Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular Phospho‐Flow cytometry reveals novel insights into TCR proximal signaling events. A comparison with Western blot

Phospho‐site specific antibodies become increasingly available, enabling the study of signaling events by Western blotting (WB) or intracellular flow cytometry (Phospho‐Flow). Here we compared data generated by WB or Phospho‐Flow regarding the kinetics and degree of phosphorylation of membrane proximal TCR signaling molecules. Phosphorylation events in Jurkat T cells were triggered by anti‐CD3 stimulation (OKT3) or by oxidative stress (H2O2) and were analyzed by Phospho‐Flow or WB. Both techniques showed that OKT3‐ or H2O2‐induced, transient phosphorylation of ZAP70 or LAT was dependent on functional Lck. Phospho‐Flow data revealed differences in the kinetics and the degree of H2O2‐ or OKT3‐mediated protein phosphorylation compared with WB data. In addition, using Phospho‐Flow we discovered that H2O2‐induced phosphorylation of TCR signaling proteins was inhibited by small molecular weight kinase inhibitors far more potently than OKT3‐triggered protein phosphorylation, despite a superior induction of phosphorylation by H2O2.This finding was confirmed by WB. Interestingly, we identified by Phospho‐Flow that, in P116 Jurkat cells lacking ZAP70 protein expression, H2O2 potently triggered the phosphorylation of ZAP70 residues Y493 and Y292 but not Y319. The phosphorylation of these ZAP70 tyrosine residues cells was blocked by an Lck inhibitor, suggesting the existence of an Lck‐coupled truncated ZAP70 protein or a novel isoform of ZAP70 in P116 cells. Phospho‐Flow is a largely quantitative technology with excellent throughput, highly suited in studying the function or inhibition of TCR signaling pathways and allowing the detection of novel pathway insights. It can serve as a good complement to Western blot analysis. © 2008 International Society for Advancement of Cytometry
Evaluation of two techniques for measurement of respiratory resistance by forced oscillation

The measurement of respiratory resistance by forced oscillation requires minimal patient co-operation and should be a useful test in children. Sixty-eight children and adolescents with obstructive lung disease were studied using two different techniques. In patients with severe obstructive lung disease, unexpectedly low values for respiratory resistance were found when the measurement was made at points of peak flow (write-out method). Measurements made at simulated resonant frequency (subtraction method) in these patients were more in keeping with other tests of respiratory function; however, they probably did not reflect true respiratory resistance. The subtraction method of measuring respiratory resistance would seem to be of value in separating the normal from the abnormal, but the absolute values in obstructed subjects are difficult to interpret.
Introducing deglitched-feedback plus convergent encoding for straight hardware implementation of asynchronous finite state machines

Asynchronous finite state machines (AFSMs) are of interest in a number of areas, particularly when simplifying the hardware and/or reducing power consumption are essential. The design of reliable standalone (no handshake signals needed) AFSMs, however, is complex due to especially possible signal races, which seriously limit their widespread use. We introduce a fundamental modification, which consists of replacing the delays in the feedback loop with deglitchers. This simple modification, combined with a proposed convergent state encoding, allows standalone AFSMs to finally be implemented nearly as easily as conventional (synchronous) FSMs, even for burst-mode operation. A helpful tool for analyzing AFSMs is also introduced. The benefits of the proposed approach are confirmed in the experiments, developed with VHDL and FPGAs.
Immunolocalization of superoxide dismutase in Dirofilaria immitis adult worms

Superoxide dismutase (SOD) may not only perform a housekeeping role in filarial worms but also assist in defense against oxidants generated by host immune cells. Both Dirofilaria and Onchocerca adult filariae and microfilariae contain relatively high activities of the antioxidant enzyme SOD; adult Dirofilaria worms also secrete SOD in vitro. In addition, superoxide radicals are relatively impotent against Dirofilaria and Onchocerca microfilariae in vitro. In assessing the role of SOD, we determined the anatomic localization of SOD in D. immitis adult worms by immunolocalization at the light-microscopic level. We found that anti-D. immitis SOD did not stain parasite tissues homogeneously, in support of the hypothesis that SOD does not have only a housekeeping role and that the pattern of staining may suggest another role(s) for SOD.
Use of interrupted saccade paradigm to study spatial and temporal dynamics of saccadic burst cells in superior colliculus in monkey.

