Miracle-dz/UniFAR-FTUs huggingface dataset:
A critical evaluation of mass isotopomer distribution analysis of gluconeogenesis in vivo.

There are conflicting reports concerning the reliability of mass isotopomer distribution analysis (MIDA) for estimating the contribution of gluconeogenesis to total glucose production (f) during [13C]glycerol infusion. 1 We have evaluated substrate-induced effects on rate of appearance (Ra) of glycerol and glucose and f during [2-13C]glycerol infusion in vivo. Five groups of mice were fasted for 30 h and then infused with [2-13C]glycerol at variable rates and variable 13C enrichments ( group I: 20 μmol ⋅ kg-1 ⋅ min-1, 99% 13C; group II: 60 μmol ⋅ kg-1 ⋅ min-1, 60% 13C; group III: 60 μmol ⋅ kg-1 ⋅ min-1, 99% 13C; group IV: 120 μmol ⋅ kg-1 ⋅ min-1, 40% 13C; or group V: 120 μmol ⋅ kg-1 ⋅ min-1, 99% 13C). The total glycerol Ra increased from ∼104 to ∼157 and to ∼210 μmol ⋅ kg-1 ⋅ min-1as the infusion of [2-13C]glycerol increased from 20 to 60 and to 120 μmol ⋅ kg- 1 ⋅ min-1, respectively. As the amount of 99% enriched [2-13C]glycerol increased from 20 to 60 and to 120 μmol ⋅ kg-1 ⋅ min-1( groups I, III, and V, respectively), plasma glycerol enrichment increased from ∼21 to ∼42 and to ∼57% and the calculated f increased from ∼27 to ∼56 and to ∼87%, respectively. Similar plasma glycerol enrichments were observed in groups I, II, and IV (i.e., ∼21-24%), yet f increased from ∼27 to ∼57 and to ∼86% in groups II and IV, respectively. Estimates of absolute gluconeogenesis increased from ∼14 to ∼33 and ∼86 μmol ⋅ kg-1 ⋅ min-1as the infusion of [2-13C]glycerol increased from 20 to 60 and 120 μmol ⋅ kg-1 ⋅ min-1. Plausible estimates of f were obtained only under conditions that increased total glycerol Ra∼2-fold ( P < 0.001) and increased glucose Ra ∼1.5-fold ( P < 0.01) above basal. We conclude that in 30-h fasted mice, 1) estimates of f by MIDA with low infusion rates of [2-13C]glycerol yield erroneous results and 2) reasonable estimates of f are obtained at glycerol infusion rates that perturb glycerol and glucose metabolism.
Increased centrosome number in BRCA‐related breast cancer specimens determined by immunofluorescence analysis

BRCA‐related breast carcinoma can be prevented through prophylactic surgery and an intensive follow‐up regimen. However, BRCA genetic tests cannot be routinely performed, and some BRCA mutations could not be defined as deleterious mutations or normal variants. Therefore, an easy functional assay of BRCA will be useful to evaluate BRCA status. As it has been reported that BRCA functions in the regulation of centrosome number, we focused on centrosome number in cancer tissues. Here, 70 breast cancer specimens with known BRCA status were analyzed using immunofluorescence of γ‐tubulin (a marker of centrosome) foci. The number of foci per cell was higher in cases with BRCA mutation compared to wild‐type cases, that is, 1.9 (95% confidence interval [CI], 1.5‐2.3) vs 0.5 (95% CI, 0.2‐0.8) (P < .001). Specifically, foci numbers per cell in BRCA1 and BRCA2 mutation cases were 1.2 (95% CI, 0.6‐1.8) and 2.2 (95% CI, 1.7‐2.6), respectively, both higher than those in wild‐type cases (P = .042 and P < .0001, respectively). The predictive value of γ‐tubulin foci as determined by area under the curve (AUC = 0.86) for BRCA status was superior to BRCAPRO (AUC = 0.69), Myriad Table (AUC = 0.61), and KOHBRA BRCA risk calculator (AUC = 0.65) pretest values. The use of γ‐tubulin foci to predict BRCA status had sensitivity = 83% (19/23), specificity = 89% (42/47), and positive predictive value = 77% (20/26). Thus, γ‐tubulin immunofluorescence, a functional assessment of BRCA, can be used as a new prospective test of BRCA status.
Metabolic acidosis regulates rat renal Na-Si cotransport activity.

