Miracle-dz/UniFAR-FTUs huggingface dataset:
The rec locus, a competence-induced operon in Streptococcus pneumoniae

To study competence and the process of transformation (TFN) in pneumococci, we developed a method for isolating TFN- mutants using insertional inactivation coupled with fusions to the gene for alkaline phosphatase (phoA). One TFN- mutant transformed 2 log units less efficiently than the parent strain. Reconstitution of the mutated region revealed a locus, rec, that contains two polycistronic genes, exp10 and the previously identified recA (B. Martin, J. M. Ruellan, J. F. Angulo, R. Devoret, and J. P. Claverys, Nucleic Acids Res. 20:6412, 1992). Exp10 is likely to be a membrane-associated protein, as it has a prokaryotic signal sequence and an Exp10-PhoA fusion localized with cell membranes. On the basis of sequence similarity, pneumococcal RecA is a member of bacterial RecA proteins responsible for homologous recombination of DNA. DNA-RNA hybridization analysis showed that this locus is transcribed as a polycistronic message, with increased transcription occurring during competence. With an Exp10-PhoA chimera used as a reporter, there was a 10-fold increase in the expression of the rec locus during competence while there was only minimal expression under growth conditions that repressed competence. The TFN- mutant containing the exp10-phoA fusion produced activator, a small extracellular polypeptide that induces competence, and the expression of rec was induced in response to activator. Therefore, the rec locus is directly required for genetic transformation and is regulated by the cell signaling mechanism that induces competence.
The Arabidopsis sickle Mutant Exhibits Altered Circadian Clock Responses to Cool Temperatures and Temperature-Dependent Alternative Splicing

The Arabidopsis SICKLE gene plays a role in pre-mRNA metabolism that influences alternative splicing of core circadian clock transcripts, temperature entrainment, and temperature compensation. The circadian clock allows plants to anticipate and respond to daily changes in ambient temperature. Mechanisms establishing the timing of circadian rhythms in Arabidopsis thaliana through temperature entrainment remain unclear. Also incompletely understood is the temperature compensation mechanism that maintains consistent period length within a range of ambient temperatures. A genetic screen for Arabidopsis mutants affecting temperature regulation of the PSEUDO-RESPONSE REGULATOR7 promoter yielded a novel allele of the SICKLE (SIC) gene. This mutant, sic-3, and the existing sic-1 mutant both exhibit low-amplitude or arrhythmic expression of core circadian clock genes under cool ambient temperature cycles, but not under light-dark entrainment. sic mutants also lengthen free running period in a manner consistent with impaired temperature compensation. sic mutant alleles accumulate LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1) splice variants, among other alternatively spliced transcripts, which is exacerbated by cool temperatures. The cca1-1 lhy-20 double mutant is epistatic to sic-3, indicating the LHY and CCA1 splice variants are needed for sic-3 circadian clock phenotypes. It is not expected that SIC is directly involved in the circadian clock mechanism; instead, SIC likely contributes to pre-mRNA metabolism, and the splice variants that accumulate in sic mutants likely affect the circadian clock response to cool ambient temperature.
Hormontherapie in der Peri- und Postmenopause und Mammakarzinom-Risiko

Die Hormontherapie (HT) in Peri- und Postmenopause mit Ostrogenen und Gestagenen ist mit einem erhohten Mammakarzinomrisiko assoziiert. Hormone spielen eine wichtige Rolle im Entstehungsprozess dieser malignen Erkrankung. Fur das Risiko, ein Mammakarzinom zu entwickeln, haben reproduktive Faktoren einen relevanten Einfluss. Die Anwendung von Sexualsteroiden im Rahmen einer HT stellt einen potentiellen Risikofaktor dar. Zu der Fragestellung wurden in den letzten Jahren eine Reihe von Beobachtungs- und randomisierten Studien publiziert. Diese Ubersicht gibt einen Uberblick der derzeitigen Datenlage zu diesem Thema.
The inactivation of foot and mouth disease, Aujeszky's disease and classical swine fever viruses in pig slurry

