Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Canine Transmissible Venereal Tumor Cells Using in Situ Polymerase Chain Reaction and the Stable Sequence of the Long Interspersed Nuclear Element

Canine transmissible venereal tumor (CTVT) is a unique tumor that can be transplanted across the major histocompatibility complex (MHC) barrier by viable tumor cells. In dogs, CTVT grows progressively for a few months and then usually regresses spontaneously. A long interspersed nuclear element (LINE) insertion is found specifically and constantly in the 5′ end of the CTVT cell c-myc gene, outside the first exon. The rearranged LINE—c-myc gene sequence has been used with polymerase chain reaction (PCR) to diagnose CTVT. However, in CTVT cells, the total length of the inserted LINE gene is not constant. In this experiment, variation in the inserted LINE gene was studied to determine which parts of the LINE sequence can be used as primers to identify CTVT cells with in situ PCR (IS PCR). The LINE gene was inserted between the TATA boxes in the promoter region of c-myc. In CTVT cells, deletions of different lengths are frequent in this gene. However, the 550-bp segment at the 5′ end of the LINE—c-myc gene was stable. Thus, primers were designed to cover the stable 0.55-kb segment from the 5′ end outside the first exon of the c-myc gene to the 5′ end of LINE gene stable segment. With these primers and IS PCR, individual CTVT cells in formalin-fixed tissue sections and CTVT cultures were identified. Cells from other canine tumors were negative for this gene. In addition, the CTVT-specific, 0.55-kb segment was not found in any spindle-shaped cells from progressive or regressive phase CTVT. The IS PCR technique also did not detect any positive spindle-shaped cells in CTVT cell cultures. Thus, fibroblastic terminal differentiation is less likely to be a mechanism for spontaneous regression of CTVT cells.
Optimization of Object-Oriented Design using Coupling Metrics

In spite of large acceptance of object-oriented paradigm, many programmers don’t have a firm grip on the design principles and the intimate mechanisms of object-orientation and this result into to a lot of poor designed large scale OO systems. Coupling in the software is one of the most vibrant internal quality attribute to measure the design performance. In this paper, we propose Message Received Coupling (MRC) and Degree of Coupling (DC) metrics for the automatic detection of a set of design problems along with an algorithm to apply these metrics to redesign an object-oriented source code, if necessary. We also design a Method Calling Graph (MCG) that helps in calculating the value of proposed metrics. The revised set of metrics helps the developers to decide whether a design needs to be changed or left in its original form. General Terms Analysis, Metrics, Object-Oriented Design.
Evaluation of the accuracy of Lachman and Anterior Drawer Tests with KT1000 ın the follow-up of anterior cruciate ligament surgery

Ligament laxity measurement is clinically valuable to diagnose the injury and also to compare the laxity before and after surgical procedure. The aim of the study was to compare the accuracy of the Lachman and Anterior Drawer Tests to evaluate the knee examination with the KT1000 arthrometer after the anterior cruciate ligament (ACL) surgery in early follow-up period. Fourty ACL reconstructed knees were examined with the Lachman and Anterior Drawer Tests, and KT1000 arthrometer with compariable intact knee of the same patients. Physical emanination findings were compared with the KT1000 arthrometer with each power. Spearman correlation and receiver operating characteristic (ROC) analysis were used for the evaluation of relations between parameters. Significance was evaluated in P<0.1 and P<0.05. The mean age was 28.18±6.21 yr, and the mean follow-up was 23.09±9.08 months. The mean KT1000 measurements of 40 operated knees state at 6.8, 9.1, 13.6 kg and maxium anterior displacement forces were 4.9, 6.7, 8.7, and 11.9 mm, respectively. The same values for the same acting forces of intact knees were 4.2, 5.9, 7.8, and 10.2, respectively. In Spearman’s correlation and ROC analysis at 13.6-kg power on KT1000 arthrometer statistically matched with pyhsical examinations (P<0.1, P<0.01). In our study, correlation of physical examinations with KT1000 arthrometer is a worthy evaluation technique that can be added to examination of ACL reconstructed knee to control with inexperinced examiners’ findings. We suggest that at 13.6-kg power with KT1000 arthrometer findings perfectly match the Lachman and Anterior Drawer Tests of the knee.
Removal of Muscle Artifacts from Single-Channel EEG Based on Ensemble Empirical Mode Decomposition and Multiset Canonical Correlation Analysis