1. We recorded the spatial and temporal dynamics of saccade-related burst neurons (SRBNs) found in the intermediate layers of the superior colliculus (SC) in the alert, behaving monkey. These burst cells are normally the first neurons recorded during radially directed microelectrode penetrations of the SC after the electrode has left the more dorsally situated visual layers. They have spatially delimited movement fields whose centers describe the well-studied motor map of the SC. They have a rather sharp, saccade-locked burst of activity that peaks just before saccade onset and then declines steeply during the saccade. Many of these cells, when recorded during saccade trials, also have an early, transient visual response and an irregular prelude of presaccadic activity. 2. Because saccadic eye movements normally have very stereotyped durations and velocity trajectories that vary systematically with saccade size, it has been difficult in the past to establish quantitatively whether the activity of SRBNs temporally codes dynamic saccadic control signals, e.g., dynamic motor error or eye velocity, where dynamic motor error is defined as a signal proportional to the instantaneous difference between desired final eye position and the actual eye position during a saccade. It has also not been unequivocally established whether SRBNs participate in an organized spatial shift of ensemble activity in the intermediate layers of the SC during saccadic eye movements. 3. To address these issues, we studied the activity of SRBNs using an interrupted saccade paradigm. Saccades were interrupted with pulsatile electrical stimulation through a microelectrode implanted in the omnipauser region of the brain stem while recordings were made simultaneously from single SRBNs in the SC. 4. Shortly after the beginning of the stimulation (which was electronically triggered at saccade onset), the eyes decelerated rapidly and stopped completely. When the high-frequency (typically 300-400 pulses per second) stimulation was terminated (average duration 12 ms), the eye movement was reinitiated and a resumed saccade was made accurately to the location of the target. 5. When we recorded from SRBNs in the more caudal colliculus, which were active for large saccades, cell discharge was powerfully and rapidly suppressed by the stimulation (average latency = 3.8 ms). Activity in the same cells started again just before the onset of the resumed saccade and continued during this saccade even though it has a much smaller amplitude than would normally be associated with significant discharge for caudal SC cells. (ABSTRACT TRUNCATED AT 400 WORDS)
Active learning through collaborative knowledge building using an automatic free-text scoring system in a b-learning environment

ABSTRACT According to active learning, students should be responsible for their own learning. Automatic free-text scoring allows teachers to provide open-ended questions with their correct answers to a computer system, so when students answer the questions, they get immediate feedback (a score, a comment, or both). However, teachers are usually overloaded with many tasks, and they may not have time to create the questions with the correct answers. Therefore, in the 2012/2013 academic year, we asked a group of 124 Pre-Primary and Primary Education students to become the creators of the questions and their correct answers in groups in a free-text scoring system, so the questions use learners’ language, not teachers’ language. From them, 41 students (group of involved students, GIS) fulfilled all the requirements during the course. Our hypothesis was that GIS would be able to increase their academic performance and levels of engagement compared to the rest of the students. The results gathered provide statistic evidence to support that hypothesis. This study pretends to help teachers who want to increase the academic performance and levels of engagement of their students in courses that they may find boring and unrelated to the main topic of their degree, or not directly related with their main academic interests.
Relative validity and reproducibility of a 14-item semi-quantitative food frequency questionnaire for cardiovascular prevention

