Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitation of Cancer Treatment Response by 18F-FDG PET/CT: Multicenter Assessment of Measurement Variability

The aim of this study was to assess the interobserver variability of quantitative 18F-FDG PET/CT parameters used in assessments of treatment response across multiple sites and readers. Methods: Paired pre- and posttreatment 18F-FDG PET/CT images of 30 oncologic patients were distributed to 22 readers across 15 U.S. and international sites. One reader was aware of the full medical history (readreference) of the patients, whereas the 21 other readers were unaware. The readers selected the single hottest tumor from each study, and made SUV measurements from this target lesion and the liver. Descriptive statistics, percentage changes in the measurements, and their agreements were obtained. Results: The intraclass correlation coefficient for the percentage change in SUVmax (%ΔSUVmax) of the hottest tumor was 0.894 (95% confidence interval [CI], 0.813–0.941), and the individual equivalence coefficient was 1.931 (95% CI, 0.568–6.449) when all reads were included (n = 638). When only the measurements that selected the same target tumor as the readreference (n = 486) were included, the intraclass correlation coefficient for the %ΔSUVmax was 0.944 (95% CI, 0.841–0.989), and the individual equivalence coefficient was −0.688 (95% CI, −1.810 to −0.092). The absolute change in SUVmean of liver corrected for lean body mass showed upper and lower limits of agreement (average bias ± 2 SDs) of 0.13 and −0.13 g/mL. Conclusion: The quantitative tumor SUV changes measured across multiple sites and readers show a high correlation. Selection of the same tumor target among readers further increased the degree of correlation.
The effects of dietary lipids on gene expression and apoptosis

The beneficial effects of dietary FO with respect to autoimmune disease, CVD and some types of cancer are well established. Studies conducted over the last 10-15 years have established the potent effects of FO on gene expression in the previously mentioned diseases. The effects of dietary FO appear to be selective in nature, with the expression of individual genes simultaneously being increased, decreased or completely unaffected. In order to elucidate the molecular mechanism(s) involved, recent studies have focused on analysing the effects of the long-chain polyunsaturated n-3 fatty acids EPA and DHA which are highly enriched in FO and thought to be the primary mediators of its biological activity. Indeed, it has been found that EPA and DHA appear to both directly and indirectly modulate gene expression in vivo, depending on the gene examined. The direct effects of EPA and DHA are most probably mediated by their ability to bind to positive and/or negative regulatory transcription factors, while the indirect effects appear to be mediated through alterations in the generation of intracellular lipid second messengers (e.g. diacylglycerol and ceramide). Future studies need to be focused on further elucidation of the inter- and intracellular signalling events mediated by dietary n-3 fatty acids. Understanding the molecular mechanism(s) modified by dietary FO will ultimately lead to improved dietary strategies to aid in the prevention of autoimmune disease, CVD and/or certain types of cancer.
The unfolded protein response mediates fibrogenesis and collagen I secretion through regulating TANGO1 in mice

Fibrogenesis encompasses the deposition of matrix proteins, such as collagen I, by hepatic stellate cells (HSCs) that culminates in cirrhosis. Fibrogenic signals drive transcription of procollagen I, which enters the endoplasmic reticulum (ER), is trafficked through the secretory pathway, and released to generate extracellular matrix. Alternatively, disruption of procollagen I ER export could activate the unfolded protein response (UPR) and drive HSC apoptosis. Using a small interfering RNA screen, we identified Transport and Golgi organization 1 (TANGO1) as a potential participant in collagen I secretion. We investigated the role of TANGO1 in procollagen I secretion in HSCs and liver fibrogenesis. Depletion of TANGO1 in HSCs blocked collagen I secretion without affecting other matrix proteins. Disruption of secretion led to procollagen I retention within the ER, induction of the UPR, and HSC apoptosis. In wild‐type (WT) HSCs, both TANGO1 and the UPR were induced by transforming growth factor β (TGFβ). As the UPR up‐regulates proteins involved in secretion, we studied whether TANGO1 was a target of the UPR. We found that UPR signaling is responsible for up‐regulating TANGO1 in response to TGFβ, and this mechanism is mediated by the transcription factor X‐box binding protein 1 (XBP1). In vivo, murine and human cirrhotic tissue displayed increased TANGO1 messenger RNA levels. Finally, TANGO1+/– mice displayed less hepatic fibrosis compared to WT mice in two separate murine models: CCl4 and bile duct ligation. Conclusion: Loss of TANGO1 leads to procollagen I retention in the ER, which promotes UPR‐mediated HSC apoptosis. TANGO1 regulation during HSC activation occurs through a UPR‐dependent mechanism that requires the transcription factor, XBP1. Finally, TANGO1 is critical for fibrogenesis through mediating HSC homeostasis. The work reveals a unique role for TANGO1 and the UPR in facilitating collagen I secretion and fibrogenesis. (Hepatology 2017;65:983‐998).
Biological sensitivity to context moderates the effects of the early teacher–child relationship on the development of mental health by adolescence

