Miracle-dz/UniFAR-FTUs huggingface dataset:
Frailty and patient-reported outcomes in subjects with chronic obstructive pulmonary disease: are they independent entities?

Introduction There is a hypothesis that chronic obstructive pulmonary disease (COPD) is an accelerated ageing disease. Frailty is a geriatric syndrome characterised by physical, psychological and social vulnerability, thought to be a feature of ageing. The authors aimed to explore the relationship between frailty and physiological and patient-reported outcomes (PROs) in subjects with stable COPD. Methods We administered the Kihon Checklist that has been validated for frailty screening. We also assessed patient-reported measurements of health status and dyspnoea using the COPD Assessment Test (CAT), the St. George’s Respiratory Questionnaire (SGRQ), the Hyland Scale, the Medical Outcomes Study 36-item short-form (SF-36), the Baseline Dyspnea Index (BDI) and the Dyspnea-12 (D-12). Pulmonary function was also measured. Results Of 79 consecutive COPD outpatients, 38 (48.1%), 24 (30.4%) and 17 (21.5%) patients were classified as robust, prefrail and frail, respectively. The total Kihon Checklist score was significantly weakly to moderately correlated with the CAT score (Spearman’s rank correlation coefficient (Rs)=0.38, p<0.01), the SGRQ total score (Rs=0.65, p<0.01), the Hyland Scale score (Rs=−0.54, p<0.01), all subscale scores of the SF-36 (Rs=−0.64 to −0.31, p<0.01), the BDI score (Rs=−0.46, p<0.01) and the D-12 score (Rs=0.41, p<0.01). We found no or only weak correlations between the total Kihon Checklist score and lung function measurements. We found statistically significant between-group (robust, prefrail and frail) differences in most PRO scores. Using stepwise multiple regression analyses to identify the variables that predicted the total Kihon Checklist score, the SGRQ total score alone significantly explained 49.1% of the variance (p<0.01). Discussion Frailty was significantly correlated with PROs, especially health status, unlike lung function. Frailty should be assessed in addition to PROs separately from lung function as part of multidimensional analyses of COPD.
The Spatial LASSO With Applications to Unmixing Hyperspectral Biomedical Images

Hyperspectral imaging (HSI) is a spectroscopic method that uses densely sampled measurements along the electromagnetic spectrum to identify the unique molecular composition of an object. Traditionally HSI has been associated with remote sensing-type applications, but recently has found increased use in biomedicine, from investigations at the cellular to the tissue level. One of the main challenges in the analysis of HSI is estimating the proportions, also called abundance fractions of each of the molecular signatures. While there is great promise for HSI in the area of biomedicine, large variability in the measurements and artifacts related to the instrumentation has slow adoption into more widespread practice. In this article, we propose a novel regularization and variable selection method called the spatial LASSO (SPLASSO). The SPLASSO incorporates spatial information via a graph Laplacian-based penalty to help improve the model estimation process for multivariate response data. We show the strong performance of this approach on a benchmark HSI dataset with considerable improvement in predictive accuracy over the standard LASSO. Supplementary materials for this article are available online.
Etiological diagnosis of bacterial pneumonia by gram stain and quantitative culture of expectorates. Leukocytes or alveolar macrophages as indicators of sample representativity.

Sputum samples from 151 patients admitted to Roslagstull Hospital for Infectious Diseases, Stockholm, from Sept. 1978 through May 1979 with acute community-acquired lower respiratory tract disease and roentgenological evidence of acute pneumonia were examined by direct microscopy of gram-stained smears and semiquantitative culture. It was carefully noted if the specimen was collected before or after initiation of antibiotic therapy. For an estimate of the suitability of the samples for bacteriological examination 2 criteria were applied: (i) presence of alveolar macrophages, and (ii) purulence, i.e. a ratio leukocytes/squamous epithelial cells of greater than 5. The latter was found to be a good indicator of sample suitability, while the presence of macrophages was not. Of the 266 samples examined 76% were deemed purulent. Potentially pathogenic bacteria in numbers of greater than or equal to 10(5) colony forming units/ml were found in 67% of the purulent sputum samples obtained before antibiotic therapy but in only 36% if such treatment had already been started. Pneumococci were isolated from 52% of pre-treatment samples but from only 8% after treatment. H. influenzae was found as often in post-treatment samples (17%) as in pre-treatment ones (15%) and enteric gram-negative rods twice as often in post-treatment samples (11 vs. 6%). The use of gram-stained smears was a valuable aid in the interpretation of the culture results and the results could be made available to the clinician within minutes after receipt of the specimen. The results were in agreement with those of the cultures for about 75% of the purulent samples.
Identifying influential individuals in linkage analysis: Application to a quantitative trait locus detected in the COGA data

