Miracle-dz/UniFAR-FTUs huggingface dataset:
An essential role for IL‐13 in maintaining a non‐healing response following Leishmania mexicana infection

A comparison of the growth of Leishmania mexicana in IL‐4–/–, IL‐4Rα–/– and wild‐type BALB/c mice demonstrated a disease exacerbative role for IL‐13 as well as IL‐4. Thus, while both IL‐4–/– and IL‐4Rα–/– mice were more resistant than wild‐type controls to infection with L. mexicana, IL‐4Rα–/– mice, which are unresponsive to IL‐13 as well as IL‐4, were significantly more resistant to parasite growth than their IL‐4–/– counterparts. Cytokine and antibody analysis revealed a Th1‐biased specific response in both infected IL‐4–/– and IL‐4Rα–/– mice compared with wild‐type animals. Reconstituting SCID mice with IL‐4–/–, IL‐4Rα–/– or wild‐type splenocytes prior to infection demonstrated that the early onset of lesion growth was dependent on the presence of lymphocytes responding to IL‐4 and/or IL‐13, as lesions failed to develop in only the SCID IL‐4Rα–/– reconstituted mice. An independent role for IL‐13 in L. mexicana infection was demonstrated by comparing disease progression in IL‐13–/–, IL‐4–/–/IL‐13–/– and wild‐type B6/129 mice. In contrast to IL‐4–/–/IL‐13–/– mice, which were resistant, IL‐13–/– mice developed lesions similar in size to wild‐type animalsup to week 8 post infection. However, in contrast to wild‐type mice in which disease continued to progress, lesions eventually healed in IL‐13–/– mice, in association with the development of a Th1 response. Collectively our results suggest that IL‐4 plays a critical role in early lesion development, and that IL‐13 plays a crucial part in maintaining a chronic non‐healing infection.
Machine learning can differentiate venom toxins from other proteins having non-toxic physiological functions

Ascribing function to sequence in the absence of biological data is an ongoing challenge in bioinformatics. Differentiating the toxins of venomous animals from homologues having other physiological functions is particularly problematic as there are no universally accepted methods by which to attribute toxin function using sequence data alone. Bioinformatics tools that do exist are difficult to implement for researchers with little bioinformatics training. Here we announce a machine learning tool called ‘ToxClassifier’ that enables simple and consistent discrimination of toxins from non-toxin sequences with >99% accuracy and compare it to commonly used toxin annotation methods. ‘ToxClassifer’ also reports the best-hit annotation allowing placement of a toxin into the most appropriate toxin protein family, or relates it to a non-toxic protein having the closest homology, giving enhanced curation of existing biological databases and new venomics projects. ‘ToxClassifier’ is available for free, either to download (https://github.com/rgacesa/ToxClassifier) or to use on a web-based server (http://bioserv7.bioinfo.pbf.hr/ToxClassifier/).
Who is afraid of reviewers’ comments? Or, why anything can be published and anything can be cited

We were surprised recently when an associate editor informed us that a manuscript was a resubmission of a paper that had been already peer-reviewed and rejected by our journal last year. The authors did not supply any rebuttal to the previous reviewers’ comments. Then, we received another manuscript that was a copy of a previously peer-reviewed and rejected paper. The two versions were identical, with two exceptions. The title had changed and the study design had been metamorphosed from retrospective to prospective. Again, the cover letter made no allusion to the previous submission. Then, we received a paper that, on close scrutiny, we had already rejected twice after peer-review. In the first submission the study was comparative; in the second submission the study was cut to one-arm description; in the third submission the study had become again comparative. The authors made no allusion to the previous submissions and reviewer comments. Obviously all these covert resubmissions were rejected. The submitting authors of these second-shots apparently thought that peer-review was a lottery. If you try hard enough, anything can be published even in the same journal that rejected the paper upfront; maybe it will go to different editors and reviewers; no need to address or even mention the problems identified by previous reviewers! This rationale leads to a parody of science and peer-review. We don’t know how extensive this practice is at other journals, but editors should beware. Such incidents make us think also about wider issues. How about the thousands of papers that are rejected at one journal and then resubmitted elsewhere without any consideration of previous reviewers’ comments? Rejection is currently the most common outcome to a journal submission. While many papers are rejected summarily based on screening by editors, most rejections receive input from peer-reviewers. We have little evidence on how frequently the authors take these comments into account when they resubmit elsewhere. However, we suspect that comments are often ignored. An evaluation of randomized trials submitted to BMJ showed that the published versions of the papers (usually at some other journal) differed minimally compared with the original
Hyperuricemia in primary and renal hypertension.

