Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional analysis of the murine T-cell receptor beta enhancer and characteristics of its DNA-binding proteins

The minimal T-cell receptor (TCR) beta-chain (TCR beta) enhancer has been identified by transfection into lymphoid cells. The minimal enhancer was active in T cells and in some B-lineage cells. When a larger fragment containing the minimal enhancer was used, its activity was apparent only in T cells. Studies with phytohemagglutinin and 4 beta-phorbol-12,13-dibutyrate revealed that the enhancer activity was increased by these agents. By a combination of DNase I footprinting, gel mobility shift assay, and methylation interference analysis, seven different motifs were identified within the minimal enhancer. Furthermore, competition experiments showed that some of these elements bound identical or similar factors that are known to bind to the TCR V beta promoter decamer or to the immunoglobulin enhancer kappa E2 or muEBP-E motif. These shared motifs may be important in the differential gene activity among the different lymphoid subsets.
Hyperglycemia Reduces Survival and Impairs Function of Circulating Blood-Derived Progenitor Cells

Objective—Function and availability of circulating progenitor cells (CPC) have been shown to be impaired in patients with diabetes mellitus (DM). Therefore, the aim of the present study was to analyze possible mechanisms leading to the reduction of CPC amount and function. Methods and Results—Peripheral blood mononuclear cells (MNCs) of healthy donors (n=15) were cultivated under hyperglycemia (HG) conditions (12 mmol/L D-Glucose) or in osmotic control medium (Con) (5 mmol/L D-Glucose plus 7 mmol/L L-Glucose) for 7 days. CPC amount was determined by uptake of acetylated low-density lipoprotein and lectin binding. On the functional level, cell cycle status, nitric oxide (NO) production, and migrational and integrative capacity of CPCs were assessed. HG conditions caused a significant decrease in CPC amount derived from healthy MNCs. Furthermore, HG conditions led to a functional impairment, reflected in a decreased NO production and matrix metalloproteinase (MMP)-9 activity, as well as an impairment of the migrational and integrative capacities. Conclusion—HG, a main feature of DM, affects important functional characteristics of CPCs. These results may provide further insight into the pathomechanism of endothelial dysfunction in HG.
Retinal, anterior segment and full eye imaging using ultrahigh speed swept source OCT with vertical-cavity surface emitting lasers

We demonstrate swept source OCT utilizing vertical-cavity surface emitting laser (VCSEL) technology for in vivo high speed retinal, anterior segment and full eye imaging. The MEMS tunable VCSEL enables long coherence length, adjustable spectral sweep range and adjustable high sweeping rate (50–580 kHz axial scan rate). These features enable integration of multiple ophthalmic applications into one instrument. The operating modes of the device include: ultrahigh speed, high resolution retinal imaging (up to 580 kHz); high speed, long depth range anterior segment imaging (100 kHz) and ultralong range full eye imaging (50 kHz). High speed imaging enables wide-field retinal scanning, while increased light penetration at 1060 nm enables visualization of choroidal vasculature. Comprehensive volumetric data sets of the anterior segment from the cornea to posterior crystalline lens surface are also shown. The adjustable VCSEL sweep range and rate make it possible to achieve an extremely long imaging depth range of ~50 mm, and to demonstrate the first in vivo 3D OCT imaging spanning the entire eye for non-contact measurement of intraocular distances including axial eye length. Swept source OCT with VCSEL technology may be attractive for next generation integrated ophthalmic OCT instruments.
Performance and nutrient digestibility in weanling pigs as influenced by yeast culture additions to starter diets containing dried whey or one of two fiber sources.

