Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioinformatic Integration of Molecular Networks and Major Pathways Involved in Mice Cochlear and Vestibular Supporting Cells

Background: Cochlear and vestibular epithelial non-hair cells (ENHCs) are the supporting elements of the cellular architecture in the organ of Corti and the vestibular neuroepithelium in the inner ear. Intercellular and cell-extracellular matrix interactions are essential to prevent an abnormal ion redistribution leading to hearing and vestibular loss. The aim of this study is to define the main pathways and molecular networks in the mouse ENHCs. Methods: We retrieved microarray and RNA-seq datasets from mouse epithelial sensory and non-sensory cells from gEAR portal (http://umgear.org/index.html) and obtained gene expression fold-change between ENHCs and non-epithelial cells (NECs) against HCs for each gene. Differentially expressed genes (DEG) with a log2 fold change between 1 and −1 were discarded. The remaining genes were selected to search for interactions using Ingenuity Pathway Analysis and STRING platform. Specific molecular networks for ENHCs in the cochlea and the vestibular organs were generated and significant pathways were identified. Results: Between 1723 and 1559 DEG were found in the mouse cochlear and vestibular tissues, respectively. Six main pathways showed enrichment in the supporting cells in both tissues: (1) “Inhibition of Matrix Metalloproteases”; (2) “Calcium Transport I”; (3) “Calcium Signaling”; (4) “Leukocyte Extravasation Signaling”; (5) “Signaling by Rho Family GTPases”; and (6) “Axonal Guidance Si”. In the mouse cochlea, ENHCs showed a significant enrichment in 18 pathways highlighting “axonal guidance signaling (AGS)” (p = 4.37 × 10−8) and “RhoGDI Signaling” (p = 3.31 × 10−8). In the vestibular dataset, there were 20 enriched pathways in ENHCs, the most significant being “Leukocyte Extravasation Signaling” (p = 8.71 × 10−6), “Signaling by Rho Family GTPases” (p = 1.20 × 10−5) and “Calcium Signaling” (p = 1.20 × 10−5). Among the top ranked networks, the most biologically significant network contained the “auditory and vestibular system development and function” terms. We also found 108 genes showing tonotopic gene expression in the cochlear ENHCs. Conclusions: We have predicted the main pathways and molecular networks for ENHCs in the organ of Corti and vestibular neuroepithelium. These pathways will facilitate the design of molecular maps to select novel candidate genes for hearing or vestibular loss to conduct functional studies.
Perioperative implication of the endothelial glycocalyx

The endothelial glycocalyx (EG) is a gel-like layer lining the luminal surface of healthy vascular endothelium. Recently, the EG has gained extensive interest as a crucial regulator of endothelial funtction, including vascular permeability, mechanotransduction, and the interaction between endothelial and circulating blood cells. The EG is degraded by various enzymes and reactive oxygen species upon pro-inflammatory stimulus. Ischemia-reperfusion injury, oxidative stress, hypervolemia, and systemic inflammatory response are responsible for perioperative EG degradation. Perioperative damage of the EG has also been demonstrated, especially in cardiac surgery. However, the protection of the EG and its association with perioperative morbidity needs to be elucidated in future studies. In this review, the present knowledge about EG and its perioperative implication is discussed from an anesthesiologist’s perspective.
Long-Term Effects of Traffic-Related Air Pollution on Mortality in a Dutch Cohort (NLCS-AIR Study)

