Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization and quantification of endogenous fatty acid nitroalkene metabolites in human urine[S]

The oxidation and nitration of unsaturated fatty acids transforms cell membrane and lipoprotein constituents into mediators that regulate signal transduction. The formation of 9-NO2-octadeca-9,11-dienoic acid and 12-NO2-octadeca-9,11-dienoic acid stems from peroxynitrite- and myeloperoxidase-derived nitrogen dioxide reactions as well as secondary to nitrite disproportionation under the acidic conditions of digestion. Broad anti-inflammatory and tissue-protective responses are mediated by nitro-fatty acids. It is now shown that electrophilic fatty acid nitroalkenes are present in the urine of healthy human volunteers (9.9 ± 4.0 pmol/mg creatinine); along with electrophilic 16- and 14-carbon nitroalkenyl β-oxidation metabolites. High resolution mass determinations and coelution with isotopically-labeled metabolites support renal excretion of cysteine-nitroalkene conjugates. These products of Michael addition are in equilibrium with the free nitroalkene pool in urine and are displaced by thiol reaction with mercury chloride. This reaction increases the level of free nitroalkene fraction >10-fold and displays a KD of 7.5 × 10−6 M. In aggregate, the data indicates that formation of Michael adducts by electrophilic fatty acids is favored under biological conditions and that reversal of these addition reactions is critical for detecting both parent nitroalkenes and their metabolites. The measurement of this class of mediators can constitute a sensitive noninvasive index of metabolic and inflammatory status.
Deep Learning for Jazz Walking Bass Transcription

In this paper, we focus on transcribing walking bass lines, which provide clues for revealing the actual played chords in jazz recordings. Our transcription method is based on a deep neural network (DNN) that learns a mapping from a mixture spectrogram to a salience representation that emphasizes the bass line. Furthermore, using beat positions, we apply a late-fusion approach to obtain beat-wise pitch estimates of the bass line. First, our results show that this DNN-based transcription approach outperforms state-of-the-art transcription methods for the given task. Second, we found that an augmentation of the training set using pitch shifting improves the model performance. Finally, we present a semi-supervised learning approach where additional training data is generated from predictions on unlabeled datasets.
Redox-Mediated Enrichment of Self-Renewing Adult Human Pancreatic Cells That Possess Endocrine Differentiation Potential

Objectives: The limited availability of transplantable human islets has stimulated the development of methods needed to isolate adult pancreatic stem/progenitor cells capable of self-renewal and endocrine differentiation. The objective of this study was to determine whether modulation of intracellular redox state with N-acetyl-l-cysteine (NAC) would allow for the propagation of pancreatic stem/progenitor cells from adult human pancreatic tissue. Methods: Cells were propagated from human pancreatic tissue using a serum-free, low-calcium medium supplemented with NAC and tested for their ability to differentiate when cultured under different growth conditions. Results: Human pancreatic cell (HPC) cultures coexpressed &agr;-amylase, albumin, vimentin, and nestin. The HPC cultures, however, did not express other genes associated with differentiated pancreatic exocrine, duct, or endocrine cells. A number of transcription factors involved in endocrine cell development including Beta 2, Islet-1, Nkx6.1, Pax4, and Pax6 were expressed at variable levels in HPC cultures. In contrast, pancreatic duodenal homeobox factor 1 (Pdx-1) expression was extremely low and at times undetectable. Overexpression of Pdx-1 in HPC cultures stimulated somatostatin, glucagon, and carbonic anhydrase expression but had no effect on insulin gene expression. HPC cultures could form 3-dimensional islet-like cell aggregates, and this was associated with expression of somatostatin and glucagon but not insulin. Cultivation of HPCs in a differentiation medium supplemented with nicotinamide, exendin-4, and/or LY294002, an inhibitor of phosphatidylinositol-3 kinase, stimulated expression of insulin mRNA and protein. Conclusion: These data support the use of intracellular redox modulation for the enrichment of pancreatic stem/progenitor cells capable of self-renewal and endocrine differentiation.
Hyaluronic acid and oxidized regenerated cellulose prevent adhesion reformation after adhesiolysis in rat models