Three experiments were conducted using crossbred weanling pigs (7.2 to 8.6 kg; 25 to 29 d of age) to determine the effect on performance and nutrient digestibility of . 75% yeast culture (YC) additions to starter diets containing whey or one of two fiber sources. An 18% CP corn-soybean meal basal diet was used in all experiments. In Exp. 1 (n = 192), the addition of YC did not affect ADG, ADFI, or gain: feed ratios (G:F) of pigs fed diets without or with 15% dried whey in two 5-wk trials. In Exp. 2 (n = 174), ADG and ADFI were not affected by YC addition to diets containing no added fiber, 8% soybean hulls (SH), or 8% peanut hulls (PH) in two 5-wk trials. The addition of SH or PH did not affect ADG or ADFI; however, a YC x SH interaction (P < .05) and a YC x PH interaction (P < .10) for G:F indicated that the addition of SH or PH to the diet in the absence of YC reduced G:F, but in the presence of YC, G:F were maintained. In a 3-wk grower phase of one trial in Exp. 2 (n = 54), SH and PH additions decreased ADG (P < .005), whereas YC additions improved ADG (P < .01), particularly for pigs fed diets that also contained SH (P < .05). (ABSTRACT TRUNCATED AT 250 WORDS)
Analysis About Overshoot Peaks Appearing in the Current Loop With Resonant Controller

Resonant controller is considered ideal for harmonics current control, with advantages of zero steady-state error and computation efficiency. The commonly employed proportional-resonant (PR) controller is widely accepted, but its limited ability in dealing with higher order harmonics, or named limited regulation bandwidth, is also recognized from practical applications. This paper points out that regulation bandwidth of resonant controller is related to the overshoot peaks around resonant frequency in the current loop. The overshoot peaks are caused by open-loop phase lag around resonant frequency, which comes from delay link and R-L plant. The phase lag from delay link could be canceled by the proposed delay-compensated forms for both PR and vector resonant (VR) controller; but toward phase lag from R-L plant, the two types resonant controller perform different: PR controller does not give full consideration about R-L plant, leading to inherent obvious overshoot peaks in current loop, whereas VR controller provides proper leading phase to cancel the phase lag from R-L plant, greatly reducing the overshoot peaks and promising wider regulation bandwidth. The comparisons and analysis reveal the principle and relations of PR and VR controllers, which help to deepen the understanding for further improving the resonant controller.
High Rate CPFSK Space-Time Trellis Codes

Space-time trellis coding is an established diversity technique that reduces the effects of multipath fading over wireless communication channels. Here, we consider high rate space-time trellis codes (STTC) with continuous phase frequency shift keying (CPFSK). We present optimized rate-2/3 STTC implemented with 3 transmit antennas. These codes provide system throughputs of 4 and 6 bits per channel use with 4-ary and 8-ary CPFSK respectively. Simulated error rate performance of the optimized codes with receive diversity is presented. We show that although the schemes do not achieve full transmit diversity, they provide excellent coding gains compared to full rank schemes that have equivalent throughput, but higher order modulations and greater complexity.
Molecular Characterization of Extended-Spectrum Beta-Lactamases producing Escherichia coli and Klebsiella pneumoniae Blood Isolates from Egyptian Pediatric Cancer Patients

The occurrence of Extended-Spectrum Beta-Lactamases(ESBLs) producing bacteria in Egypt has been well documented. However, investigations on blood stream infections (BSIs) caused by these bacteria in pediatric cancer patients are limited. The present study was carried out to assess the prevalence of and to characterize the ESBLs types in K. pneumoniae and E . coli causing BSIs in pediatric cancer patients. Fifty four ESBL producing K. pneumoniae and E . coli blood isolates collected from pediatric patients with malignancies at the National Cancer Institute, Cairo, Egypt, were investigated for ESBLs production by phenotypic and genotypic methods. These isolates were recognized as ESBLs producers. Molecular characterization of ESBLs types revealed the presence of the Ambler class A ESBLs types. bla TEM type was the predominant in all E. coli and in 70.8 % of K. pneumoniae isolates. bla SHV gene was more frequent in K. pneumoniae as being in 87.5 % of the isolates. bla CTX-M gene was detected in high percentages in both E. coli (93.3 %) and K. pneumonia isolates (91.6 %) as well. All isolates were co-producers of the ESBLs types. It is concluded that a random and/or empirical use of the antibiotics in cancer patients should be restricted as far as possible.
Stability polygons reshaping and morphing for smooth multi-contact transitions and force control of humanoid robots

