endometrial carcinoma were examined for evidence of MI using a consensus panel of microsatellite markers. Fourteen cases (25%) displayed unequivocal evidence of MI, consistent with previously published estimates of the incidence of MI+ sporadic endometrial carcinoma. These cases were subjected to a mutation screen of the coding regions and exon-intron boundaries of the mismatch repair genes MSH2 and MLH1. Although several polymorphisms were detected, no clearly deleterious mutations were found in either of these genes. Notably, however, hypermethylation of the MLH1 promoter region was identified in 10 of 14 (71%) MI+ cases. Somatic mutations in coding region microsatellite repeats in the TGFbetaIIR, IGFIIR, BAX, E2F4, MSH3, MSH6, BRCA1, and BRCA2 genes were generally rare. Four MI+ tumors (29%) contained somatic mutations in the PTEN gene, only one of which was likely the result of MI. These data indicate that somatic mutational inactivation of known mismatch repair genes does not account for the great majority of sporadic endometrial carcinomas with MI and that a significant fraction of these cases may instead be causally associated with hypermethylation of the MLH1 promoter. Furthermore, genes with coding region microsatellites that are frequently mutated in MI+ gastrointestinal cancers are rarely mutated in MI+ endometrial cancers, implying the existence of alternative molecular targets for the tumorigenic effects of MI in this tumor type.
Photoelastic Analysis of Stresses Transmitted by Universal Cast to Long Abutment on Implant-Supported Single Restorations Under Static Occlusal Loads

ObjectivesThe aim of this study was to compare the stresses resulting from cemented or screw-retained dental prostheses using universal cast to long abutment by the photoelastic method. Material and MethodsA photoelastic resin model was fabricated to simulate a segment of the mandibular arch with resin replicas of a first premolar and a second molar, and two 3.75 × 11-mm implants replacing the second premolar and the first molar. Vertical static loads were individually applied on the occlusal surface of the premolar and the molar (5 kgf) and simultaneously on both crowns (10 kgf). ResultsResults found variable stress patterns around each implant and concentrated stresses in the individually loaded crowns. Force transfer characteristics of each situation and quantification of the isochromatic fringes were evaluated. ConclusionsWithin the limitations of this study and based on the results obtained for implant-supported prosthesis with internal hexagon connection/universal cast to long abutment, it could be concluded that single adjacent screw-retained prosthetic restorations lead to higher stresses around the implants when compared with cement-retained restorations.
Efficient and Scalable Execution of Fine-Grained Dynamic Linear Pipelines

We present Pipelite, a dynamic scheduler that exploits the properties of dynamic linear pipelines to achieve high performance for fine-grained workloads. The flexibility of Pipelite allows the stages and their data dependences to be determined at runtime. Pipelite unifies communication, scheduling, and synchronization algorithms with suitable data structures. This unified design introduces the local suspension mechanism and a wait-free enqueue operation, which allow efficient dynamic scheduling. The evaluation on a 44-core machine, using programs from three widely used benchmark suites, shows that Pipelite implies low overhead and significantly outperforms the state of the art in terms of speedup, scalability, and memory usage.
Human Activity Recognition via an Accelerometer-Enabled-Smartphone Using Kernel Discriminant Analysis

Nowadays many people use smartphones with built-in accelerometers which makes these smartphones capable of recognizing daily activities. However, mobile phones are carried along freely instead of a firm attachment to a body part. Since the output of any body-worn triaxial accelerometer varies for the same physical activity at different positions on a subject's body, the acceleration data thus could vary significantly for the same activity which could result in high within-class variance. Therefore, realization of activity-aware smartphones requires a recognition method that could function independent of phone's position along subjects' bodies. In this study, we present a method to address this problem. The proposed method is validated using five daily physical activities. Activity data is collected from five body positions using a smartphone with a built-in triaxial accelerometer. Features including autoregressive coefficients and signal magnitude area are calculated. Kernel Discriminant Analysis is then employed to extract the significant non-linear discriminating features which maximize the between-class variance and minimize the within-class variance. Final classification is performed by means of artificial neural nets. The average accuracy of about 96\% illustrates the effectiveness of the proposed method.
Robust novelty detection in the framework of a contamination neighbourhood

A novelty detection robust model is studied in the paper. It is based on contaminated robust models which produce a set of probability distributions of data points instead of the empirical distribution. The minimax and minimin strategies are used to construct optimal separating functions. An algorithm for computing the optimal parameters of the novelty detection model is reduced to a finite number of standard SVM tasks with weighted data points. Experimental results with synthetic and some real data illustrate the proposed novelty detection robust model.
[Identification of digital differential expression patterns of a novel human gene (UBAP1) by an expressed sequence tag strategy].