Recently, we cloned a cDNA (NaSi-1) localized to rat renal proximal tubules and encoding the brush-border membrane (BBM) Na gradient-dependent inorganic sulfate (Si) transport protein (Na-Si cotransporter). The purpose of the present study was to determine the effect of metabolic acidosis (MA) on Na-Si cotransport activity and NaSi-1 protein and mRNA expression. In rats with MA for 24 h (but not 6 or 12 h), there was a significant increase in the fractional excretion of Si, which was associated with a 2.4-fold decrease in BBM Na-Sicotransport activity. The decrease in Na-Si cotransport correlated with a 2.8-fold decrease in BBM NaSi-1 protein abundance and a 2.2-fold decrease in cortical NaSi-1 mRNA abundance. The inhibitory effect of MA on BBM Na-Si cotransport was also sustained in rats with chronic (10 days) MA. In addition, in Xenopus laevis oocytes injected with mRNA from kidney cortex, there was a significant reduction in the induced Na-Si cotransport in rats with MA compared with control rats, suggesting that MA causes a decrease in the abundance of functional mRNA encoding the NaSi-1 cotransporter. These findings indicate that MA reduces Si reabsorption by causing decreases in BBM Na-Si cotransport activity and that decreases in the expression of NaSi-1 protein and mRNA abundance, at least in part, play an important role in the inhibition of Na-Si cotransport activity during MA.
Biofunctionalized Scaffold in Bone Tissue Repair

Bone tissue engineering is based on bone grafting to repair bone defects. Bone graft substitutes can contribute to the addition of mesenchymal stem cells (MSCs) in order to enhance the rate and the quality of defect regeneration. The stem cell secretome contains many growth factors and chemokines, which could affect cellular characteristics and behavior. Conditioned medium (CM) could be used in tissue regeneration avoiding several problems linked to the direct use of MSCs. In this study, we investigated the effect of human periodontal ligament stem cells (hPDLSCs) and their CM on bone regeneration using a commercially available membrane scaffold Evolution (EVO) implanted in rat calvarias. EVO alone or EVO + hPDLSCs with or without CM were implanted in Wistar male rats subjected to calvarial defects. The in vivo results revealed that EVO membrane enriched with hPDLSCs and CM showed a better osteogenic ability to repair the calvarial defect. These results were confirmed by acquired micro-computed tomography (CT) images and the increased osteopontin levels. Moreover, RT-PCR in vitro revealed the upregulation of three genes (Collagen (COL)5A1, COL16A1 and transforming growth factor (TGF)β1) and the down regulation of 26 genes involved in bone regeneration. These results suggest a promising potential application of CM from hPDLSCs and scaffolds for bone defect restoration and in particular for calvarial repair in case of trauma.
Effect of Vertical Annealing on the Nitrogen Dioxide Response of Organic Thin Film Transistors

Nitrogen dioxide (NO2) sensors based on organic thin-film transistors (OTFTs) were fabricated by conventional annealing (horizontal) and vertical annealing processes of organic semiconductor (OSC) films. The NO2 responsivity of OTFTs to 15 ppm of NO2 is 1408% under conditions of vertical annealing and only 72% when conventional annealing is applied. Moreover, gas sensors obtained by vertical annealing achieve a high sensing performance of 589% already at 1 ppm of NO2, while showing a preferential response to NO2 compared with SO2, NH3, CO, and H2S. To analyze the mechanism of performance improvement of OTFT gas sensors, the morphologies of 6,13-bis(triisopropylsilylethynyl)-pentacene (TIPS-pentacene) films were characterized by atomic force microscopy (AFM) in tapping mode. The results show that, in well-aligned TIPS-pentacene films, a large number of effective grain boundaries inside the conducting channel contribute to the enhancement of NO2 gas sensing performance.
Embedding structured contour and location prior in siamesed fully convolutional networks for road detection