Postsurgical adhesion formation is the most common complication in abdominal and pelvic surgery. Adhesiolysis is the most commonly applied treatment for adhesion formation but is often followed by adhesion reformation. Therefore, an efficient strategy should be adopted to solve these problems. This study aimed to explore whether hyaluronic acid and oxidized regenerated cellulose (ORC) could prevent adhesion formation and reformation. Thirty female Sprague Dawley rats were randomly divided into three groups (n=10 each) and subjected to different treatments during the first and second surgery. The control group was treated with isotonic sodium chloride, the ORC group was treated with ORC (1.5×1 cm), and the medical sodium hyaluronate (MSH) group was treated with 1% MSH (0.5 mL). At 2 weeks after the first surgery, adhesion scores in the MSH group (1.90±0.99) and the ORC group (1.40±0.97) were significantly lower than those in the control group (3.00±0.82) (P=0.005). Similarly, 2 weeks after the second surgery, adhesion scores in the MSH group (2.00±0.82) and the ORC group (1.50±1.27) were significantly lower than those in the control group (3.50±0.53) (P=0.001). In addition, body weights in the MSH group and the ORC group did not change significantly, whereas the control group showed a consistent decrease in body weight during the experiment. Histological examination revealed that inflammatory infiltration was involved in both adhesion formation and reformation. In conclusion, hyaluronic acid and ORC were both efficient in reducing adhesion formation and reformation in the rat model.
PENGARUH URUTAN BUKTI, GAYA KOGNITIF, DAN PERSONALITAS TERHADAP PROSES REVISI KEYAKINAN

Researches that tried to examines effect of evidence order and individual psychological dimensions, consist of cognitive style and personality, to auditors’ judgment never been examined in auditing, especially, in belief-revision context. Present research is first. Present research focused on examination the influence of evidence order, cognitive style, and personality to auditors’ judgment. Judgment in this research is define to how auditor revised his believe based on evidence that evaluated step-by-step. Experiment method use in this research. Using a case study out of to 88 auditor, this research found that: (i) auditors’ judgment were affected by order in which audit evidences was evaluated;(ii) when auditor evaluated evidences in reverse order (- - + + vs. + + - -), recency effect occur. This finding show that auditor will weighted disconfirmation evidence more important than confirmation evidence; (iii) interaction exist between evidence order, cognitive style, and personality to affect auditors’ judgment.
PMI-cool at SemEval-2016 Task 3: Experiments with PMI and Goodness Polarity Lexicons for Community Question Answering

We describe our submission to SemEval-2016 Task 3 on Community Question Answering. We participated in subtask A, which asks to rerank the comments from the thread for a given forum question from good to bad. Our approach focuses on the generation and use of goodness polarity lexicons, similarly to the sentiment polarity lexicons, which are very popular in sentiment analysis. In particular, we use a combination of bootstrapping and pointwise mutual information to estimate the strength of association between a word (from a large unannotated set of question-answer threads) and the class of good/bad comments. We then use various features based on these lexicons to train a regression model, whose predictions we use to induce the ﬁnal comment ranking. While our system was not very strong as it lacked important features, our lexicons contributed to the strong performance of another top-performing system.
A Verbal Illusion

The sentence, No head injury is too trivial to be ignored, tends to be systematically misconstrued to mean that one should not ignore head injuries. It is argued that the sentence is anomalous in two ways. It is semantically anomalous because the relation between the adjective and the verb is the same as in the sentence, No sinner is too wicked to be condemned. It is pragmatically anomalous because the relation between the noun and the verb expresses an injunction which is inconsistent with commonly held beliefs. An experiment was conducted to investigate the effect of this pragmatic anomaly on comprehension. Four pragmatic and four non-pragmatic sentences were paraphrased. The prediction was confirmed that the pragmatic sentences were paraphrased more accurately than the non-pragmatic sentences. Some alternative explanations are considered.
Prevalence of Listeria sp. in droppings from urban rooks (Corvus frugilegus)

