Miracle-dz/UniFAR-FTUs huggingface dataset:
Postischemic inflammation: a role for mast cells in intestine but not in skeletal muscle.

The objective of this study was to directly study a role for mast cells in ischemia-reperfusion (I/R)-induced mucosal and microvascular dysfunction. I/R was induced in the intestine and skeletal muscle (gastrocnemius and cremaster muscle) of wild-type mice and mast cell-deficient mice ( W/ Wv ). Changes in mucosal permeability (blood-to-lumen clearance of51Cr-EDTA), leukocyte infiltration (myeloperoxidase activity in the intestine and intravital microscopy in the cremaster muscle), and vascular permeability (tissue wet-to-dry weight ratio and FITC-albumin leakage) were measured as indexes of tissue dysfunction. In wild-type animals, intestinal I/R induced a significant increase in mucosal permeability, leukocyte infiltration, and vascular permeability. Mast cell-deficient animals were completely protected from I/R-induced mucosal dysfunction. However, skeletal muscle I/R induced a significant increase in leukocyte infiltration, FITC-albumin leakage, and edema formation to the same degree in both wild-type and mast cell-deficient animals. These data suggest that mast cells may be important mediators of I/R-induced mucosal and microvascular dysfunction in the intestine but not of microvascular dysfunction in skeletal muscle.
Visual Mismatch and Predictive Coding: A Computational Single-Trial ERP Study

Predictive coding (PC) posits that the brain uses a generative model to infer the environmental causes of its sensory data and uses precision-weighted prediction errors (pwPEs) to continuously update this model. While supported by much circumstantial evidence, experimental tests grounded in formal trial-by-trial predictions are rare. One partial exception is event-related potential (ERP) studies of the auditory mismatch negativity (MMN), where computational models have found signatures of pwPEs and related model-updating processes. Here, we tested this hypothesis in the visual domain, examining possible links between visual mismatch responses and pwPEs. We used a novel visual “roving standard” paradigm to elicit mismatch responses in humans (of both sexes) by unexpected changes in either color or emotional expression of faces. Using a hierarchical Bayesian model, we simulated pwPE trajectories of a Bayes-optimal observer and used these to conduct a comprehensive trial-by-trial analysis across the time × sensor space. We found significant modulation of brain activity by both color and emotion pwPEs. The scalp distribution and timing of these single-trial pwPE responses were in agreement with visual mismatch responses obtained by traditional averaging and subtraction (deviant-minus-standard) approaches. Finally, we compared the Bayesian model to a more classical change model of MMN. Model comparison revealed that trial-wise pwPEs explained the observed mismatch responses better than categorical change detection. Our results suggest that visual mismatch responses reflect trial-wise pwPEs, as postulated by PC. These findings go beyond classical ERP analyses of visual mismatch and illustrate the utility of computational analyses for studying automatic perceptual processes. SIGNIFICANCE STATEMENT Human perception is thought to rely on a predictive model of the environment that is updated via precision-weighted prediction errors (pwPEs) when events violate expectations. This “predictive coding” view is supported by studies of the auditory mismatch negativity brain potential. However, it is less well known whether visual perception of mismatch relies on similar processes. Here we combined computational modeling and electroencephalography to test whether visual mismatch responses reflected trial-by-trial pwPEs. Applying a Bayesian model to series of face stimuli that violated expectations about color or emotional expression, we found significant modulation of brain activity by both color and emotion pwPEs. A categorical change detection model performed less convincingly. Our findings support the predictive coding interpretation of visual mismatch responses.
In vivo diffusion of immunoglobulin G in muscle: effects of binding, solute exclusion, and lymphatic removal.

