Miracle-dz/UniFAR-FTUs huggingface dataset:
Nonholonomic Orthogonal Learning Algorithms for Blind Source Separation

Independent component analysis or blind source separation extracts independent signals from their linear mixtures without assuming prior knowledge of their mixing coefficients. It is known that the independent signals in the observed mixtures can be successfully extracted except for their order and scales. In order to resolve the indeterminacy of scales, most learning algorithms impose some constraints on the magnitudes of the recovered signals. However, when the source signals are nonstationary and their average magnitudes change rapidly, the constraints force a rapid change in the magnitude of the separating matrix. This is the case with most applications (e.g., speech sounds, electroencephalogram signals). It is known that this causes numerical instability in some cases. In order to resolve this difficulty, this article introduces new nonholonomic constraints in the learning algorithm. This is motivated by the geometrical consideration that the directions of change in the separating matrix should be orthogonal to the equivalence class of separating matrices due to the scaling indeterminacy. These constraints are proved to be nonholonomic, so that the proposed algorithm is able to adapt to rapid or intermittent changes in the magnitudes of the source signals. The proposed algorithm works well even when the number of the sources is overestimated, whereas the existent algorithms do not (assuming the sensor noise is negligibly small), because they amplify the null components not included in the sources. Computer simulations confirm this desirable property.
A Design Approach for Low Phase Noise 5GHz Complementary Quadrature Oscillator

A novel complementary quadrature LC oscillator is presented for achieving lower phase noise. One proposed and three conventional structures, designed in a 0.18 mum CMOS technology, are simulated in both the triple-well and the twin-well (exactly the quasi twin-well) process technologies and each phase noise is compared. These circuits operate at 5 GHz and draw 8.6 mA from a 1.8 V supply. In the triple-well environment 1-4 dBc/Hz over the entire offset frequency is improved, for the twin-well 2-5 dBc/Hz. The best-case, the proposed circuit in the triple-well, the phase noise is -130.0 dBc/Hz at 1 MHz offset frequency.
Induction of neutralization antibodies in mice by Dengue-2 envelope DNA vaccines.

BACKGROUND Dengue (DEN) viruses have become a public health problem that affects approximately 100 million people worldwide each year. Prevention measures rely on vector control programs, which are inefficient. Therefore, a vaccine is urgently needed. METHODS The main goal of our laboratory is to develop an efficient tetravalent DEN DNA vaccine. In this study, we constructed four DEN-2 DNA vaccines expressing prM/env genes, using the homologous leader sequence (VecD2, VRD2E) or the tissue plasminogen activator (tPA) secretory signal (VecD2tpa, VRD2tpa). In vitro expression was tested by transient transfections and Western blot. The immunogenicity and protective efficacy of the vaccine candidates was evaluated in BALB/c mice, using intramuscular (IM) and intradermal (ID) vaccination routes. RESULTS Envelope (E) protein expression was detected in transfected COS-7 or 293T cells. We found statistical differences in the antibody responses induced by these vaccine candidates. In addition, the strongest antibody responses and protection were observed when the vaccines were delivered intramuscularly. Moreover, the tPA leader sequence did not significantly improve the vaccine immunogenicity since VecD2 and VecD2tpa induced similar antibody responses. CONCLUSIONS We demonstrated that most of our DNA vaccine candidates could induce antibody responses and partial protection against DEN-2 virus in mice. These results provide valuable information for the design and construction of a tetravalent DEN DNA vaccine.
[Study on monoamine neurotransmitters in rat serum and brain tissue by high performance liquid chromatography with electrochemical detection].