Once linkage is detected to a quantitative trait locus (QTL), the next step towards localizing the gene involved may be to identify those families, or individuals, in whom the putative mutations are segregating. In this paper, we describe a jackknife procedure for identifying individuals (and families) who contribute disproportionately to the linkage. Following initial detection of linkage to a QTL, the strategy involves sequentially removing each individual (or each family) from the analysis and recomputing the lod score associated with the linked region using data from all remaining subjects (or families). This procedure can be used to determine if particular observations have substantial impact on evidence for linkage. Identification of such observations may provide insights for further efforts to localize the QTL.
CO2 cost pass-through and windfall profits in the power sector

Abstract In order to cover their CO2 emissions, power companies receive most of the required EU ETS allowances for free. In line with economic theory, these companies pass on the costs of these allowances in the price of electricity. This article analyses the implications of the EU ETS for the power sector, notably the impact of free allocation of CO2 emission allowances on the price of electricity and the profitability of power generation. As well as some theoretical reflections, the article presents empirical and model estimates of CO2 cost pass-through for Germany and The Netherlands, indicating that pass-through rates vary between 60 and 100% of CO2 costs, depending on the carbon intensity of the marginal production unit and various other market- or technology-specific factors. As a result, power companies realize substantial windfall profits, as indicated by the empirical and model estimates presented in the article.
Context-Sensitive Code Completion Tool for Better API Usability

Developers depend on APIs of frameworks and libraries to support the development process. Due to the large number of existing APIs, it is difficult to learn, remember, and use them during the development of a software. To mitigate the problem, modern integrated development environments provide code completion facilities that free developers from remembering every detail. In this paper, we introduce CSCC, a simple, efficient context-sensitive code completion tool that leverages previous code examples to support method completion. Compared to other existing code completion tools, CSCC uses new sources of contextual information together with lightweight source code analysis to better recommend API method calls.
A Validation of DRAM RAPL Power Measurements

Recent Intel processors support the Running Average Power Level (RAPL) interface, which among other things provides estimated energy measurements for the CPUs, integrated GPU, and DRAM. These measurements are easily accessible by the user, and can be gathered by a wide variety of tools, including the Linux perf_event interface. This allows unprecedented easy access to energy information when designing and optimizing energy-aware code. While greatly useful, on most systems these RAPL measurements are estimated values, generated on the fly by an on-chip energy model. The values are not documented well, and the results (especially the DRAM results) have undergone only limited validation. We validate the DRAM RAPL results on both desktop and server Haswell machines, with multiple types of DDR3 and DDR4 memory. We instrument the hardware to gather actual power measurements and compare them to the RAPL values returned via Linux perf_event. We describe the many challenges encountered when instrumenting systems for detailed power measurement. We find that the RAPL results match overall energy and power trends, usually by a constant power offset. The results match best when the DRAM is being heavily utilized, but do not match as well in cases where the system is idle, or when an integrated GPU is using the memory. We also verify that Haswell server machines produce more accurate results, as they include actual power measurements gathered through the integrated voltage regulator.
Ultraviolet Pasteurization for Food Industry

This article reviews the status and scope of ultraviolet (UV) light technology in food processing industry for control of foodborne pathogens and spoilage organisms for food safety and shelf life extension. The literature suggests that there have been extensive studies on application of ultraviolet light for disinfection of apple ciders. FDA acceptable reduc- tion of pathogens and spoilage organisms were reported by UV treatment of for apple cider. Several recent studies on UV treatment of milk suggest that there is more work needed to improve design of UV reactors for raw milk processing. Fresh produce industry will also benefit from UV processing so that occurrence of frequent outbreaks can be avoided. A brief review of recent applications in produce industry has also been reported. Finally a recommendation was made for future direction of UV application research in food processing industry. Deterioration of foods by pathogenic and spoilage mi- croorganisms can be minimized by food processing and preservation techniques. Frequent outbreaks of foodborne pathogens are associated with fresh produce, milk and fruit juices. Currently, produce industry uses chemicals and fu- migants to control pathogens in packing and handling in- dustries. The liquid foods and dairy industry uses thermal pasteurization methods to disinfect food pathogens and ex- tend the shelf-life of products. Though thermal methods are effective in inactivating microorganisms, thermal process- ing negatively affects foods through losses in vitamins; and changes in sensory properties, such as color, flavor and wholesomeness (Montenegro et al. 2002). Moreover, ther- mal processing is not practical in fresh produce industry. Thermal pasteurization also affects enzyme inactivation, lipid oxidation, protein denaturation and non-enzymatic browning. Therefore nonthermal processing methods are being studies as alternative food processing techniques. Currently several nonthermal technologies are under re- search. Some of these technologies are ultrasound (US), high-pressure processing (HPP), pulsed electric fields (PEF), pulsed light treatment (PL), ultraviolet light (UV), and non-thermal atmospheric pressure plasma (NTAP). These novel non-thermal methods may be useful in inactivating foodborne pathogens and spoilage microorganisms from a
Biosynthetic genes and activity spectrum of antifungal polyynes from Collimonas fungivorans Ter331.

