Miracle-dz/UniFAR-FTUs huggingface dataset:
BRAF mutation is not predictive of long-term outcome in papillary thyroid carcinoma

The BRAF mutation occurs commonly in papillary thyroid carcinoma (PTC). Previous investigations of its utility to predict recurrence‐free survival (RFS) and disease‐specific survival (DSS) have reported conflicting results and its role remains unclear. The purpose of this retrospective study was to determine the incidence of the BRAF mutation and analyze its relationship to clinicopathologic risk factors and long‐term outcomes in the largest, single‐institution American cohort to date. BRAF mutational status was determined in 508 PTC patients using RFLP analysis. The relationships between BRAF mutation status, patient and tumor characteristics, RFS, and DSS were analyzed. The BRAF mutation was present in 67% of patients. On multivariate analysis, presence of the mutation predicted only for capsular invasion (HR, 1.7; 95% CI, 1.1–2.6), cervical lymph node involvement (HR, 1.7; 95% CI, 1.1–2.7), and classic papillary histology (HR, 1.8; 95% CI 1.1–2.9). There was no significant relationship between the BRAF mutation and RFS or DSS, an observation that was consistent across univariate, multivariate, and Kaplan–Meier analyses. This is the most extensive study to date in the United States to demonstrate that BRAF mutation is of no predictive value for recurrence or survival in PTC. We found correlations of BRAF status and several clinicopathologic characteristics of high‐risk disease, but limited evidence that the mutation correlates with more extensive or aggressive disease. This analysis suggests that BRAF is minimally prognostic in PTC. However, prevalence of the BRAF mutation is 70% in the general population, providing the opportunity for targeted therapy.
Long-Term Effects of Interprofessional Biopsychosocial Rehabilitation for Adults with Chronic Non-Specific Low Back Pain: A Multicentre, Quasi-Experimental Study

Background Improvement of the long-term effectiveness of multidisciplinary ortho-paedic rehabilitation (MOR) in the management of chronic non-specific low back pain (CLBP) remains a central issue for health care in Germany. We developed an interprofessional and interdisciplinary, biopsychosocial rehabilitation concept named “PASTOR” to promote self-management in adults with CLBP and compared its effectiveness with the current model of MOR. Methods A multicentre quasi-experimental study with three measurement time points was implemented. 680 adults aged 18 to 65 with CLBP were assed for eligibil-ity in three inpatient rehabilitation centres in Germany. At first the effects of the MOR, with a total extent of 48 hours (control group), were assessed. Thereafter, PASTOR was implemented and evaluated in the same centres (intervention group). It consisted of six interprofessional modules, which were provided on 12 days in fixed groups, with a total extent of 48 hours. Participants were assessed with self-report measures at baseline, discharge, and 12 months for functional ability (primary outcome) using the Hannover Functional Ability Questionnaire (FFbH-R) and vari-ous secondary outcomes (e.g. pain, health status, physical activity, pain coping, pain-related cognitions). Results In total 536 participants were consecutively assigned to PASTOR (n=266) or MOR (n=270). At 12 months, complete data of 368 participants was available. The adjusted between-group difference in the FFbH-R at 12 months was 6.58 (95% CI 3.38 to 9.78) using complete data and 3.56 (95% CI 0.45 to 6.67) using available da-ta, corresponding to significant small-to-medium effect sizes of d=0.42 (p<0.001) and d=0.10 (p=0.025) in favour of PASTOR. Further improvements in secondary out-comes were also observed in favour of PASTOR. Conclusion The interprofessional and interdisciplinary, biopsychosocial rehabilita-tion program PASTOR shows some improvements of the long-term effectiveness of inpatient rehabilitation in the management of adults with CLBP. Further insights into mechanisms of action of complex intervention programs are required. Trial Registration ClinicalTrials.gov NCT02056951
Bounds on Maximum Likelihood Decoding Performance for Linear Codes at Low Rates

For a given linear code (ensemble), upper bounds on the error probability under maximum likelihood decoding are investigated at low rates. A class of symmetric memoryless channels suitable for Bhattacharyya-type bounds, which are particularly of importance at low rates, is introduced. Over a symmetric channel, a lower bound on the error exponent is derived for a given linear code. A sufficient condition for achieving the expurgated exponent, which is the best among known error exponents at low rates, within a fixed discrepancy is given. Over a general discrete memoryless channel, the same analysis provides a lower bound on the average error exponent for an ensemble of coset codes generated by a given linear code. The bounding technique is extended to the case of generalized maximum likelihood decoding with erasure and list- decoding options.
Learning sparse, overcomplete representations of time-varying natural images