BACKGROUND & OBJECTIVES This study was designed to identify differential expression patterns in tumor and normal tissues of the human novel gene, UBAP1, a putative nasopharyngeal carcinoma (NPC) relate gene, which is located at human chromosome 9p21-22 where loss of heterozygosity frequently occurs in NPC. METHODS Based on the generation of expressed sequence tags (ESTs), in the authors' electronic Northern blot, complete cDNA of ubap1 gene was taken as a "probe" sequence, and human EST Database search of GenBank was carried out using BLASTn programs. A report generated in a BLAST search of ubap1 gene sequence against an EST database consisting of such 'pedigree' ESTs allows the inference of the gene's tissue distribution. Furthermore, differential RT-PCR was used to describe the expression patterns of ubap1 in partial tumor tissues. RESULTS Database surveys indicated ubap1 gene was not only ubiquitously expressed in many normal tissues with various levels but also differentially expressed in different tumor tissues, especially down-regulated in multiple neoplastic tissues such as brain, breast, skin, colon, testis, and uterus tumor tissues. Furthermore, differential RT-PCR analysis demonstrated expression of ubap1 was down-regulated or absent in 7 of 11(64%) meningioma samples and 13 of 18 (72%) colorectal tumor tissues respectively. CONCLUSIONS The authors present an EST approach that proved to be useful for the identification of differential expression patterns of ubap1 in different tumors. These findings could be valuable for the investigation of the mechanism of UBAP1 gene exhibiting differential expression, potentially involved in the progression of multiple cancers.
Detecting Steps Walking at very Low Speeds Combining Outlier Detection, Transition Matrices and Autoencoders from Acceleration Patterns

In this paper, we develop and validate a new algorithm to detect steps while walking at speeds between 30 and 40 steps per minute based on the data sensed from a single tri-axial accelerometer. The algorithm concatenates three consecutive phases. First, an outlier detection is performed on the sensed data based on the Mahalanobis distance to pre-detect candidate points in the acceleration time series that may contain a ground contact segment of data while walking. Second, the acceleration segment around the pre-detected point is used to calculate the transition matrix in order to capture the time dependencies. Finally, autoencoders, trained with data segments containing ground contact transition matrices from acceleration series from labeled steps are used to reconstruct the computed transition matrices at each pre-detected point. A similarity index is used to assess if the pre-selected point contains a true step in the 30–40 steps per minute speed range. Our experimental results, based on a database from three different participants performing similar activities to the target one, are able to achieve a recall = 0.88 with precision = 0.50 improving the results when directly applying the autoencoders to acceleration patterns (recall = 0.77 with precision = 0.50).
On Additive and Multiplicative QoS-QoE Models for Multiple QoS Parameters

Generic relationships between QoE and QoS have been inten-sively discussed in literature for single QoS parameters and of-ten found to be logarithmic or exponential. While there are many experimental studies investigating statistically the inﬂuence of several parameters on QoE, the generic relationship between them, and how to best model it, have not been discussed so far. For communication networks, however, there is a major interest from different stakeholders to have multi-dimensional QoE models. The contribution of this paper is an analysis of the generic relationship between QoS and QoE for multiple QoS parameters and its implications. We address the question of whether multi-dimensional QoE models for several parameters are additive or multiplicative. In an analytic model and with examples involving HTTP non-adaptive video streaming, we show that a multiplicative model has different properties than the current additive QoE model proposed in ITU-T standards. We want to raise sensitivity in the community on multi-factor QoE models, their properties, and the need for multi-factor studies to conﬁrm the appropriate models.
An automated method for breast mass segmentation

Breast cancer continues to be a significant health problem in the world. The most familiar breast anomalies types are mass and microcalcification. However Automatic methods for detecting these abnormalities can identify breast cancer at an early stage. In this paper, we propose a marker-controlled watershed algorithm to locate breast masses. The preprocessing step has been introduced to remove all undesirable areas from mammogram. Foreground and background markers are then selected in order to apply a watershed segmentation algorithm that identifies the location of tumor region in mammogram. The proposed method was successful to segment mass anomalies. It has been tested on publicly available Mammographic Image Analysis Society (MIAS) database and it has achieved an overall mass detection rate of 90.83% and an area Az of 0.913 under the receiver operating characteristic curve ROC for mass segmentation.
PTSD and pain: exploring the impact of posttraumatic cognitions in veterans seeking treatment for PTSD.

