Miracle-dz/UniFAR-FTUs huggingface dataset:
Acute Down‐Regulation of Antibody Production Following Spinal Cord Injury: Role of Systemic Catecholamines

We investigated whether antibody production to antigens arising in the subarachnoid space is depressed acutely after spinal cord injury (SCI), and whether such depression is due to abnormal catecholamine levels. To assess antibody responses, ovalbumin (OVA) was injected into the spinal subarachnoid space (i.t.) of rats via an indwelling catheter after SCI at T4 or laminectomy (LAM). Antibody responses tested at days 0, 7, and 14 (d0, d7, d14) postinjury revealed that SCI animals exhibited an antibody response significantly lower than LAM animals on d7, but one that reached control levels by d14. ELISPOT assays indicated that the cervical lymph nodes, known to be innervated by superior cervical ganglia (SCG), processed i.t. OVA. The reduction in antibody production after SCI could not be mimicked with surgical deafferentation of the SCG. However, blockade of β-adrenergic receptors prior to SCI did reverse the decrease, suggesting an adverse effect of the surge of catecholamines that accompanies the injury. Surgical removal of sympathetic inputs to the cervical lymph nodes prior to SCI failed to reverse the effect on antibody production, suggesting a systemic source of catecholamines. We conclude that antibody responses against i.t. antigens are attenuated acutely after SCI due to the massive release of systemic catecholamines that accompanies SCI.
In vitro evidence of two-component system phosphorylation between the Mycobacterium tuberculosis TrcR/TrcS proteins.

Two-component regulatory proteins, histidine kinases and response regulators, function in bacteria as sensing and adaptive factors in response to a wide range of environmental stimuli. Conserved histidine and glycine regions of histidine kinase sensor proteins were used to design degenerate oligonucleotide primers for amplification of DNA fragments from Mycobacterium tuberculosis. Two adjacent genes, trcR and trcS, which encode a response regulator and a histidine kinase, respectively, have been identified. Full-length and truncated TrcR and TrcS proteins have been expressed in Escherichia coli. Difficulties in expressing recombinant full-length TrcS and a truncated N -terminal form of TrcS reveal that the transmembrane domains are toxic to E. coli. Overexpressed truncated C-terminal transmitter domains of TrcS have been autophosphorylated in vitro and have transphosphorylated both the full-length recombinant TrcR protein and the N -terminal receiver/regulator domain of TrcR. In vitro autophosphorylation of TrcS requires the presence of Mn2+or Ca2+as a divalent cation cofactor and subsequent transphosphorylation of TrcR is evident in the presence of TrcS-phosphate and Ca2+. Transphosphorylation between these two proteins provides evidence that these M. tuberculosis genes encode functional two-component system regulatory proteins that are members of a signal transduction circuit.
Microchip CGE linked to immunoprecipitation as an alternative to Western blotting

A novel approach for protein identification is presented, which combines the specificity of an immunoprecipitation approach with the sensitivity of protein detection in microchip CGE. This method involves derivatization of the sample proteins with a fluorescent dye, target protein isolation with specific antibodies and Protein A coated magnetic beads, and automated sizing and quantification of the eluted samples on microchips. The performance of the new technique was demonstrated with glutathion‐S‐transferase‐ and polyHistidine‐tagged target proteins in an Escherichia coli background. A specific detection of target proteins was possible down to 0.001% or 1 ng target protein in a background of 100 μg E. coli protein. With this approach, proteins ranging from 10 to 220 kDa could be identified with a panel of different target‐specific antibodies. The reproducibility of the method was very similar to standard microchip CGE methods. In a direct comparison to Western blotting, a similar sensitivity and specificity of both techniques was observed. However, the new approach compares favorably to Western blotting in terms of time‐to‐result, usability and labor intensity, antibody consumption and access to quantitative data.
Analysis and Development of Novel Three-Phase Hybrid Magnetic Paths Switched Reluctance Motors Using Modular and Segmental Structures for EV Applications