Previously, we demonstrated that immunoglobulin G (IgG), dissolved in an isotonic solution in the peritoneal cavity, transported rapidly into the abdominal wall when the intraperitoneal (ip) pressure was >2 cmH2O. We hypothesized that this was chiefly caused by convection and that diffusion of IgG was negligible. To investigate the role of diffusion, we dialyzed rats with no pressure gradient across the abdominal wall muscle for 2 or 6 h with an ip isotonic solution containing125I-labeled IgG. At the end of the experiment, the animal was euthanized and frozen and abdominal wall tissue was processed to produce cross-sectional autoradiograms. Quantitative densitometric analysis resulted in IgG concentration profiles with far lower magnitude than profiles from experiments in which convection dominated. In other in vivo experiments, we determined the lymph flow rate to be 0.8 × 10-4ml ⋅ min-1 ⋅ g-1and the fraction of extravascular tissue (θs) available to the IgG to be 0.041 ± 0.001. An in vitro binding assay was used to determine the time-dependent, nonsaturable binding constant: 0.0065 min-1 × duration of exposure. A non-steady-state diffusion model that included effects of θs, time-dependent binding, and lymph flow was fitted to the diffusion profile data, and the IgG diffusivity within the tissue void was estimated to be 2 × 10-7cm2/s, a value much higher than that published by other groups. We also demonstrate from our previous data that convection of IgG through tissue dominates over diffusion at ip pressures >2 cmH2O, but diffusion may not be negligible. Furthermore, nonsaturable binding must be accounted for in the interpretation of tissue protein concentration profiles.
Fetal cardiovascular and breathing responses to an adenosine A2a receptor agonist in sheep.

CGS-21680 (CGS), a highly selective adenosine A2a receptor agonist, may excite the fetal carotid bodies. This study was designed to determine 1) whether CGS stimulates fetal breathing and 2) whether sinoaortic denervation abolishes CGS-induced tachycardia. In eight intact fetuses (>0.8 term), intra-arterial CGS infusion (6 μg ⋅ min-1 ⋅ kg estimated fetal wt-1) increased mean arterial [Formula: see text] by 3-7 Torr, reduced fetal arterial[Formula: see text] by 2-5 Torr, and produced a mild metabolic acidemia. Heart rate increased from 154 ± 7 (control) to 249 ± 12 beats/min, but mean arterial pressure was not significantly affected. CGS initially increased the frequency, amplitude, and incidence of fetal breathing, but this hyperpnea was followed by prolonged respiratory depression that was not reversed with blockade of adenosine A1 receptors. Denervation of both carotid bodies together with interruption of the vagi abolished the hyperpnea without altering the respiratory depression or the maximum rise in heart rate. We conclude that CGS induces 1) tachycardia by a mechanism independent of the peripheral arterial chemoreceptors, 2) hyperpnea by stimulating peripheral adenosine A2areceptors, and 3) respiratory depression by activating central A2a receptors.
Differential effects of amitriptyline on perception of somatic and visceral stimulation in healthy humans.

Tricyclic antidepressants treat chronic pain both in patients with somatic illness and with functional bowel disorders. We compared the effects of amitriptyline on perception of cutaneous and gastrointestinal stimulation to assess differential analgesic effects of tricyclics on somatic and visceral pain. Cutaneous electrical stimulation and rectal and esophageal distension were performed before and after 21 days of double-blind 50 mg amitriptyline vs. placebo in healthy volunteers. Amitriptyline increased currents that elicited cutaneous threshold, moderate discomfort, and moderate pain compared with basal ( P < 0.05), whereas placebo had no effect. Amitriptyline had no effect on perception of rectal and esophageal distension and did not alter luminal compliance; thus the lack of effect on perception is not due to altered visceral elastic wall properties. In conclusion, amitriptyline reduces perception of cutaneous stimulation but does not alter visceral perception or compliance. This investigation demonstrates differential effects of tricyclics on somatic and visceral afferent function in healthy humans and provides insight into mechanisms of action in chronic pain both from somatic disease and from functional bowel disorders.
Robust fetal ECG extraction and detection from abdominal leads