In this paper we provide hindsight on how to use the information provided by the explicit computation of the stability polygon and build on task-based QP controllers to achieve both stable multi-contact smooth transitions and force control without jeopardizing stability. This entails computing stability polygons with unilateral and bilateral contacts and devising a method to continuously constrain the CoM position throughout multi-contact motion in order to effectively regulate the forces applied on the environment while avoiding hard constraints on the CoM and discontinuity between stances.
Transcriptomic Characterization of Tambaqui (Colossoma macropomum, Cuvier, 1818) Exposed to Three Climate Change Scenarios

Climate change substantially affects biodiversity around the world, especially in the Amazon region, which is home to a significant portion of the world’s biodiversity. Freshwater fishes are susceptible to increases in water temperature and variations in the concentrations of dissolved gases, especially oxygen and carbon dioxide. It is important to understand the mechanisms underlying the physiological and biochemical abilities of fishes to survive such environmental changes. In the present study, we applied RNA-Seq and de novo transcriptome sequencing to evaluate transcriptome alterations in tambaqui when exposed to five or fifteen days of the B1, A1B and A2 climate scenarios foreseen by the IPCC. The generated ESTs were assembled into 54,206 contigs. Gene ontology analysis and the STRING tool were then used to identify candidate protein domains, genes and gene families potentially responsible for the adaptation of tambaqui to climate changes. After sequencing eight RNA-Seq libraries, 32,512 genes were identified and mapped using the Danio rerio genome as a reference. In total, 236 and 209 genes were differentially expressed at five and fifteen days, respectively, including chaperones, energetic metabolism-related genes, translation initiation factors and ribosomal genes. Gene ontology enrichment analysis revealed that mitochondrion, protein binding, protein metabolic process, metabolic processes, gene expression, structural constituent of ribosome and translation were the most represented terms. In addition, 1,202 simple sequence repeats were detected, 88 of which qualified for primer design. These results show that cellular response to climate change in tambaqui is complex, involving many genes, and it may be controlled by different cues and transcription/translation regulation mechanisms. The data generated from this study provide a valuable resource for further studies on the molecular mechanisms involved in the adaptation of tambaqui and other closely related teleost species to climate change.
Predictive Technology Model for Nano-CMOS Design Exploration

Predictive MOSFET model is critical for early circuit design research. In this work, a new generation of predictive technology model (PTM) is developed, covering emerging physical effects and alternative structures. Based on physical models and early stage silicon data, PTM of bulk and double-gate devices are successfully generated from 130nm to 32nm technology nodes, with effective channel length down to 13nm. By tuning only ten primary parameters, PTM can be easily customized to cover a wide range of process uncertainties. The accuracy of PTM predictions is comprehensively verified with published silicon data: the error of the current is below 10% for both NMOS and PMOS. Furthermore, the new PTM correctly captures process sensitivities in the nanometer regime
Amlodipine bioequivalence study: quantification by liquid chromatography coupled to tandem mass spectrometry

Objective—To assess the bioequivalence of two amlodipine tablet formulations (Amlodipine® 5 mg tablet from Merck S.A. Indústrias Químicas, Brazil as test formulation and Norvasc® 5 mg tablet from Laboratórios Pfizer Ltd., Brazil as reference formulation) in 24 healthy volunteers of both sexes.
Topography dominates the hemispheric asymmetry of Stratospheric Sudden Warmings

Stratospheric Sudden Warmings (SSWs) predominantly occur in the Northern Hemisphere with only 1 major event recorded in the Southern Hemisphere in the satellite era. Investigating factors that contribute to this asymmetry can help to reveal the cause of SSWs and lead to improved forecasts. Here we use climate model simulations to investigate the impact of boundary conditions (topography and ocean circulation) on the asymmetry. Flattening topography eliminates Northern Hemisphere SSWs, while removing the ocean meridional overturning circulation reduces their frequency by half. The SSW response to boundary conditions is controlled by decrease in hemispheric asymmetry of eddy heat ﬂux. The reduction is driven by a decrease in amplitude of both eddy meridional wind and eddy temperature, as well as an increase in the diﬀerence between their phases. The results suggest boundary conditions play an important role in shaping SSWs, especially topographic forcing, but that the boundary condition interactions are nonlinear.
Submitted to Ieee Transactions on Medical Imaging 1 Identifying Virus-cell Fusion in Two-channel Fluorescence Microscopy Image Sequences Based on a Layered Probabilistic Approach

