Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimized Nanocrystalline Silicon Oxide Impedance Immunosensor Electronic Tongue for Subfemtomolar Estimation of Multiple Food Toxins

Nanocrystalline silicon oxide (nc-SiO2) immunosensor array-based electronic tongue (E-tongue) has been recently reported to simultaneously detect multiple food toxins with subfemtomolar sensitivity. However, the quantification in these reports is quite imprecise leading to an error of more than 100%. In this paper, the quantification accuracy of multiple food toxin detection in the subfemtomolar range has been improved by more than 90% through upgraded design of the E-tongue system by incorporating two major modifications. First, the pore geometry of the nc-SiO2 immunosensors has been optimized to obtain the best combination of sensitivity, selectivity, and reproducibility through the evaluation of a figure of merit. Second, in the multivariate data processing using partial least squares discriminate analysis, additional input parameters corresponding to selectivity and standard deviations of the experimentally measured data have been incorporated. The final set of input parameters include peak frequency corresponding to maximum impedance sensitivity, bandwidth of the impedance sensitivity characteristics, cutoff frequency from noise spectroscopy, and their standard deviations. The optimized E-tongue system is capable of quantifying 0.1 fg/ml Aflatoxin B1 and Ochratoxin A with an error of only 10% and 20%, respectively, which is a remarkable achievement in the domain of food toxin detection. The proposed E-tongue system is low cost with minimal operator dependence and hence has immense potential for commercial deployment.
Disrupted Structural and Functional Networks and Their Correlation with Alertness in Right Temporal Lobe Epilepsy: A Graph Theory Study

Previous studies have shown that temporal lobe epilepsy (TLE) involves abnormal structural or functional connectivity in specific brain areas. However, limited comprehensive studies have been conducted on TLE associated changes in the topological organization of structural and functional networks. Additionally, epilepsy is associated with impairment in alertness, a fundamental component of attention. In this study, structural networks were constructed using diffusion tensor imaging tractography, and functional networks were obtained from resting-state functional MRI temporal series correlations in 20 right temporal lobe epilepsy (rTLE) patients and 19 healthy controls. Global network properties were computed by graph theoretical analysis, and correlations were assessed between global network properties and alertness. The results from these analyses showed that rTLE patients exhibit abnormal small-world attributes in structural and functional networks. Structural networks shifted toward more regular attributes, but functional networks trended toward more random attributes. After controlling for the influence of the disease duration, negative correlations were found between alertness, small-worldness, and the cluster coefficient. However, alertness did not correlate with either the characteristic path length or global efficiency in rTLE patients. Our findings show that disruptions of the topological construction of brain structural and functional networks as well as small-world property bias are associated with deficits in alertness in rTLE patients. These data suggest that reorganization of brain networks develops as a mechanism to compensate for altered structural and functional brain function during disease progression.
Choice reaction time in patients with post‐operative cognitive dysfunction *

Background: Post‐operative cognitive dysfunction (POCD) is detected by administration of a neuropsychological test battery. Reaction time testing is at present not included as a standard test. Choice reaction time (CRT) data from the first International Study of Post‐operative Cognitive Dysfunction study were collected, but the association between POCD and reaction time has not been presented before. We hypothesized that CRT could be used as a screening tool for POCD.
Non-contact Sleep Apnea Syndrome Detection Based on What Random Forests Learned

This paper analyzes the differences between obstructive sleep apnea syndrome (OSAS) patients and healthy subjects focusing on the WAKE stage (shallow sleep) classification rule generated by Random Forests. In particular, our method generates the classification rules of WAKE/Non-WAKE stage for each subject from the power spectrums of mattress sensor outputs and extracts the most used frequency for the classification of WAKE/Non-WAKE stage. In cooperation with medical institutions, we conducted the experiments with nine OSAS subjects (four mild patients and five moderate patients) and nine healthy subjects (age 20 to 60) to analyze the differences between OSAS subjects and healthy subjects. The analysis of the rules derives the following implications: (1) the high frequencies (more than 1Hz) which are affected by the large body movements tend to be employed for the classification of WAKE/Non-WAKE in healthy subjects; (2) the low frequencies (i.e., 0.90 Hz, 0.53 Hz and 0.31 Hz) which are included in the range of respiration and heart beats but not directly related to them tend to be employed for the classification in OSAS subjects.
Three-Dimensional Reconstruction of Single Particle Electron Microscopy: The Voltage Sensitive Sodium Channel Structure