OBJECTIVE A rapid, reliable and simple method detecting monoamine neurotransmitters in rat serum and brain tissue by high performance liquid chromatography with electrochemical detector was developed. METHODS An ODS column was selected as separation column at room temperature,and the mobile phase (pH4.50) consisted of 0.02 mol/L trisodium citrate and 0.05 mol/L disodium phosphate, containing 15% methanol (volume ratio)in distilled water. The mobile phase was pumped at a flow rate of 1.0 ml/min and the oxidation potential was set at +0.065 mV. Dihydroxybenzylamine was used as the internal standard for quantification. Four compounds, epinephrine (E), dopamine (DA) and 5-hydroxytryptamine(5-HT) in the brain tissue ((whole cerebral cortex, hippocampus, striatum, midbrain, cerebellum) and serum were simultaneously separated and determined under the above conditions. RESULTS RSD of the retention times and peak areas of standard sample was in the range 0.29%-0.67% and 0.09%-0.36%. The recoveries of all analytes were over 85%. The detection limits of 0.083 ng/ml for NE, 0.51 ng/ml for E, 0.046 ng/ml for DA and 0.078ng/ml for 5-HT were achieved with standard solutions. The linearity is over the range 1.0-100 ng/ml for NE, 5.0-80 ng/ml for E,1.0-80 ng/ ml for DA and 1.0-60 ng/ml for 5-HT. CONCLUSION The assay had been applied successfully to measure simultaneously cortex and serum concentrations of these four monoamines in rats.
Characterization of the 5'-terminal structure of simian virus 40 early mRNA's

RPC-5 reverse-phase chromatography has been used to isolate fragments of simian virus 40 DNA generated by appropriate digestions with restriction endonucleases. Ten specific DNA fragments, mapping successively in a counterclock-wise direction from 0.67 to 0.515 on the simian virus 40 genome, were each hybridized to cytoplasmic mRNA obtained during the early phase of simian virus 40 infection. Primer extension methods with reverse transcriptase were used to characterize the 5' ends of two species of viral mRNA which were fractionated on sucrose gradients. Analysis of the complementary DNA products demonstrated the presence of two different spliced structures of simian virus 40 early mRNA's, both of which had the same 5'-end sequences (AUU), located at residues 18 to 20 on the viral genome. The mRNA for small-t contained a segment 588 bases in length (residues 18 to 605) spliced to residues 672. A 66-nucleotide segment rich in adenine-thymine was spliced out of this mRNA. The mRNA for large-T contained a segment 308 bases in length (residues 18 to 325) which is also spliced to residue 672. A 346-base segment was spliced from this mRNA. The results suggest that there are two levels for control of genetic expression. One would be the regulation of initiation of transcription at a common promoter; the other involves post-transcriptional splicing.
Distributionally Robust Co-Optimization of Energy and Reserve Dispatch

This paper proposes a two-stage distributionally robust optimization model for the joint energy and reserve dispatch (D-RERD for short) of bulk power systems with significant renewable energy penetration. Distinguished from the prevalent uncertainty set-based and worst-case scenario oriented robust optimization methodology, we assume that the output of volatile renewable generation follows some ambiguous distribution with known expectations and variances, the probability distribution function (pdf) is restricted in a functional uncertainty set. D-RERD aims at minimizing the total expected production cost in the worst renewable power distribution. In this way, D-RERD inherits the advantages from both stochastic optimization and robust optimization: statistical characteristic is taken into account in a data-driven manner without requiring the exact pdf of uncertain factors. We present a convex optimization-based algorithm to solve the D-RERD, which involves solving semidefinite programming (SDP), convex quadratic programming (CQP), and linear programming (LP). The performance of the proposed approach is compared with the emerging adaptive robust optimization (ARO)-based model on the IEEE 118-bus system. Their respective features are discussed in case studies.
Radioguided Surgery Using Intravenous 99mTc Sestamibi Associated with Breast Magnetic Resonance Imaging for Guidance of Breast Cancer Resection