Background Several studies have found an effect on mortality of between-city contrasts in long-term exposure to air pollution. The effect of within-city contrasts is still poorly understood. Objectives We studied the association between long-term exposure to traffic-related air pollution and mortality in a Dutch cohort. Methods We used data from an ongoing cohort study on diet and cancer with 120,852 subjects who were followed from 1987 to 1996. Exposure to black smoke (BS), nitrogen dioxide, sulfur dioxide, and particulate matter ≤mu;M2.5), as well as various exposure variables related to traffic, were estimated at the home address. We conducted Cox analyses in the full cohort adjusting for age, sex, smoking, and area-level socioeconomic status. Results Traffic intensity on the nearest road was independently associated with mortality. Relative risks (95% confidence intervals) for a 10-μg/m3 increase in BS concentrations (difference between 5th and 95th percentile) were 1.05 (1.00–1.11) for natural cause, 1.04 (0.95–1.13) for cardiovascular, 1.22 (0.99–1.50) for respiratory, 1.03 (0.88–1.20) for lung cancer, and 1.04 (0.97–1.12) for mortality other than cardiovascular, respiratory, or lung cancer. Results were similar for NO2 and PM2.5, but no associations were found for SO2. Conclusions Traffic-related air pollution and several traffic exposure variables were associated with mortality in the full cohort. Relative risks were generally small. Associations between natural-cause and respiratory mortality were statistically significant for NO2 and BS. These results add to the evidence that long-term exposure to ambient air pollution is associated with increased mortality.
A multicenter evaluation of a new EUS core biopsy needle: Experience in 200 patients

Background and Objectives: We present a multicenter study of a new endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) needle (Acquire, Boston Scientific, Natick, MA). The aim of the study was to analyze the needle's clinical performance when sampling solid lesions and to assess the safety of this device. Methods: We performed a multicenter retrospective study of patients undergoing EUS-FNB during July 1–November 15, 2016. Results: Two hundred patients (121 males and 79 females) underwent EUS-FNB of solid lesions with the Acquire needle. Lesions included solid pancreatic masses (n = 109), adenopathy (n = 45), submucosal lesions (n = 34), cholangiocarcinoma (n = 8), liver lesions (n = 6), and other (n = 8). Mean lesion size was 30.6 mm (range: 3–100 mm). The mean number of passes per target lesion was 3 (range: 1–7). Rapid onsite cytologic evaluation (ROSE) by a cytologist was performed in all cases. Tissue obtained by EUS-FNB was adequate for evaluation and diagnosis by ROSE in 197/200 cases (98.5%). Data regarding the presence or absence of a core of tissue obtained after EUS-FNB were available in 145/200 procedures. In 131/145 (90%) of cases, a core of tissue was obtained. Thirteen out of 200 patients (6.5%) underwent some form of repeat EUS-based tissue acquisition after EUS-FNB with the Acquire needle. There were no adverse events. Conclusion: Overall, this study showed a high rate of tissue adequacy and production of a tissue core with this device with no adverse events seen in 200 patients. Comparative studies of different FNB needles are warranted in the future to help identify which needle type and size is ideal in different clinical settings.
New Perspectives on Nitrogen Fixation Measurements Using 15N2 Gas

Recently, the method widely used to determine 15N2 fixation rates in marine and freshwater environments was found to underestimate rates because the dissolution of the added 15N2 gas bubble in seawater takes longer than theoretically calculated. As a solution to the potential underestimate of rate measurements, the usage of the enriched water method was proposed to provide constant 15N2 enrichment. Still, the superiority of enriched water method over the previously used bubble injection remains inconclusive. To clarify this issue, we performed laboratory based experiments and implemented the results into an error analysis of 15N2 fixation rates. Moreover, we conducted a literature search on the comparison of the two methods to calculate a mean effect size using a meta-analysis approach. Our results indicate that the error potentially introduced by an equilibrium phase of the 15N2 gas is -72% at maximum for experiments with very short incubation times of 1 hour. In contrast, the underestimation was negligible for incubations lasting 12 to 24 hours (error is -0.2%). Our meta-analysis indicates that 84 % of the measurements in the two groups will overlap and there is a 61% chance that a sample picked at random from the enriched water group will have a higher value than one picked at random from the bubble group. Overall, the underestimation of N2 fixation rates when using the bubble method relative to the enriched water method is highly dependent on incubation time and other experimental conditions and cannot be generalized.
Do biometeorological indices improve modeling outcomes of heat-related mortality?

