Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid and sensitive insulated isothermal PCR for point-of-need feline leukaemia virus detection

Objectives Feline leukaemia virus (FeLV), a gamma retrovirus, causes diseases of the feline haematopoietic system that are invariably fatal. Rapid and accurate testing at the point-of-need (PON) supports prevention of virus spread and management of clinical disease. This study evaluated the performance of an insulated isothermal PCR (iiPCR) that detects proviral DNA, and a reverse transcription (RT)-iiPCR that detects both viral RNA and proviral DNA, for FeLV detection at the PON. Methods Mycoplasma haemofelis, feline coronavirus, feline herpesvirus, feline calicivirus and feline immunodeficiency virus were used to test analytical specificity. In vitro transcribed RNA, artificial plasmid, FeLV strain American Type Culture Collection VR-719 and a clinical FeLV isolate were used in the analytical sensitivity assays. A retrospective study including 116 clinical plasma and serum samples that had been tested with virus isolation, real-time PCR and ELISA, and a prospective study including 150 clinical plasma and serum samples were implemented to evaluate the clinical performances of the iiPCR-based methods for FeLV detection. Results Ninety-five percent assay limit of detection was calculated to be 16 RNA and five DNA copies for the RT-iiPCR, and six DNA copies for the iiPCR. Both reactions had analytical sensitivity comparable to a reference real-time PCR (qPCR) and did not detect five non-target feline pathogens. The clinical performance of the RT-iiPCR and iiPCR had 98.82% agreement (kappa[κ] = 0.97) and 100% agreement (κ = 1.0), respectively, with the qPCR (n = 85). The agreement between an automatic nucleic extraction/RT-iiPCR system and virus isolation to detect FeLV in plasma or serum was 95.69% (κ = 0.95) and 98.67% (κ = 0.85) in a retrospective (n = 116) and a prospective (n = 150) study, respectively. Conclusions and relevance These results suggested that both RT-iiPCR and iiPCR assays can serve as reliable tools for PON FeLV detection.
Abnormal Uterine Bleeding- evaluation by Endometrial Aspiration

Endometrial evaluation is generally indicated in cases presenting with abnormal uterine bleeding (AUB), especially in women more than 35 years of age. AUB encompasses a variety of presentation, for example, heavy menstrual bleeding, frequent bleeding, irregular vaginal bleeding, postcoital and postmenopausal bleeding to name a few. Many methods are used for the evaluation of such cases, with most common being sonography and endometrial biopsy with very few cases requiring more invasive approach like hysteroscopy. Endometrial aspiration is a simple and safe office procedure used for this purpose. Materials and Methods: We retrospectively analyzed cases of AUB where endometrial aspiration with Pipette (Medgyn) was done in outpatient department between January 2015 and April 2016. Case records (both paper and electronic) were used to retrieve data. Results: One hundred and fifteen cases were included in the study after applying inclusion and exclusion criteria. Most cases were between 46 and 50 years of age followed by 41–45 years. No cases were below 25 or more than 65 years of age. Heavy menstrual bleeding was the most common presentation of AUB. Adequate samples were obtained in 86% of cases while 13.9% of cases' sample was inadequate for opinion, many of which were later underwent hysteroscopy and/or dilatation and curettage (D and C) in operation theater; atrophic endometrium was the most common cause for inadequate sample. Uterine malignancy was diagnosed in three cases. Discussion: Endometrial aspiration has been compared with traditional D and C as well as postoperative histopathology in various studies with good results. Many such studies are done in India as well as in western countries confirming good correlation with histopathology and adequate tissue sample for the pathologist to give a confident diagnosis. No complication or side effect was noted with the use of this device. Conclusion: Endometrial aspiration is a simple, safe, and effective method to sample endometrium in cases of AUB avoiding risk of anesthesia and is less time-consuming. Many similar devices are also available in the market and need to be popularized in all parts of the country.
Phenotypic characterization of an older adult male with late-onset epilepsy and a novel mutation in ASXL3 shows overlap with the associated Bainbridge-Ropers syndrome