Abstract: The purpose of this study was to evaluate the feasibility of surgery radioguided with intravenous 99mTc sestamibi associated with magnetic resonance imaging (MRI) of the breast to detect tumor extent and guide complete tumor resection. A descriptive experimental study was developed with 10 breast cancer patients (stage IIA–IIB) who underwent mastectomy. From 2 to 10 days before surgery, the patients underwent breast MRI with 0.1 mmol/kg of gadolinium and scintimammography with a 740 MBq of 99mTc sestamibi. A region of interest was drawn around the tumor image and an uptake curve as a function of time was plotted to calculate the optimal time to perform radioguided surgery. In the perioperative period, the same dose of 99mTc sestamibi was intravenously injected into the patients. Tumor resection was performed under the guidance of a gamma probe. MRI was used to evaluate the skin and deep fascia involvement and to detect occult tumor foci which were also excised. Subsequently a modified radical mastectomy was performed. Tumor and residual breast were histopathologically examined. In a series of 10 women, all demonstrated 99mTc sestamibi uptake in tumor cells. Eight patients showed no disease in the residual breast, one presented with one foci of invasive ductal carcinoma measuring 0.5 cm in diameter located 5 cm from the tumor bed, and one presented with one foci of ductal carcinoma in situ measuring 0.8 cm at the resection margin. The mean tumor size in the histopathologic assessment was 3.3 cm and in MRI was 5.0 cm. Radioguided surgery using 99mTc sestamibi associated with MRI is a feasible technique that can be employed in tumor resection.
Alcohol exposure in utero perturbs retinoid homeostasis in adult rats.

BACKGROUND Maternal alcohol exposure and adult alcohol intake have been shown to perturb the metabolism of various micro- and macro-nutrients, including vitamin A and its derivatives (retinoids). Therefore, it has been hypothesized that the well-known detrimental consequences of alcohol consumption may be due to deregulations of the metabolism of such nutrients rather than to a direct effect of alcohol. Alcohol exposure in utero also has long-term harmful consequences on the health of the offspring with mechanisms that have not been fully clarified. Disruption of tissue retinoid homeostasis has been linked not only to abnormal embryonic development, but also to various adult pathological conditions, including cancer, metabolic disorders and abnormal lung function. We hypothesized that prenatal alcohol exposure may permanently perturb tissue retinoid metabolism, predisposing the offspring to adult chronic diseases. METHODS Serum and tissues (liver, lung and prostate from males; liver and lung from females) were collected from 60-75 day-old sprague dawley rats born from dams that were: (I) fed a liquid diet containing 6.7% alcohol between gestational day 7 and 21; or (II) pair-fed with isocaloric liquid diet during the same gestational window; or (III) fed ad libitum with regular rat chow diet throughout pregnancy. Serum and tissue retinoid levels were analyzed by reverse-phase high-performance liquid chromatography (HPLC). Serum retinol-binding protein (RBP) levels were measured by western blot analysis, and liver, lung and prostate mRNA levels of lecithin-retinol acyltransferase (LRAT) were measured by qPCR. RESULTS Retinyl ester levels were significantly reduced in the lung of both males and females, as well as in the liver and ventral prostate of males born from alcohol-fed dams. Tissue LRAT mRNA levels remained unchanged upon maternal alcohol treatment. CONCLUSIONS Prenatal alcohol exposure in rats affects retinoid metabolism in adult life, in a tissue- and sex-dependent manner. We propose that the alcohol-induced perturbations of vitamin A metabolism may predispose to detrimental consequnces on adult health.
Molecular characterization of phenyllactate dehydratase and its initiator from Clostridium sporogenes