The aim of the study was to investigate the decontamination of pig slurry containing exotic viruses of pigs, foot and mouth disease virus (FMDV), Aujeszky's disease virus (ADV) and classical swine fever virus (CSFV). Laboratory‐scale decontamination experiments showed that FMDV, ADV and CSFV were heat inactivated in slurry within 3 min at 67 °C, 3 min at 62 °C and 3 min at 60 °C and in Glasgow Eagles medium within 5 min at 67 °C, 4 min at 65 °C and 2 min at 65 °C, respectively. At pilot scale, FMDV was heat inactivated at 66 °C in water and 61 °C in slurry, ADV at 61 °C in water or slurry and CSFV at 62 °C in water and 50 °C in slurry. Treatment of pig slurry for the inactivation of exotic viruses may be achieved through the use of a thermal pilot plant operating in continuous mode. The work demonstrates the suitability of thermal treatment in ensuring the safety of pig slurry following a disease outbreak.
An Active Contour Model with Improved Shape Priors using Fourier Descriptors

Snakes or active contours are widely used for image segmentation. There are many different implementationsof snakes. No matter which implementation is being employed, the segmentation results suffer greatly inpresence of occlusions, noise, concavities or abnormal modification of shape. If some prior knowledge aboutthe shape of the object is available, then its addition to an existing model can greatly improve the segmentationresults. In this work inclusion of such shape constraints for explicit active contours is presented. Theseshape priors are introduced through the use of Fourier based descriptors which makes them invariant to thetranslation, scaling and rotation factors and enables the deformable model to converge towards the prior shapeeven in the presence of occlusion and context noise. These shape constraints have been computed in descriptorspace so no reconstruction is required. Experimental results clearly indicate that the inclusion of these shapepriors greatly improved the segmentation results in comparison with the original snake model.
Safety of Radial Access for Primary Percutaneous Intervention in Patients With ST-Elevation Acute Myocardial Infarction: Results From a Low-Volume Center

Radial access for primary percutaneous coronary intervention (pPCI) in patients with ST-elevation acute myocardial infarction (STEMI) is recommended in high-volume experienced centers. This study investigated whether radial access for pPCI is safe even in a low-volume center. We performed radial access for pPCI in 171 patients. Major adverse cardiac events (total death, myocardial infarction, stroke) rate was 1.2%. The overall incidence of bleeding complications was 2.4%; there was no vascular complication at the access site. In patients with STEMI undergoing pPCI, the results of radial access in a low-volume center were acceptable. These findings support the safety of radial access in patients with STEMI.
Rule-based fuzzy systems with weighted power mean firing operator as universal approximators

Certain classes of fuzzy rule-based systems have been shown to be universal approximators, capable of approximating any continuous mapping on a compact subset of the domain. In previous cases, this property has been proven for fuzzy systems employing t-norms to determine the firing level of each rule. In this paper, we prove that use of the weighted power mean to determine rule firing levels also results in a universal approximator. While it is only a t-norm in certain special cases, the weighted power mean is a more general aggregation operator, capable of providing greater logical flexibility in a rule. This will be of particular interest in computing with words (CWW) applications, where such flexibility is needed the better to mimic human reasoning.
Characterization and Structure of the Vaccinia Virus NF-κB Antagonist A46 *