I show how to adapt an overcomplete dictionary of space-time functions so as to represent time-varying natural images with maximum sparsity. The basis functions are considered as part of a probabilistic model of image sequences, with a sparse prior imposed over the coefficients. Learning is accomplished by maximizing the log-likelihood of the model, using natural movies as training data. The basis functions that emerge are space-time inseparable functions that resemble the motion-selective receptive fields of simple-cells in mammalian visual cortex. When the coefficients are computed via matching-pursuit in space and time, one obtains a punctuate, spike-like representation of continuous time-varying images. It is suggested that such a coding scheme may be at work in the visual cortex.
Pulmonary artery blood temperature at admission to the intensive care unit is predictive of outcome after on‐pump coronary artery bypass surgery

Objective—To evaluate whether pulmonary artery blood (PA) temperature on admission to the intensive care unit (ICU) is predictive of postoperative outcome after isolated on‐pump coronary artery bypass grafting (CABG). Design—A retrospective study on 1639 patients who underwent isolated on‐pump CABG in whom PA temperature at admission to the ICU was available for review. Results—Thirty‐three patients (2.0%) died during the in‐hospital stay and 87 patients (5.3%) developed low cardiac output syndrome. PA temperature at admission to the ICU was significantly associated with an increased risk of overall postoperative death (p = 0.002), cardiac death (p = 0.03), and low cardiac output syndrome (p < 0.0001), and was significantly correlated with prolonged length of ICU stay (p < 0.0001) and postoperative bleeding (p = 0.001). Patients with high PA temperature had significantly more severe comorbidities, and longer aortic cross‐clamping and cardiopulmonary bypass time. The receiver operating characteristic curve showed that PA temperature at admission to the ICU in predicting postoperative death had an area under the curve of 0.660 (p = 0.002) and its best cut‐off value was 36.4°C (sensitivity: 63.6%, specificity: 65.2%). When the PA temperature at admission to the ICU was ≥36.4°C, the postoperative mortality and low cardiac output syndrome rates were 3.6 and 8.3%, whereas they were 1.1 and 3.7% when the PA temperature at admission to the ICU was <36.4°C (p = 0.001, p < 0.0001), respectively. Conclusion—Patients having a PA temperature ≥36.4°C at admission to the ICU after CABG seem to be at higher risk of poor postoperative outcome.
Obtaining oil from macauba kernels by ultrasound-assisted extraction using ethyl acetate as the solvent

Abstract The objective of this work was to evaluate the efficacy of ethyl acetate as a solvent in the extraction of macauba kernel oil (MKO) using ultrasonic-assisted extraction (UAE). It was shown that more MKO oil could be extracted with the use of larger amounts of solvent, higher temperatures and longer extraction times. Thus the maximum oil yield (40.61%) was obtained by UAE at 60 °C for 45 min, using a solvent to kernel ratio of 12 (mL g-1), obtaining a higher yield than that obtained with n-hexane under the same experimental conditions. UAE was favorable for this oil extraction (p < 0.05), presenting a yield close to that reported for classical extraction but with a shorter extraction time and smaller solvent volume. Lauric acid corresponded to ~44% of the MKO composition. The oils presented low free fatty acid contents (<0.80% wt), and the phytosterols, campesterol and β-sitosterol, were identified in the MKO with higher levels in the oil obtained by UAE.
A comparison of clinical characteristics and outcome in pyogenic liver abscess patients with and without diabetes mellitus: A case-control study