AN increased incidence of hyperuricemia in patients with primary hypertension has been cited in several reports.1 2 3 The present investigation of the population of the Hypertension-Nephritis Clinic of the Presbyterian Hospital in New York City confirms this observation among patients with either primary or renal hypertension, treated and untreated. The data from a related series of studies suggest that the hyperuricemia in both types of hypertension results from diminished renal excretion of urate. Altered lactic acid metabolism in hypertensive disease may account in part for the altered renal transport of uric acid.4 The results also raise the possibility that elevations of .
Miniaturized “Dark Eyes” antenna for pulsed microwave sensing: Complete microstrip-fed design

In this work, we reported on an antenna design with a complete microstrip feed suited for near-field microwave imaging centered at 6GHz. The antenna is compact and has a planar structure. Future work will be directed toward studying the antenna efficiency and fidelity for different values of surface resistivity. In addition, the antenna will be studied in an array configuration for near-field imaging applications.
Faster Defect Resolution with Higher Technical Quality of Software

We performed an empirical study of the relation between technical quality of software products and the defect resolution performance of their maintainers. In particular, we tested the hypothesis that ratings for source code maintainability, as employed by the SIG quality model, are correlated with ratings for defect resolution speed. This study revealed that all but one of the metrics of the SIG quality model show significant positive correlation Preprint accepted for publication in the proceedings of the 4th International Workshop on Software Quality and Maintainability (SQM 2010), Madrid (Spain) 15-18 March, 2010
Real-time novelty detection in video using background subtraction techniques: State of the art a practical review

Autonomously detecting novelties using background subtraction has quickly become a very important area of image analysis with many different approaches to novelty detection and the output therein. The ultimate goal of the approaches is to be robust to false detections and noise whilst using as little computational power as possible. This review focuses on some of the most prominent pixel-wise background subtraction techniques currently in use, and compares and contrasts their attributes and capabilities. The purpose of this review is to practically summarize the pixel-wise approaches and suggest a way forward from these techniques.
Tools and techniques for Java API testing

With the advent of object-oriented languages and the portability of Java APIs, the development and use of reusable software components is becoming a reality. Effective component reuse depends on component reliability, which in turn depends on thorough testing. The literature, however, provides few approaches to component testing that are practical for the input generation and output checking of the large number of test cases required. In this paper, we present the "Roast" tool and techniques for the testing of Java APIs. The tool and techniques are illustrated on two non-trivial components, and quantitative results are presented to substantiate the practicality and effectiveness of the approach.
Research Trends in Knowledge Management: Analyzing the Past and Predicting the Future

Through a meta-data analysis of the literature over a 34-year period, this article aims to provide a review and investigation into the knowledge management field in terms of how the domain is represented along a number of dimensions including unit of analysis, research paradigm employed, and the research topics/issues investigated. Information on a series of variables was extracted after conducting a review of 1,043 articles on KM, published in various peer-reviewed journals between 1974–2008. The findings suggest that a combination of positivist, empirical, conceptual/descriptive, and multi-method approaches have been predominantly used in the area. Organizational as well as systems and environmental context-based KM research were found to be the most widely published topics within the KM domain. Further, the authors identified literature gaps that require more exploration and conceptual refinement in the context of knowledge management research.
White paper defining optimal palliative care in older people with dementia: A Delphi study and recommendations from the European Association for Palliative Care