The heterotrimeric phenyllactate dehydratase from Clostridium sporogenes, FldABC, catalyses the reversible dehydration of (R)‐phenyllactate to (E)‐cinnamate in two steps: (i) CoA‐transfer from the cofactor cinnamoyl‐CoA to phenyllactate to yield phenyllactyl‐CoA and the product cinnamate mediated by FldA, a (R)‐phenyllactate CoA‐transferase; followed by (ii) dehydration of phenyllactyl‐CoA to cinnamoyl‐CoA mediated by heterodimeric FldBC, a phenyllactyl‐CoA dehydratase. Phenyllactate dehydratase requires initiation by ATP, MgCl2 and a reducing agent such as dithionite mediated by an extremely oxygen‐sensitive initiator protein (FldI) present in the cell‐free extract. All four genes coding for these proteins were cloned and shown to be clustered in the order fldAIBC, which shares over 95% sequence identity of nucleotide and protein levels with a gene cluster detected in the genome of the closely related Clostridium botulinum Hall strain A. FldA shows sequence similarities to a new family of CoA‐transferases, which apparently do not form covalent enzyme CoA‐ester intermediates. An N‐terminal Strep II‐Tag containing enzymatically active FldI was overproduced and purified from Escherichia coli. FldI was characterized as a homodimeric protein, which contains one [4Fe‐4S]1+/2+ cluster with an electron spin S= 3/2 in the reduced form. The amino acid sequence as well as the chemical and EPR‐properties of the pure protein are very similar to those of component A of 2‐hydroxyglutaryl‐CoA dehydratase from Acidaminococcus fermentans (HgdC), which was able to replace FldI in the activation of phenyllactate dehydratase. Only in the oxidized state, FldI and component A exhibit significant ATPase activity, which appears to be essential for unidirectional electron transfer. Both subunits of phenyllactyl‐CoA dehydratase (FldBC) show significant sequence similarities to both subunits of 2‐hydroxyglutaryl‐CoA dehydratase (HgdAB). The fldAIBC gene cluster resembles the hadAIBC gene cluster in the genome of Clostridium difficile and the hadABC,I genes in C. botulinum. The four subunits of these deduced 2‐hydroxyacid dehydratases (65–81% amino acid sequence identity between the had genes) probably code for a 2‐hydroxyisocaproate dehydratase involved in leucine fermentation. This enzyme could be the target for metronidazole in the treatment of pseudomembranous enterocolitis caused by C. difficile.
Validation of mood measures for people with multiple sclerosis.

BACKGROUND Valid assessments are needed in order to identify anxiety and depression in people with multiple sclerosis (MS). The objective of this study was to assess the validity of questionnaire measures of mood in people with MS. METHODS People with MS were recruited from a clinic database and asked to complete and return a questionnaire containing the Beck Anxiety Inventory (BAI), Beck Depression Inventory-II (BDI-II), and Hospital Anxiety and Depression Scale (HADS). Those who returned the questionnaire were invited to complete a structured clinical interview, which was blind to the results of the questionnaire. RESULTS The BDI-II and HADS were both found to be valid measures to detect depression and anxiety in people with MS. An optimum cutoff score of 23 for the BDI-II yielded high sensitivity (85%) and high specificity (76%). An optimum cutoff score of 11 for the HADS demonstrated high sensitivity and specificity for both the Anxiety subscale (sensitivity 90%, specificity 92%) and the Depression subscale (sensitivity 77%, specificity 81%). The BAI had high sensitivity (80%) but poor specificity (46%) for detecting anxiety. CONCLUSION The BDI-II and HADS can be used to identify mood disorders in people with MS.
Increased Risk of Very Low Birth Weight, Rapid Postnatal Growth, and Autism in Underweight and Obese Mothers

Purpose. To determine whether prepregnancy weight was associated with children's birth weight, early physical growth, and autism diagnosis. Design. Early Childhood Longitudinal Study–Birth Cohort data. Setting. United States. Subjects. Representative sample of U.S. children followed from birth through kindergarten (n = 4800). Also, a subpopulation of the very low birth weight children was examined (n = 500). Measures. Maternal variables included age and prepregnancy body mass index. Changes in children's height, weight, and head circumference between 9 months and 2 years were used as growth metrics. Children's sex, age, birth weight, and reported autism were also considered. Analysis. Logistic and multinomial logistic models assessed the impact of prepregnancy weight on birth weight and children's subsequent rate of physical growth and autism. Results. Children born to underweight or obese mothers had increased odds of very low birth weight. Very low birth weight was related to rapid height and weight growth and more than twice the likelihood to subsequently be diagnosed with autism. For the subgroup of very low birth weight children, rapid head growth was related to a fivefold increase in the odds of autism. After accounting for the impact birth weight and growth rates, we found prepregnancy weight indirectly impacted autism risk. Conclusion. Being underweight or obese during prepregnancy indirectly increased risk for autism from increased odds of low birth weight and accelerated postnatal growth.
Desaturation and oxygenation of 1,2-dihydronaphthalene by toluene and naphthalene dioxygenase