Electroencephalogram (EEG) recordings are often contaminated with muscle artifacts. This disturbing muscular activity strongly affects the visual analysis of EEG and impairs the results of EEG signal processing such as brain connectivity analysis. If multichannel EEG recordings are available, then there exist a considerable range of methods which can remove or to some extent suppress the distorting effect of such artifacts. Yet to our knowledge, there is no existing means to remove muscle artifacts from single-channel EEG recordings. Moreover, considering the recently increasing need for biomedical signal processing in ambulatory situations, it is crucially important to develop single-channel techniques. In this work, we propose a simple, yet effective method to achieve the muscle artifact removal from single-channel EEG, by combining ensemble empirical mode decomposition (EEMD) with multiset canonical correlation analysis (MCCA). We demonstrate the performance of the proposed method through numerical simulations and application to real EEG recordings contaminated with muscle artifacts. The proposed method can successfully remove muscle artifacts without altering the recorded underlying EEG activity. It is a promising tool for real-world biomedical signal processing applications.
Delta‐like 1 participates in the specification of ventral midbrain progenitor derived dopaminergic neurons

Delta‐like 1 (Dlk1), a member of the Delta/Notch protein family, is expressed in the mouse ventral midbrain (VM) as early as embryonic day 11.5 (E11.5) followed by exclusive expression in tyrosine 3‐monooxygenase (TH) positive neurons from E12.5 onwards. To further elucidate the yet unknown function of Dlk1 in VM neuron development, we investigated the effect of soluble Dlk1 protein as well as the intrinsic Dlk1 function in the course of VM progenitor expansion and dopaminergic (DA) neuron differentiation in vitro. Dlk1 treatment during expansion increased DA progenitor proliferation and the proportion of NR4A2+ neurons expressing TH after differentiation, whereas Dlk1 treatment during the course of DA precursor differentiation did not alter TH+ neuron counts. In contrast, silencing of endogenously expressed Dlk1 prior to DA precursor differentiation partially prevented the expression of DA neuron markers, which was not accompanied with alteration of overall or local proliferation. Due to the latter finding in combination with the absence of Dlk1 negative DA neurons in differentiated cultures, we suggest that Dlk1 expression might have a permissive effect on DA neuron differentiation in vitro. The study presented here is the first publication identifying Dlk1 effects on ventral midbrain‐derived DA precursor differentiation.
School, Activism and Politics at the Movies: Educator Reactions to the Film Waiting for “Superman”

Context The documentary film about U.S. education reform, Waiting for “Superman,” was met with acclaim and controversy when released to theaters in 2010, and again when launching its grassroots “host a screening” campaign in 2011. The campaign ran concurrent with 2011 state legislative sessions, during which several states (e.g., Ohio, Indiana, New Jersey, and Wisconsin) voted on education reform bills regarding teacher merit pay, probationary teacher contracts, school vouchers, changes to the school funding formula, charter school funding, and limiting teachers’ (and public workers’) collective bargaining rights—all issues touched on in the film. Purpose To shed light on the relationship between popular media, public opinion, and social action regarding education, I examine responses to Waiting for “Superman” across different viewer demographics and relate responses to educational policy stances. The following research questions are considered: 1. Why did people watch Waiting for “Superman”? 2. How did different education stakeholders (preservice teachers, current teachers, academics, community members, etc.) react to the film? Were some groups more likely to accept, negotiate with, or oppose the film's message? 3. What role, if any, did the film play in viewers’ stances on education reform or intention to take social action in the education reform movement? Participants Participants include 168 self-selected audience members attending free public film screenings at a midwestern university. Research Design Mixed methods research design compares audiences’ descriptive statistics alongside open-ended survey responses and interview data. Results Viewers were majority young and female. Most attended because they were interested in the topic, wanted to learn more, or came with a friend. Audience responses were complex and nuanced, i.e., 38% volunteered positive reactions to the film and 30% criticized it in some way (not mutually exclusive). Emotional reactions were common (38%). Audience members tended to respond to the film based on their direct prior experience (or lack thereof) with the U.S. public education system. The majority of current teachers in the audience chose not to participate in the study, perhaps because of the contentious political climate. Fifteen percent of audience members were “inspired” to act after viewing, and half of those were preservice teachers, but none were current teachers. Conclusions In vilifying teachers’ unions, thereby marginalizing some great teachers, the film's producers may have missed the chance to effect lasting change in the education system. While potentially polarizing, popular film may be an effective way to engage preservice teachers in complex education topics. Contextualizing discussion with a multiperspective panel afterward is recommended.
GABAergic Networks in the Prefrontal Cortex and Working Memory