—The entry process of virus particles into cells is decisive for infection. In this work, we investigate fusion of virus particles with the cell membrane via time-lapse fluorescence microscopy. To automatically identify fusion for single particles based on their intensity over time, we have developed a layered probabilistic approach. The approach decomposes the action of a single particle into three abstractions: the intensity over time, the underlying temporal intensity model, as well as a high level behavior. Each abstraction corresponds to a layer and these layers are represented via stochastic hybrid systems and Hidden Markov Models. We use a maxbelief strategy to efficiently combine both representations. To compute estimates for the abstractions we use a hybrid particle filter and the Viterbi algorithm. Based on synthetic image sequences, we characterize the performance of the approach as a function of the image noise. We also characterize the performance as a function of the tracking error. We have also successfully applied the approach to real image sequences displaying pseudotyped HIV-1 particles in contact with host cells and compared the experimental results with ground truth obtained by manual analysis.
Sexual Offender Subtyping: The Incest Offender Question

Aim/Background: Current wisdom in the risk assessment of sexual offenders is that incest offenders have a small chance of re-offending. Previous research has shown that re-offense rates even for untreated offenders who choose victims from within the family, range from 4-10%. Flowing from this belief are further assumptions that they are less dangerous and do not require intensive treatment, if they require any at all. Material/Methods: The paper summarizes the findings of two prior reports which examined a sample of in-patient child molesters attending treatment at the Phoenix Program. Results: Findings reveal a great deal of overlap between categories with incestuous offenders having numerous non-incestuous victims, and non-incestuous offenders also having incestuous victims. There was also a great deal of overlap between these two groups in terms of their erotic preference testing responses. This was the finding even when biologically related fathers were examined separately, and when exclusively incestuous fathers were considered. Conclusions: If there were a (cid:147)pure(cid:148) form of incest offender who poses little risk to other children, it is virtually impossible to discriminate who fits this category at the outset of treatment. Neither index offense nor erotic preference testing are very helpful in distinguishing this group from extrafamilial offenders. Beliefs about treatment requirements for incest offenders and their potential risk to victims outside their own family need to be reconsidered.
Measures of auditory-visual integration for speech understanding: a theoretical perspective.

Recent studies of auditory-visual integration have reached diametrically opposed conclusions as to whether individuals differ in their ability to integrate auditory and visual speech cues. A study by Massaro and Cohen [J. Acoust. Soc. Am. 108(2), 784–789 (2000)] reported that individuals are essentially equivalent in their ability to integrate auditory and visual speech information, whereas a study by Grant and Seitz [J. Acoust. Soc. Am. 104(4), 2438–2450 (1998)] reported substantial variability across subjects in auditory-visual integration for both sentences and nonsense syllables. This letter discusses issues related to the measurement of auditory-visual integration and modeling efforts employed to separate information extraction from information processing.
A Loss Function Analysis for Classification Methods in Text Categorization

This paper presents a formal analysis of popular text classification methods, focusing on their loss functions whose minimization is essential to the optimization of those methods, and whose decomposition into the training-set loss and the model complexity enables cross-method comparisons on a common basis from an optimization point of view. Those methods include Support Vector Machines, Linear Regression, Logistic Regression, Neural Network, Naive Bayes, K-Nearest Neighbor, Rocchio-style and Multi-class Prototype classifiers. Theoretical analysis (including our new derivations) is provided for each method, along with evaluation results for all the methods on the Reuters-21578 benchmark corpus. Using linear regression, neural networks and logistic regression methods as examples, we show that properly tuning the balance between the training-set loss and the complexity penalty would have a significant impact to the performance of a classifier. In linear regression, in particular, the tuning of the complexity penalty yielded a result (measured using macro-averaged F1) that outperformed all text categorization methods ever evaluated on that benchmark corpus, including Support Vector Machines.
Developmental synergism of steroidal estrogens in sex determination.