Road detection from the perspective of moving vehicles is a challenging issue in autonomous driving. Recently, many deep learning methods spring up for this task because they can extract high-level local features to find road regions from raw RGB data, such as Convolutional Neural Networks (CNN) and Fully Convolutional Networks (FCN). However, how to detect the boundary of road accurately is still an intractable problem. In this paper, we propose a siamesed fully convolutional network (named as “s-FCN-loc”) based on VGG-net architecture, which is able to consider RGB-channel, semantic contour and location prior simultaneously to segment road region elaborately. To be specific, the s-FCN-loc has two streams to process original RGB images and contour maps respectively. At the same time, the location prior is directly appended to the last feature map to promote the final detection performance. Experiments demonstrate that the proposed s-FCN-loc can learn more discriminative features of road boundaries and converge 30% faster than the original FCN during the training stage. Finally, the proposed approach is evaluated on KITTI road detection benchmark, and achieves a competitive result.
A meta‐analysis of the association between substance use and emerging adult development using the IDEA scale

BACKGROUND AND OBJECTIVES Much debate exists surrounding Arnett's theory of emerging adulthood in terms of its breadth and application. Researchers have attempted to capture dimensions of emerging adulthood (eg, experimentation, negativity/instability, other-focus, self-focus, and feeling in-between) through self report assessment, using variations of the Inventory of the Dimensions of Emerging Adulthood or IDEA. Results from studies investigating this relationship have been mixed. We conducted a meta-analysis on the association between substance use and the IDEA. METHOD Data were extracted to calculate correlational associations with substance use as well as typical moderators found in the literature. Twelve studies were meta-analyzed. RESULTS We found small associations (range: ρ = -.03 to .15; d = .06 to 30) between the IDEA scores and substance use. We found higher severity (dependence diagnosis) of participants yielded larger associations across all dimensions (ρ = .16), and proportion of college students to be a subscale-specific moderator (experimentation, negativity/instability, other-focus, self-focus, and feeling in-between). Alcohol use outcomes also provided larger subscale-specific associations (experimentation, negativity/instability, other-focus, self-focus). CONCLUSIONS The dimensions of emerging adulthood may be less effective in predicting substance use among non-college samples and those studies focusing on drug use. Further research should prioritize exploring variation in the transition to emerging adulthood among non-college samples and the longitudinal associations between IDEA and substance use. SCIENTIFIC SIGNIFICANCE Important contributions include the modest association between IDEA and substance use as well as specific participant characteristics that amplify or mitigate the association between IDEA and substance use. (Am J Addict 2018;27:166-176).
Differing rates of antibody acquisition to merozoite antigens in malaria: implications for immunity and surveillance

Antibodies play a key role in acquired human immunity to Plasmodium falciparum (Pf) malaria and target merozoites to reduce or prevent blood‐stage replication and the development of disease. Merozoites present a complex array of antigens to the immune system, and currently, there is only a partial understanding of the targets of protective antibodies and how responses to different antigens are acquired and boosted. We hypothesized that there would be differences in the rate of acquisition of antibodies to different antigens and how well they are boosted by infection, which impacts the acquisition of immunity. We examined responses to a range of merozoite antigens in 2 different cohorts of children and adults with different age structures and levels of malaria exposure. Overall, antibodies were associated with age, exposure, and active infection, and the repertoire of responses increased with age and active infection. However, rates of antibody acquisition varied between antigens and different regions within an antigen following exposure to malaria, supporting our hypothesis. Antigen‐specific responses could be broadly classified into early response types in which antibodies were acquired early in childhood exposure and late response types that appear to require substantially more exposure for the development of substantial levels. We identified antigen‐specific responses that were effectively boosted after recent infection, whereas other responses were not. These findings advance our understanding of the acquisition of human immunity to malaria and are relevant to the development of malaria vaccines targeting merozoite antigens and the selection of antigens for use in malaria surveillance.
Cartilage Regeneration in Full-Thickness Patellar Chondral Defects Treated with Particulated Juvenile Articular Allograft Cartilage: An MRI Analysis