OBJECTIVE Previous research has demonstrated a significant relationship between posttraumatic stress disorder (PTSD) and pain. While several models attempt to explain this relationship, significant questions remain regarding factors that may play a role in this interaction. The purpose of this study was to determine whether posttraumatic cognitions mediate the relationship between PTSD and pain. DESIGN The sample comprised 136 veterans who presented to the VA Ann Arbor Health Care System seeking evaluation and treatment in the PTSD clinic. Participants completed the Clinician-Administered PTSD Scale, the Posttraumatic Cognitions Inventory, and Brief Pain Inventory-Short Form, along with other assessments as part of their evaluation. RESULTS This study showed that the majority of patients (86.8%) reported some problems with pain. Further, the findings indicate that there is a significant relationship between PTSD severity and pain severity. Posttraumatic cognitions were not related to the level of pain experienced, but they were related to pain interference in this population. CONCLUSIONS In particular, negative cognitions regarding the self were associated with the level of pain-related interference, and partially mediated the relationship between PTSD and pain. The clinical implications of these findings are discussed.
Sequence heterogeneity of NS5A and core proteins of hepatitis C virus and virological responses to pegylated‐interferon/ribavirin combination therapy

Both host and viral factors have been implicated in influencing the response to pegylated‐interferon/ribavirin (PEG‐IFN/RBV) therapy for hepatitis C virus (HCV) infection. Among the viral factors, sequence heterogeneity within NS5A and core regions has been proposed. This study aimed to clarify the relationship between virological responses to PEG‐IFN/RBV therapy and sequence heterogeneity within NS5A, including the IFN/RBV resistance‐determining region (IRRDR), the interferon sensitivity‐determining region (ISDR) and the core region. Pretreatment sequences of NS5A and the core regions were analyzed in 57 HCV‐1b‐infected patients who were to be treated with PEG‐IFN/RBV. Of 40 patients infected with HCV having an IRRDR with four or more mutations (IRRDR ≥ 4), 28 (70%) patients achieved a sustained virological response (SVR). On the other hand, only 4 (24%) of 17 patients infected with HCV having an IRRDR with three or fewer mutations (IRRDR ≤ 3) achieved a SVR (P= 0.001). Similarly, 22 (71%) of 31 patients infected with HCV and having an ISDR with one or more mutations (ISDR ≥ 1) achieved a SVR while 10 (38%) of 26 patients infected with HCV and having an ISDR without any mutations (ISDR = 0) achieved a SVR (P= 0.014). As for the core region, there was significant correlation between a single mutation at position 70 (Gln70) and non‐SVR (P= 0.02). Notably, Gln70 was more prominently associated with the null response (P= 0.0007). In conclusion, sequence heterogeneity within the IRRDR and ISDR, and a single point mutation at position 70 of the core region of HCV‐1b are likely to be correlated with virological responses to PEG‐IFN/RBV therapy.
Bmc Microbiology a New Short-term Toxicity Assay Using Aspergillus Awamori with Recombinant Aequorin Gene

Background: Most currently available short-term toxicity assays are based on bacterial cells. Therefore there is a need for novel eukaryotic microbial bioassays that will be relevant to higher eukaryotes such as animals and plants. Ca 2+ is a universal intracellular signalling molecule found in all organisms from prokaryotes to highly specialized animal cells. In fungi calcium has been demonstrated to be involved in control of many important processes. The recombinant aequorin gene from the jellyfish Aequorea victoria responsible for the expression of the Ca 2+-sensitive aequorin photoprotein has been cloned in the filamentous fungus Aspergillus awamori. This has allowed real life monitoring of [Ca 2+ ] c changes in living fungal cells. When subjected to different physico-chemical stimuli fungal cells respond by transiently changing the concentration of free Ca 2+ in the cytosol ([Ca 2+ ] c) and the pattern of these changes (Ca 2+ signature) is specific to each particular stimulus. Therefore it was interesting to investigate whether different environmental toxicants would be able to affect the pattern of [Ca 2+ ] c changes in a reproducible and dose dependant manner.
On a reduced-order two-track car model including longitudinal and lateral load transfer

In this paper we propose a novel reduced-order car model that captures some key features for aggressive maneuvering of complex car vehicles. The proposed model, called RigidCar, consists of a rigid body interacting with the ground at four contact points (two-track car) and including tire models and load transfer. The model does not include suspension models, thus keeping a reasonable level of complexity. Load transfer (both longitudinal and lateral) is taken into account by explicitly imposing the holonomic constraints and computing the reaction forces of the ground at the four contact points. Since the vehicle interacts with the ground at four contact points, it results to be a hyper-static structure so that reaction forces are not uniquely determined. We use the Principle of Least Work to get a compatibility equation and thus resolving the indeterminateness. We provide numerical computations validating the proposed model with respect to a multi-body virtual prototype on an aggressive ISO lane-change maneuver.
Unobservable Re-authentication for Smartphones