Gonadal sex in the red-eared slider turtle, Trachemys scripta, is determined by incubation temperature during embryonic development. Evidence suggests that temperature determines sex by influencing steroid hormone metabolism and/or sensitivity: steroidogenic enzyme inhibitors or exogenous sex steroid hormones and their man-made analogs override (or enhance) temperature effects on sex determination. Specifically, nonaromatizable androgens and aromatase inhibitors induce testis differentiation at female-producing temperatures, whereas aromatizable androgens and estrogens induce ovary differentiation at male-producing temperatures. Moreover, natural estrogens and temperature synergize to produce more females than would be expected if estrogens and temperature had purely additive effects on sex determination. In this study, we use sex reversal of turtle embryos incubated at a male-producing temperature to examine synergism among steroidal estrogens: estrone, 17ss-estradiol, and estriol. A low dose of 17ss-estradiol (200 ng) showed significant synergism when administered with a single low dose of estriol (10 ng). Likewise, a single low dose of estrone (250 ng) had a synergistic effect when combined with the same low dose of estriol (10 ng). We conclude that the weak natural estrogens estrone and 17ss-estradiol synergize with a low dose of the more potent estriol to reverse gonadal sex during the critical period of sexual differentiation. These results suggest that weak environmental estrogens may also synergize with stronger natural estrogens. ImagesFigure 1Figure 2Figure 3Figure 4
Wrapper method for feature selection to classify cardiac arrhythmia

Efficient monitoring of cardiac patients can save tremendous amount of lives. Cardiac disease prediction and classification has gained utmost significance in this regard during the past few years. This paper presents a predictive model for classification of arrhythmias. The model works by selecting best features using wrapper algorithm around random forest, followed by implementing various machine learning classifiers on the selected features. Cardiac arrhythmia dataset from University of California, Irvine (UCI) machine learning repository has been used for the experimental purpose. After normalizing the data, repeated cross validation with 10 folds is applied on support vector machine (SVM), K nearest neighbor (KNN), Naïve Bayes, random forest, and Multi-Layer perceptron (MLP). The experimental results demonstrate that MLP beats other classifiers by achieving an average accuracy of 78.26%, while accuracies calculated for KNN and SVM are 76.6% and 74.4% respectively, outperforming the accuracies of previous models.
Extraovarian pelvic yolk sac tumor: Case report and review of published work

Extraovarian pelvic yolk sac tumors are rare, with only nine cases documented previously in the published work. We report a case of extraovarian pelvic yolk sac tumor occurring synchronously with breast carcinoma. The patient underwent resection of the pelvic tumor and hepatic implant, omentectomy and breast lumpectomy with sentinel axillary lymph node biopsy. The uterus and bilateral adnexa were preserved. Postoperative adjuvant therapy for the yolk sac tumor included three cycles of the bleomycin, etoposide and cisplatin (BEP) regimen. This was followed by adjuvant chemotherapy and radiotherapy for the breast carcinoma. It is concluded that in women with extraovarian pelvic yolk sac tumor who wish to preserve childbearing capacity, fertility‐saving surgery followed by fertility‐preserving cisplatin‐based chemotherapy is adequate and appropriate treatment.
Transition between Friction Modes in Adhesive Contacts of a Hard Indenter and a Soft Elastomer: An Experiment

: The tangential adhesive contact (friction) between a rigid steel indenter and a soft elastomer at shallow indentation depths, where the contact exists mainly due to adhesion, is investigated experimentally. The dependencies of friction force, contact area, average tangential stresses, and the coordinates of the front and back edges of the contact boundary on the indenter displacement are studied. It is found that first a stick–slip mode of friction is established, which is then replaced by another, more complex mode where the phase of a global slip of the elastomer on the indenter surface is absent. In both regimes, the evolutions of friction force and contact area are analyzed in detail.