Background Dietary habits play a major role in cardiovascular disease risk but few simple nutrition assessment tools are available for clinical practice. We developed a 14-item food frequency questionnaire to evaluate dietary patterns in relation with coronary risk in a French population. Design and methods This food frequency questionnaire gave different scores of intake: saturated fatty acids (six questions), mono-unsaturated fatty acids, Ω-3 and Ω-6/Ω-3 polyunsaturated fatty acids (five questions), and fruits and vegetables (three questions). Validity was assessed against a 7-day dietary history (n = 49 subjects) and against biomarkers (n = 181). The food frequency questionnaire was also administered twice with an interval of 15 days to evaluate its reproducibility (n = 20). Results Validity against dietary history was assessed with Spearman correlation coefficients which ranged from 0.47 (fruits and vegetables) to 0.63 (polyunsaturated fatty acids/saturated fatty acids) (all P < 0.05), with a mean value of 0.54. On average, 39% of the subjects were classified in the same quartile with the food frequency questionnaire and the dietary history and 84% in the same or adjacent quartile. Biomarker-based validity using Spearman correlation coefficients varied from 0.21 (saturated fatty acids) to 0.53 (Ω-3 polyunsaturated fatty acids) (all P < 0.05), with a mean value of 0.35. On average, 37% of the participants were classified in the same quartile with the food frequency questionnaire and the corresponding biomarkers and 73% in the same or adjacent quartile. Reproducibility assessed by the intraclass correlation coefficient ranged from 0.71 (mono-unsaturated fatty acids) to 0.93 (global score), with a mean value of 0.81. Conclusion We validated a short food frequency questionnaire for dietary pattern assessment in coronary prevention.
A Sequential Sensing Data Transmission and Fusion Approach for Large Scale Cognitive Radios

Cognitive radios are efficient techniques to improve the utilization of the spectrum. Spectrum sensing is the key functionality to improve the spectrum efficiency and avoid harmful interference to the licensed users. By exploiting the spatial diversity of the different secondary users, cooperative sensing can achieve better sensing performance compared to the local sensing, thereby, receiving much attention recently. However, in large scale cognitive radio networks, such as Wireless Regional Area Network (WRAN) defined by IEEE 802.22, the secondary users may have quite different sensing SNRs due to the different pass loss and other environment parameters. How to efficiently transmit and fuse the sensing data of cooperative sensing in large scale cognitive radios have not been fully studied yet. This paper presents a sequential sensing data transmission and fusion approach for large scale cognitive radios to minimize the average sensing time by dividing the users into different sets according to their SNR parameters. The analytical and simulation results both show that the proposed approach not only decreases the sensing time but also certifies the accuracy of detection.
Seroprevalence of Toxoplasma gondii in Canadian Pinnipeds

Sera (n=328) collected from phocids (1995–97) from the east coast of Canada, including harp seals (Phoca groenlandica), hooded seals (Cystophora cristata), grey seals (Halichoerus grypus), and harbor seals (Phoca vitulina), were diluted 1:25, 1:50, and 1:500 and tested by a modified agglutination test for antibodies to Toxoplasma gondii. Titers equal to or greater than 1:25 were considered evidence of exposure. Grey seal (11/122, 9%), harbor seal (3/34, 9%), and hooded seal (1/60, 2%) had titers of 1:25 and 1:50. Harp seals (n=112) were seronegative. Probable maternal antibody transfer was observed in one harbor and one grey seal pup at 10 and 14 day of age, respectively. Transmission of T. gondii in the marine environment is not understood. The discovery of T. gondii in marine mammals might indicate natural infections unknown because of lack of study or might indicate recent contamination of the marine environment from the terrestrial environment by natural or anthropogenic activities.
CIST System Report for SIGdial MultiLing 2015

This report provides a description of the methods applied in our CIST system participating two tasks in SIGdial MultiLing 2015. For the task of MMS, we adopt hLDA modeling for documents and sentence extraction to generate a summary. For the task of On-ForumS, we utilize Word Embedding Model in deep learning and compute sentence similarity for content linking; then implement LDA topic modeling for argument label and sentiment analysis for sentiment label. According to the published evaluation results, we have got the best performance for both argument label and sentiment label.
Introduction to Volume 11, Issue 1 and Proceedings of the Faculty for Undergraduate Neuroscience Workshops at Pomona College, Claremont, CA, July 28 to July 31, 2011

Bruce R. Johnson, Eric P. Wiertelak, Julio J. Ramirez, and Karen Parfitt 1 Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853; 2 Department of Psychology and Neuroscience Studies Program, Macalester College, St. Paul, MN 55105; 3 Department of Psychology and Neuroscience Program, Davidson College, Davidson, NC 28035; 4 Department of Neuroscience, Pomona College, Claremont, CA 91711
Self-Orthogonal Convolutional Coding for the DPCM-AQB Speech Encoder