### Introduction Working memory, the ability to briefly store and act on mental representations of information, even when that information is no longer associated with sensory input, is crucial to completing goal-directed behaviors ([Goldman-Rakic, 1996][1]; [Miller and Cohen, 2001][2]). This type
A Decoupled Architecture for Scalability in Text Mining Applications

Sophisticated Text Mining features such as visualization, summarization, and clustering are becoming increasingly common in software applications. In Text Mining, documents are processed using techniques from different areas which can be very expensive in computation cost. This poses a scalability challenge for real-life ap- plications in which users behavior can not be entirely predicted. This paper proposes a decoupled architecture for document processing in Text Mining applications, that allows applications to be scalable for large corpora and real-time processing. It con- tributes a software architecture designed around these requirements and presents TML, a Text Mining Library that implements the architecture. An experimental evaluation on its scalability using a standard corpus is also presented, and empirical evidence on its performance as part of an automated feedback system for writing tasks used by real students.
Object-Based Unequal Error Protection

This report investigates the application of forward-error-correcting codes to data organized as multiple, independent multimedia objects and encoded with modern embedded coders. Capitalizing on the strict importance-ordering characteristic of embedded encodings, the strength of the error protection is optimized such that data that is more important to the reconstructed quality of the dataset is assigned stronger protection. The focus of the investigation is on providing this optimization while maintaining the ability to independently access the individual multimedia objects. Experimental results are presented for still-image objects that illustrate that the desired independent-access ability comes at a cost in reconstruction quality. In addition, it is observed that this cost increases as the channel-loss conditions actually experienced degrade from those for which the optimal-protection arrangement was designed.
Performance evaluation of ballistic silicon nanowire transistors with atomic-basis dispersion relations

In this letter, we explore the band structure effects on the performance of ballistic silicon nanowire transistors (SNWTs). The energy dispersion relations for silicon nanowires are evaluated with an sp3d5s* tight binding model. Based on the calculated dispersion relations, the ballistic currents for both n-type and p-type SNWTs are evaluated by using a seminumerical ballistic model. For large diameter nanowires, we find that the ballistic p-SNWT delivers half the ON-current of a ballistic n-SNWT. For small diameters, however, the ON-current of the p-type SNWT approaches that of its n-type counterpart. Finally, the carrier injection velocity for SNWTs is compared with those for planar metal-oxide-semiconductor field-effect transistors, clearly demonstrating the impact of quantum confinement on the performance limits of SNWTs.
Learning Meronyms from Biomedical Text

The part-whole relation is of special importance in biomedicine: structure and process are organised along partitive axes. Anatomy, for example, is rich in part-whole relations. This paper reports preliminary experiments on part-whole extraction from a corpus of anatomy definitions, using a fully automatic iterative algorithm to learn simple lexico-syntactic patterns from multiword terms. The experiments show that meronyms can be extracted using these patterns. A failure analysis points out factors that could contribute to improvements in both precision and recall, including pattern generalisation, pattern pruning, and term matching. The analysis gives insights into the relationship between domain terminology and lexical relations, and into evaluation strategies for relation learning.
A Machine Learning Approach for Text and Document Mining