Background: Dementia is a life-limiting disease without curative treatments. Patients and families may need palliative care specific to dementia. Aim: To define optimal palliative care in dementia. Methods: Five-round Delphi study. Based on literature, a core group of 12 experts from 6 countries drafted a set of core domains with salient recommendations for each domain. We invited 89 experts from 27 countries to evaluate these in a two-round online survey with feedback. Consensus was determined according to predefined criteria. The fourth round involved decisions by the core team, and the fifth involved input from the European Association for Palliative Care. Results: A total of 64 (72%) experts from 23 countries evaluated a set of 11 domains and 57 recommendations. There was immediate and full consensus on the following eight domains, including the recommendations: person-centred care, communication and shared decision-making; optimal treatment of symptoms and providing comfort (these two identified as central to care and research); setting care goals and advance planning; continuity of care; psychosocial and spiritual support; family care and involvement; education of the health care team; and societal and ethical issues. After revision, full consensus was additionally reached for prognostication and timely recognition of dying. Recommendations on nutrition and dehydration (avoiding overly aggressive, burdensome or futile treatment) and on dementia stages in relation to care goals (applicability of palliative care) achieved moderate consensus. Conclusion: We have provided the first definition of palliative care in dementia based on evidence and consensus, a framework to provide guidance for clinical practice, policy and research.
A Fast Iterative Blind image restoration algorithm

Successful blind image deconvolution algorithms require the exact estimation of the Point Spread Function size, PSF. In the absence of any priori information about the imagery system and the true image, this estimation is normally done by trial and error experimentation, until an acceptable restored image quality is obtained. This paper, presents an exact estimation of the PSF size that yields the optimum restored image quality. The paper also describes a least squares PSF estimation, instead of the slow iterative update, that is commonly used in Iterative Blind Deconvolution software, IBD. Moreover, a technique is also proposed to improve the sharpness of the deconvolved images, by constrained maximization of the detail wavelet-coefficient entropies. Several simulations are given to verify these results.
Reproduction of Spatio-Temporal Patterns of Major Mediterranean Phytoplankton Groups from Remote Sensing OC-CCI Data

During the last two decades, several satellite algorithms have been proposed to retrieve information about phytoplankton groups using ocean colour data. One of these algorithms, the so-called PHYSAT-Med, was developed specifically for the Mediterranean Sea due to the optical peculiarities of this basin. The method allows the detection from ocean colour images of the dominant Mediterranean phytoplankton groups, namely nanoeukaryotes, Prochlorococcus, Synechococcus, diatoms, coccolithophorids and Phaeocystis-like phytoplankton. Here, we present a new version of PHYSAT-Med applied to the Ocean Colour – Climate Change Initiative (OC-CCI) database. The OC-CCI database consists of a multi-sensor, global ocean-colour product that merges observations from four different sensors. This retuned version presents improvements with respect to the previous version, as it increases the temporal range (since 1998), decreases the cloud cover, improves the bias correction and a validation exercise was performed in the NW Mediterranean Sea. In particular, the PHYSAT-Med version has been used here to analyse the annual cycles of the major phytoplankton groups in the Mediterranean Sea. Wavelet analyses were used to explore the spatial variability in dominance both in the time and frequency domains in several Mediterranean sub-regions, such as the Alboran Sea, Ligurian Sea, Northern Adriatic Sea and Levantine basin. Results extended the interpretation of previously detected patterns, indicating the dominance of Synechococcus-like versus prochlorophytes throughout the year at the basin level, and the predominance of nanoeukaryotes during the winter months. The method successfully reproduced the diatom blooms normally detected in the basin during the spring season (March to April), especially in the Adriatic Sea. According to our results, the PHYSAT-Med OC-CCI algorithm represents a useful tool for the spatio-temporal monitoring of dominant phytoplankton groups in Mediterranean surface waters. The successful applications of other regional ocean colour algorithms to the OC-CCI database will give rise to extended time series of phytoplankton functional types, with promising applications to the study of long-term oceanographic trends in a global change context.
Suicidal ideation among students of the 7th, 8th, and 9th grades in the State of Lara, Venezuela: the Global School Health Survey.