A fixed-tap differential pulse code modulation (DPCM) system with a robust backward-adaptive Jayant quantizer is investigated for speech encoding at 16-40 kbits/s using binary phase shift keying over an additive white Gaussian noise channel. The performance of this system becomes unacceptable as the channel bit error rate (P_{b}) approaches 10-2. Using high-rate, long constraint length, self-orthogonal convolutional codes, the DPCM system performance is much-improved for 10^{-4} depending on the transmitted data rate. The use of high-rate (n - 1)/n, n = 2,3,4, , and 5 codes minimizes the number of bits allocated to channel coding, and decoding complexity is reduced by employing self-orthogonal codes which admit threshold decoding. Subjectively, while there is additional quantization noise with channel coding, the irritating popping and squeaking sounds due to channel errors are eliminated.
Loss of retinitis pigmentosa 2 (RP2) protein affects cone photoreceptor sensory cilium elongation in mice

Degeneration of photoreceptors (rods and cones) results in blindness. As we rely almost entirely on our daytime vision mediated by the cones, it is the loss of these photoreceptors that results in legal blindness and poor quality of life. Cone dysfunction is usually observed due to two mechanisms: noncell‐autonomous due to the secondary effect of rod death if the causative gene is specifically expressed in rods and cell autonomous, if the mutation is in a cone‐specific gene. However, it is difficult to dissect cone autonomous effect of mutations in the genes that are expressed in both rods and cones. Here we report a property of murine cone photoreceptors, which is a cone‐autonomous effect of the genetic perturbation of the retinitis pigmentosa 2 (Rp2) gene mutated in human X‐linked RP. Constitutive loss of Rp2 results in abnormal extension of the cone outer segment (COS). This effect is phenocopied when the Rp2 gene is ablated specifically in cones but not when ablated in rods. Furthermore, the elongated COS exhibits abnormal ultrastructure with disorganized lamellae. Additionally, elongation of both the outer segment membrane and the microtubule cytoskeleton was observed in the absence of RP2. Taken together, our studies identify a cone morphological defect in retinal degeneration due to ablation of RP2 and will assist in understanding cone‐autonomous responses during disease and develop targeted therapies. © 2015 Wiley Periodicals, Inc.
The complete mitochondrial genome of the hybrid of Culter alburnus (♀) × Ancherythroculter nigrocauda (♂)

Abstract In this study, the complete mitochondrial genome sequence of the hybrid of Culter alburnus (♀) × Ancherythroculter nigrocauda (♂) was determined and analyzed for the first time. The total length of the mitogenome is 16,621 bp, with the base composition of 31.20% A, 24.78% T, 27.78% C, and 16.24% G. It contains the typical structure as that of most other vertebrates, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 main non-coding regions (the origin of the light strand replication and the control region). The complete mitogenome of the hybrid of C. alburnus (♀) × A. nigrocauda (♂) provides an important data set for study in mitochondrial inheritance mechanism.
Rings with annihilator chain conditions and right distributive rings

We prove that if a right distributive ring R , which has at least one completely prime ideal contained in the Jacobson radical, satisfies either a.c. c or d.c.c. on principal right annihilators, then the prime radical of R is the right singular ideal of R and is completely prime and nilpotent. These results generalize a theorem by Posner for right chain rings.
Multi-rate frequency-dependent line (FD-Line) model for simulations of EMTs in power systems

This paper presents a multi-rate FD-Line model for executing more efficient simulations of EMTs in power networks with multiple time steps. Basically, this line model takes advantage of its two decoupled-in-time Norton equivalents for splitting a power network in two resulting sub-networks for its subsequent parallel execution in a PC-cluster. These sub-networks are solved in the PSB/Simulink toolbox with cosimulations. Finally, the time-steps assigned to each sub-network are in full accordance with its internal dynamic.
Propofol Pretreatment Reduces Ceramide Production and Attenuates Intestinal Mucosal Apoptosis Induced by Intestinal Ischemia/Reperfusion in Rats