The additional sex combs like 3 gene is considered to be causative for the rare Bainbridge-Ropers syndrome (BRPS), which is characterized by severe intellectual disability, neonatal hypotonia, nearly absent development of speech and language as well as several facial dysmorphisms. Apart from disruptive autistiform behaviors, sleep disturbances and epileptic phenomena may be present. Here, a 47-year-old severely intellectually disabled male is described in whom exome sequencing disclosed a novel heterozygous frameshift mutation in the ASXL3 gene leading to a premature stopcodon in the last part of the last exon. Mutations in this very end 3′ of the gene have not been reported before in BRPS. The phenotypical presentation of the patient including partially therapy-resistant epilepsy starting in later adulthood shows overlap with BRPS, and it was therefore concluded that the phenotype is likely explained by the identified mutation in ASXL3.
The Role of Stem Cells in Ovarian Cancer : A Review

Ovarian cancer causes themost deaths amonggynecological cancers.Oneof themajor reasons for its lethality despite improved surgical techniques and improved chemotherapeutic agents in recent years is the recurrence due to chemoresistance. There have been several proposed mechanisms for chemoresistance of which the existence of cancer stem cells has recently been brought to attention. Cancer stem cells represent a small proportion of cells within a tumor with the ability to proliferate in order to increase the number of cancer stemcells, aswell as the ability to differentiate into heterogeneous-nontumorigenic cancer cell types. Also in ovarian cancer as in other types of cancer, different populations of cancer stemcells were isolated from tumors. In literature the cancer stem cells are represented by different cell populations expressing different phenotypes and characteristics. The most commonly used markers for their isolation are CD44, CD133, CD24, CD117 and ALDH, which are often used in combinations. In vitro and in vivo studies confirmed that these isolated cells behave as cancer stem cells and use different mechanisms tominimize the effect of chemotherapeutic agents. Also proteins,which are generally knownaspluripotent stemcell markers of normal stem cells, such as NANOG, OCT-4A, SOX-2 and c-MYC, have an important role in ovarian cancer development and chemoresistance. Additionally, it was demonstrated that the expression of the mentioned markers in ovarian tumors can be used as a prognostic tool, where usually the over-expression of a specificmarker correlateswith a poor prognosis. However, the conclusions of the prognostic value of cancer stem cell markers are still under debate. The reason for vague conclusions may lay in the fact that stem cells expressing the same markers can be also found in "healthy" ovaries, which could represent a bias in cancer studies. Evenmore, since stem cells located in "healthy" ovaries, including small stem cells resembling very small embryonic-like stemcells, represent themost of the cells that divide andproliferate, they seem tobe the best candidate to undergomalignant transformation andcould serve as tumor initiating cells. Therefore, the knowledgeon stemcells, expressing the pluripotency-related markers in "healthy" ovaries is a prerequisite to better understand the ovarian cancer.
Examining Features for Android Malware Detection

With the constantly increasing use of mobile devices, the need for effective malware detection algorithms is constantly growing. The research presented in this paper expands upon previous work that applied machine learning techniques to the area of Android malware detection by examining Java API call data as a method for malware detection. In addition to examining a new feature, a significant amount of work has been done in understanding how the model works and various ways of improving its accuracy. Ultimately a classification accuracy of around 80-85% was achieved using the JAVA API call feature.
Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data

Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution rates. The genetic substitution rates of Hanwoo and Holstein cattle were estimated using NGS data. Our main findings was to calculate the gene’s substitution rates. Through estimation of genetic substitution rates, we found: diving region of altered substitution density exists. This region may indicate a boundary between protected and unprotected genes. The protected region is mainly associated with the gene ontology terms of regulatory genes. The genes that distinguish Hanwoo from Holstein in terms of substitution rate predominantly have gene ontology terms related to blood and circulatory system. This might imply that Hanwoo and Holstein evolved with dissimilar mutation rates and processes after domestication. The difference in meat quality between Hanwoo and Holstein could originate from differential evolution of the genes related to these blood and circulatory system ontology terms.
On position angle errors in the Tremaine-Weinberg method