Single particle analysis in electron microscopy allows direct observation of the reconstructed three-dimensional structures of protein molecules. This method enables a more comprehensive study of membrane proteins which have been problematic in structural studies using X-ray crystallography. These membrane proteins include the voltage-sensitive ion channel proteins, which play an important rule in neural activities, and have great medical significance. The method described is supported by the development of cryo-electron microscopy and the angular reconstitution method. This review summarizes certain principles governing single particle analysis employing angular reconstitution. This method was applied to our study of the voltage-sensitive sodium channel, and the results are discussed. With improvements in resolutions and statistical analyses, the single particle technique is considered to be advantageous in studies of the structural changes and molecular interactions of protein molecules.
Band Subset Selection for Anomaly Detection in Hyperspectral Imagery

This paper presents a new approach, called band subset selection (BSS)-based hyperspectral anomaly detection (AD), which selects multiple bands simultaneously as a band subset rather than selecting multiple bands one at a time as the tradition band selection (BS) does, referred to as sequential multiple BS (SQMBS). Its idea is to first use virtual dimensionality (VD) to determine the number of multiple bands, <inline-formula> <tex-math notation="LaTeX">$n_{\mathrm {BS}}$ </tex-math></inline-formula> needed to be selected as a band subset and then develop two iterative process, sequential BSS (SQ-BSS) algorithm and successive BSS (SC-BSS) algorithm to find an optimal band subset numerically among all possible <inline-formula> <tex-math notation="LaTeX">$n_{\mathrm {BS}}$ </tex-math></inline-formula> combinations out of the full band set. In order to terminate the search process the averaged least-squares error (ALSE) and 3-D receiver operating characteristic (3D ROC) curves are used as stopping criteria to evaluate performance relative to AD using the full band set. Experimental results demonstrate that BSS generally performs better background suppression while maintaining target detection capability compared to target detection using full band information.
BadR, a New MarR Family Member, Regulates Anaerobic Benzoate Degradation by Rhodopseudomonas palustris in Concert with AadR, an Fnr Family Member

ABSTRACT A cluster of genes for the anaerobic degradation of benzoate has been described for the phototrophic bacterium Rhodopseudomonas palustris. Here we provide an initial analysis of the regulation of anaerobic benzoate degradation by examining the contributions of two regulators: a new regulator, BadR, encoded by the benzoate degradation gene cluster, and a previously described regulator, AadR, whose gene lies outside the cluster. Strains with single mutations in eitherbadR or aadR grew slowly on benzoate but were relatively unimpaired in growth on succinate and several intermediates of benzoate degradation. A badR aadR double mutant was completely defective in anaerobic growth on benzoate. Effects of the regulators on transcriptional activation were monitored with anR. palustris strain carrying a chromosomal fusion of ′lacZ to the badE gene of thebadDEFG operon. This operon encodes benzoyl-coenzyme A (benzoyl-CoA) reductase, an unusual oxygen-sensitive enzyme that catalyzes the benzene ring reduction reaction that is the rate-limiting step in anaerobic benzoate degradation. Expression ofbadE::′lacZ was induced 100-fold when cells grown aerobically on succinate were shifted to anaerobic growth on succinate plus benzoate. The aadR gene was required for a 20-fold increase in expression that occurred in response to anaerobiosis, and badR was responsible for a further 5-fold increase in expression that occurred in response to benzoate. Further studies with the badE::′lacZ fusion strain grown with various kinds of aromatic acids indicated that BadR probably responds to benzoyl-CoA acting as an effector molecule. Sequence information indicates that BadR is a member of the MarR family of transcriptional regulators. These studies expand the range of functions regulated by MarR family members to include anaerobic aromatic acid degradation and provide an example of a MarR-type protein that acts as a positive regulator rather than as a negative regulator, as do most MarR family members. AadR resembles the Escherichia coli Fnr regulator in sequence and contains cysteine residues that are spaced appropriately to serve in the capacity of a redox-sensing protein.
Enumeration, Isolation, and Characterization of N2-Fixing Bacteria from Seawater