BACKGROUND Suicidal behavior among adolescents is not a well-explored public health problem. Health policy decision-making on suicidal behavior needs reliable information on the prevalence of suicidal ideation (SI) and its associated risk factors to produce health promotion and prevention programs. METHODS The Global School Health Survey is a self-administered survey done on a random probabilistic sample among students of the 7th, 8th, and 9th grades in the Lara State, Venezuela, school period 2003 to 2004. Point prevalence of SI and associated factors were included and the odds (OR) of having SI was calculated given selected factors. RESULTS Two-thousand seventy (2070) respondents, of which 13.5 % reported having SI in the last 12 months, and in females more than males (14.6% vs. 11.7%). The OR for SI, according to an associated risk factor, were among (a) females: age > or = 14 years (2.2), worries (3.42), loneliness (8.8), ever had sexual intercourse (5.58), alcohol (8.43) and (b) males: having only one or non close friends (3.69), alcohol (12.36), ever had sexual intercourse (2.73). CONCLUSION Behavioral risk factors are relatively new in the field of surveillance systems; therefore, results on SI should be cautiously taken into consideration and a wide discussion should be encouraged as we learn how to best use the results for health promotion and disease prevention.
Localized magnetic states in biased bilayer and trilayer graphene

We study the localized magnetic states of an impurity in biased bilayer and trilayer graphene. It is found that the magnetic boundary for bilayer and trilayer graphene shows mixed features of Dirac and conventional fermions. For zero gate bias, as the impurity energy approaches the Dirac point, the impurity magnetization region diminishes for bilayer and trilayer graphene. When a gate bias is applied, the dependence of impurity magnetic states on the impurity energy exhibits a different behavior for bilayer and trilayer graphene due to the opening of a gap between the valence and the conduction band in the bilayer graphene with an applied gate bias. The magnetic moment and the corresponding magnetic transition of the impurity in bilayer graphene are also investigated.
Inhibition of Notch signaling enhances transdifferentiation of the esophageal squamous epithelium towards a Barrett's-like metaplasia via KLF4

Barrett's esophagus (BE) is defined as an incomplete intestinal metaplasia characterized generally by the presence of columnar and goblet cells in the formerly stratified squamous epithelium of the esophagus. BE is known as a precursor for esophageal adenocarcinoma. Currently, the cell of origin for human BE has yet to be clearly identified. Therefore, we investigated the role of Notch signaling in the initiation of BE metaplasia. Affymetrix gene expression microarray revealed that BE samples express decreased levels of Notch receptors (NOTCH2 and NOTCH3) and one of the the ligands (JAG1). Furthermore, BE tissue microarray showed decreased expression of NOTCH1 and its downstream target HES1. Therefore, Notch signaling was inhibited in human esophageal epithelial cells by expression of dominant-negative-Mastermind-like (dnMAML), in concert with MYC and CDX1 overexpression. Cell transdifferentiation was then assessed by 3D organotypic culture and evaluation of BE-lineage specific gene expression. Notch inhibition promoted transdifferentiation of esophageal epithelial cells toward columnar-like cells as demonstrated by increased expression of columnar keratins (K8, K18, K19, K20) and glandular mucins (MUC2, MUC3B, MUC5B, MUC17) and decreased expression of squamous keratins (K5, K13, K14). In 3D culture, elongated cells were observed in the basal layer of the epithelium with Notch inhibition. Furthermore, we observed increased expression of KLF4, a potential driver of the changes observed by Notch inhibition. Interestingly, knockdown of KLF4 reversed the effects of Notch inhibition on BE-like metaplasia. Overall, Notch signaling inhibition promotes transdifferentiation of esophageal cells toward BE-like metaplasia in part via upregulation of KLF4. These results support a novel mechanism through which esophageal epithelial transdifferentiation promotes the evolution of BE.
[Studies on chemical constituents in Huangjuhua (flowers of Chrysanthemum morifolium)].