BACKGROUND:Apoptosis has been shown to be a major mode of intestinal epithelial cell death caused by intestinal ischemia/reperfusion (II/R), a condition that is associated with increased oxidative stress. Ceramide has been proposed as a messenger of apoptosis. We investigated if pretreatment with propofol, an anesthetic with antioxidant properties, could reduce ceramide production, and consequently, mucosal epithelial apoptosis induced by II/R in rats. METHODS:Rat II/R injury was produced by clamping the superior mesenteric artery for 1 h followed by 3 h of reperfusion. Thirty rats were randomly allocated into control, injury (II/R) and propofol (pretreatment) groups (n = 10 per group). In the propofol group, propofol 50 mg/kg, a dose that has been shown to cause the loss of reflex responses to a painful stimulus while remaining sensitive to skin incision in rats, was administered intraperitoneally 30 min before inducing intestinal ischemia, while animals in control and untreated injury groups received an equal volume of intralipid. Intestinal mucosal epithelial apoptosis was detected via electron microscopy and TUNEL analysis. Lipid oxidation product malondialdehyde and the activities of superoxide dismutase were assessed by colorimetric analyses. Ceramide generation and sphingomyelinase mRNA expression in intestinal mucosa were determined by high performance thin layer chromatography and reverse transcriptase polymerase chain reaction, respectively. RESULTS:II/R caused intestinal mucosal epithelial apoptosis and over-production of ceramide accompanied by up-regulation of sphingomyelinase mRNA expression and increases in lipid oxidation (all P < 0.01 versus control). Propofol pretreatment significantly attenuated these changes (all P < 0.01, propofol versus injury). CONCLUSION:The findings indicate that propofol pretreatment attenuates II/R-induced intestinal epithelial apoptosis, which might be attributable to its antioxidant property modulating the ceramide pathway.
Oropharyngeal cancer and human papilloma virus: evolving diagnostic and management paradigms

The significant increase in human papilloma virus (HPV)‐associated oropharyngeal carcinoma (OPC) over recent years has lead to a surge in research and an improved understanding of the disease. Most patients with HPV‐associated OPC present with cystic nodal metastases with a small primary tumour, and respond well to all treatment modalities including primary surgery and primary chemoradiotherapy. Current research is evaluating treatment de‐escalation to reduce long‐term treatment‐associated morbidities. Transoral robotic surgery (TORS) is particularly relevant as the transoral approach allows small primary tumours to be removed with lower morbidity than traditional surgical approaches. The current American Joint Committee on Cancer staging system for oropharyngeal cancer does not appropriately stratify HPV‐associated OPC; hence, alternative risk stratification and staging classifications are being proposed.
The Assessment of Dietary Habits in Obese Women: Influence of Eating Behavior Patterns

The objective of this cross-sectional, observational study was to compare the dietary history and the 7-day record method to assess dietary habits in obese women. The second goal was to investigate whether eating behavior characteristics influence self-reported dietary intake. The study took place at the Obesity Outpatient Clinic, University Hospital Gasthuisberg, Leuven, Belgium. Subjects were 137 obese women with a mean age of 40 ± 12 years and a mean body mass index of 38.2 ± 6.0 kg/m2. Dietary intake was assessed both by the dietary history and by the 7-day record method. Resting energy expenditure was measured by continuous indirect calorimetry. Physical activity level was estimated using the Baecke questionnaire. To study different aspects of eating behaviour, the “Dutch Eating Behaviour Questionnaire” was used. Absolute energy intake, as assessed by the 7-day record, was consistently lower than with the dietary history method. Sixteen percent of the obese women were overreporters while 66% clearly underreported energy intake, using dietary history as standard method. Restrained eating was associated with underreporting, while all aspects of emotional and external eating behavior were significantly higher in the group of overreporters. No relationship could be observed between the degree of underreporting and age, body weight or body mass index. Energy intake, as assessed by the dietary history method, correlated better with measured energy expenditure in obese subjects than the 7-day record. Eating behavior characteristics influence the accuracy of self-reported dietary intake in obese women. This study was supported in part by the Fonds voor Wetenschappelijk Onderzoek – Vlaanderen (Project G.0178.96 and ‘Krediet aan Navorsers’ 1.5.006.95).