Various biometeorological indices and temperature measures have been used to assess heat-related health risks. Composite indices are expected to assess human comfort more accurately than do temperature measures alone.Theperformancesofseveralcommonbiometeorologicalindicesandtemperaturemeasuresinevaluating the heat-related mortality in Brisbane, Australia—a city with a subtropical climate—were compared. Daily counts of deaths from organic causes [International Statistical Classification of Diseases and Related Health Problems, 9th Revision, (ICD9) codes 001‐799 and ICD, 10th Revision, (ICD10) codes A00‐R99] during the periodfrom 1 January 1996 to30 November 2004were used. Several composite biometeorological indices were considered, such as apparent temperature, relative strain index, Thom discomfort index, the humidex, and wetbulb globe temperature. Hot days were defined as those days falling into the 95th percentile of each thermal stress indicator. Case-crossover analysis was applied to estimate the relationship between exposure to heat and mortality. The performances of various biometeorological indices and temperature measures were compared using the jackknife resampling method.The results showthat more deathswerelikelytooccur on hot daysthan on other (i.e., control) days regardless of the temperature measure or biometeorological index that is considered. The magnitude of the odds ratios varied with temperature indicators, between 1.08 [95% confidence interval (CI): 1.02‐1.14] and 1.41 (95% CI: 1.22‐1.64) after adjusting for air pollutants (particulate matter with aerodynamic diameter less than 10 mm and ozone). Average temperature performedsimilarly tothe composite indices, but minimum and maximum temperatures performed relatively poorer. Thus, average temperature may be suitable for the development of weather‐health warning systems if the findings presented herein are confirmed in different locations.
Electrochemical sensors with screen printed Ag|AgCl|KCl reference electrodes

This paper presents the printed thick film Ag|AgCl|KCl reference electrodes for electrochemical or biosensors application and theirelectrochemical and analytical performance. The reference electrode exhibits a stable potential against standard glass reference electrode with a potential difference of 5 mV in the deionized water. The anodic and cathodic peak current of the electrode increase with the increase in scan rate in the range of 25–150 mVs−1. The open circuit potential response of thick film reference electrode in the NaCl concentrations range (30–100 mM) was measured and it shows a stable potential in each test solution. The fabricated reference electrode shows an excellent application for an electrochemical pH sensor.
Characteristics of Synchronous and Metachronous Multiple Gastric Tumors after Endoscopic Submucosal Dissection of Early Gastric Neoplasm

Background/Aims Endoscopic submucosal dissection (ESD) has been widely accepted as a method of treatment of early gastric tumor. This study aimed to identify the incidence and characteristics of multiple gastric tumors after ESD. Methods Patients with early gastric tumors who were treated by ESD from January 2004 to June 2012 and followed up with endoscopic examination periodically for at least 1 year were enrolled. All multiple gastric lesions were subsequently treated with ESD and the medical records of the patients were retrospectively reviewed. Results In total, 643 patients were included. The mean duration of endoscopic follow-up was 45.27±27.59 (range, 12–148) months. Overall, 144 patients (22.4%) showed multiple gastric tumors during the follow-up period (44 synchronous [6.8%] and 100 metachronous [15.5%]). The cumulative incidence rate steadily increased during the follow-up period. More than 50% of the tumors that developed at the same longitudinal location of the stomach were of the same macroscopic and histological type as the primary lesions. Conclusions Because synchronous and/or metachronous gastric tumors are common, considerable attention should be paid to detect multiple gastric lesions after ESD of early gastric neoplasm.
1 Broadband Terahertz Light-Matter Interaction 2 Enhancement for Precise Spectroscopy of Thin Films 3 and Micro-Samples 4

In biology molecules and macromolecules like sugars, proteins, DNA, and RNA are of 10 utter importance. Detecting their presence as well as their conformation is still a challenge in many 11 cases. It is well known that the vibrational states of such molecules lie from the infrared to the 12 TeraHertz range. Spectroscopy can be used to detect such compounds and probe their 13 conformation. Still, terahertz spectroscopy on biosample is a challenge for two main reasons: water 14 absorption; and the small size of the samples. The sample volume is smaller than the cube of the 15 TeraHertz wavelength; the light matter interactions are thus extremely reduced. In this paper, we 16 present the design, fabrication, characterization and the first typical uses of a biophotonic device 17 aiming at increasing light matter interaction to enable terahertz spectroscopy of minute samples on 18 a broad band (0.2–2 THz). We demonstrate time domain spectroscopy experiments on few μl 19 samples showing the validity of our approach. 20
Low-dose folic acid supplementation does not influence plasma methionine concentrations in young non-pregnant women