The classical switched reluctance motors (SRMs) often suffer from drawbacks such as low power and torque densities, high torque ripple, mutual coupling, etc., which limit their industrial applications. This paper presents the analysis and development of two novel three-phase SRMs with hybrid magnetic paths comprising six E-shaped modular stators and three segmental common rotors, termed as the modular SRMs (MSRMs), for electric vehicle applications. The machine topologies with different winding arrangements are described. The voltage and output power equations are analytically derived, and some design particularities and parameters are discussed. The field distributions and static magnetic characteristics of an MSRM with double coil are analyzed by using 3-D finite-element method. After that, two MSRMs with different winding arrangements, namely a double-coil MSRM and single-coil MSRM, are analyzed and compared to evaluate the distinct features of this novel MSRM, accompanied with a classical three-phase 6/4 SRM. The comparison includes static magnetic characteristics, mass of iron core, normal dynamic, and fault-tolerant performances. It is shown that the double-coil MSRM appears to have better characteristics such as higher torque production capability, lower torque ripple and cost, higher torque and output power densities, and higher reliability and fault tolerance. For experimental verification, laboratory testing of a double-coil MSRM is developed, and the simulated and measured static inductance characteristics and dynamic performances correlate well.
Circularization of the Herpes Simplex Virus Type 1 Genome upon Lytic Infection

ABSTRACT For many years, the generally accepted model for the replication of the double-stranded DNA genome of herpes simplex virus type 1 (HSV-1) incorporated initial circularization of linear molecules in the cell nucleus. Ensuing DNA synthesis resulted in the generation of head-to-tail concatemers which were subsequently cleaved into monomeric units and packaged into the nascent viral capsid. Recently, however, it has been proposed that circularization of HSV-1 genomes does not occur at the onset of lytic infection and moreover that this event is specifically inhibited by the HSV-1 transcriptional transactivator, ICP0 (S.A. Jackson and N.A. DeLuca, Proc. Natl. Acad. Sci. USA 100:7871-7876, 2003). To further investigate genome circularization, we have generated HSV-1 derivatives in which the viral a sequences, which contain the cleavage-packaging signals, have been replaced by a minimal packaging element located in the thymidine kinase gene. In contrast to wild-type HSV-1, fusion of the genomic termini of these viruses produces a novel fragment in circular or concatemeric DNA which can be detected by Southern blot hybridization. Utilizing these viruses, we demonstrate that fusion of the genomic termini occurred rapidly upon infection and in the presence of inhibitors of viral DNA or protein synthesis. We provide evidence indicating that the end joining represented circularization rather than concatemerization of input molecules and that circularized molecules functioned as templates for replication. Since the termini of these viruses lack direct repeats, our findings indicate that circularization can be mediated by direct end-to-end ligation of linear input genomes.
Impact of therapeutic hypothermia in the treatment of patients with out-of-hospital cardiac arrest from the J-PULSE-HYPO study registry.

BACKGROUND Mild hypothermia is an effective therapy for patients with return of spontaneous circulation (ROSC) after out-of-hospital cardiac arrest. However, evidence of the effectiveness of therapeutic hypothermia (TH) remains unclear. METHODS AND RESULTS A multicenter registry in Japan (J-PULSE-HYPO study registry) was conducted to investigate the effectiveness of TH for post-resuscitation neurological dysfunction developing after out-of-hospital cardiac arrest from 14 institutions, between January 2005 and December 2009. The committee entrusted each hospital with the timing of cooling, cooling methods, target temperature, duration, and rewarming. There were 452 patients (375 men) enrolled into the registry. The mean age was 58.6 ± 13.5 years. Initial electrocardiogram rhythm at the time of occurrence of the cardiac arrest showed 68.9% had ventricular fibrillation or pulseless ventricular tachycardia, 13.7% had pulseless electrical activity, and 9.1% had asystole. The median interval from the occurrence of cardiac arrest to ROSC was 26 min. The target core temperature during TH was 33.9 ± 0.4°C and the mean duration of cooling was 31.5 ± 13.9 h. Intra-aortic balloon pumping was used in 40.1% and percutaneous cardiopulmonary support in 22.6% of patients. At 30 days after cardiac arrest, the proportion of survival was 80.1% and the proportion of patients with favorable neurological functions, with a cerebral performance category score of 1 or 2, was 55.3%. CONCLUSIONS The J-PULSE-HYPO study registry showed a clinical aspect of TH.
Electrical coupling of astrocytes in rat hippocampal slices under physiological and simulated ischemic conditions