The fetal ECG derived from abdominal leads provides an alternative to standard means of fetal monitoring. Furthermore, it permits long-term and ambulant recordings, which expands the range diagnostic possibilities for evaluating the fetal health state. However, due to the temporal and spectral overlap of maternal and fetal signals, the usage of abdominal leads imposes the need for elaborated signal processing routines. In this work a modular combination of processing techniques is presented. Its core consists of two maternal ECG estimation techniques, namely the extended Kalman smoother (EKS) and template adaption (TA) in combination with an innovative detection algorithm. Our detection method employs principles of evolutionary computing to detect fetal peaks by considering the periodicity and morphological characteristics of the fetal signal. In a postprocessing phase, single channel detections are combined by means of kernel density estimation and heart rate correction. The described methodology was presented during the Computing in Cardiology Challenge 2013. The entry was the winner of the closed-source events with average scores for events 4/5 with 15.1/3.32 (TA) and 69.5/4.58 (EKS) on training set-A and 20.4/4.57 (TA) and 219/7.69 (EKS) on test set-B, respectively. Using our own clinical data (24 subjects each 20 min recordings) and statistical measures beyond the Challenge’s scoring system, we further validated the proposed method. For our clinical data we obtained an average detection rate of 82.8% (TA) and 83.4% (EKS). The achieved results show that the proposed methods are able produce reliable fetal heart rate estimates from a restricted number of abdominal leads.
Effect of Disposition on Feedlot Gain and Quality Grade

A total of 13,315 beef calves fed at eight Iowa feedyards were used to evaluate the effect of disposition during the feedlot period on feedlot gain and carcass quality. The calves, representing 12 states, were consigned to the Iowa Tri-County Steer Carcass Futurity and were weighed upon arrival, after 35 days, at reimplant, and prior to harvest. A disposition score (Beef Improvement Federation Six Point Scoring System – 1 = very docile and 6 = very aggressive) was assigned at on test weighing, re-implant time, and pre-harvest, and these disposition scores were averaged to calculate a mean disposition score. The mean disposition score was used to classify calves into three groups for analysis – 1 and 2 = docile (n=9,642), 3 and 4 = restless (n=2,915), and 5 and 6 = aggressive (n=758). A common diet and health program was utilized at each feedlot. Calves were sorted and harvested when they were visually evaluated to have 0.4 inches of fat cover. Arrival weight (lb) and ADG (lb/day) were 630.5 and 3.17; 626.4 and 3.11; and 610.8 and 2.91 for docile, restless, and aggressive calves, respectively. Morbidity rate was significantly (P=.0009) affected by disposition class 19.23, 16.82 and 16.18% for docile, restless and aggressive calves, respectively. However, disposition score did not affect mortality rate (P=.1985). The percent prime, choice, select, and standard carcasses for docile, restless, and aggressive calves were 1.69, 72.45, 23.29, and 2.55; 1.17, 67.91, 27.49, and 3.43; and 0.13, 58.12, 36.20, and 5.55, respectively. Disposition score influenced the percentages of carcasses in each quality grade (P<.001). Acceptance rates for black-hided Angus-type calves eligible for the Certified Angus Beef ® Program (CAB) were 29.07, 22.83, and 14.31 (P<.0001) for docile, restless, and aggressive calves, respectively. When considering the effect of disposition on quality and yield grade, feedlot gain, death loss, and treatment costs, docile calves returned $62.19/head more than aggressive calves. Calves with poor disposition were lighter upon arrival at the feedlot, gained less, had reduced quality grade, and reduced CAB acceptance rates compared with docile calves.
Heterogeneity of the proliferative capacity of rat cholangiocytes after bile duct ligation.

We previously introduced the concept that intrahepatic bile duct epithelial cells, or cholangiocytes, are functionally heterogeneous. This concept is based on the observation that secretin receptor (SR) gene expression and secretin-induced cAMP synthesis are present in cholangiocytes derived from large (>15 μm in diameter) but not small (<15 μm in diameter) bile ducts. In work reported here, we tested the hypothesis that cholangiocytes are heterogeneous with regard to proliferative capacity. We assessed cholangiocyte proliferation in vivo by measurement of [3H]thymidine incorporation and in vitro by both [3H]thymidine incorporation and H3 histone gene expression in small ( fraction 1) and large ( fraction 2) cholangiocytes isolated from rats after bile duct ligation (BDL). In the two cholangiocyte subpopulations, we also studied basal somatostatin receptor (SSTR2) gene expression as well as the effects of somatostatin on 1) SR gene expression and secretin-induced cAMP synthesis and 2) [3H]thymidine incorporation and H3 histone gene expression. In normal rat liver, cholangiocytes, unlike hepatocytes, were mitotically dormant; after BDL, incorporation of [3H]thymidine markedly increased in cholangiocytes but not hepatocytes. When subpopulations of cholangiocytes were isolated after BDL, DNA synthesis assessed by both techniques was limited to large cholangiocytes, as was SSTR2 steady-state gene expression. In vitro, somatostatin inhibited SR gene expression and secretin-induced cAMP synthesis only in large cholangiocytes. Moreover, compared with no hormone, somatostatin inhibited DNA synthesis solely in large cholangiocytes. These results support the concept of the heterogeneity of cholangiocytes along the biliary tree, extend this concept to cholangiocyte proliferative activity, and imply that the proliferative compartment of cholangiocytes after BDL is located principally in the cholangiocytes lining large (>15 μm) bile ducts.
Open Set Logo Detection and Retrieval