The antifungal activity of bacteria from the genus Collimonas has been well documented, but the chemistry and gene functions that underlie this phenotype are still poorly understood. Screening of a random plasposon insertion library of Collimonas fungivorans Ter331 for loss-of-function mutants revealed the importance of gene cluster K, which is annotated to code for the biosynthesis of a secondary metabolite and which features genes for fatty acid desaturases and polyketide synthases. Mutants in gene cluster K had lost the ability to inhibit hyphal growth of the fungus Aspergillus niger and were no longer able to produce and secrete several metabolites that after extraction and partial purification from wildtype strain Ter331 were shown to share a putative ene-triyne moiety. Some but not all of these metabolites were able to inhibit growth of A. niger, indicating functional variation within this group of Collimonas-produced polyyne-like 'collimomycins'. Polymerase chain reaction analysis of isolates representing different Collimonas species indicated that the possession of cluster K genes correlated positively with antifungal ability, further strengthening the notion that this cluster is involved in collimomycin production. We discuss our findings in the context of other bacterially produced polyynes and the potential use of collimomycins for the control of harmful fungi.
Trusting Our Memories: Dissociating the Neural Correlates of Confidence in Veridical versus Illusory Memories

Although memory confidence and accuracy tend to be positively correlated, people sometimes remember with high confidence events that never happened. How can confidence correlate with accuracy but apply also to illusory memories? One possible explanation is that high confidence in veridical versus illusory memories depends on different neural mechanisms. The present study investigated this possibility using functional magnetic resonance imaging and a modified version of the Deese-Roediger-McDermott false-memory paradigm. Participants read short lists of categorized words, and brain activity was measured while they performed a recognition test with confidence rating. The study yielded three main findings. First, compared with low-confidence responses, high-confidence responses were associated with medial temporal lobe (MTL) activity in the case of true recognition but with frontoparietal activity in the case of false recognition. Second, these regions showed significant confidence-by-veridicality interactions. Finally, only MTL regions showed greater activity for high-confidence true recognition than for high-confidence false recognition, and only frontoparietal regions showed greater activity for high-confidence false recognition than for high-confidence true recognition. These findings indicate that confidence in true recognition is mediated primarily by a recollection-related MTL mechanism, whereas confidence in false recognition reflects mainly a familiarity-related frontoparietal mechanism. This account is consistent with the fuzzy trace theory of false recognition. Correlation analyses revealed that MTL and frontoparietal regions play complementary roles during episodic retrieval. In sum, the present study shows that when one focuses exclusively on high-confidence responses, the neural correlates of true and false memory are clearly different.
A Theory of Universal Artificial Intelligence based on Algorithmic Complexity

Decision theory formally solves the problem of rational agents in uncertain worlds if the true environmental prior probability distribution is known. Solomono’s theory of universal induction formally solves the problem of sequence prediction for unknown prior distribution. We combine both ideas and get a parameterless theory of universal Artificial Intelligence. We give strong arguments that the resulting AI model is the most intelligent unbiased agent possible. We outline for a number of problem classes, including sequence prediction, strategic games, function minimization, reinforcement and supervised learning, how the AI model can formally solve them. The major drawback of the AI model is that it is uncomputable. To overcome this problem, we construct a modified algorithm AI tl , which is still eectively more intelligent than any other time t and space l bounded agent. The computation time of AI tl is of the order t·2 l . Other discussed topics are formal definitions of intelligence order relations, the horizon problem and relations of the AI theory to other AI approaches.
One Security, Four Markets: Canada-US Cross-Listed Options and Underlying Equities

In this paper we examine the relative contributions of US and Canadian markets to price discovery for Canadian cross-listed options and their cross-listed underlying stocks. We use two different econometric approaches in assessing the contributions of each market to price discovery, the information shares approach and the common factor approach. Our empirical results are consistent in both approaches. We show that on average price discovery for cross-listed Canadian stocks and options takes place overwhelmingly in the underlying asset markets, where Canadian equity markets dominate the discovery process. The results show that option markets information shares remain comparable, although slightly higher in the US, which contrasts with the fact that its relative volume is almost ten times greater than that of Canadian options markets. The results also indicate a high degree of integration between Canadian and US markets for the underlying stocks of cross-listed options and show that the foreign exchange market does not contribute to the co integration between these markets to any significant extent. An analysis of the determinants of the relative information shares between firms with all markets analyzed simultaneously shows that the most important factor explaining the information shares is the volatility of underlying returns.
Roles of base excision repair subpathways in correcting oxidized abasic sites in DNA

