Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of a goal maintenance task for use in clinical applications.

BACKGROUND We sought to develop a Dot Pattern Expectancy task (DPX) to assess goal maintenance for use in clinical trials. Altering the standard task created 5 versions of the DPX to compare-a standard version and 4 others. Alterations in the interstimulus interval (ISI) length and the strength of a learned prepotent response distinguished the different tasks. These adjustments were designed to decrease administration time and/or improve reliability of the data. METHODS We determined participant eligibility in an initial session (the first of 3) using clinical interviewing tools. The initial session also included a demographic assessment and assessments of community functioning and symptom severity. All versions of the DPX were administered, across 3 sessions. Specific deficits on the context processing compared with difficulty control condition were evaluated using mixed-effects logistic regression within a hierarchical linear model. RESULTS We analyzed the data from 136 control participants and 138 participants with schizophrenia. Relative to a difficulty control condition, patients performed worse than controls on context processing conditions that required goal maintenance. ISI did not predict errors. Stronger prepotency was associated with increased errors in the difficulty control relative to context processing condition for controls, which improved the interpretability of findings for patients. Reliability was acceptable for a version of the task with a 10-minute running time. CONCLUSIONS The best compromise between task duration and interpretability occurred on a version with a short ISI and a strong prepotency.
The minimal solar activity in 2008–2009 and its implications for long‐term climate modeling

Variations in the total solar irradiance (TSI) associated with solar activity have been argued to influence the Earth's climate system, in particular when solar activity deviates from the average for a substantial period. One such example is the 17th Century Maunder Minimum during which sunspot numbers were extremely low, as Earth experienced the Little Ice Age. Estimation of the TSI during that period has relied on extrapolations of correlations with sunspot numbers or even more indirectly with modulations of galactic cosmic rays. We argue that there is a minimum state of solar magnetic activity associated with a population of relatively small magnetic bipoles which persists even when sunspots are absent, and that consequently estimates of TSI for the Little Ice Age that are based on scalings with sunspot numbers are generally too low. The minimal solar activity, which measurements show to be frequently observable between active‐region decay products regardless of the phase of the sunspot cycle, was approached globally after an unusually long lull in sunspot activity in 2008–2009. Therefore, the best estimate of magnetic activity, and presumably TSI, for the least‐active Maunder Minimum phases appears to be provided by direct measurement in 2008–2009. The implied marginally significant decrease in TSI during the least active phases of the Maunder Minimum by 140 to 360 ppm relative to 1996 suggests that drivers other than TSI dominate Earth's long‐term climate change.
ProteinProcessor: A probabilistic analysis using mass accuracy and the MS spectrum

Current approaches to protein identification rely heavily on database matching of fragmentation spectra or precursor peptide ions. We have developed a method for MALDI TOF‐TOF instrumentation that uses peptide masses and their measurement errors to confirm protein identifications from a first pass MS/MS database search. The method uses MS1‐level spectral data that have heretofore been ignored by most search engines. This approach uses the distribution of mass errors of peptide matches in the MS1 spectrum to develop a probability model that is independent of the MS/MS database search identifications. Peptide mass matches can come from both precursor ions that have been fragmented as well as those that are tentatively identified by accurate mass alone. This additional corroboration enables us to confirm protein identifications to MS/MS‐based scores that are otherwise considered to be only of moderate quality. Straightforward and easily applicable to current proteomic analyses, this tool termed “ProteinProcessor” provides a robust and invaluable addition to current protein identification tools.
ON THE BEHAVIOR OF FIXED-b TREND BREAK TESTS UNDER FRACTIONAL INTEGRATION

Testing for the presence of a broken linear trend when the nature of the persistence in the data is unknown is not a trivial problem, because the test needs to be both asymptotically correctly sized and consistent, regardless of the order of integration of the data. In a recent paper, Sayginsoy and Vogelsang (2011, Econometric Theory 27, 992–1025) (SV) show that tests based on fixed-b asymptotics provide a useful solution to this problem in the case where the shocks may be either weakly dependent or display strong dependence within the near-unit-root class. In this paper we analyze the performance of these tests when the shocks may be fractionally integrated, an alternative model paradigm that allows for either weak or strong dependence in the shocks. We demonstrate that the fixed-b trend break statistics converge to well-defined limit distributions under both the null and local alternatives in this case (and retain consistency against fixed alternatives), but that these distributions depend on the fractional integration parameter δ. As a result, it is only when δ is either zero or one that the SV critical values yield correctly sized tests. Consequently, we propose a procedure that employs δ-adaptive critical values to remove the size distortions in the SV test. In addition, use of δ-adaptive critical values also allows us to consider a simplification of the SV test that is (asymptotically) correctly sized across δ but can also provide a significant increase in power over the standard SV test when δ = 1.
Lipids of human meibum: mass-spectrometric analysis and structural elucidation1 Published, JLR Papers in Press, July 12, 2007.