Current logo retrieval research focuses on closed set scenarios. We argue that the logo domain is too large for this strategy and requires an open set approach. To foster research in this direction, a large-scale logo dataset, called Logos in the Wild, is collected and released to the public. A typical open set logo retrieval application is, for example, assessing the effectiveness of advertisement in sports event broadcasts. Given a query sample in shape of a logo image, the task is to find all further occurrences of this logo in a set of images or videos. Currently, common logo retrieval approaches are unsuitable for this task because of their closed world assumption. Thus, an open set logo retrieval method is proposed in this work which allows searching for previously unseen logos by a single query sample. A two stage concept with separate logo detection and comparison is proposed where both modules are based on task specific CNNs. If trained with the Logos in the Wild data, significant performance improvements are observed, especially compared with state-of-the-art closed set approaches.
Meta-analysis of programmed cell death 1 polymorphisms with systemic lupus erythematosus risk

The association of polymorphisms in programmed cell death 1 (PDCD1) gene with systemic lupus erythematosus (SLE) risk is inconsistent across different studies. This meta-analysis is aimed to provide reliable evidence to the association of five common PDCD1 polymorphisms (PD1.1, PD1.2, PD1.3, PD1.5 and PD1.6) with SLE risk. A total of 28 studies with 4,344 SLE cases and 5,474 healthy controls were included in this meta-analysis. PD1.3 polymorphism was significantly associated with SLE in the overall population (A vs. G: OR = 1.35, 95% CI = 1.12-1.63; GA vs.GG: OR = 1.41, 95% CI = 1.12-1.76; AA+GA vs. GG: OR = 1.41, 95% CI = 1.13-1.7). In the stratified analyses based on ethnicity, we found a significant association in Caucasians and in Mexicans. In the subgroup analyses by gender, a significant association was found between PD1.3 polymorphism and SLE risk in males. The results also suggested an association between the PD1.6 polymorphism and decreased SLE risk (A vs. G: OR = 0.84, 95% CI = 0.73-0.96). Our meta-analysis revealed that PD1.3 polymorphism may increase the susceptibility to SLE, particularly in Caucasians, while PD1.6 may be a protective factor to SLE.
Stem Cell Properties of Normal Human Keratinocytes Determine Transformation Responses to Human Papillomavirus 16 DNA

ABSTRACT Human papillomavirus (HPV) infection of the genital tract is common; however, only about 10 to 15% of infections persist, and approximately 10 to 15% of these persistent infections result in cancer. Basal epidermal stem cells are the presumed target cells for HPV infection, providing a reservoir of latently infected cells that persist over time and initiate lesions. However, it is not known whether stem cell density has any influence on transformation of human keratinocytes by HPV. We explored the relationship between stem cell properties of normal human keratinocytes and their susceptibility to transformation by HPV16 DNA. Normal human keratinocyte isolates (NHKc) derived from different donors were cultured in three-dimensional anchorage-free suspension to assess their spheroid-forming ability. NHKc spheroids were then plated back into plastic monolayer culture and transfected with full-length HPV16 DNA, which we have previously shown to integrate into the host cell genome upon transfection. Spheroid-derived NHKc (SD-NHKc) and fluorescence-activated cell sorting-purified populations of basal stem-like keratinocytes, expressing low levels of epidermal growth factor receptor and high levels of integrin alpha 6 (EGFRlo/ITGα6hi), responded to transfection with HPV16 DNA with more vigorous proliferation, greater immortalization efficiency, and faster progression to differentiation resistance than autologous mass-cultured cells. Conversely, cells committed to terminal differentiation (EGFRhi/ITGα6lo) grew slowly after transfection with HPV16 and failed to generate immortalized or DR clones. HPV16 DNA induced stem cell properties in mass-cultured NHKc. We conclude that HPV16 preferentially immortalizes basal keratinocytes with stem cell properties and that these cells readily achieve a differentiation-resistant phenotype upon immortalization by HPV16. IMPORTANCE This paper explores the relationship between the stem cell properties of normal human epidermal cells in culture and these cells' susceptibility to transformation by HPV16 DNA, the HPV type present in about 50% of cervical cancers. We report variable susceptibilities to HPV16-mediated transformation among different keratinocyte isolates derived from neonatal foreskin. Our findings provide strong experimental evidence that HPV16 preferentially transforms basal keratinocytes with stem cell properties. Insights gained from these studies increase our understanding of the host cell-specific factors influencing individual susceptibility to HPV-driven transformation and the contributing factors leading to preneoplastic and neoplastic progression of HPV-positive lesions.
Using Positive or Negative Reinforcement in Neurofeedback Games for Training Self-Regulation