Text Classification or Text Categorization is performed to automatically categorize a set of documents into its respective categories. With the rapid growth of World Wide Web and increasing electronic documents, the Text Categorization becomes an essential method for knowledge discovery and organizing the information. Different tools of Information Retrieval (IR) and Machine Learning (ML) are used for the classification process. A review on machine learning approach for text classification have been done in this paper and also a new system has been proposed for efficient classification. KNN (K Nearest Neighbor) is one of the most promising classification methods for Information retrieval. The main disadvantage of this method is that it has very high computational complexity. This is due to the fact that it considers all the training samples. A combination of traditional KNN classification algorithm and K-Means clustering algorithm has been proposed to overcome this difficulty. The terms are weighted using Term FrequencyInverse Document Frequency after the Preprocessing steps are performed. Then the K-Means clustering algorithm will be used to group all the training samples and the cluster centers will be considered as the new training samples. The KNN classification algorithm is then performed to find out the category of the documents. A Decision Tree algorithm will then be performed to find out the sub category of the documents. The accuracy will be evaluated using precision, recall and F measure. KeywordsText classification, KNN classification algorithm, Cluster, Decision tree
Smoking, Smoking Cessation, and Risk for Type 2 Diabetes Mellitus

BACKGROUND Cigarette smoking is an established predictor of incident type 2 diabetes mellitus, but the effects of smoking cessation on diabetes risk are unknown. OBJECTIVE To test the hypothesis that smoking cessation increases diabetes risk in the short term, possibly owing to cessation-related weight gain. DESIGN Prospective cohort study. SETTING The ARIC (Atherosclerosis Risk in Communities) Study. PATIENTS 10,892 middle-aged adults who initially did not have diabetes in 1987 to 1989. MEASUREMENTS Smoking was assessed by interview at baseline and at subsequent follow-up. Incident diabetes was ascertained by fasting glucose assays through 1998 and self-report of physician diagnosis or use of diabetes medications through 2004. RESULTS During 9 years of follow-up, 1254 adults developed type 2 diabetes. Compared with adults who never smoked, the adjusted hazard ratio of incident diabetes in the highest tertile of pack-years was 1.42 (95% CI, 1.20 to 1.67). In the first 3 years of follow-up, 380 adults quit smoking. After adjustment for age, race, sex, education, adiposity, physical activity, lipid levels, blood pressure, and ARIC Study center, compared with adults who never smoked, the hazard ratios of diabetes among former smokers, new quitters, and continuing smokers were 1.22 (CI, 0.99 to 1.50), 1.73 (CI, 1.19 to 2.53), and 1.31 (CI, 1.04 to 1.65), respectively. Further adjustment for weight change and leukocyte count attenuated these risks substantially. In an analysis of long-term risk after quitting, the highest risk occurred in the first 3 years (hazard ratio, 1.91 [CI, 1.19 to 3.05]), then gradually decreased to 0 at 12 years. LIMITATION Residual confounding is possible even with meticulous adjustment for established diabetes risk factors. CONCLUSION Cigarette smoking predicts incident type 2 diabetes, but smoking cessation leads to higher short-term risk. For smokers at risk for diabetes, smoking cessation should be coupled with strategies for diabetes prevention and early detection.
Social support, psychological distress, and natural killer cell activity in ovarian cancer.