Background Full-thickness cartilage lesions of the patella represent a common source of pain and dysfunction. Previously reported surgical treatment options include marrow stimulation, cell-based treatments, and osteochondral transfer. Minced juvenile allograft cartilage is a novel treatment option that allows for a single stage approach for these lesions. Hypothesis Particulated juvenile allograft cartilage (PJAC) for the treatment of chondral defects of the patella would offer acceptable lesion fill rates, mature over time, and not be associated with any negative biologic effects on the surrounding tissue. Methods A retrospective chart review of prospectively collected data was conducted to identify consecutive patients who were treated with PJAC for a full thickness symptomatic cartilage lesion. Qualitative (fast spin echo) and quantitative (T2 mapping) magnetic resonance imaging (MRI) was undertaken at the 6-, 12-, and 24-month postoperative mark. Numerous patient, lesion, and graft specific factors were assessed against MRI scores and percent defect fill of the graft. Graft maturation over time was also assessed. Results Forty-five patients total were included in the study. Average age at the time of surgery was 26.5 years (range 13-45 years), average lesion size was 208 mm2 (range 4-500 mm2), and average donor age was 49.5 months (range 3-120 months). Sixty percent of the patients were female, while 93% of all patients underwent a concomitant procedure at the time of the index operation. Six-month MRI findings revealed that no patient-, graft-, or donor-specific factors correlated with MR scores, and 82% of the knees demonstrated good to excellent fill. Twelve-month MRI findings revealed that T2 relaxation times of deep graft demonstrated negative correlation with patient age (P = 0.049) and donor age (P = 0.006), the integration zone showed a negative correlation with donor age (P = 0.026). In all, 85% of patients at 12 months displayed good to moderate fill of the graft. At 24 months, patient age demonstrated negative correlation with average T2 relaxation times of the deep and superficial graft (P = 0.005; P = 0.0029) and positive correlation with the superficial zone of the adjacent cartilage (P = 0.001). Donor age showed negative correlation with grayscale score (P = 0.004) and T2 relaxation times at deep integration zone (P = 0.018). T2 relaxation times of deep and superficial graft and integration zone improved over time (P < 0.001) and between each time point. Conclusions Particulated juvenile allograft tissue appears to be an acceptable reconstructive option for full-thickness cartilage lesions of the patella, offering satisfactory tissue defect fill at 6, 12, and 24 months after surgery. Imaging of the repaired cartilage demonstrates progressive graft maturation over time.
Quick Sepsis‐related Organ Failure Assessment, Systemic Inflammatory Response Syndrome, and Early Warning Scores for Detecting Clinical Deterioration in Infected Patients outside the Intensive Care Unit

Rationale: The 2016 definitions of sepsis included the quick Sepsis‐related Organ Failure Assessment (qSOFA) score to identify high‐risk patients outside the intensive care unit (ICU). Objectives: We sought to compare qSOFA with other commonly used early warning scores. Methods: All admitted patients who first met the criteria for suspicion of infection in the emergency department (ED) or hospital wards from November 2008 until January 2016 were included. The qSOFA, Systemic Inflammatory Response Syndrome (SIRS), Modified Early Warning Score (MEWS), and the National Early Warning Score (NEWS) were compared for predicting death and ICU transfer. Measurements and Main Results: Of the 30,677 included patients, 1,649 (5.4%) died and 7,385 (24%) experienced the composite outcome (death or ICU transfer). Sixty percent (n = 18,523) first met the suspicion criteria in the ED. Discrimination for in‐hospital mortality was highest for NEWS (area under the curve [AUC], 0.77; 95% confidence interval [CI], 0.76‐0.79), followed by MEWS (AUC, 0.73; 95% CI, 0.71‐0.74), qSOFA (AUC, 0.69; 95% CI, 0.67‐0.70), and SIRS (AUC, 0.65; 95% CI, 0.63‐0.66) (P < 0.01 for all pairwise comparisons). Using the highest non‐ICU score of patients, ≥2 SIRS had a sensitivity of 91% and specificity of 13% for the composite outcome compared with 54% and 67% for qSOFA ≥2, 59% and 70% for MEWS ≥5, and 67% and 66% for NEWS ≥8, respectively. Most patients met ≥2 SIRS criteria 17 hours before the combined outcome compared with 5 hours for ≥2 and 17 hours for ≥1 qSOFA criteria. Conclusions: Commonly used early warning scores are more accurate than the qSOFA score for predicting death and ICU transfer in non‐ICU patients. These results suggest that the qSOFA score should not replace general early warning scores when risk‐stratifying patients with suspected infection.
Shape smoothing with feature preserving weighted filters