Base excision DNA repair (BER) is fundamentally important in handling diverse lesions produced as a result of the intrinsic instability of DNA or by various endogenous and exogenous reactive species. Defects in the BER process have been associated with cancer susceptibility and neurodegenerative disorders. BER funnels diverse base lesions into a common intermediate, apurinic/apyrimidinic (AP) sites. The repair of AP sites is initiated by the major human AP endonuclease, Ape1, or by AP lyase activities associated with some DNA glycosylases. Subsequent steps follow either of two distinct BER subpathways distinguished by repair DNA synthesis of either a single nucleotide (short‐patch BER) or multiple nucleotides (long‐patch BER). As the major repair mode for regular AP sites, the short‐patch BER pathway removes the incised AP lesion, a 5′‐deoxyribose‐5‐phosphate moiety, and replaces a single nucleotide using DNA polymerase (Polβ). However, short‐patch BER may have difficulty handling some types of lesions, as shown for the C1′‐oxidized abasic residue, 2‐deoxyribonolactone (dL). Recent work indicates that dL is processed efficiently by Ape1, but that short‐patch BER is derailed by the formation of stable covalent crosslinks between Ape1‐incised dL and Polβ. The long‐patch BER subpathway effectively removes dL and thereby prevents the formation of DNA–protein crosslinks. In coping with dL, the cellular choice of BER subpathway may either completely repair the lesion, or complicate the repair process by forming a protein–DNA crosslink.
Elucidating Rice Cell Metabolism under Flooding and Drought Stresses Using Flux-Based Modeling and Analysis1[C][W][OPEN]

A metabolic/regulatory network of rice incorporates two important tissue types, germinating seeds and photorespiring leaves, is validated through experiments with rice suspension cultures, and applied to analyze metabolic capability under flooding and drought conditions. Rice (Oryza sativa) is one of the major food crops in world agriculture, especially in Asia. However, the possibility of subsequent occurrence of flood and drought is a major constraint to its production. Thus, the unique behavior of rice toward flooding and drought stresses has required special attention to understand its metabolic adaptations. However, despite several decades of research investigations, the cellular metabolism of rice remains largely unclear. In this study, in order to elucidate the physiological characteristics in response to such abiotic stresses, we reconstructed what is to our knowledge the first metabolic/regulatory network model of rice, representing two tissue types: germinating seeds and photorespiring leaves. The phenotypic behavior and metabolic states simulated by the model are highly consistent with our suspension culture experiments as well as previous reports. The in silico simulation results of seed-derived rice cells indicated (1) the characteristic metabolic utilization of glycolysis and ethanolic fermentation based on oxygen availability and (2) the efficient sucrose breakdown through sucrose synthase instead of invertase. Similarly, flux analysis on photorespiring leaf cells elucidated the crucial role of plastid-cytosol and mitochondrion-cytosol malate transporters in recycling the ammonia liberated during photorespiration and in exporting the excess redox cofactors, respectively. The model simulations also unraveled the essential role of mitochondrial respiration during drought stress. In the future, the combination of experimental and in silico analyses can serve as a promising approach to understand the complex metabolism of rice and potentially help in identifying engineering targets for improving its productivity as well as enabling stress tolerance.
CHARACTERIZATION AND EXPRESSION PROFILES OF FIVE POSSIBLE CYTOCHROME P450 GENES FROM Liposcelis entomophila (ENDERLEIN) (PSOCOPTERA: LIPOSCELIDIDAE).

In this study, the cDNAs of five cytochromes P450 genes (named CYP345P1, CYP358B1, CYP4FD2, CYP4CD2, and CYP6JN1) contained open reading frames from 1,500 to 1,554 nucleotides that encoded 499 to 517 amino acids were cloned from the psocid Liposcelis entomophila. They are characterized by predicted molecular weights from 57.67 to 59.64 kDa and theoretical isoelectric points of 5.57-9.07. Quantitative real-time PCR analysis showed these five genes were expressed at all tested developmental stages and higher expressions were observed in adults. CYP358B1 was expressed at higher levels in egg and adult compared to the larval stages. mRNA abundances of five genes were detected in both sexes and were relatively more abundant in adult females than in adult males. Synergism bioassay showed that the synergic ratio was 2.20 and 2.45 when insects were treated with the mixture of deltamethrin or malathion with the synergist piperonyl butoxide (PBO). Because PBO induces cytochrome P450s in some insects, this suggested to us that cytochromes P450 might participate in detoxification of these insecticides. The transcripts of the five cytochromes P450 genes in adult psocids could be induced to the highest level at 12 h after the exposure to malathion. After exposure to deltamethrin, CYP358B1 reached maximum expression at 24 h. The maximum expression of the other four genes occurred at 36 h. Treatments with the carbamate propoxur did not influence transcription of the cytochromes P450 gene. The induction profiles suggested that these five cytochrome P450 genes may be associated with deltamethrin and malathion metabolism in psocids.