Background: Pyogenic liver abscess (PLA) is a relatively rare and potentially life-threatening disease. The incidence of PLA has been increasing steadily over the past few decades. PLA is relatively common in patients with diabetes mellitus (DM). Although multiple studies have explored the relationship between PLA and DM, it remains controversial, and the evidence comes primarily from case reports. Because of this, more studies are necessary to compare the characteristics of PLA patients with and without DM to explore the relationship between PLA and DM. Materials and Methods: A total of 115 PLA patients admitted in Beijing Luhe Hospital from December 2012 to August 2017 were divided into two groups based on the presence of DM (the DM group and the non-DM group) for the comparison of clinical characteristics and outcomes of patients. Chi-square, Fisher's exact, and t-tests were used to analyze the differences between the two groups. Results: Of 115 patients included, 50.4% of patients had DM. The DM group had a lower prevalence of abdominal pain (28% vs. 51%, P = 0.011) and pain to palpation (48% vs. 67%, P = 0.046). Moreover, the DM group had a higher prevalence of misdiagnosis (45% vs. 16%, P = 0.001) and poor outcomes (9% vs. 0%, P = 0.03). Conclusions: We found that patients with DM may have less typical symptoms of PLA than those without DM, which may explain the higher prevalence of misdiagnosis of PLA in patients with DM. Moreover, patients with DM have worse outcomes than those without DM.
The use of combined single photon emission computed tomography and X-ray computed tomography to assess the fate of inhaled aerosol.

BACKGROUND Gamma camera imaging is widely used to assess pulmonary aerosol deposition. Conventional planar imaging provides limited information on its regional distribution. In this study, single photon emission computed tomography (SPECT) was used to describe deposition in three dimensions (3D) and combined with X-ray computed tomography (CT) to relate this to lung anatomy. Its performance was compared to planar imaging. METHODS Ten SPECT/CT studies were performed on five healthy subjects following carefully controlled inhalation of radioaerosol from a nebulizer, using a variety of inhalation regimes. The 3D spatial distribution was assessed using a central-to-peripheral ratio (C/P) normalized to lung volume and for the right lung was compared to planar C/P analysis. The deposition by airway generation was calculated for each lung and the conducting airways deposition fraction compared to 24-h clearance. RESULTS The 3D normalized C/P ratio correlated more closely with 24-h clearance than the 2D ratio for the right lung [coefficient of variation (COV), 9% compared to 15% p < 0.05]. Analysis of regional distribution was possible for both lungs in 3D but not in 2D due to overlap of the stomach on the left lung. The mean conducting airways deposition fraction from SPECT for both lungs was not significantly different from 24-h clearance (COV 18%). Both spatial and generational measures of central deposition were significantly higher for the left than for the right lung. CONCLUSIONS Combined SPECT/CT enabled improved analysis of aerosol deposition from gamma camera imaging compared to planar imaging. 3D radionuclide imaging combined with anatomical information from CT and computer analysis is a useful approach for applications requiring regional information on deposition.
Relation of Cholesterol Level to Dietary Fat Intake in Patients of IschemicHeart Disease

Objective: To study the association of cholesterol level and dietary habits in patients of ischemic heart disease admitted with acute coronary syndromes. Materials and Methods: A total of 404 patients of ischemic heart disease admitted at the Punjab Institute of Cardiology, Lahore were included in the study. Patients were divided into four groups. Group I: 176(45.5%) patients with normal cholesterol levels and low fat diet. Group II: 76(18.2%) patients with normal cholesterol levels on high fat diet. Group III: 113(27.9%) patients with high cholesterol levels on low fat diet. Group IV: 39(9.6%) patients with high cholesterol levels on high fat diet. Results: Mean age of the study population was 55.6 ± 12.3 years. Mean age was similar in all the groups (p< 0.127). Overall 308(76.2%) patients were males and 96(23.8%) were females. Mean caloric intake of the study patients was 2570.5 ± 936.7. Caloric intake was highest in Group I followed by Group III. Group II and IV had lower caloric intake than groups I and III (p< 0.0001). Similarly percent fat was also lower in Group I and III as compared to Groups II and IV (p<0.008). Mean cholesterol level of the study population was 154.5 ± 42.6 mg/dl. Mean cholesterol level was highest in Group III, 195.9 ± 38.8 mg/dl (despite on low fat diet) followed by Group IV, 193.6 ± 39.5 (on high fat diet). Mean cholesterol was similar in Group I, 130.3 ± 19.6 and Group II, 129.1 ± 20.4 (p< 0.0001) irrespective of dietary intake of fat. Low HDL in Group I and II patients even having normal cholesterol level lead to acute myocardial infarction. Conclusion: Dietary intake of fat has no influence on cholesterol levels. Low HDL is an important risk factor leading to acute myocardial infarction and is not influenced by fat intake in diet.
Tumor Infection by Oncolytic Reovirus Primes Adaptive Antitumor Immunity