I show that Tremaine-Weinberg (TW) measurements of bar pattern speeds are sensitive to errors in the position angle of the disc, PA d i s c . I use an N-body experiment to measure these errors; for typical random PA d i s c errors, the resulting scatter in the measured values of the dimensionless bar speed parameter R (defined as the ratio of the corotation radius to the bar semi-major axis) is of the order of the scatter in the observed values. I also consider how the systematic PA d i s c errors produced by disc ellipticities affect TW measurements. The scatter produced by these errors may be significant, depending on the ellipticity distribution. Conversely, by using the sample of TW observations, I find that an upper limit of the typical disc (density) ellipticity is 0.07 at the 90 per cent confidence level, which is in good agreement with previous measurements. Taken together, the random and systematic scatter suggest that the intrinsic distribution of R of gas-poor early-type barred galaxies may be as narrow as that of the gas-rich later types.
Experiments and Modeling of Ternary Alloy Semiconductors

Experiments and Modeling of Ternary Alloy Semiconductors by Stephanie Tritchler Results of the growth ofGat-xlnxSb crystals as the pseudobinary Gat-x SblnxSb are presented. Special focus is given to the relationship between crystal composition and the cut-off wavelength of transmission for the crystal using Fourier Transform Infrared (FTIR) and Ultra Violet-Visual Wavelength (UV-Vis) spectroscopy. This provides a fast, easy method to determine the composition. A Matlab model to determine the composition of a crystal grown using the Bridgman method is developed. This compares the ideal to the regular solution models for Gat-xlnxSb. These two models are used to predict the composition of the grown crystals. The regular solution yields a more accurate pseudo-binary phase diagram and thus a much closer fit to the experimental data.
Integrated Molecular Characterization of Gastrointestinal Stromal Tumors (GIST) Harboring the Rare D842V Mutation in PDGFRA Gene

Gastrointestinal stromal tumors (GIST) carrying the D842V activating mutation in the platelet-derived growth factor receptor alpha (PDGFRA) gene are a very rare subgroup of GIST (about 10%) known to be resistant to conventional tyrosine kinase inhibitors (TKIs) and to show an indolent behavior. In this study, we performed an integrated molecular characterization of D842V mutant GIST by whole-transcriptome and whole-exome sequencing coupled with protein–ligand interaction modelling to identify the molecular signature and any additional recurrent genomic event related to their clinical course. We found a very specific gene expression profile of D842V mutant tumors showing the activation of G-protein-coupled receptor (GPCR) signaling and a relative downregulation of cell cycle processes. Beyond D842V, no recurrently mutated genes were found in our cohort. Nevertheless, many private, clinically relevant alterations were found in each tumor (TP53, IDH1, FBXW7, SDH-complex). Molecular modeling of PDGFRA D842V suggests that the mutant protein binds imatinib with lower affinity with respect to wild-type structure, showing higher stability during the interaction with other type I TKIs (like crenolanib). D842V mutant GIST do not show any actionable recurrent molecular events of therapeutic significance, therefore this study supports the rationale of novel TKIs development that are currently being evaluated in clinical studies for the treatment of D842V mutant GIST.
System Identification Modeling for Flight Control Design

Flight control analyses require accurate models of the bare airframe and its associated uncertainties, as well as the integrated system (block diagrams) across the frequency range of interest. Frequency domain system identification methods have proven to efficiently fulfill these requirements in recent rotorcraft flight control applications. This paper presents integrated system identification methods for flight control modeling for flight test examples of the Fire Scout MQ-8B, S-76, and ARH-70A. The paper also looks toward how system identification could be used in new modeling challenges such as the Joint Heavy Lift rotorcraft as well as small unique unmanned configurations.
Tailored Therapist-Guided Internet-Based Cognitive Behavioral Treatment for Psoriasis: A Randomized Controlled Trial