Marine pelagic N2-fixing bacteria have not, in general, been identified or quantified, since low or negligible rates of N2 fixation have been recorded for seawater when blue-green algae (cyanobacteria) are absent. In the study reported here, marine N2-fixing bacteria were found in all samples of seawater collected and were analyzed by using a most-probable-number (MPN) method. Two different media were used which allowed growth of microaerophiles, as well as that of aerobes and facultative anaerobes. MPN values obtained for N2-fixing bacteria ranged from 0.4 to 1 � 103 per liter for water collected off the coast of Puerto Rico and from 2 to 5.5 � 102 per liter for Chesapeake Bay water. Over 100 strains of N2-fixing bacteria were isolated from the MPN tubes and classified, yielding four major groups of NaCl-requiring bacteria based on biochemical characteristics. Results of differential filtration studies indicate that N2-fixing bacteria may be associated with phytoplankton. In addition, when N2-fixing bacteria were inoculated into unfiltered seawater and incubated in situ, nitrogenase activity could be detected within 1 h. However, no nitrogenase activity was detected in uninoculated seawater or when bacteria were incubated in 0.2-μm-filtered (phytoplankton-free) seawater. The ability of these isolates to fix N2 at ambient conditions in seawater and the large variety of N2-fixing bacteria isolated and identified lead to the conclusion that N2 fixation in the ocean may occur to a greater degree than previously believed.
Repeat Transsphenoidal Surgery for the Treatment of Remaining or Recurring Pituitary Tumors in Acromegaly

BACKGROUND:Acromegaly is a disorder characterized by hypersecretion of growth hormone caused by a growth hormone–secreting pituitary adenoma. OBJECTIVE:To evaluate the long-term efficacy and safety of repeat transsphenoidal surgery for persistent or recurrent acromegaly. METHODS:We retrospectively reviewed records for 53 acromegalic patients who underwent repeat transsphenoidal surgery for persistent or progressive acromegaly at Toranomon Hospital between 1987 and 2006. Multivariate logistic regression was performed to evaluate preoperative factors influencing the surgical outcome. RESULTS:Thirty-one patients (58.5%) met the criteria for cure on long-term follow-up endocrine findings. Furthermore, 17 patients were well controlled with normal insulin-like growth factor I levels without (2 patients) or with medication (15 patients), whereas insulin-like growth factor I levels were still above normal in 5 patients after postoperative adjuvant therapy. Only 1 patient was undergoing additional hormonal replacement after surgery, although transient cerebrospinal fluid leak, transient abducens nerve palsy, severe nasal bleeding, and pituitary abscess occurred in each patient, respectively. Multivariate analysis clarified that a favorable surgical outcome was achieved in patients without cavernous sinus invasion (hazard ratio 12.56), tumor segmentation (hazard ratio 5.82), or in those older than 40 years old (hazard ratio 3.21). CONCLUSION:Repeat surgery can be performed safely with an approximately 60% long-term cure rate in this series. Reoperation should therefore be considered for persistent or recurrent disease in acromegalic patients in whom adjuvant therapy is not effective enough or cannot be accepted. The careful study of initial or preoperative magnetic resonance imaging and the use of micro-Doppler, endoscope, and eye movement monitoring device during surgery can help increase cure rate with a lower complication rate.
Nucleolar Proteins and Nuclear Ultrastructure in Preimplantation Bovine Embryos Produced In Vitro1