Background: Vaccinia virus encodes several anti-inflammatory proteins that interfere with host signaling pathways. Results: The protein A46 has a similar fold to other vaccinia virus anti-inflammatory proteins but uses a different dimer interface. Conclusion: Variations in quaternary structure can affect the specificity of interactions of anti-inflammatory proteins. Significance: The structure illustrates how viruses can generate versatility of function from the same protein fold. Successful vaccinia virus (VACV) replication in the host requires expression of viral proteins that interfere with host immunity, such as antagonists of the activation of the proinflammatory transcription factor NF-κB. Two such VACV proteins are A46 and A52. A46 interacts with the Toll-like receptor/interleukin-1R (TIR) domain of Toll-like receptors and intracellular adaptors such as MAL (MyD88 adapter-like), TRAM (TIR domain-containing adapter-inducing interferon-β (TRIF)-related adaptor molecule), TRIF, and MyD88, whereas A52 binds to the downstream signaling components TRAF6 and IRAK2. Here, we characterize A46 biochemically, determine by microscale thermophoresis binding constants for the interaction of A46 with the TIR domains of MyD88 and MAL, and present the 2.0 Å resolution crystal structure of A46 residues 87–229. Full-length A46 behaves as a tetramer; variants lacking the N-terminal 80 residues are dimeric. Nevertheless, both bind to the Toll-like receptor domains of MAL and MyD88 with KD values in the low μm range. Like A52, A46 also shows a Bcl-2-like fold but with biologically relevant differences from that of A52. Thus, A46 uses helices α4 and α6 to dimerize, compared with the α1-α6 face used by A52 and other Bcl-2 like VACV proteins. Furthermore, the loop between A46 helices α4-α5 is flexible and shorter than in A52; there is also evidence for an intramolecular disulfide bridge between consecutive cysteine residues. We used molecular docking to propose how A46 interacts with the BB loop of the TRAM TIR domain. Comparisons of A46 and A52 exemplify how subtle changes in viral proteins with the same fold lead to crucial differences in biological activity.
Description and Evaluation of a Short Writing Assignment in Historical Geology.

A writing assignment in an introductory historical geology class introduces students to technical writing, provides an opportunity for them to critically review other student papers, and increases their understanding of the subject material. The students write a short paper in which they describe and interpret the history of a geologic feature of their choice. They constructively criticize two other student papers and then revise their own papers based on the peer reviews. Topics have included specific outcrops, beach sediments, hand samples, building stones and fossil specimens. Students responded enthusiastically to the writing exercise and review process. More than 90 percent of the students who received comments on their papers considered the critiques helpful. This assignment actively involves students in the learning process and challenges them to apply classroom knowledge to the outside world.
Subclasses of IgG Antibodies in Immune Thrombocytopenic Purpura (ITP)

Summary. The subclasses of platelet‐associated IgG were measured on the platelets of patients with immune thrombocytopenic purpura (ITP) by modification of the antiglobulin consumption test. All subclasses were found. In most patients, one subclass was predominant; this was usually IgG1. The platelet‐associated IgG in normal donors is predominantly IgGl and IgG2.
Treatment of Vogt-Koyanagi-Harada Disease by Corticosteroids and Immunosuppresive Agents

Narsing A. Rao, MD Doheny Eye Institute, University of Southern California, Los Angeles, CA, USA Vogt-Koyanagi-Harada syndrome (VKH), also referred to as Vogt-KoyanagiHarada disease, is characterized by its distinct clinical and histopathologic features. The clinical features include symptoms of meningeal irritation, followed by signs of bilateral intraocular inflammation commonly associated with multifocal serous retinal detachments in the posterior pole and/or serous exudative detachment involving the inferior retina. Associated features include the presence of disc hyperemia and/or swelling in the vast majority of the cases and dysacusis in some individuals. All of these features are observed during the acute phase of the disease. In contrast, those patients who progress to chronic or chronic recurrent phases of the disease show signs of integumentory depigmentation, poliosis, and sunset glow fundus with peripheral nummular chorioretinal scars. The clinical features of VKH thus differ depending on the phase of the disease. Moreover, several studies have revealed that not all VKH patients experience cutaneous and auditory changes. In those patients who present with ocular changes only, laboratory detection of cerebrospinal fluid pleocytosis, fluorescein angiographic documentation of multiple focal leaks at the level of the retinal pigment epithelium, and ultrasonographic detection of choroid thickening primarily in the juxtapapillary area have been helpful for establishing the diagnosis.1,2 Once the diagnosis of VKH is established, most clinicians with expertise in the field of uveitis initially prescribe a high-dose corticosteroid, either orally (1 to 1.5 mg/kg/day) or through a short course of intravenous delivery, followed by oral administration of the agent. A majority of those patients who show improvement when their VKH is treated with a 4to 6-month initial course of high-dose corticosteroids with gradual tapering do not go on to develop chronic VKH. These patients, therefore, avoid such common complications as subretinal neovascularization, proliferation of retinal pigment epithelium (subretinal fibrosis), cataract, and glaucoma.1 These complications, along with chronic intraocular inflammation, result in significant loss of vision. Of course, those patients who cannot tolerate prolonged high-dose treatment with corticosteroids require immunomodulatory agents such as cyclosporine, methotrexate, azathioprin, mycophenolate mofetil (Cell Cept), and rarely, cyclophosphamide. Moreover, those patients who present with chronic phase or chronic recurrent disease often require the concurrent use of immunomodulatory agents and corticosteroids to suppress the ocular inflammation.
Lupus anticoagulants and the risk of a first episode of deep venous thrombosis