Objective: Patients with somatic conditions, such as psoriasis, frequently suffer from high burden of their disease in daily life and might benefit from internet-based cognitive behavioral therapy (ICBT) tailored to their adjustment problems. The aim of this multicenter randomized controlled trial was to examine the effects of therapist-guided, individually tailored ICBT in a clinical sample of patients with psoriasis. Methods: A total of 131 patients with psoriasis, who were screened for a psychological risk profile, were randomized to either care as usual (CAU, n = 66) or ICBT in addition to CAU (n = 65). Participants filled out standardized self-report questionnaires assessing physical and psychological functioning and impact on daily activities at baseline, posttreatment assessment, and 6-month follow-up. Results: In covariate-controlled linear mixed-model analyses, significantly larger improvements in ICBT compared to CAU were found in the primary outcomes physical functioning (p = 0.03, d = 0.36) and impact on daily activities (p = 0.04, d = 0.35), but not in psychological functioning (p = 0.32), up to 6 months after treatment compared to baseline. In explorative analyses, the working alliance measured at the beginning of ICBT treatment predicted improved physical (p = 0.02) and psychological (p < 0.001) outcomes. Conclusions: Results underline the promise of therapist-guided, individually tailored ICBT to improve physical functioning and reduce the impact of psoriasis on daily activities in patients with a psychological risk profile. Establishing a good therapeutic relationship early on may be an important factor that influences treatment outcomes in personalized ICBT interventions. Further research is needed to evaluate ICBT effectiveness in additional samples and to explore its underlying mechanisms.
Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma

Purpose As a typical hypervascular tumor, clear cell renal cell carcinoma (ccRCC) is the most common type of RCC. This study was aimed to explore the prognostic genes for ccRCC, focusing on the roles of vascular endothelial growth factor A (VEGFA) and Delta-like ligand 4 (DLL4) in the disease. Materials and methods The mRNA-sequencing data of kidney renal clear cell carcinoma (KIRC) were obtained from The Cancer Genome Atlas (TCGA) database, including 469 tumor samples and 68 adjacent normal samples. Using limma package, differentially expressed genes (DEGs) were analyzed by differential expression and subgroup analyses and confirmed using validation dataset GSE53757. Followed by enrichment analysis, protein–protein interaction (PPI) network analysis and protein subcellular localization were performed using multifaceted analysis tool for human transcriptome tool, and Cytoscape software and InnateDB database, respectively. Moreover, survival analysis was conducted to identify key prognosis-associated genes. In addition, VEGFA and DLL4 levels were detected using real-time quantitative PCR (qRT-PCR). Results A total of 1,984 DEGs were screened in the KIRC tumor samples. VEGFA was located in extracellular space and could interact with placental growth factor (PGF) and angiopoietin 2 (ANGPT2) in the PPI network. Subgroup analysis suggested that VEGFA was significantly upregulated in stages I, II, and III ccRCC tumor samples. Survival analysis showed that TIMP1 was among the top four prognosis-associated genes. qRT-PCR analysis confirmed that the expression levels of DLL4 and VEGFA were significantly upregulated in tumor samples. Conclusion VEGFA and DLL4 might be prognostic genes for ccRCC. Besides, PGF, ANGPT2, and TIMP1 might also be related to the prognosis of ccRCC patients.
Transforming the short-term sensing stimuli to long-term e-skin memory

A Tantalum Pentoxide (Ta2O5) based resistive nonvolatile memory device with bipolar switching behaviour was developed to demonstrate the new concept of memory in e-skin. The memory device showed stable switching behavior under preprogrammed voltage stimuli after an initial forming process. The memory cell was then integrated with a commercial tactile sensor with a new interface circuit, which enabled the switching of the memory cell through the electrical output from the sensor. This study provides a novel method for handling the transport and storage of large tactile data and will trigger advances towards memorable e-skin.
HIV Clustering in Mississippi: Spatial Epidemiological Study to Inform Implementation Science in the Deep South