Mammalian protoplasmic astrocytes are extensively coupled through gap junction channels but the biophysical properties of these channels under physiological and ischemic conditions in situ are not well defined. Using confocal morphometric analysis of biocytin‐filled astrocytic syncytia in rat hippocampal CA1 stratum radiatum we found that each astrocyte directly couples, on average, to 11 other astrocytes with a mean interastrocytic distance of 45 μm. Voltage‐independent and bidirectional transjunctional currents were always measured between directly coupled astrocyte pairs in dual voltage‐clamp recordings, but never from astrocyte–NG2 glia or astrocyte–interneuron pairs. The electrical coupling ratio varied considerably among astrocytes in developing postnatal day 14 rats (P14, 0.5–12.4%, mean = 3.6%), but became more constant in young adult P21 rats (0.18–3.9%, mean = 1.6%), and the coupling ratio declined exponentially with increasing pair distance. Electrical coupling was not affected by short‐term oxygen–glucose deprivation (OGD) treatment, but showed delayed inhibition in an acidic extracellular pH of 6.4. Combination of acidic pH (6.4) and OGD, a condition that better represents cerebral ischemia in vivo, accelerated the inhibition of electrical coupling. Our results show that, under physiological conditions, 20.7–24.2% of K+ induced currents can travel from any astrocytic soma in CA1 stratum radiatum to the gap junctions of the nearest neighbor astrocytes, but this should be severely inhibited as a consequence of the OGD and acidosis seen in the ischemic brain. © 2009 Wiley‐Liss, Inc.
[Alcohol dependence in the Italian general population: diagnostic criteria according to general practitioners and to the Composite International Diagnostic Interview (CIDI)].

OBJECTIVES to identify the criteria used by general practitioners (GPs) for the diagnosis of alcohol dependence (AD) and to compare them with the criteria of the Composite International Diagnostic Interview (CIDI). DESIGN cross-sectional correlational study. SETTING AND PARTICIPANTS the 55 GPs of Friuli Venezia Giulia Region (Northern Italy) and Tuscany Region (Central Italy) who took part in the research conducted a clinical evaluation of the first 40 patients who came for a medical examination. MAIN OUTCOME MEASURES prevalence of AD diagnosed by GPs and CIDI and their association with sociodemographic variables, other diseases, and alcohol consumption. RESULTS AD prevalence assessed by the GPs was 5.4%, while AD prevalence assessed by the CIDI was 4.4%, with an overlap of about 26%. Patients identified as AD by the GPs were older and more frequently suffering from liver disease and hypertension than patients identified by the CIDI. CONCLUSIONS the limited overlap between diagnoses of AD made by GPs and the one made by the CIDI is problematic. GPs appear to identify mainly more severe forms of AD, in which excessive consumption of alcohol is associated with the presence of liver disease, while the CIDI could identify younger patients who have not yet developed diseases. GPs' recognition of AD could be increased by using their expertise along with standardised questionnaires which measure alcohol consumption.
Mapping Quantitative Trait Loci in Noninbred Mosquito Crosses