The widespread usage of smartphones gives rise to new security and privacy concerns. Smartphones are becoming a personal entrance to networks, and may store private information. Due to its small size, a smartphone could be easily taken away and used by an attacker. Using a victim’s smartphone, the attacker can launch an impersonation attack, which threatens the security of current networks, especially online social networks. Therefore, it is necessary to design a mechanism for smartphones to re-authenticate the current user’s identity and alert the owner when necessary. Such a mechanism can help to inhibit smartphone theft and safeguard the information stored in smartphones. In this paper, we propose a novel biometric-based system to achieve continuous and unobservable re-authentication for smartphones. The system uses a classifier to learn the owner’s finger movement patterns and checks the current user’s finger movement patterns against the owner’s. The system continuously re-authenticates the current user without interrupting user-smartphone interactions. Experiments show that our system is efficient on smartphones and achieves high accuracy.
Economic effects and Energy Use Efficiency of Incorporating Alfalfa and Fertilizer into Grass- Based Pasture Systems

A ten-year grazing study was conducted at the Agriculture and Agri-Food Canada Brandon Research Centre in Manitoba to study the effect of alfalfa inclusion and fertilizer (N, P, K, and S) addition on economics and efficiency of non-renewable energy use in meadow brome grass-based pasture systems for beef production. Fertilizing grass-only or alfalfa-grass pastures to full soil test recommendations improved pasture productivity, but did not improve profitability compared to unfertilized pastures. Fertilizing grass-only pastures resulted in the highest net loss of any pasture management strategy in this study. Adding alfalfa at the time of seeding, with no added fertilizer, was economically the best pasture improvement strategy in this study. Because of moisture limitations, adding commercial fertilizer to full soil test recommendations is probably not economically justifiable in most years, especially with the rising cost of fertilizer. Improving grass-only pastures by adding fertilizer and/or alfalfa required additional non-renewable energy inputs; however, the additional energy required for unfertilized alfalfa-grass pastures was minimal compared to the fertilized pastures. Of the four pasture management strategies, adding alfalfa to grass pastures without adding fertilizer had the highest efficiency of energy use. Based on energy use and economic performance, the unfertilized alfalfa-grass pasture was the most efficient and sustainable pasture system.
Online banking malware ontology

Due to the ever increasing popularity of the Internet, institutions are migrating their services to the digital realm. Banks are among the most representative examples: in order to better meet their clients’ requirements, but also to reduce operational costs, online banking platforms were created and their use stimulated. However, the users’ mass adoption to this novel technology without proper awareness campaigns resulted in a large increase of online banking fraud occurrence rates. This poses great challenges to Law Enforcement Agencies dedicated to cybercrime investigation: in addition to personnel skills training, there is an urgent need for new approaches correlating the horizontally sparse and concealed evidence resulted from such offence. As semantic technologies enable the more intelligent use of computer resources regarding data from a specific domain, this paper proposes the creation of an online banking malware investigation ontology.
Chlorophytum borivilianum as potential terminator of free radicals in various in vitro oxidation systems

Chlorophytum borivilianum is a very popular herb in traditional Indian medicine and used as a potent “Rasayana” drug in “Ayurveda” as a rejuvenator. Currently, a large body of evidence supports the key role of free radicals in diverse pathological conditions such as aging and atherosclerosis. The present investigation essentially focuses on the comprehensive account of in vitro antioxidant activity exerted by C.borivilianum root extracts (i.e., aqueous and ethanolic), to clarify the pharmacological antagonism of chemicals/metals-mediated oxidation. Graded-dose (25 to 1000 µg/ml) of aqueous extract exhibited higher antioxidant potency as evidenced by powerful nitric oxide, superoxide, hydroxyl, DPPH and ABTS·+ radicals scavenging activity along with reducing capacity (Fe3+/ferricyanide complex and FRAP assays), metal chelating ability, as well as markedly suppressed the lipid peroxidation in mitochondrial fractions as compared to ethanolic extract. Further, aqueous extract significantly decreased (P < 0.05) copper-mediated human serum and kinetics of LDL oxidation, as demonstrated by prolongation of lag phase time with decline of oxidation rate, conjugated dienes, lipid hydroperoxides and thiobarbituric acid reactive substances. In addition, the total polyphenol and flavonoid contents of aqueous extract were higher than that of ethanolic extract, which indicated a positive correlation between antioxidant activity and contents of total phenols. The IC50 values of both extracts were also compared with appropriate antioxidant standards. Overall, aqueous extract of C.borivilianum root has significant powerful antioxidant activity and may favorably affect atherosclerosis risk status by reducing LDL oxidation susceptibility.