Abstract The aim of the present investigation was to describe the basic cell biology of the postfertilization activation of rRNA genes using in vitro-produced bovine embryos as a model. We used immunofluorescence confocal laser scanning microscopy and transmission electron microscopy to study nucleolar development in the nuclei of embryos up to the fifth postfertilization cell cycle. During the first cell cycle (1-cell stage), fibrillarin, upstream binding factor (UBF), nucleolin (C23), and RNA polymerase I were localized to distinct foci in the pronuclei, and, ultrastructurally, compact spherical fibrillar masses were the most prominent pronuclear finding. During the second cell cycle (2-cell stage), the findings were similar except for a lack of nucleolin and RNA polymerase I labeling. During the third cell cycle (4-cell stage), fibrillarin, UBF, nucleophosmin, and nucleolin were localized to distinct foci. Ultrastructurally, spherical fibrillar masses that developed a central vacuole over the course of the cell cycle were observed. Early in the fourth cell cycle (8-cell stage), fibrillarin, nucleophosmin, and nucleolin were localized to small bodies that with time developed a central vacuole. UBF and topoisomerase I were localized to clusters of small foci. Ultrastructurally, spherical fibrillar masses with a large eccentric vacuole and later small peripheral vacuoles were seen. Late in the fourth cell cycle, nucleophosmin and nucleolin were localized to large shell-like bodies; and fibrillarin, UBF, topoisomerase I, and RNA polymerase I were localized to clusters of small foci. Ultrastructurally, a presumptive dense fibrillar component (DFC) and fibrillar centers (FCs) were observed peripherally in the vacuolated spherical fibrillar masses. Subsequently, the presumptive granular component (GC) gradually became embedded in the substance of this entity, resulting in the formation of a fibrillo-granular nucleolus. During the fifth cell cycle (16-cell stage), a spherical fibrillo-granular nucleolus developed from the start of the cell cycle. In conclusion, the nucleolar protein compartment in in vitro-produced preimplantation bovine embryos is assembled over several cell cycles. In particular, RNA polymerase I and topoisomerase I are detected for the first time late during the fourth embryonic cell cycle, which coincides with the first recognition of the DFC, FCs, and GC at the ultrastructural level.
Inflammation and chronic colonization of Haemophilus influenzae in sputum in COPD patients related to the degree of emphysema and bronchiectasis in high-resolution computed tomography

The presence of bacteria in the lower airways in COPD results in inflammation, further airway structural damage, and might lead to repeated exacerbations. We have previously shown that chronic colonization of Haemophilus influenzae during stable disease is related to increased inflammation, and we now aimed to relate previous findings of bacterial colonization and inflammation to the degree of radiological findings of bronchiectasis and emphysema. Thirty-nine patients with COPD were included in their stable state, and a high-resolution computed tomography of the lung was performed. They were followed-up monthly for up to a maximum of 6 months or until exacerbation, and they answered questionnaires, performed spirometry, and induced sputum at every visit. Thirty-five patients had emphysema with an emphysema degree of median 20% (interquartile range 10–50), and five patients had bronchiectasis, of which only four could expectorate sputum. The degree of emphysema correlated with several inflammatory mediators in sputum, such as interleukin-8 concentration, myeloperoxidase activity, and Leukotriene B4 concentration. Ten patients were chronically colonized with H. influenzae (ie, had a positive culture for H. influenzae at all visits). The four sputum patients with bronchiectasis were chronically colonized with H. influenzae and showed higher degree of H. influenzae growth compared to patients without bronchiectasis. During exacerbation, there was no longer any correlation between emphysema degree and inflammation, but patients with bronchiectasis showed higher sputum purulence score than patients without bronchiectasis. Emphysema and bronchiectasis in COPD patients show different clinical features. The presence of emphysema is more related to inflammation, while bronchiectasis is associated with bacterial colonization. We believe that both emphysema and bronchiectasis are therefore COPD phenotypes of highest impact and need evaluation to prevent further disease progression.
A- and B-utrophin Have Different Expression Patterns and Are Differentially Up-regulated in mdx Muscle*