Abstract The moderating effects of biological sensitivity to context (physiological and behavioral stress reactivity) on the association between the early teacher–child relationship and the development of adolescent mental health problems were examined in a community sample of 96 children. Grade 1 measures of biological sensitivity to context included physiological (i.e., slope of mean arterial pressure across a 20- to 30-min stress protocol) and behavioral (i.e., temperamental inhibition/disinhibition) markers. Grade 1 measures of the teacher–child relationship included positive (i.e., closeness) and negative (i.e., conflict) qualities. Mental health symptoms were assessed at Grades 1 and 7. Results of a multiple regression analysis indicated substantial association of the teacher–child relationship with the development of adolescent mental health symptoms, especially for more reactive children. In addition to teacher–child relationship main effects, all four Reactivity × Teacher–Child Relationship interaction terms were statistically significant when controlling for Grade 1 symptom severity, suggesting that both physiological and behavioral reactivity moderate the association of both adverse and supportive aspects of the teacher–child relationship with Grade 7 symptom severity over and above Grade 1 severity. There were important differences, depending on which stress reactivity measure was considered. The importance of these findings for recent theoretical arguments regarding biological sensitivity to context and differential susceptibility is discussed.
The Relationship of Intellectual Functioning and Cognitive Performance to Brain Structure in Schizophrenia

Background Schizophrenia (SZ) is often characterized by cognitive and intellectual impairment. However, there is much heterogeneity across individuals, suggesting different trajectories of the illness. Recent findings have shown brain volume differences across subgroups of individuals with psychosis (SZ and bipolar disorder), such that those with intellectual and cognitive impairments presented evidence of early cerebral disruption, while those with cognitive but not intellectual impairments showed evidence of progressive brain abnormalities. Our aim was to investigate the relations of cognition and intellectual functioning with brain structure abnormalities in a sample of SZ compared to unaffected individuals. Methods 92 individuals with SZ and 94 healthy controls part of the Northwestern University Schizophrenia Data and Software Tool (NUSDAST) underwent neuropsychological assessment and structural magnetic resonance imaging (MRI). Individuals with SZ were divided into subgroups according their estimated premorbid crystallized intellectual (ePMC-IQ) and cognitive performance. Brain volumes differences were investigated across groups. Results SZ with ePMC-IQ and cognitive impairments had reduced total brain volume (TBV), intracranial volume (ICV), TBV corrected for ICV, and cortical gray matter volume, as well as reduced cortical thickness, and insula volumes. SZ with cognitive impairment but intact ePMC-IQ showed only reduced cortical gray matter volume and cortical thickness. Conclusions These data provide additional evidence for heterogeneity in SZ. Impairments in cognition associated with reduced ePMC-IQ were related to evidence of broad brain structural alterations, including suggestion of early cerebral disruption. In contrast, impaired cognitive functioning in the context of more intact intellectual functioning was associated with cortical alterations that may reflect neurodegeneration.
Spectrum Efficient MIMO-FBMC System Using Filter Output Truncation