The purpose of this study was to structurally characterize the major lipid species present in human meibomian gland secretions (MGS) of individual subjects by means of ion trap atmospheric pressure ionization mass spectrometry analysis (API MSn). The samples of MGS and authentic lipid standards were analyzed in direct infusion and high-pressure liquid chromatography (HPLC) experiments with API MSn detection of the analytes (HPLC API MSn). The major precursor ions were isolated and subjected to further sequential fragmentation in MSn experiments, and their fragmentation patterns were compared with those of authentic lipid standards. Multiple precursor ions were observed in the positive-ion mode. Among those, previously identified cholesterol (Chl; m/z 369; [M − H2O + H]+) and oleic acid (OA; m/z 283; [M + H]+) were found. The other major compounds of the general molecular formula CnH2n-2O2 were consistent with wax esters (WEs), with OA as fatty acyl component. Accompanying them were two homologous series of compounds that fit the molecular formulas CnH2n-4O2 and CnH2nO2. Subset 2 was found to be a homolog series of linoleic acid-based WEs, whereas subset 3 was, apparently, a mixture of stearic acid-based WEs. HPLC API MSn analysis revealed the presence of large quantities of cholesteryl esters (Chl-Es) in all of the tested samples. Less than 0.1% (w/w) of oleamide was detected in human MGS. In the negative-ion mode, three major compounds with m/z values of 729, 757, and 785 that were apparently related to anionogenic lipids of the diacylglyceryl family were found in all of the samples. Common phospholipids and ceramides (Cers) were not present among the major MGS lipids. Phosphocholine-based lipids were found in MGS in quantities less than 0.01% (w/w), if at all. This ratio is two orders of magnitude lower than reported previously. These observations suggest that MGS are a major source of nonpolar lipids of the WE and Chl-E families for the tear film lipid layer, but not of its previously reported (phospho)lipid, Cer, and fatty acid amide components.
Patterns of structural and defense investments in fine roots of Scots pine (Pinus sylvestris L.) across a strong temperature and latitudinal gradient in Europe

Plant functional traits may be altered as plants adapt to various environmental constraints. Cold, low fertility growing conditions are often associated with root adjustments to increase acquisition of limiting nutrient resources, but they may also result in construction of roots with reduced uptake potential but higher tissue persistence. It is ultimately unclear whether plants produce fine roots of different structure in response to decreasing temperatures and whether these changes represent a trade‐off between root function or potential root persistence. We assessed patterns of root construction based on various root morphological, biochemical and defense traits including root diameter, specific root length (SRL), root tissue density (RTD), C:N ratio, phenolic compounds, and number of phellem layers across up to 10 root orders in diverse populations of Scots pine along a 2000‐km climatic gradient in Europe. Our results showed that different root traits are related to mean annual temperature (MAT) and expressed a pattern of higher root diameter and lower SRL and RTD in northern sites with lower MAT. Among absorptive roots, we observed a gradual decline in chemical defenses (phenolic compounds) with decreasing MAT. In contrast, decreasing MAT resulted in an increase of structural protection (number of phellem layers) in transport fine roots. This indicated that absorptive roots with high capacity for nutrient uptake, and transport roots with low uptake capacity, were characterized by distinct and contrasting trade‐offs. Our observations suggest that diminishing structural and chemical investments into the more distal, absorptive roots in colder climates is consistent with building roots of higher absorptive capacity. At the same time, roots that play a more prominent role in transport of nutrients and water within the root system saw an increase in structural investment, which can increase persistence and reduce long‐term costs associated with their frequent replacement.
Disseminated community-acquired USA300 methicillin-resistant Staphylococcus aureus pyomyositis and septic pulmonary emboli in an immunocompetent adult.

BACKGROUND Recent reports have increasingly recognized methicillin-resistant Staphylococcus aureus (MRSA) as an important etiology of pyomyositis, an uncommon disease entity. Specific virulence factors such as the Panton-Valentine leukocidin protein have been identified that may play a role in the pathophysiology of pyomyositis, especially when community-acquired MRSA is implicated. METHODS We review a case of disseminated pyomyositis and septic pulmonary emboli in an immunocompetent adult in whom a pvl+ USA300 clone was isolated. RESULTS The degree of dissemination in this patient suggests an emerging level of virulence for community-acquired MRSA that has not been reported previously. CONCLUSION The clinical history and management of severe disseminated pyomyositis, including diagnostic modalities, antimicrobial therapy, and surgical drainage, require an aggressive approach.
Fine-Grained Algorithm Design for Matching