Purpose: Early clinical trials are under way exploring the direct oncolytic potential of reovirus. This study addresses whether tumor infection by reovirus is also able to generate bystander, adaptive antitumor immunity. Experimental Design: Reovirus was delivered intravenously to C57BL/6 mice bearing lymph node metastases from the murine melanoma, B16-tk, with assessment of nodal metastatic clearance, priming of antitumor immunity against the tumor-associated antigen tyrosinase-related protein-2, and cytokine responses. In an in vitro human system, the effect of reovirus infection on the ability of Mel888 melanoma cells to activate and load dendritic cells for cytotoxic lymphocyte (CTL) priming was investigated. Results: In the murine model, a single intravenous dose of reovirus reduced metastatic lymph node burden and induced antitumor immunity (splenocyte response to tyrosinase-related protein-2 and interleukin-12 production in disaggregated lymph nodes). In vitro human assays revealed that uninfected Mel888 cells failed to induce dendritic cell maturation or support priming of an anti-Mel888 CTL response. In contrast, reovirus-infected Mel888 cells (reo-Mel) matured dendritic cells in a reovirus dose-dependent manner. When cultured with autologous peripheral blood lymphocytes, dendritic cells loaded with reo-Mel induced lymphocyte expansion, IFN-γ production, specific anti-Mel888 cell cytotoxicity, and cross-primed CD8+ T cells specific against the human tumor-associated antigen MART-1. Conclusion: Reovirus infection of tumor cells reduces metastatic disease burden and primes antitumor immunity. Future clinical trials should be designed to explore both direct cytotoxic and immunotherapeutic effects of reovirus.
Appearance can be deceptive: Dentigerous cyst crossing the midline

Dentigerous cyst is a developmental odontogenic cyst, which develops by accumulation of fluid between reduced enamel epithelium and the tooth crown of an unerupted tooth. Dentigerous cysts are usually solitary, slow growing, asymptomatic lesions that are incidentally found during routine radiographs They most frequently involve the mandibular third molar followed in order of frequency by the maxillary canine, mandibular second pre-molar and maxillary third molar. Occasionally, these cysts become painful when infected causing swelling and erythema. The cyst is usually small, however, when large, results in the expansion and thinning of the cortex leading to pathological fracture. Radiographic features are specific to the lesion characterized by a well-defined radiolucency circumscribed by a sclerotic border, associated with the crown of an impacted or unerupted tooth. Dentigerous cysts are treated most commonly by enucleation, Marsupialization and decompression of cyst by fenestration. The criteria for selecting the treatment modality is based on the age, size, location, stage of root development, position of the involved tooth and relation of the lesion to the adjacent tooth and vital structure. The prognosis is an excellent when the cyst is enucleated and recurrence is rare. In this article, we present a case of a Dentigerous cyst in an 80-year-old man in the anterior aspect of the mandible enveloping an impacted canine and crossing the midline but with no clinical expansion or discomfort.
Glycogen Synthase Kinase 3 Inhibition Slows Mitochondrial Adenine Nucleotide Transport and Regulates Voltage-Dependent Anion Channel Phosphorylation

Inhibition of glycogen synthase kinase (GSK)-3 reduces ischemia/reperfusion injury by mechanisms that involve the mitochondria. The goal of this study was to explore possible molecular targets and mechanistic basis of this cardioprotective effect. In perfused rat hearts, treatment with GSK inhibitors before ischemia significantly improved recovery of function. To assess the effect of GSK inhibitors on mitochondrial function under ischemic conditions, mitochondria were isolated from rat hearts perfused with GSK inhibitors and were treated with uncoupler or cyanide or were made anoxic. GSK inhibition slowed ATP consumption under these conditions, which could be attributable to inhibition of ATP entry into the mitochondria through the voltage-dependent anion channel (VDAC) and/or adenine nucleotide transporter (ANT) or to inhibition of the F1F0-ATPase. To determine the site of the inhibitory effect on ATP consumption, we measured the conversion of ADP to AMP by adenylate kinase located in the intermembrane space. This assay requires adenine nucleotide transport across the outer but not the inner mitochondrial membrane, and we found that GSK inhibitors slow AMP production similar to their effect on ATP consumption. This suggests that GSK inhibitors are acting on outer mitochondrial membrane transport. In sonicated mitochondria, GSK inhibition had no effect on ATP consumption or AMP production. In intact mitochondria, cyclosporin A had no effect, indicating that ATP consumption is not caused by opening of the mitochondrial permeability transition pore. Because GSK is a kinase, we assessed whether protein phosphorylation might be involved. Therefore, we performed Western blot and 1D/2D gel phosphorylation site analysis using phos-tag staining to indicate proteins that had decreased phosphorylation in hearts treated with GSK inhibitors. Liquid chromatographic–mass spectrometric analysis revealed 1 of these proteins to be VDAC2. Taken together, we found that GSK-mediated signaling modulates transport through the outer membrane of the mitochondria. Both proteomics and adenine nucleotide transport data suggest that GSK regulates VDAC and that VDAC may be an important regulatory site in ischemia/reperfusion injury.
CO(1-0), CO(2-1), and Neutral Gas in NGC 6946: Molecular Gas in a Late-Type, Gas-Rich, Spiral Galaxy