Bacterial strains expressing toluene and naphthalene dioxygenase were used to examine the sequence of reactions involved in the oxidation of 1,2-dihydronaphthalene. Toluene dioxygenase of Pseudomonas putida F39/D oxidizes 1,2-dihydronaphthalene to (+)-cis-(1S,2R)-dihydroxy-1,2,3,4-tetrahydronaphthalene, (+)-(1R)-hydroxy-1,2-dihydronaphthalene, and (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. In contrast, naphthalene dioxygenase of Pseudomonas sp. strain NCIB 9816/11 oxidizes 1,2-dihydronaphthalene to the opposite enantiomer, (-)-cis-(1R,2S)-dihydroxy-1,2,3,4-tetrahydronaphthalene and the identical (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. Recombinant Escherichia coli strains expressing the structural genes for toluene and naphthalene dioxygenases confirmed the involvement of these enzymes in the reactions catalyzed by strains F39/D and NCIB 9816/11. 1-Hydroxy-1,2-dihydronaphthalene was not formed by strains expressing naphthalene dioxygenase. These results coupled with time course studies and deuterium labelling experiments indicate that, in addition to direct dioxygenation of the olefin, both enzymes have the ability to desaturate (dehydrogenate) 1,2-dihydronaphthalene to naphthalene, which serves as a substrate for cis dihydroxylation.
An Integrated Photonic Gas Sensor Enhanced by Optimized Fano Effects in Coupled Microring Resonators With an Athermal Waveguide

Microresonator-based photonic gas sensors exhibit unique advantages of building a CMOS-compatible, cost-effective, and portable sensing system fully integrated on a single chip. In this paper, we propose gas sensors featured by nanoscale waveguide layers using titanium dioxide to achieve athermal device operation, at close to visible wavelengths. Sensitivity and limit of detection are enhanced by Fano effects in coupled-microresonator devices (also called photonic molecules). Sharp Fano lineshapes are obtained by optimizing the dual-ring structures in terms of coupling coefficients and resonance offsets, with minimized cavity loss including material absorption, scattering and bending losses, and substrate leakage. Various types of dual-ring resonator configurations have been comprehensively compared. Overall performance of the on-chip sensing systems including integrated light sources and detectors is carefully analyzed by taking into account the imperfections of each component, such as relative intensity noise of laser, laser linewidth and frequency jitter, and detector noise. We outline the similarity and difference of three dual-ring systems and provide design guidelines to optimize the sensor with balanced consideration between device performance and its tolerance to fabrication imperfections.
Data compression can discriminate broilers by selection line, detect haplotypes, and estimate genetic potential for complex phenotypes

ABSTRACT Accurately establishing the relationships among individuals lays the foundation for genetic analyses such as genome‐wide association studies and identification of selection signatures. Of particular interest to the poultry industry are estimates of genetic merit based on molecular data. These estimates can be commercially exploited in marker‐assisted breeding programs to accelerate genetic improvement. Here, we test the utility of a new method we have recently developed to estimate animal relatedness and applied it to genetic parameter estimation in commercial broilers. Our approach is based on the concept of data compression from information theory. Using the real‐world compressor gzip to estimate normalized compression distance (NCD) we have built compression‐based relationship matrices (CRM) for 988 chickens from 4 commercial broiler lines—2 male and 2 female lines. For all pairs of individuals, we found a strong negative relationship between the commonly used genomic relationship matrix (GRM) and NCD. This reflects the fact that “similarity” is the inverse of “distance. ” The CRM explained more genetic variation than the corresponding GRM in 2 of 3 phenotypes, with corresponding improvements in accuracy of genomic‐enabled predictions of breeding value. A sliding‐window version of the analysis highlighted haplotype regions of the genome apparently under selection in a line‐specific manner. In the male lines, we retrieved high population‐specific scores for IGF‐1 and a cognate receptor, INSR. For the female lines, we detected an extreme score for a region containing a reproductive hormone receptor (GNRHR). We conclude that our compression‐based method is a valid approach to established relationships and identify regions under selective pressure in commercial lines of broiler chickens.