Due to the use of an appropriately designed pulse shaping prototype filter, filter bank multicarrier (FBMC) system can achieve low out of band (OoB) emissions and is also robust to the channel and synchronization errors. However, it comes at a cost of long filter tails, which may reduce the spectral efficiency significantly when the block size is small. Filter output truncation (FOT) can reduce the overhead by discarding the filter tails but may also significantly destroy the orthogonality of FBMC system, by introducing intercarrier interference (ICI) and intersymbol interference (ISI) terms in the received signal. As a result, the signal-to-interference ratio (SIR) is degraded. In addition, the presence of intrinsic interference terms in FBMC also proves to be an obstacle in combining multiple-input multiple-output (MIMO) with FBMC. In this paper, we present a theoretical analysis on the effect of FOT in an MIMO-FBMC system. First, we derive the matrix model of MIMO-FBMC system, which is subsequently used to analyze the impact of finite filter length and FOT on the system performance. The analysis reveals that FOT can avoid the overhead in the time domain but also introduces extra interference in the received symbols. To combat the interference terms, we then propose a compensation algorithm that considers odd and even overlapping factors as two separate cases, where the signals are interfered by the truncation in different ways. The general form of the compensation algorithm can compensate all the symbols in a MIMO-FBMC block and can improve the SIR values of each symbol for better detection at the receiver. It is also shown that the proposed algorithm requires no overhead and can still achieve a comparable bit error rate (BER) performance to the case with no filter truncation.
Effects of whey protein in carbohydrate-electrolyte drinks on post-exercise rehydration

Abstract The purpose of this study was to examine the effects of different amounts of whey protein in carbohydrate–electrolyte (CE) drinks on post-exercise rehydration. Ten males completed 5 trials in a randomised cross-over design. A 4-h recovery was applied after a 60-min run at 65% VO2peak in each trial. During recovery, the participants ingested a high-carbohydrate CE drink (CE-H), a low-carbohydrate CE drink (CE-L), a high-whey-protein (33 g·L−1) CE drink (CW-H), a medium-whey-protein (22 g·L−1) CE drink (CW-M) or a low-whey-protein (15 g·L−1) CE drink (CW-L) in a volume equivalent to 150% of their body mass (BM) loss. The drinks were provided in six equal boluses and consumed by the participants within 150 min in each trial. After exercise, a BM loss of 2.15% ± 0.05% was achieved. Urine production was less in the CW-M and CW-H trials during recovery, which induced a greater fluid retention in the CW-M (51.0% ± 5.7%) and CW-H (55.4% ± 3.8%) trials than in any other trial (p < .05). The plasma albumin content was higher in the CW-H trial than in the CE-H and CE-L trials at 2 h (p < .05) and 3 h (p < .01) during recovery. The aldosterone concentration was lower in the CE-H trial than in the CW-M and CW-H trials after recovery (p < .05). It is concluded that the rehydration was improved when whey protein was co-ingested with CE drinks during a 4-h recovery after a 60-min run. However, this additive effect was only observed when whey protein concentration was at least 22 g·L−1 in the current study.
MIS in the Congested Clique Model in O(log log Δ) Rounds

We give a maximal independent set (MIS) algorithm that runs in $O(\log \log \Delta)$ rounds in the congested clique model, where $\Delta$ is the maximum degree of the input graph. This improves upon the $O(\frac{\log(\Delta) \cdot \log \log \Delta}{\sqrt{\log n}} + \log \log \Delta )$ rounds algorithm of [Ghaffari, PODC '17], where $n$ is the number of vertices of the input graph. In the first stage of our algorithm, we simulate the first $O(\frac{n}{\text{poly} \log n})$ iterations of the sequential random order Greedy algorithm for MIS in the congested clique model in $O(\log \log \Delta)$ rounds. This thins out the input graph relatively quickly: After this stage, the maximum degree of the residual graph is poly-logarithmic. In the second stage, we run the MIS algorithm of [Ghaffari, PODC '17] on the residual graph, which completes in $O(\log \log \Delta)$ rounds on graphs of poly-logarithmic degree.
Learning Compact Neural Networks with Regularization