Droppings from 112 urban rooks (Corvus frugilegus) were cultured for the presence of Listeria sp. Overall, 46% of rooks sampled harboured one or more Listeria species. Of all birds examined, 33%, 24% and 8%, respectively, were infected with Listeria monocytogenes, Listeria innocua and Listeria seeligeri. Differentiation of L. monocytogenes and L. seeligeri carried out by several phenotypic typing methods proved the diversity of strains and the major role of rooks which widely contribute to spreading this bacteria in our environment. The results also suggest that the ability to recover specific Listeria strains from the same sample is at least partially dependent on the methodology. These findings reinforce the need for strain‐specific typing of multiple L. monocytogenes isolates from the same sample.
Langerhans cells in benign, premalignant and malignant skin lesions of renal transplant recipients and the effect of retinoid therapy

Langerhans cells (LC) are a unique population of antigen‐presenting cells in the epidermis which may play a role in the defense mechanisms against skin tumors. Renal transplant recipients (RTRs) have a significantly increased incidence of premalignant and malignant skin lesions. Langerhans cells, which are important for local immune surveillance, may be depleted or downregulated in skin neoplasms of RTRs, facilitating their growth. We investigated the Langerhans cell densities in 29 squamous cell carcinomas (SCCs), five basal cell carcinomas (BCCs), four Bowen's disease, eight dysplastic lesions (actinic keratoses), and three viral warts from 15 RTRs and compared these to the Langerhans cell densities in normal control skin. Eleven RTRs were receiving low‐dose etretinate as chemoprophylaxis for recurrent skin cancer and the effect of low‐dose retinoid therapy on Langerhans cell densities in SCCs from these patients was also assessed. Langerhans cells in frozen tissue sections were stained with the anti‐human Leu‐6 monoclonal antibody.
A motor isolation effect: When object manipulability modulates recall performance

Previous studies suggested that the language production architecture is recruited during verbal retention, and others proposed that spatial memory relies on the oculomotor system. The objective of the present study was to investigate the role of the motor system in object memory, by examining the effect of objects’ affordances on retention. In a serial recall task, we manipulated the manipulability of objects to retain in memory. We used an isolation paradigm where we isolated the manipulability level of one object from the list. We showed that recall performance improved for the isolated object (Experiment 1) and that this advantage was abolished when participants were required to perform motor suppression during the task (Experiment 2). In Experiment 3, we showed that the abolition of the motor isolation effect in Experiment 2 was not due to an effect of distraction since motor suppression was shown not to interfere with a semantic isolation effect. It is argued that motor affordances play a role in object memory, but only when the motor characteristics of an object allow discriminating it from the other objects in the list.
Higher dose rate Gamma Knife radiosurgery may provide earlier and longer-lasting pain relief for patients with trigeminal neuralgia.