Neurofeedback training can reduce symptoms related to epileptic seizures, attention deficits, and Asperger's Syndrome, and often uses games to motivate participation over the long term needed to see improvements. Most neurofeedback games use negative reinforcement to guide players -- i.e., a barrier to progressing in the game is removed when players achieve a desirable state -- which is considered to be less effective than reinforcing behaviour through positive feedback when players do well. We investigate whether using positive reinforcement is more successful than negative reinforcement through the design and evaluation of the experience and efficacy of a custom neurofeedback training game. We showed that positive reinforcement was more effective in encouraging players to keep their brain activity regulated. Furthermore it generated more positive affect and motivated more investment of effort in players, suggesting that positive reinforcement in neurofeedback games may provide a better and more effective neurofeedback training experience.
Mechanical and Thermal Properties of Dental Composites Cured with CAD/CAM Assisted Solid-State Laser

Over the last three decades, it has been frequently reported that the properties of dental restorative composites cured with argon laser are similar or superior to those achieved with conventional halogen and light emitting diode (LED) curing units. Whereas laser curing is not dependent on the distance between the curing unit and the material, such distance represents a drawback for conventional curing units. However, a widespread clinical application of this kind of laser remains difficult due to cost, heavy weight, and bulky size. Recently, with regard to the radiation in the blue region of the spectrum, powerful solid-state lasers have been commercialized. In the current research, CAD (computer-aided design)/CAM (computer-aided manufacturing) assisted solid-state lasers were employed for curing of different dental restorative composites consisting of micro- and nanoparticle-reinforced materials based on acrylic resins. Commercial LED curing units were used as a control. Temperature rise during the photopolymerisation process and bending properties were measured. By providing similar light energy dose, no significant difference in temperature rise was observed when the two light sources provided similar intensity. In addition, after 7 days since curing, bending properties of composites cured with laser and LED were similar. The results suggested that this kind of laser would be suitable for curing dental composites, and the curing process does not suffer from the tip-to-tooth distance.
Perception and measurement of food texture: Solid foods.

There is still a gap between instrumental measurement and sensory evaluation because of the complexity of food texture in spite of many efforts. In sensory evaluation, the terms describing the texture should be well understood by panelists, which poses a problem of establishing lexicons and training panelists. In the instrumental measurement, more efforts are required to understand the large deformation and fracture behavior of foods. The texture profile analysis (TPA) proposed by Alina Szczesniak, Malcolm Bourne, and Sherman has been applied to many foods, and was useful to develop the understanding of textures. But sometimes confusion of the interpretation of TPA parameters appeared. Many new techniques have been introduced to quantify TPA parameters. Recent efforts to fill the gap between sensory evaluation and instrumental measurements, human measurements, or physiological measurements have been introduced. This endeavor is an effort of synthesizing the dentistry and biomedical approach, sensory and psychological approach, and material science approach, and therefore, the collaboration among these disciplines is necessary. This manuscript mainly discusses texture studies for solid foods. PRACTICAL APPLICATIONS To fill the gap between the sensory evaluation and the instrumental measurement of texture, it is necessary to examine the physical change of foods during the oral processing. This will give us the designing principle of palatable and safe foods.