PURPOSE Psychosocial stress has been related to impaired immunity in cancer patients. However, the extent to which these relationships exist in immune cells in the tumor microenvironment in humans has not been explored. We examined relationships among distress, social support, and natural killer (NK) cell activity in ovarian cancer patients in peripheral-blood mononuclear cells (PBMC), ascitic fluid, and tumor-infiltrating lymphocytes (TIL). PATIENTS AND METHODS Patients awaiting surgery for a pelvic mass suspected of being ovarian cancer completed psychological questionnaires and gave a presurgical sample of peripheral blood. Samples of tumor and ascites were taken during surgery, lymphocytes were then isolated, and NK cytotoxicity and percentage were determined. The final sample, which was confirmed by surgical diagnosis, included 42 patients with epithelial ovarian cancer and 23 patients with benign masses. RESULTS Peripheral NK cell activity was significantly lower among ovarian cancer patients than in patients with benign masses. Among ovarian cancer patients, NK cytotoxicity in TIL was significantly lower than in PBMC or ascitic fluid. Social support was related to higher NK cytotoxicity in PBMC and TIL, adjusting for stage. Distress was related to lower NK cytotoxicity in TIL. A multivariate model indicated independent associations of both distress and social support with NK cell activity in TIL. CONCLUSION Psychosocial factors, such as social support and distress, are associated with changes in the cellular immune response, not only in peripheral blood, but also at the tumor level. These relationships were more robust in TIL. These findings support the presence of stress influences in the tumor microenvironment.
Frequency range extension of the ITU-R NLOS path loss models applicable for urban street environments with 28 GHz measurements

Since millimeter-wave (mmWave) frequency bands are strong candidates in new spectra for 5G mobiles, standardized propagation channel models are anticipated to be developed for 5G system evaluation and interference analysis. Instead of developing a new model, this paper takes the tact of examining the practicality of applying already existing, and commonly-used, ITU-R path loss models to the mmWave bands. Specifically, we focus on NLOS (non-line-of-sight) propagation in urban street canyon environments, where the radio waves propagate along the street roads and the obstruction sources are building corners. To do this, we compare measurements collected in Seoul at 28 GHz to the two ITU-R path loss models: (1) the ITU-R P.1411 Street Canyons NLOS path loss model and (2) the ITU-R M.2135 UMi (urban microcell) Manhattan-grid NLOS path loss model. The results show that the prediction of the original ITU-R models do, in fact, deviate from our 28 GHz measurement data. However, by modifying certain parameters of the ITU-R P.1411 model, we are able to generate predictions more nearly in line with the measurement data. Thusly, without modifying parameter values, the existing ITU-R P.1411 model can be still applicable to 28 GHz.
Prevalence of obesity in adolescents and the impact of sexual maturation stage on body mass index in obese adolescents

OBJECTIVE Puberty is a high-risk period for the development of obesity. The aim of this study was to determine the prevalence of obesity in adolescents admitted to an outpatient adolescent clinic and investigate the relationships between the increase of body mass index and sexual maturation stages in obese adolescents. MATERIAL AND METHODS We recruited 6,462 adolescents, aged 9-16 years, admitted to the outpatient clinic of our Adolescent Unit, between May 1999 and September 2000. BMI was calculated as weight per height with weight in kilograms and height in meters. Adolescents with a BMI > or = 95th percentile for age and sex were defined as obese, with BMI's > or = 90th percentile but < 95th percentile were defined as overweight and considered at risk for obesity. Obese adolescents, with endocrine problems identified to cause obesity, were excluded from this study. Pearson correlation coefficients were used to assess the relationships between BMI and age. The differences between the sexual maturation stages were evaluated with Mann-whitney U Test. RESULTS Out of 6,462 cases screened, 151 obese adolescents were found. Prevalence of obesity for the total sample surveyed was estimated at 2.3%. BMI values were significantly correlated with age in both sexes. In girls, only the increase of BMI values from stage I to stage II was found to be statistically significant. In boys, BMI values did not differ significantly between the sexual maturation stages but the number of obese cases were high in stages I and II. DISCUSSION AND CONCLUSION The pubertal growth spurt (timing determined by sexual maturation stage) effects the amount of fat accumulation and the distribution of fat in different ways in boys and girls. So, not only the age and sex but also the sexual maturation stage has to be taken into account while evaluating the BMI values for investigating the risk of obesity in puberty.