OBJECTIVE To study the chemical constituents in Huangjuhua (flowers of Chrysanthemum morifolium). METHOD The chemical constituents were isolated by various column chromatographic methods and structurally elucidated by NMR and MS evidences. RESULT Eleven compounds were obtained and identified as luteolin (1), quercetin (2), acacetin 7-O-beta-D-(3"-acetyl) -glucopyranoside (3), luteolin 7-O-beta-D-(6"-acetyl)-glucopyranoside (4), hesperetin 7-O-beta-D-glucopyranoside (5), acacetin 7-O-beta-D-glucopyranoside (6), diosmetin 7-O-beta-D-glucopyranoside (7), apigenin 7-O-beta-D-glucopyranoside (8), hesperidin (9), linarin (10), and luteolin 7-O-beta-D-glucopyranoside (11). CONCLUSION Compounds 4, 5 were isolated from the plant for the first time.
OF THE EXPERIMENTAL ANALYSIS OF BEHAVIOR VARIABLE-INTERVAL SCHEDULE PERFORMANCE IN OPEN AND CLOSED ECONOMIES

In two experiments, pigeons obtained food according to variable-interval schedules. In the first experiment, equivalent variable-interval schedules with average interreinforcer intervals ranging between 10 and 80 s in different conditions were studied in both open and closed economies. Response rates increased as reinforcement frequency decreased in the closed economy. By contrast, in the open economy response rates decreased for 1 bird and were variable for the other as reinforcement frequency decreased. The second experiment showed that the differences in the functions between responding and reinforcement frequency in the two types of economies were not due to changes in deprivation level. These results suggest that open and closed economies yield different behavioral effects. This conclusion is supported further by a reconsideration of previous findings that appear counter to the conclusion.
Prediction of catalytic site of proteins based on amino acid triads approach using non parametric function

In this study, we present a method for the catalytic site prediction of proteins rest on the triads of amino acids residues using non parametric function - artificial neural network. Using this method, we can efficiently predict that whether the amino acid triads of a protein are the part of catalytic site or not. For the preparation of training and test datasets, catalytic site residues of protein are downloaded from the database of catalytic site atlas and residues for non catalytic site are taken which are not participating in the formation of catalytic site of protein. This method used the numerical value of six physiochemical properties of amino acids along with the difference between centers of mass of whole protein and amino acids triads as the input for the neural network. Our analysis shows that this method is worked with the efficiency of 83.66% which is higher than other existing model for the prediction of catalytic site of protein. Our analysis is based on the residues physiochemical and topological properties and not on the evolutionary and sequence similarities so, In future, this work may help the researchers to develop tool and predicting the nature of residues of catalytic or active site of protein and may be helpful in ligand designing and molecular docking.
WEATHER ON OTHER WORLDS. I. DETECTION OF PERIODIC VARIABILITY IN THE L3 DWARF DENIS-P J1058.7-1548 WITH PRECISE MULTI-WAVELENGTH PHOTOMETRY

Photometric monitoring from warm Spitzer reveals that the L3 dwarf DENIS-P J1058.7-1548 varies sinusoidally in brightness with a period of hr and an amplitude of 0.388% ± 0.043% (peak-to-valley) in the 3.6 μm band, confirming the reality of a 4.31 ± 0.31 hr periodicity detected in J-band photometry from the SOAR telescope. The J-band variations are a factor of 2.17 ± 0.35 larger in amplitude than those at 3.6 μm, while 4.5 μm Spitzer observations yield a 4.5 μm/3.6 μm amplitude ratio of only 0.23 ± 0.15, consistent with zero 4.5 μm variability. This wide range in amplitudes indicates rotationally modulated variability due to magnetic phenomena and/or inhomogeneous cloud cover. Weak Hα emission indicates some magnetic activity, but it is difficult to explain the observed amplitudes by magnetic phenomena unless they are combined with cloud inhomogeneities (which might have a magnetic cause). However, inhomogeneous cloud cover alone can explain all our observations, and our data align with theory in requiring that the regions with the thickest clouds also have the lowest effective temperature. Combined with published vsin (i) results, our rotation period yields a 95% confidence lower limit of R* ⩾ 0.111 R☉, suggesting upper limits of 320 Myr and 0.055 M☉ on the age and mass. These limits should be regarded cautiously because of ∼3σ inconsistencies with other data; however, a lower limit of 45° on the inclination is more secure. DENIS-P J1058.7-1548 is only the first of nearly two dozen low-amplitude variables discovered and analyzed by the Weather on Other Worlds project.