Several techniques for arbitrary shape recovery from scanned data attempt to recognize and further regularize shape. For arbitrary shape, one can recognize several shape features which should be guided with global shape parameters. Smoothed curves and surfaces created with subdivision can visually improve recovery when overall smoothness is expected. Local features such as sharp edges are not preserved during smoothing. In this paper we show procedural approach to preserve such features while globally smoothing shape. Weighted filters are applied according to local shape variations. For flat and smooth areas, weighted mean face is dominant. Sharp features are detected with normal difference variation and dominated by nearest face normal. After suggested face normals are calculaced, vertices are moved by simplified version of nonlinear diffusion. Performance of proposed method is compared with other methods for mesh smoothing and edge creasing on "CAD" and "media" models.
Posttraumatic stress disorder symptoms and cognitive function in a large cohort of middle‐aged women

Posttraumatic stress disorder (PTSD) has been linked to cognitive decline, but research in women is generally lacking. We examined whether trauma and elevated PTSD symptoms were associated with worse cognitive function in middle‐aged civilian women. A secondary objective was to investigate the possible role of depression in the relation of PTSD symptoms to cognitive function.
Melanoma cell adhesion molecule–positive CD8 T lymphocytes mediate central nervous system inflammation

Although Tc17 lymphocytes are enriched in the central nervous system (CNS) of multiple sclerosis (MS) subjects and of experimental autoimmune encephalomyelitis (EAE) animals, limited information is available about their recruitment into the CNS and their role in neuroinflammation. Identification of adhesion molecules used by autoaggressive CD8+ T lymphocytes to enter the CNS would allow further characterization of this pathogenic subset and could provide new therapeutic targets in MS. We propose that melanoma cell adhesion molecule (MCAM) is a surface marker and adhesion molecule used by pathogenic CD8+ T lymphocytes to access the CNS.
Individual differences in pain: understanding the mosaic that makes pain personal

The experience of pain is characterized by tremendous inter-individual variability. Multiple biological and psychosocial variables contribute to these individual differences in pain, including demographic variables, genetic factors, and psychosocial processes. For example, sex, age and ethnic group differences in the prevalence of chronic pain conditions have been widely reported. Moreover, these demographic factors have been associated with responses to experimentally-induced pain. Similarly, both genetic and psychosocial factors contribute to clinical and experimental pain responses. Importantly, these different biopsychosocial influences interact with each other in complex ways to sculpt the experience of pain. Some genetic associations with pain have been found to vary across sex and ethnic group. Moreover, genetic factors also interact with psychosocial factors, including stress and pain catastrophizing, to influence pain. The individual and combined influences of these biological and psychosocial variables results in a unique mosaic of factors that contributes pain in each individual. Understanding these mosaics is critically important in order to provide optimal pain treatment, and future research to further elucidate the nature of these biopsychosocial interactions is needed in order to provide more informed and personalized pain care.
Multislot Simultaneous Spectrum Sensing and Energy Harvesting in Cognitive Radio

In cognitive radio (CR), the spectrum sensing of the primary user (PU) may consume some electrical power from the battery capacity of the secondary user (SU), resulting in a decrease in the transmission power of the SU. In this paper, a multislot simultaneous spectrum sensing and energy harvesting model is proposed, which uses the harvested radio frequency (RF) energy of the PU signal to supply the spectrum sensing. In the proposed model, the sensing duration is divided into multiple sensing slots consisting of one local-sensing subslot and one energy-harvesting subslot. If the PU is detected to be present in the local-sensing subslot, the SU will harvest RF energy of the PU signal in the energy-harvesting slot, otherwise, the SU will continue spectrum sensing. The global decision on the presence of the PU is obtained through combining local sensing results from all the sensing slots by adopting “Or-logic Rule”. A joint optimization problem of sensing time and time splitter factor is proposed to maximize the throughput of the SU under the constraints of probabilities of false alarm and detection and energy harvesting. The simulation results have shown that the proposed model can clearly improve the maximal throughput of the SU compared to the traditional sensing-throughput tradeoff model.