Duchenne muscular dystrophy (DMD) is a fatal childhood disease caused by mutations that abolish the expression of dystrophin in muscle. Utrophin is a paralogue of dystrophin and can functionally replace it in skeletal muscle. A method to induce utrophin up-regulation in muscle should therefore be therapeutically useful in DMD. We have previously shown that there are two full-length utrophin mRNA species: A and B. Here we describe the generation and characterization of antibodies specific to A- and B-utrophin. We show that both mRNA isoforms are translated into full-length proteins, which have very different expression patterns. B-utrophin is expressed in vascular endothelial cells; A-utrophin is expressed at the neuromuscular junction, choroid plexus, pia mater, and renal glomerulus. We have analyzed the expression of A- and B-utrophin protein and RNA in dystrophin-deficient tissues. We conclude that (i) the previously described expression patterns of utrophin represent a composite of A- and B-utrophin, (ii) A- but not B-utrophin is up-regulated in dystrophin-deficient striated muscle, and (iii) this up-regulation occurs post-transcriptionally with an additional transcriptional component in skeletal muscle. These results have important implications for understanding the biology of utrophin and are crucial for future studies aiming to effect its therapeutic up-regulation in DMD patients.
Antibody fragments, expressed by a fowl adenovirus vector, are able to neutralize infectious bursal disease virus

Single-chain variable fragments (scFv) contain the heavy and light chain variable domains of immunoglobulin, joined by a short peptide linker. Previously, our laboratory has produced neutralizing scFv to epitopes of infectious bursal disease virus (IBDV). The in vitro delivery and expression of one of these scFv with and without the CH2-CH4 Fc domain of chicken IgY attached (scFv-Fc) by a serotype 8 fowl adenovirus (FAdV-8) vector was investigated in the present study. A panel of FAdV-8 vectors was constructed, each containing a different transgene (scFv or scFv-Fc), a different promoter to drive scFv and scFv-Fc transcription (CMVie or the fowl adenovirus major late promoter), and a different sized, right-hand end genomic deletion (52 bp or 2.3 kb). This panel was used to establish what effect these variables had on protein production, viral replication and scFv transcription, as measured by enzyme-linked imunosorbent assay and real-time polymerase chain reaction. Our results showed that, using a FAdV-8 vector containing the optimal CMVie promoter/2.3 kb deletion combination, we successfully expressed a secreted form of both scFv and scFv-Fc that were able to neutralize IBDV both in vitro and in ovo. These studies indicate that the FAdV-8 vector may be a promising candidate to deliver and express therapeutic molecules such as scFv and scFv-Fc in vivo in poultry.
Human taste detection of glucose oligomers with low degree of polymerization

Studies have reported that some animals, including humans, can taste mixtures of glucose oligomers (i.e., maltooligosaccharides, MOS) and that their detection is independent of the known T1R2/T1R3 sweet taste receptor. In an effort to understand potential mechanisms underlying the taste perception of glucose oligomers in humans, this study was designed to investigate: 1) the variability of taste sensitivity to MOS with low degree-of-polymerization (DP), and 2) the potential role of hT1R2/T1R3 in the MOS taste detection. To address these objectives, a series of food grade, narrow-DP-range MOS were first prepared (DP 3, 3–4, 5–6, and 6–7) by fractionating disperse saccharide mixtures. Subjects were then asked to discriminate these MOS stimuli as well as glucose (DP 1) and maltose (DP 2) from blanks after the stimuli were swabbed on the tongue. All stimuli were presented at 75 mM with and without a sweet taste inhibitor (lactisole). An α-glucosidase inhibitor (acarbose) was added to all test stimuli to prevent oral digestion of glucose oligomers. Results showed that all six stimuli were detected with similar discriminability in normal tasting conditions. When the sweet receptor was inhibited, DP 1, 2, and 3 were not discriminated from blanks. In contrast, three higher-DP paired MOS stimuli (DP 3–4, 5–6, and 6–7) were discriminated from blanks at a similar degree. Overall, these results support the presence of a sweet-independent taste perception mechanism that is stimulated by MOS greater than three units.