OBJECT Gamma Knife radiosurgery (GKRS) utilizes cobalt-60 as its radiation source, and thus dose rate varies as the fixed source decays over its half-life of approximately 5.26 years. This natural decay results in increasing treatment times when delivering the same cumulative dose. It is also possible, however, that the biological effective dose may change based on this dose rate even if the total dose is kept constant. Because patients are generally treated in a uniform manner, radiosurgery for trigeminal neuralgia (TN) represents a clinical model whereby biological efficacy can be tested. The authors hypothesized that higher dose rates would result in earlier and more complete pain relief but only if measured with a sensitive pain assessment tool. METHODS One hundred thirty-three patients were treated with the Gamma Knife Model 4C unit at a single center by a single neurosurgeon during a single cobalt life cycle from January 2006 to May 2012. All patients were treated with 80 Gy with a single 4-mm isocenter without blocking. Using an output factor of 0.87, dose rates ranged from 1.28 to 2.95 Gy/min. The Brief Pain Inventory (BPI)-Facial was administered before the procedure and at the first follow-up office visit 1 month from the procedure (mean 1.3 months). Phone calls were made to evaluate patients after their procedures as part of a retrospective study. Univariate and multivariate linear regression was performed on several independent variables, including sex, age in deciles, diagnosis, follow-up duration, prior surgery, and dose rate. RESULTS In the short-term analysis (mean 1.3 months), patients' self-reported pain intensity at its worst was significantly correlated with dose rate on multivariate analysis (p = 0.028). Similarly, patients' self-reported interference with activities of daily living was closely correlated with dose rate on multivariate analysis (p = 0.067). A 1 Gy/min decrease in dose rate resulted in a 17% decrease in pain intensity at its worst and a 22% decrease in pain interference with activities of daily living. In longer-term follow-up (mean 1.9 years), GKRS with higher dose rates (> 2.0 Gy/min; p = 0.007) and older age in deciles (p = 0.012) were associated with a lower likelihood of recurrence of pain. DISCUSSION Prior studies investigating the role of dose rate in Gamma Knife radiosurgical ablation for TN have not used validated outcome tools to measure pain preoperatively. Consequently, differences in pain outcomes have been difficult to measure. By administering pain scales both preoperatively as well as postoperatively, the authors have identified statistically significant differences in pain intensity and pain interference with activities of daily living when comparing higher versus lower dose rates. Radiosurgery with a higher dose rate results in more pain relief at the early follow-up evaluation, and it may result in a lower recurrence rate at later follow-up.
Age-Related Difference in Functional Brain Connectivity of Mastication

The age-related decline in motor function is associated with changes in intrinsic brain signatures. Here, we investigated the functional connectivity (FC) associated with masticatory performance, a clinical index evaluating general masticatory function. Twenty-six older adults (OA) and 26 younger (YA) healthy adults were recruited and assessed using the masticatory performance index (MPI) and resting-state functional magnetic resonance imaging (rs-fMRI). We analyzed the rs-fMRI FC network related to mastication, which was constructed based on 12 bilateral mastication-related brain regions according to the literature. For the OA and the YA group, we identified the mastication-related hubs, i.e., the nodes for which the degree centrality (DC) was positively correlated with the MPI. For each pair of nodes, we identified the inter-nodal link for which the FC was positively correlated with the MPI. The network analysis revealed that, in the YA group, the FC between the sensorimotor cortex, the thalamus (THA) and the cerebellum was positively correlated with the MPI. Consistently, the cerebellum nodes were defined as the mastication-related hubs. In contrast, in the OA group, we found a sparser connection within the sensorimotor regions and cerebellum and a denser connection across distributed regions, including the FC between the superior parietal lobe (SPL), the anterior insula (aINS) and the dorsal anterior cingulate cortex (dACC). Compared to the YA group, the network of the OA group also comprised more mastication-related hubs, which were spatially distributed outside the sensorimotor regions, including the right SPL, the right aINS, and the bilateral dACC. In general, the findings supported the hypothesis that in OA, higher masticatory performance is associated with a widespread pattern of mastication-related hubs. Such a widespread engagement of multiple brain regions associated with the MPI may reflect an increased demand in sensorimotor integration, attentional control and monitoring for OA to maintain good mastication.
Finding the Lesser of Two Evils: Treating Refractory Status Epilepticus