Finding maximum-cardinality matchings in undirected graphs is arguably one of the most central graph problems. For $m$-edge and $n$-vertex graphs, it is well-known to be solvable in $O(m\sqrt{n})$ time; however, for several applications this running time is still too slow. Improving this worst-case upper bound resisted decades of research. In this paper we mainly focus on parameterizations of the input with respect to several kinds of distance to triviality, i.e. how far is the input from some linear-time solvable cases. Our contribution is twofold. First we focus on linear-time fixed-parameter algorithms (with low polynomial parameter dependence). To this end we develop the first linear-time algorithm for maximum matching on cocomparability graphs; this algorithm is based on the recently discovered Lexicographic Depth First Search (LDFS) and is of independent interest. Using this algorithm we derive an $O(k(n+m))$-time algorithm for general graphs, where $k$ is the vertex deletion distance to cocomparability graphs. Second we focus on linear-time kernelization. We start a deeper and systematic study of various "distance to triviality"-parameters for the maximum matching problem. We design linear (and almost linear) time computable kernels of size $O(k)$, $O(k^2)$, $O(k^3)$, and $2^{O(k)}$, respectively, where $k$ is the considered parameter in each case. Investigating linear-time kernelization of a polynomial-time solvable problem, such as maximum matching, leads to a rich number of new and combinatorially interesting challenges. Based on our results, we postulate that maximum matching has the clear potential to become the "drosophila" of "FPT in P studies" analogously to the path-breaking role vertex covering played for classical FPT studies for NP-hard problems.
Attitudes Toward Homosexuality Among Young Adults: Connections to Gender Role Identity, Gender-Typed Activities, and Religiosity

Individual differences in attitudes toward homosexuality have been linked to numerous personality and demographic variables. This study investigated the influence that gender role identity, involvement in gender-typed activities, and religiosity plays in this relationship. The sample included 194 undergraduate students from a Northeastern university. Analyses revealed that both males and females who held a more masculine gender role identity and individual commitment to religion scored higher on measures of homophobia and heteronormativity, whereas there was no association between spiritual meaning in life and attitudes toward homosexuality. Among males, but not females, more masculine gender identity and less spiritual meaning in life was associated with greater homophobia. The importance of the findings for research on the origins of attitudes toward individuals with a homosexual orientation are discussed, as well as the potential directions for future research on connections between gender role identity, religious affiliation, and attitudes toward gays and lesbians.
Clinical, nutritional and immunological characteristics of HIV-infected children in an area of high HIV prevalence.

OBJECTIVES To evaluate the clinical, nutritional and neurodevelopment status of HIV-infected children in a high HIV prevalence area. METHODS All HIV-infected children under 15 years of age attending an outpatient clinic of Mozambique between April and May 2010 were recruited. Clinical data were collected and physical examination was performed. RESULTS In all, 140 children were recruited. The median age at HIV diagnosis was 2.1 years. Fifty-one percent of the children were classified in WHO clinical Stages 3 or 4. Median age of antiretroviral treatment commencement was 3.9 years. Overall, 68% were undernourished, mainly stunted. Forty-four percent failed to pass the national psychomotor developmental test. CONCLUSIONS The pathways for early HIV diagnosis and start of antiretrovirals in children should be improved in Mozambique. Malnutrition, especially stunting, and developmental delay were highly prevalent. Further research focused on early diagnosis of neurocognitive disorders and on the indications of antiretroviral treatment commencement based on chronic malnutrition is required.
Free-space optical communication in the presence of atmospheric angular spread

In this paper, different optical detection schemes are investigated in the presence of turbulence-induced effects. Both log-amplitude fluctuations and angle-of-arrival (AOA) fluctuations introduced by atmospheric turbulence are taken into account in channel modelling. The impact of the angular spread can be thus determined based on the performance of the FSO receivers. For direct detection, we find the optimal receiver field-of-view (FOV) to improve the performance. We further show the benefit of coherent detection over direct detection in the presence of angular spread. Moreover, spatial diversity receivers which are able to significantly improve the performance of atmospheric optical systems are discussed in detail.
A study on the twin screw extrusion-cooking of plant-meat pet food mixtures

A b s t r a c t. A study was conducted on the possibility of application of “dry” extrusion-cooking technology for the processing of plant-meat mixtures. The effect of the concentration of the meat material (meat-bone pulp), leguminous material (faba bean), wheat grain meal and extrusion temperature on the process run, physicochemical properties and on the microstructure of the extrudates was investigated. It was demonstrated that extrusion-cooking with a twin-screw extruder permits the processing of blends with up to 30% meat-bone pulp content. Increase in the content of the meat material caused a decrease of specific density and water solubility index (WSI) of the extrudates. At the same time, a significant increase in the content of proteins, fat, and ash was observed. Extrusion temperature increase from 130 to 250°C caused an increase in the degree of expansion ratio and impact strength of the extrudates and a decrease in specific density of the products. At the same time, the microstructure of the products was changed from cohesive and compacted to more expanded and porous. K e y w o r d s: extrusion-cooking, faba been, meat-bone pulp, pet food, wheat
A Plucking Model of Business Cycles