We study the impact of regularization for learning neural networks. Our goal is speeding up training, improving generalization performance, and training compact models that are cost efficient. Our results apply to weight-sharing (e.g.~convolutional), sparsity (i.e.~pruning), and low-rank constraints among others. We first introduce covering dimension of the constraint set and provide a Rademacher complexity bound providing insights on generalization properties. Then, we propose and analyze regularized gradient descent algorithms for learning shallow networks. We show that problem becomes well conditioned and local linear convergence occurs once the amount of data exceeds covering dimension (e.g.~\# of nonzero weights). Finally, we provide insights on layerwise training of deep models by studying a random activation model. Our results show how regularization can be beneficial to overcome overparametrization.
Hematinic deﬁciencies in patients with recurrent aphthous stomatitis: variations by gender and age

Background The aim of this study was to evaluate the association between hematinic deficiencies and recurrent aphthous stomatitis (RAS). Material and Methods 517 RAS patients and 187 healthy controls were enrolled in the present study. Hematinic deficiencies, including serum ferritin, folic acid, and vitamin B12 deficiencies were assessed for each participant. Gender and age were taken into account and the collected data were statistically analysed. Results Compared with the healthy controls, a significantly higher overall frequency of hematinic deficiencies was found in RAS patients (p<0.001). When gender and age were taken into account, significant differences in hematinic deficiencies were observed among RAS patients. Serum ferritin deficiency was much more common in young and middle-aged female RAS patients (age<60). Serum folate deficiency and serum vitamin B12 deficiency were both much more common in the young adult group of male RAS patients (21–40 years of age). Logistic regression analysis revealed that both gender and age have significant correlation with the presence of hematinic deficiencies in the RAS patients. Conclusions Significant variations in hematinic deficiencies were demonstrated in RAS patients across different genders and age groups. We suggest that further studies on the hematinic deficiencies of RAS patients should take into account the gender and age of participants. Key words:Recurrent aphthous stomatitis, hematinic deﬁciencies, gender, age.
The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Here, Mikhaylichenko et al. investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. The authors demonstrate that while the timing of enhancer transcription is correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers and conclude that this is likely an inherent sequence property of the elements themselves.
Copy number variation in the mouse genome: implications for the mouse as a model organism for human disease

Individuals within a species have genetic differences which ultimately result in the spectrum of phenotypic variation that we observe. Genetic variation exists at the nucleotide level in the form of single nucleotide polymorphisms (SNPs), and at a structural level as inversions, deletions and amplifications of larger stretches of nucleotides. Profiling of human and mouse genomes has identified numerous genomic segmental copy number variations (CNVs) throughout these genomes. Since inbred mice are widely used laboratory models for the study of both normal and disease biology, it is crucial that we understand the full scope of genetic variation, including CNVs, within these animals. These genetic differences can inform us about the history of a population or species, enlighten us on gene function, and guide our selection of a model system for the study of human disease.
Nutritional implications and metabolizable energy value of D-xylose and L-arabinose in chicks.

An experiment was conducted to examine the effects of graded levels (2.5, 5.0, 7.5, 10.0, and 15.0%) of dietary D-xylose or L-arabinose on chick performance. As reference, D-glucose was included in the experiment. A second experiment was performed to determine the AMEn of D-xylose and L-arabinose. Results of Experiment 1 showed a significant linear decrease (P less than .05) in weight gain and efficiency of feed utilization when the dietary level of either D-xylose or L-arabinose was increased. The same was true for daily feed intake of the D-xylose treatments. Water intake was linearly (P less than .05) increased as dietary level of both pentose sugars increased, and, as a result, dry matter content of the droppings decreased. Results of Experiment 2 showed that the AMEn value of either pentose sugar was dose related. The AMEn values for D-xylose at 5 and 10% dietary inclusion were 2,660 and 2,020 kcal/kg, respectively. Those for L-arabinose at these inclusion levels were 2,300 and 1,360 kcal/kg, respectively. Feeding equal dietary levels of either pentose sugar resulted in higher concentrations of xylose than of arabinose in blood plasma. Concentration of glucose in blood was not affected by feeding either D-xylose or L-arabinose. Cecal length and weight were markedly increased by feeding L-arabinose and intermediately by D-xylose.
A Behavioral Model of Forecasting: Naive Statistics on Mental Samples