An elevated plasma total homocysteine (tHcy) concentration is a risk factor for cardiovascular disease and for having offspring with a neural-tube defect. Folate is a methyl donor in the remethylation of homocysteine into methionine. Although folic acid supplementation decreases tHcy concentrations, effects of folic acid supplementation on plasma methionine concentrations are unclear. There is also concern that folic acid supplementation negatively affects vitamin B12 status. We studied effects of low-dose folic acid supplementation on methionine and vitamin B12 concentrations in plasma. We also investigated whether baseline plasma methionine and tHcy concentrations correlated with the baseline folate and vitamin B12 status. For a period of 4 weeks, 144 young women received either 500 μg folic acid each day, or 500 μg folic acid and placebo tablets on alternate days, or a placebo tablet each day. Plasma methionine, tHcy and plasma vitamin B12 concentrations were measured at start and end of the intervention period. Folic acid supplementation had no effect on plasma methionine or plasma vitamin B12 concentrations although it significantly decreased tHcy concentrations. Plasma methionine concentrations showed no correlation with either tHcy concentrations (Spearman rs - 0·01, P = 0·89), or any of the blood vitamin variables at baseline. Baseline tHcy concentrations showed a slight inverse correlation with baseline concentrations of plasma vitamin B12 (rs - 0·25, P < 0·001), plasma folate (rs - 0·24, P < 0·01) and erythrocyte folate (rs - 0·19, P < 0·05). In conclusion, low-dose folic acid supplementation did not influence plasma methionine or plasma vitamin B12 concentrations. Furthermore, no correlation between plasma methionine concentrations and the blood folate and vitamin B12 status was shown.
Clinical Impact of the Ankle-Brachial Index in Patients Undergoing Successful Percutaneous Coronary Intervention.

BACKGROUND Several studies have reported a relationship between clinical outcomes and the ankle-brachial index (ABI) in different populations. However, the relationship in Japanese patients or in patients undergoing percutaneous coronary intervention (PCI) has not been examined well.Methods and Results:The subjects were 1,857 patients who underwent PCI from July 2007 to May 2010 and in whom the carotid and renal arteries and abdominal aorta were examined simultaneously by ultrasonography and ABI. We investigated the relationship between ABI and major adverse cardiovascular events (MACE: all-cause death, myocardial infarction, and stroke). The median follow-up was 1,322 days (interquartile range: 1,092-1,566 days). Patients with low (<0.9), borderline (0.9-1.0) and high ABI (>1.4) had significantly higher incidence of MACE at 4 years (31%, 15%, 10%, and 29% for the low, borderline, normal, and high groups, respectively; log-rank P<0.0001) and all-cause mortality at 4 years (22%, 12%, 6.9%, and 29%, respectively; P<0.0001) compared with the normal ABI group (1.0≤ABI≤1.4). The adjusted hazard ratios for MACE were 2.35 (1.72-3.20), 1.27 (0.89-1.80) and 1.87 (0.81-3.79) for low, borderline and high ABI, respectively. CONCLUSIONS This study suggested that ABI provides additional information for cardiovascular disease risk stratification in Japanese patients undergoing PCI, even it is borderline ABI.
Benefits of Mindfulness Meditation on Emotional Intelligence, General Self-Efficacy, and Perceived Stress: Evidence from Thailand

This study investigated the benefits of mindfulness meditation practice on self-report emotional intelligence, general self-efficacy, and general perceived stress. The survey data was collected from 317 respondents in Thailand. The results analyzed using the partial least squares regression indicated that mindfulness meditation practice tended to associate positively with emotional intelligence. Practicing mindfulness meditation also negatively relates to general perceived stress directly and indirectly through emotional intelligence. However, the positive association between the meditation and general self-efficacy was only found to be mediated by emotional intelligence.
Increasing antigen presentation on HSV-1-infected cells increases lesion size but does not alter neural infection or latency