The identification of genes that affect quantitative traits has been of great interest to geneticists for many decades, and many statistical methods have been developed to map quantitative trait loci (QTL). Most QTL mapping studies in experimental organisms use purely inbred lines, where the two homologous chromosomes in each individual are identical. As a result, many existing QTL mapping methods developed for experimental organisms are applicable only to genetic crosses between inbred lines. However, it may be difficult to obtain inbred lines for certain organisms, e.g., mosquitoes. Although statistical methods for QTL mapping in outbred populations, e.g., humans, can be applied for such crosses, these methods may not fully take advantage of the uniqueness of these crosses. For example, we can generally assume that the two grandparental lines are homozygous at the QTL of interest, but such information is not be utilized through methods developed for outbred populations. In addition, mating types and phases can be relatively easy to establish through the analysis of adjacent markers due to the large number of offspring that can be collected, substantially simplifying the computational need. In this article, motivated by a mosquito intercross experiment involving two selected lines that are not genetically homozygous across the genome, we develop statistical methods for QTL mapping for genetic crosses involving noninbred lines. In our procedure, we first infer parental mating types and use likelihood-based methods to infer phases in each parent on the basis of genotypes of offspring and one parent. A hidden Markov model is then employed to estimate the number of high-risk alleles at marker positions and putative QTL positions between markers in each offspring, and QTL mapping is finally conducted through the inferred QTL configuration across all offspring in all crosses. The performance of the proposed methods is assessed through simulation studies, and the usefulness of this method is demonstrated through its application to a mosquito data set.
Rapid screening assay for precise and reliable estimation of cyanide content in sorghum

Determining the cyanogenic potential of crop plants using traditional biochemical methods are laborious and time consuming. Presently, the Feigl-Anger paper method is being employed for qualitative analysis of cyanogenic potential of plant samples in a rapid and cost effective manner. To improve this technique from its status of qualitative to a more reliable semi-quantitative assay, the Feigl-Anger Densitometry (FAD) method was developed. This method measures the intensity of blue spots on the Feigl-Anger paper, after its exposure to HCN released from sorghum leaf tissues during a freeze thaw cycle. For colour intensity measurements, a densitometric software was employed. The densitometry results obtained from test samples and standards were compared with corresponding values obtained from quantitative spectrophotometric analysis. The results of FAD in a set of 66 germplasm lines revealed high correspondence with cyanide contents estimated through widely used spectrophotometric method of Lambert (R 2 =0.9107). Further, our method was also validated with known concentrations of KCN standards (R 2 = 0.9661). Hence it was concluded that FAD can be employed to estimate HCN content in sorghum rapidly with acceptable precision in a simple lab setup. The method can be suitable for screening of large number of mutants and segregating plant populations for the selection of low hydrogen cyanide lines in breeding programmes.
Efficient fuzzy edge detection using successive Otsu's method

In this paper we propose fuzzy based edge detection using Successive Otsu's method. Edge detection has always been a vital aspect of majority in image processing techniques. In this work we describe the algorithm of Successive Otsu technique and utilize same in grouping image histogram into different partitions. The algorithm proposed here is implemented to provide the threshold parameter to classical Sobel Operator in order to enhance its edge detection capability using the fuzzy logic. The results are compared with Canny Edge Detector and finally concludes that proposed method based Sobel edge detection process behaves much alike to Canny edge detection process.
New performance metrics for ultrasound pulse compression systems

In medical ultrasound, B-mode images are log-compressed and displayed with a grayscale map, typically on a 40-60 dB dynamic range. The image formation process is the same for an ultrasound pulse compression system using coded excitation. Metrics, such as full width at half maximum (FWHM), peak sidelobe level (PSL) and integrated sidelobe level (ISL), used to evaluate pulse compression systems were adopted from radar and communications. These metrics are utilized to evaluate the performance of an auto-correlation function, which is the ideal case. In medical ultrasound imaging however, the combination of frequency and depth dependent attenuation, dispersion, harmonic generation, beamforming errors, and limited transducer bandwidth create a more complicated case for a pulse compressed system that is far from the ideal.
Parameter estimation of aircraft dynamics via unscented smoother using multiple data sets

This paper proposes a method for parameter estimation of aircraft dynamics based on multiple sets of test data. It is an extension of a method based on Unscented Rauch-Tung-Striebel Smoother (URTSS) to estimate the state and unknown parameters, combined with Expectation-Maximization (EM) algorithm to estimate unknown statistics, i.e., the mean and covariance of initial states, and the noise covariances. The developed method achieves stable convergence, because non-convex numerical optimization algorithms are not necessary. The effectiveness of the developed method is demonstrated through a parameter estimation problem of a longitudinal motion of an aircraft.
Computer-aided-diagnosis in colorectal cancer: A survey of state of the art techniques