Most operations models assume individuals make decisions based on a perfect understanding of random variables or stochastic processes. In reality, however, individuals are subject to cognitive limitations and make systematic errors. We leverage established psychology on sample naivete to model individuals’ forecasting errors and biases in a way that is portable to operations models. The model has one behavioral parameter and embeds perfect rationality as a special case. We use the model to mathematically characterize point and error forecast behavior, reflecting an individual's beliefs about the mean and variance of a random variable. We then derive 10 behavioral phenomena which are inconsistent with perfect rationality assumptions, but supported by existing empirical evidence. Finally, we apply the model to two operations settings – inventory management and queuing – to illustrate the model's portability and discuss its numerous predictions. For inventory management, we characterize order decisions assuming behavioral demand forecasting. The model predicts that even under automated cost-optimization, one should expect a pull-to-center effect. It also predicts this effect can be mitigated by separating point forecasting from error forecasting. For base stock models, it predicts safety stocks are too small (large) for short (long) lead-times. We also express the steady state behavior of a queue with balking, assuming rational joining decisions but behavioral wait-time forecasts. The model predicts that joining customers tend to be disappointed in their experienced waits. Also, for long (short) lines, it predicts customers have more (less) disperse wait-time beliefs and tend to overestimate (underestimate) the true wait-time variance.
The distribution and heterogeneity of mast cells in tongue from five different avian species

This study was conducted with the aim of determining the morphology, distribution and heterogeneity of mast cells in the tongues of seagull (Larus fuscus), common buzzard (Buteo buteo), goose (Anser anser), white stork (Ciconia ciconia) and Gerze rooster. The study used five samples of tongue material from each of the healthy adult avian species. The samples were fixed in 10% neutral‐buffered formalin (NBF) solution, then, after routine tissue follow‐up, the samples blocked with paraplast. Cross‐sections with 5–6 μm of thickness were stained with the 0.5% toluidine blue and alcian blue/safranin O (AB/SO). In all five avian species, it was found that the mast cells were in different sizes and round, oval or spindle‐shaped based on their place of distribution. Mast cell numbers were determined in stained with toluidine blue, examined ×40 objectives in a 1 mm2 area. It was observed that mast cell density in subepithelial lamina propria and microscopic papilla was higher in the tongues of all species. Mast cell distribution and heterogeneity varied through the tongue, and there were more mast cells in the dorsal side of the tongue than the ventral side. The highest amount of mast cells was found in the tongue of the Gerze rooster among all five species. In the tongue cross‐sections stained with the combined method of alcian blue/safranin O (AB/SO), the mast cells were stained as AB (+), SO (+) and AB/SO (+) (mixed).
Systematic review of interventions to encourage careers in academic medicine

Abstract Aims: Academic medicine is a career route that historically struggles to recruit and retain suitable doctors. The aim of this paper is to review the evidence for interventions to encourage careers in academic medicine by way of a descriptive systematic review. Methods: Key databases were searched in February 2017. Studies that evaluated interventions to encourage careers in academic medicine and that used a pre–post analysis or included a comparison group were included. Interventions reporting only learner satisfaction were excluded. The review was specific to medical students and graduates. Results: Twenty-four studies were identified for inclusion within the review. The included studies identified interventions across five domains: postgraduate funding, postgraduate training, mentoring, undergraduate interventions, and institutional change. The papers varied in terms of strength of conclusion and method of analysis with broad, structured, well-funded programs having the most palpable results. Conclusions: The five domains identified offer a framework that can be used by institutions who wish to develop similar programs. It also offers a body of research on which an evidence base can be built.