CD8+ T cells have a role in the control of acute herpes simplex virus (HSV) infection and may also be important in the maintenance of latency. In this study we have explored the consequences of boosting the efficacy of CD8+ T cells against HSV by increasing the amount of an MHC I-presented epitope on the surface of infected cells. To do this we used HSVs engineered to express an extra copy of the immunodominant CD8+ T cell epitope in C57Bl/6 mice, namely gB498 (SSIEFARL). Despite greater presentation of gB498 on infected cells, CD8+ T cell responses to these viruses in mice were similar to those elicited by a control virus. Further, the expression of extra gB498 did not significantly alter the extent or stability of latency in our mouse model, and virus loads in skin and sensory ganglia of infected mice were not affected. Surprisingly, mice infected with these viruses developed significantly larger skin lesions than those infected with control viruses and notably, this phenotype was dependent on MHC haplotype. Therefore increasing the visibility of HSV-infected cells to CD8+ T cell attack did not impact neural infection or latency, but rather enhanced pathology in the skin.
Integrity of Glycosylation Processing of a Glycan-Depleted Trimeric HIV-1 Immunogen Targeting Key B-Cell Lineages.

Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans, while mature bNAbs can evolve to accommodate or bypass these shielding glycans. The design of germline-targeting Env immunogens therefore includes the targeted deletion of specific glycan sites. However, the processing of glycans on Env trimers can be influenced by the density with which they are packed together, a highly relevant point given the essential contributions under-processed glycans make to multiple bNAb epitopes. We sought to determine the impact of the removal of 15 potential N-glycan sites (5 per protomer) from the germline-targeting soluble trimer, BG505 SOSIP.v4. 1-GT1, using quantitative, site-specific N-glycan mass spectrometry analysis. We find that, compared with SOSIP.664, there was little overall change in the glycan profile but only subtle increases in the extent of processing at sites immediately adjacent to where glycans had been deleted. We conclude that multiple glycans can be deleted from BG505 SOSIP trimers without perturbing the overall integrity of the glycan shield.
Ionic modulation of calcium dynamics in simulated human heart failure

Calcium mishandling observed in failing hearts is responsible for contractile dysfunction and arrhythmias. Thereby, calcium dynamics becomes an important target to explore for the restoration of the altered excitation-contraction coupling. In this study, we performed an in-silico sensitivity analysis to understand the mechanisms modulating calcium dynamics in failing human hearts. Using a modified version of the O'Hara et al. human ventricular action potential model, we simulated different failing conditions for every ionic parameter remodeled in heart failure. Calcium biomarkers from simulated endocardial cells, such as systolic and diastolic calcium concentration, were measured and analyzed. The results of this study highlight the importance of maintaining SERCA activity in its normal levels to improve contractility and point to other crucial parameters that also alter calcium handling, such as NCX.
Sketching Folds

We present the first sketch-based modeling method for developable surfaces with pre-designed folds, such as garments or leather products. The main challenge we address for building folded surfaces from sketches is that silhouette strokes on the sketch correspond to discontinuous sets of non-planar curves on the 3D model. We introduce a new zippering algorithm for progressively identifying silhouette edges on the model and tying them to silhouette strokes. Our solution ensures that the strokes are fully covered and optimally sampled by the model. This new method, interleaved with developability optimization steps, is implemented in a multiview sketching system where the user can sketch the contours of internal folds in addition to the usual silhouettes, borders, and seam lines. All strokes are interpreted as hard constraints, while developability is only optimized. The developability error map we provide then enables users to add local seams or darts where needed and progressively improve their design. This makes our method robust, even to coarse input for which no fully developable solution exists.
Stability analysis of singularly perturbed switched and impulsive linear systems

This paper proposes a new methodology for stability analysis of singularly perturbed linear systems whose dynamics is affected by switches and state jumps. The overall problem is formulated in the framework of hybrid singularly perturbed systems and we use Lyapunov-based techniques to investigate its stability. We emphasize that, beside the stability of slow and fast dynamics, we need a dwell-time condition to guarantee the overall singularly perturbed system is globally asymptotically stable. Furthermore, we characterize this dwell-time as the sum of one term related to the stabilization of systems evolving on one time-scale (slow dynamics) and one term of the order of the parameter defining the ratio between the time-scales. As highlighted in the paper the second term is required to compensate the effect of the jumps introduced in the state of the boundary layer system by the switches and impulses affecting the overall dynamics. Some numerical examples illustrates our results.