We present on-the-fly maps of the CO(1-0) and CO(2-1) emission covering a 10′ × 10′ region of NGC 6946. Using our CO maps and archival VLA H I observations we create a total gas surface density map, Σgas, for NGC 6946. The predominantly molecular inner gas disk transitions smoothly into an atomic outer gas disk, with equivalent atomic and molecular gas surface densities at R = 3.5′ (6 kpc). We estimate that the total H2 mass is 3 × 109 M⊙, roughly one-third of the interstellar hydrogen gas mass and about 2% of the dynamical mass of the galaxy at our assumed distance of 6 Mpc. The value of the CO(2-1)/CO(1-0) line ratio ranges from 0.35 to 2; 50% of the map is covered by very high ratio gas (>1). The very high ratios are predominantly from interarm regions and appear to indicate the presence of wide-spread optically thin gas. Star formation tracers are better correlated with the total neutral gas disk than with the molecular gas by itself, implying ΣSFR ∝ Σgas. Using the 100 μm and 21 cm continua from NGC 6946 as star formation tracers, we arrive at a gas consumption timescale of 2.8 Gyr, which is relatively uniform across the disk. The high star formation rate at the nucleus appears to be due to a large accumulation of molecular gas rather than a large increase in the star formation efficiency. The midplane gas pressure in the outer (R > 10 kpc) H I arms of NGC 6946 is close to the value at the radial limit (10 kpc) of our observed CO disk. If the midplane gas pressure is a factor for the formation of molecular clouds, these outer H I gas arms should contain molecular gas, which we do not see because this gas is beyond our detection limit.
Computing homomorphic program invariants

xi CHAPTER 1. OVERVIEW . 1 1.1 Fundamental Challenges of Program Analysis . 2 1.2 Contemporary Approaches to Program Analysis . 5 1.3 Research Theme . 10 1.4 Research Goals . 11 1.5 Organization . 13 CHAPTER 2. A “HUMAN-IN-THE-LOOP” APPROACH FOR RESOLVING COMPLEX SOFTWARE ANOMALIES . 15 CHAPTER 3. A SECURITY TOOLBOX FOR DETECTING NOVEL AND SOPHISTICATED SOFTWARE ANOMALIES . 20 3.1 General Purpose Program Indexers . 22 3.2 Domain-specific Semantic Indexers . 23 3.3 Automatic Program Analyzers . 24 3.4 Interactive User Interface . 25 3.5 Interactive On-demand Analysis Visualizations . 26
Simulating Quantum Circuits with Sparse Output Distributions

We show that several quantum circuit families can be simulated efficiently classically if it is promised that their output distribution is approximately sparse i.e. the distribution is close to one where only a polynomially small, a priori unknown subset of the measurement probabilities are nonzero. Classical simulations are thereby obtained for quantum circuits which---without the additional sparsity promise---are considered hard to simulate. Our results apply in particular to a family of Fourier sampling circuits (which have structural similarities to Shor's factoring algorithm) but also to several other circuit families, such as IQP circuits. Our results provide examples of quantum circuits that cannot achieve exponential speed-ups due to the presence of too much destructive interference i.e. too many cancelations of amplitudes. The crux of our classical simulation is an efficient algorithm for approximating the significant Fourier coefficients of a class of states called computationally tractable states. The latter result may have applications beyond the scope of this work. In the proof we employ and extend sparse approximation techniques, in particular the Kushilevitz-Mansour algorithm, in combination with probabilistic simulation methods for quantum circuits.