Background In recent years, more than half of new HIV infections in the United States occur among African Americans in the Southeastern United States. Spatial epidemiological analyses can inform public health responses in the Deep South by identifying HIV hotspots and community-level factors associated with clustering. Objective The goal of this study was to identify and characterize HIV clusters in Mississippi through analysis of state-level HIV surveillance data. Methods We used a combination of spatial epidemiology and statistical modeling to identify and characterize HIV hotspots in Mississippi census tracts (n=658) from 2008 to 2014. We conducted spatial analyses of all HIV infections, infections among men who have sex with men (MSM), and infections among African Americans. Multivariable logistic regression analyses identified community-level sociodemographic factors associated with HIV hotspots considering all cases. Results There were HIV hotspots for the entire population, MSM, and African American MSM identified in the Mississippi Delta region, Southern Mississippi, and in greater Jackson, including surrounding rural counties (P<.05). In multivariable models for all HIV cases, HIV hotspots were significantly more likely to include urban census tracts (adjusted odds ratio [AOR] 2.01, 95% CI 1.20-3.37) and census tracts that had a higher proportion of African Americans (AOR 3.85, 95% CI 2.23-6.65). The HIV hotspots were less likely to include census tracts with residents who had less than a high school education (AOR 0.95, 95% CI 0.92-0.98), census tracts with residents belonging to two or more racial/ethnic groups (AOR 0.46, 95% CI 0.30-0.70), and census tracts that had a higher percentage of the population living below the poverty level (AOR 0.51, 95% CI 0.28-0.92). Conclusions We used spatial epidemiology and statistical modeling to identify and characterize HIV hotspots for the general population, MSM, and African Americans. HIV clusters concentrated in Jackson and the Mississippi Delta. African American race and urban location were positively associated with clusters, whereas having less than a high school education and having a higher percentage of the population living below the poverty level were negatively associated with clusters. Spatial epidemiological analyses can inform implementation science and public health response strategies, including improved HIV testing, targeted prevention and risk reduction education, and tailored preexposure prophylaxis to address HIV disparities in the South.
Relationship of Social Cognitive Theory Concepts to Dietary Habits of Pregnant Women

Background: Nutrition during pregnancy is undoubtedly one of the most important factors affecting maternal health. In this regard, considering the cognitive-behavioral factors associated with feeding, behaviors will play an important role in the effectiveness of interventions. Therefore, this study aimed to investigate the correlation between food habits and structures of social cognitive theory in pregnant women. Materials and Methods: In this cross-sectional study, 192 pregnant women were randomly selected. Data were collected using a questionnaire based on the social cognitive theory structures and food habits questionnaire in the questioning manner and was also analyzed using Pearson correlation and multiple linear regression with the software Statistical Package for the Social Sciences, version 19. Results: There was a significant correlation between nutritional behavior with self-regulation (p = 0.001), self-efficacy (p = 0.001), outcome expectations (p = 0.001), social support (p = 0.002), and access (p = 0.001). A significant correlation was observed between lack of consumption of unnecessary and unhelpful food with self-regulation (p = 0.02). In the multivariable regression analysis, only self-regulation revealed significant and direct contribution in relation to nutritional behavior (p < 0.001). Conclusions: Results of this study showed that self-regulation is one of the important factors associated with feeding behavior in pregnant women so that it is suggested to be considered in nutritional interventions in order to improve nutritional behavior.
Eavesdropping via pilot relay attack

In this paper, we propose a new type of attack from the perspective of the eavesdropper. The full-duplex eavesdropper acts as a relay in the uplink channel estimation phase forwarding the received pilot signal from legitimate receiver to confound the legitimate transmitter. Compared to pilot spoofing attack, which needs the eavesdropper to know the pilot signal accurately, the pilot relay attack only needs the eavesdropper to know the frame structure of the legitimate transceiver pair. In this paper, we study the optimal amplify-and-forward strategy of the eavesdropper so that its eavesdropping behavior is harder to be detected by maximizing the transmission rate from the legitimate transmitter to the legitimate receiver under the constraint that the eavesdropping rate is larger than the legitimate transmission rate. Furthermore, we analyze the performance of the pilot relay attack when Eve is at different locations, the simulations have shown that different strategies should be adopted at different locations.