In standard models, economic activity fluctuates symmetrically around a “natural rate” and stabilization policies can dampen these fluctuations but do not affect the average level of activity. An alternative view—labeled the “plucking model” by Milton Friedman—is that economic fluctuations are drops below the economy’s full potential ceiling. If this view is correct, stabilization policy, by dampening these fluctuations, can raise the average level of activity. We show that the dynamics of the unemployment rate in the US display a striking asymmetry that strongly favors the plucking model: increases in unemployment are followed by decreases of similar amplitude, while the amplitude of the increase is not related to the amplitude of the previous decrease. We develop a microfounded plucking model of the business cycle. The source of asymmetry in our model is downward nominal wage rigidity, which we embed in an explicit search model of the labor market. Our search framework implies that downward nominal wage rigidity is consistent with optimizing behavior and equilibrium. In our plucking model, stabilization policy lowers average unemployment and thereby yields sizable welfare gains.
High sCD36 plasma level is associated with steatosis and its severity in patients with genotype 1 chronic hepatitis C

Summary. Soluble CD36 (sCD36) plasma levels, a known marker of cardiometabolic disorders, are associated with surrogate markers of steatosis, while experimental and human studies show a link between CD36 expression in the liver and steatosis. In a cohort of patients with genotype 1 chronic hepatitis C (G1 CHC), we tested the association of sCD36 plasma levels with host and viral factors and sustained virological response (SVR). One hundred and seventy‐five consecutive biopsy‐proven patients were studied. sCD36 plasma levels were assessed by an in‐house ELISA. All biopsies were scored by one pathologist for staging and grading (Scheuer) and graded for steatosis, which was considered moderate–severe if ≥20%. Patients underwent standard of care therapy with pegylated interferon and ribavirin. The severity of steatosis progressively increased according to sCD36 quartiles (P = 0.02); total and low‐density lipoprotein (LDL) cholesterol levels were significantly higher in patients in the lower quartile compared to all the others. Gamma‐glutamyl transferase (P = 0.02), homoeostasis model assessment (HOMA) score (P = 0.002) and sCD36 (P = 0.04) were independently associated with the severity of steatosis as continuous variable. Multivariate logistic regression analysis showed that HOMA (OR 1.243, 95% CI 1.04–1.484, P = 0.01) and sCD36 (OR 1.445, 95%CI 1.135–1.839, P = 0.003) were independently linked to steatosis ≥20%. No association was found between sCD36 and SVR. CD36 is linked to steatosis and insulin resistance in patients with G1 CHC, but does not predict response to treatment. The potential of sCD36 as a surrogate marker of steatosis should be further investigated.
Decision Tree Induction on Hyper-Spectral Cement Images

— Applying data mining techniques to multimedia data, such as images, is becoming very important yet challenging. Discovering interesting patterns from images can be very useful in many areas, such as medical science, chemical science, agriculture, and geosciences. In this paper, we present a new application of performing classification on hyper-spectral cement images. Each image dataset includes a backscattered electron image and eight X-ray images of a cement material. We apply decision tree induction to analyze the relationship among the characteristics of cement materials and the cement clinker phase. The classifier will then be used to predicate the phases of a new cement material. We test our model on extensive real datasets using individual or combined data sets as training data. Our model achieves high classification accuracy compared to Bentz’s model, which uses image segmentation to determine the cement phases.
A MORN1‐associated HAD phosphatase in the basal complex is essential for Toxoplasma gondii daughter budding

Apicomplexan parasites replicate by several budding mechanisms with two well‐characterized examples being Toxoplasma endodyogeny and Plasmodium schizogony. Completion of budding requires the tapering of the nascent daughter buds toward the basal end, driven by contraction of the basal complex. This contraction is not executed by any of the known cell division associated contractile mechanisms and in order to reveal new components of the unusual basal complex we performed a yeast two‐hybrid screen with its major scaffolding protein, TgMORN1. Here we report on a conserved protein with a haloacid dehalogenase (HAD) phosphatase domain, hereafter named HAD2a, identified by yeast two‐hybrid. HAD2a has demonstrated enzyme‐activity in vitro, localizes to the nascent daughter buds, and co‐localizes with MORN1 to the basal complex during its contraction. Conditional knockout of HAD2a in Toxoplasma interferes with basal complex assembly, which leads to incomplete cytokinesis and conjoined daughters that ultimately results in disrupted proliferation. In Plasmodium, we further confirmed localization of the HAD2a ortholog to the basal complex toward the end of schizogony. In conclusion, our work highlights an essential role for this HAD phosphatase across apicomplexan budding and suggests a regulatory mechanism of differential phosphorylation on the structure and/or contractile function of the basal complex.