Colorectal cancer is a significant health problem in the world and is one of the major contributors in deaths by cancer. It is a malignant tumor that starts out as more likely to be non-cancerous but as the growth increases on the lining of colon wall it becomes carcinogenic. With regular screening colon cancer can be detected early, when treatment is more effective and CAD scheme with its recent advancements is an effective detection tool for detecting colon polyp cancer. It's mostly non-invasive nature has substantially contributed to improve the quality of treatment. Active research is still being carried out to increase the diagnostic accuracy of CAD scheme as well as reproducibility of mammographic clarification. This survey focuses on studying the techniques used in the computer-aided-diagnosis and analysis of colon polyp cancer. This literature survey presents various methods and the importance of CAD scheme.
Perception control with improved expectation learning through multilayered neural networks

In this paper, we investigate the viability of multilayered neural network (NN)-based extension of a conventional "perception" control concept. The perception process selects and completes the information from the system to be controlled before passing it to the controlling agent so that control is not lost when sensory information from the system is incomplete. The perception process produces an expectation of the next set of information to be received from the system. The expectation is used to replace missing parts of the information received and it also influences the next perception. In the existing work, each of the expectation elements is linearly acquired such that the expectation tells only the dominant information in the recent past, i.e., this approach has no capability to sense the trend and the dynamics in the information. This handicap could become a serious problem when the perception process is applied to real physical systems. Here, we introduce an extension of the perception control process by using a radial basis function (RBF) feedforward NN to learn the trend and the dynamics in the information and produce the expectation of the next observation. Through some simulation comparisons, we show that the proposed RBFNN-based method is better than the existing one.
PNA-based microbial pathogen identification and resistance marker detection

With the rapidly growing availability of the entire genome sequences of microbial pathogens, there is unmet need for increasingly sensitive systems to monitor the gene-specific markers for diagnosis of bacteremia that enables an earlier detection of causative agent and determination of drug resistance. To address these challenges, a novel FISH-type genomic sequence-based molecular technique is proposed that can identify bacteria and simultaneously detect antibiotic resistance markers for rapid and accurate testing of pathogens. The approach is based on a synergistic combination of advanced Peptide Nucleic Acid (PNA)-based technology and signal-enhancing Rolling Circle Amplification (RCA) reaction to achieve a highly specific and sensitive assay. A specific PNA-DNA construct serves as an exceedingly selective and very effective biomarker, while RCA enhances detection sensitivity and provide with a highly multiplexed assay system. Distinct-color fluorescent decorator probes are used to identify about 20-nucleotide-long signature sequences in bacterial genomic DNA and/or key genetic markers of drug resistance in order to identify and characterize various pathogens. The technique's potential and its utility for clinical diagnostics are illustrated by identification of S. aureus with simultaneous discrimination of methicillin-sensitive (MSSA) versus methicillin-resistant (MRSA) strains. Overall these promising results hint to the adoption of PNA-based rapid sensitive detection for diagnosis of other clinically relevant organisms. Thereby, new assay enables significantly earlier administration of appropriate antimicrobial therapy and may, thus have a positive impact on the outcome of the patient.
Radio-frequency flexible electronics: Transistors and passives

Flexible electronics have customarily addressed low-frequency applications because the traditional materials for flexible electronics, such as polymer and non-crystalline inorganic semiconductors, have poor electronic properties. Fast flexible electronics that operate at radio frequencies (RF), particularly at microwave frequencies, could lead to a number of novel RF applications that rigid chip based solid-state electronics cannot easily fulfill. Single-crystal semiconductor nanomembranes that can be released from a number of wafer sources are mechanically very flexible and exhibit outstanding electronic properties that are equivalent to those of their bulk counterparts. These thin, flexible single-crystal materials can furthermore be placed, via transfer printing techniques, onto nearly any substrate, including flexible polymers, thus creating the opportunity to realize RF flexible electronics. In this paper, we will present various RF transistors made of semiconductor nanomembranes on plastic substrates, along with RF passives fabricated on the same flexible substrates. We will also elaborate on the difference between such flexible electronics and those made from thinned rigid wafers.