Summary. We have determined lupus anticoagulants, anti‐β2 glycoprotein I (β2GPI) and antiprothrombin antibodies in the Leiden Thrombophilia Study, a population‐based case–control study designed to determine risk factors for deep venous thrombosis (DVT). Lupus anticoagulant (LAC) was measured in 473 patients and 472 control subjects. Four control subjects (0.9%) and 14 patients (3.1%) had a positive LAC, resulting in a 3.6‐fold increased risk [odds ratio (OR) 3.6, 95% CI: 1.2–10.9]. Of the total population, 49 were positive for anti‐β2GPI antibodies: 15 controls (3.4%) and 34 patients (7.5%), implying a 2.4‐fold increased risk (95% CI: 1.3–4.2). Antiprothrombin antibodies were present in 114 subjects: 48 controls (11.0%) and 66 cases (14.6%) with an OR of 1.4 (95% CI: 1.0–2.1). When LAC was considered in the co‐presence of antiprothrombin or anti‐β2GPI antibodies the OR increased to 10.1 (95% CI: 1.3–79.8). A LAC without a positive anti‐β2GPI or antiprothrombin test was not associated with a risk for DVT (OR 1.3, 95% CI: 0.3–6.0). This study demonstrates that the presence of LAC, anti‐β2GPI antibodies and antiprothrombin antibodies are risk factors for DVT in a general population. The strongest association holds for the combination LAC and the presence of anti‐β2GPI or antiprothrombin antibodies.
Olanzapine in the Treatment of Refractory Migraine and Chronic Daily Headache

Background. —Olanzapine, a thienobenzodiazepine, is a new “atypical” antipsychotic drug. Olanzapine's pharmacologic properties suggest it would be effective for headaches, and its propensity for inducing acute extrapyramidal reactions or tardive dyskinesia is relatively low. We thus decided to assess the value of olanzapine in the treatment of chronic refractory headache.
Control of Voluntary Movement in Indefinite Environment - Real-time Optimization of Reaching Patterns by Constraints Emergence and Satisfaction

Humans achieve reaching movements even when environmental conditions change unexpectedly, and because the human arm is redundant, constraints should be needed in the controller. To adapt to environmental changes, we have previously proposed new constraints for reaching movement, based on realtime optimization of motion patterns. However, consistency of our model to conventional models, which were based on offline optimization, has not been investigated. In this paper, we have compared our model to the conventional minimum torque change model for a redundant three joints arm. In a slow reaching condition, our model produced similar motion to the one by minimum torque change, whereas in a fast condition, the minimum torque change was not satisfied by our model but it generated postures with comfortable joint angles. These results indicated that our model would include minimum torque change criterion along with another criterion which evaluates kinematic comfort determined by the arm posture.
Effect of preslaughter feeding and ractopamine hydrochloride supplementation on growth performance, carcass characteristics, and end product quality in market dairy cows.