OBJECTIVE: To evaluate the risks of continuously administered IV anesthetic drugs (IVADs) on the outcome of adult patients with status epilepticus (SE). METHODS: All intensive care unit patients with SE from 2005 to 2011 at a tertiary academic medical care center were included. Relative risks were calculated for the primary outcome measures of seizure control, Glasgow Outcome Scale score at discharge, and death. Poisson regression models were used to control for possible confounders and to assess effect modification. RESULTS: Of 171 patients, 37% were treated with IVADs. Mortality was 18%. Patients with anesthetic drugs had more infections during SE (43% vs 11%; p < 0.0001) and a 2.9fold relative risk for death (2.88; 95% confidence interval 1.45–5.73), independent of possible confounders (i.e., duration and severity of SE, nonanesthetic third-line antiepileptic drugs, and critical medical conditions) and without significant effect modification by different grades of SE severity and etiologies. As IVADs were used after firstand second-line drugs failed, there was a correlation between treatment-refractory SE and the use of IVADs, leading to insignificant results regarding the risk of IVADs and outcome after additional adjustment for refractory SE. CONCLUSION: Our findings heighten awareness regarding adverse effects of IVADs. Randomized controlled trials are needed to further clarify the association of IVADs with outcome in patients with SE. CLASSIFICATION OF EVIDENCE: This study provides Class III evidence that patients with SE receiving IVADs have a higher proportion of infection and an increased risk of death as compared to patients not receiving IVADs.
Psychiatric comorbidity and additional abuse of drugs in maintenance treatment with l- and d,l-methadone

Sixty d,l- or l-methadone treated patients in maintenance therapy were interviewed for additional drug abuse and psychiatric comorbidity; 51.7% of the entire population had a comorbid Axis-I disorder, with a higher prevalence in females (P=0.05). Comorbid patients tended to have higher abuse of benzodiazepines, alcohol, cannabis, and cocaine, but not of heroin. They had received a significantly lower d,l- (P<0.05) and l-methadone dose than non-comorbid subjects. The duration of maintenance treatment showed an inverse relationship to frequency of additional heroin intake (P<0.01). Patients with additional heroin intake over the past 30 days had been treated with a significantly lower l-methadone dosage (P<0.05) than patients without. Axis-I comorbidity appears to be decreased when relatively higher dosages of d,l- (and l-methadone) are administered; comorbid individuals, however, were on significantly lower dosages. Finally, l-, but not d,l-methadone seems to be more effective in reducing additional heroin abuse.
On Critical Reflection

In this article, we review empirical studies that research critical reflection based on Mezirow’s definition. The concepts of content, process, and premise reflection have often been cited, and operationalizing Mezirow’s high-level transformative learning theory and its components has been the endeavor of adult education and human resource development (HRD) researchers. By conducting a literature review, we distill 12 research studies on critical reflection that we dissect, analyze, and compare. Discovering different approaches, assessment processes, and outcomes leads us to the conclusion that there is little agreement on how to operationalize reflection. We suggest four improvements: (a) integrating different critical reflection traditions, (b) using multiple data collection pathways, (c) opting for thematic embedding, and (d) attending to feelings. By implementing these improvements, we hope to stimulate closer alignment of approaches in critical reflection research across adult education and HRD researchers.
New Perspectives on k-Support and Cluster Norms

We study a regularizer which is defined as a parameterized infimum of quadratics, and which we call the box-norm. We show that the k-support norm, a regularizer proposed by [Argyriou et al, 2012] for sparse vector prediction problems, belongs to this family, and the box-norm can be generated as a perturbation of the former. We derive an improved algorithm to compute the proximity operator of the squared box-norm, and we provide a method to compute the norm. We extend the norms to matrices, introducing the spectral k-support norm and spectral box-norm. We note that the spectral box-norm is essentially equivalent to the cluster norm, a multitask learning regularizer introduced by [Jacob et al. 2009a], and which in turn can be interpreted as a perturbation of the spectral k-support norm. Centering the norm is important for multitask learning and we also provide a method to use centered versions of the norms as regularizers. Numerical experiments indicate that the spectral k-support and box-norms and their centered variants provide state of the art performance in matrix completion and multitask learning problems respectively.
Network of Recurrent Neural Networks

We describe a class of systems theory based neural networks called "Network Of Recurrent neural networks" (NOR), which introduces a new structure level to RNN related models. In NOR, RNNs are viewed as the high-level neurons and are used to build the high-level layers. More specifically, we propose several methodologies to design different NOR topologies according to the theory of system evolution. Then we carry experiments on three different tasks to evaluate our implementations. Experimental results show our models outperform simple RNN remarkably under the same number of parameters, and sometimes achieve even better results than GRU and LSTM.