An experiment was conducted in market dairy cows to determine the effect of feeding time and ractopamine hydrochloride (RAC) on growth performance, carcass characteristics, and end product quality. In 3 replicates, 9 Holstein cows per replicate (n = 27; 659 +/- 25.3 kg initial BW) culled from 3 dairies were randomly assigned to 3 treatments: 1) slaughter immediately (control), 2) feed for 90 d (NoR), or 3) feed for 90 d with RAC (312 mg.cow(-1). d(-1)) for the final 32 d (RAC). On d 0, NoR and RAC cows were placed in individual pens and fed a high concentrate diet (86% concentrate, DM basis) for 90 d before slaughter. All cows were subjectively scored for BCS and locomotion score on d 0, and NoR and RAC cows were evaluated again after 90 d. Individual DMI was recorded daily throughout the trial, and BW was collected every 14 d. Age and age x treatment did not affect (P > 0.05) any of the traits evaluated in this study. When cows fed for 90 d (NoR and RAC combined) were compared with nonfed controls, fed cows had greater (P < 0.001) final BCS, BW and HCW, lower (P < 0.001) final locomotion score, and greater (P < 0.03) dressing percentage, external fat thickness, and marbling score. Fed cows also tended to have more desirable yield grade (P = 0.08), ribeye area (P = 0.11), fat color (P = 0.09), lean maturity (P = 0.06), and quality grade (P = 0.09) compared with control cows. Warner-Bratzler shear force was not affected (P = 0.23) by feeding. However, a 12-member trained sensory panel revealed that fed cow carcasses had more desirable (P < 0.04) tenderness, juiciness, and overall acceptability than control cow carcasses. Flavor intensity also tended (P = 0.10) to be more desirable for fed vs. control cows. No difference (P > 0.10) in off-flavor was detected among treatments. Finally, there was no effect (P > 0.10) of RAC on growth performance, carcass characteristics, or end product quality. In conclusion, feeding a high concentrate diet for 90 d improved important live animal, carcass, and end product characteristics related to the quality and palatability of beef from market dairy cows; however, no effect of RAC supplementation was observed.
Construction of geo-information conceptual classification system based on ontology

Geographic information classification is one of the important topics in Geographical Ontology research. Based on the analysis of existing geographical ontological theory research and application research achievements, combining with the particularity of geographic object, this paper has made in-depth research of geographic information classification theory by using ontology and spatial cognition theory. As an example, the classification of settlement place-a kind of social economic factors is studied here. The research is started with the meta-properties of concept, and the effects of multiplicate factors on classification of geographical elements have been considered synthetically, such as the characteristics of geo-ontology and the spatial structural attribute of geographic object, etc. The purpose of this study is to construct a complete geo-information conceptual classification system based on ontology, so as to solve the existing problems of former classification system.
Fast entity recognition in biomedical text

In biomedical text mining, entity recognition is often an early task in the pipeline of analyzing free text. MetaMap, the de facto standard software tool for this task, employs much Natural Language Processing (NLP) machinery to recognize entities in UMLS (Unified Medical Language System), the largest metathesaurus. Knowing that the NLP machinery is time-consuming, and that UMLS is rich in lexical variations, this work investigates whether a fast, string similarity-based method can achieve results comparable to those of MetaMap. We implemented an NLP-light method that performs fast MinHash lookups via character trigram features. Starting with UMLS as the dictionary of entities, we select a subset whose entity names are short and thus amenable to a string similarity-based approach. We applied the method to both scientific literature and layman-oriented texts from Internet health portals. Our proposed method achieved up to 83% precision and 78% coverage under a strict rating scheme that penalizes failure in Word Sense Disambiguation (WSD), at a throughput of 1,720 PubMed abstracts or 175 web pages per minute. When compared to MetaMap, our proposed method achieved comparable precision and 13% less coverage using less than 1% of the time.
Cascaded Multilevel Inverter Employing Three-Phase Transformers and Single DC Input

This paper proposes an isolated cascaded multilevel inverter employing low-frequency three-phase transformers and a single DC input power source. The proposed circuit configuration can reduce a number of transformers compared with traditional three-phase multilevel inverters using single-phase transformers. It controls switching phase angles to obtain an optimal switching pattern identified with the fundamental frequency of the output voltage. Owing to this control strategy, harmonic components of the output voltage and switching losses can be diminished considerably. To verify the performance of the proposed approach, we implemented computer-aided simulations and experiments using a prototype.
Restoration algorithms for imaging through atmospheric turbulence

Abstract : This research project had focused on algorithms for imaging through atmospheric turbulence. An open dataset, called OTIS (Open Turbulent Image Set), was created for the community for algorithms assessment. Anew wavelet burst accumulation method was proposed to reconstruct a restored image from a sequence of frames. We proposed a new spatio-temporal point of view for the moving object detection problem and we designed a vector field decomposition algorithm to numerically solved this problem. Finally, we mention some work currently in progress about a lucky imaging based super-resolution algorithm, as well as our current work on the simplification of the Fried kernel for deconvolution purposes.