Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of FTA Cards for Direct Sampling of Patients' Lesions in the Ecological Study of Cutaneous Leishmaniasis

ABSTRACT The FTA card (Whatman) was assessed for its utility as a molecular epidemiological tool in collecting samples from patients with leishmaniasis in Peru because the card has a variety of merits; it is less invasive for patients and easy to handle for both physicians and other medical personnel for sample collection or diagnosis, in addition to its simplicity and easy countrywide and/or intercountry transportation for analysis. Samples were collected from 132 patients suspected of having leishmaniasis, and Leishmania species were successfully identified in samples from 81 patients in 15 departments of Peru by cytochrome b and mannose phosphate isomerase gene analyses. Of these, 61.7% were identified as Leishmania (Viannia) peruviana, 22.2% as L. (V.) braziliensis, 12.3% as L. (V.) guyanensis, 2.5% as L. (V.) shawi, and 1.2% as L. (V.) lainsoni. The three predominant species, L. (V.) peruviana, L. (V.) braziliensis, and L. (V.) guyanensis, were mainly found in the Andean highlands, in the tropical rainforest, and in northern and central rainforest regions, respectively. This is the first time L. (V.) shawi has been identified outside Brazil. The present study showed that the FTA card will be a useful tool for the ecological study of different forms of leishmaniasis. Furthermore, collecting samples directly from patients' lesions by using the FTA card eliminates (i) the possibility of contamination of Leishmania isolates during short- and/or long-term passages of culture in vitro in each laboratory and (ii) pain and suffering of patients from taking samples by skin biopsy.
Lithium Controls Central Nervous System Autoimmunity through Modulation of IFN-γ Signaling

Inhibitors of glycogen synthase kinase 3 (GSK3) are being explored as therapy for chronic inflammatory diseases. We previously demonstrated that the GSK inhibitor lithium is beneficial in experimental autoimmune encephalomyelitis (EAE), the mouse model of multiple sclerosis. In this study we report that lithium suppresses EAE induced by encephalitogenic interferon-γ (IFN-γ)-producing T helper (Th1) cells but not by interleukin (IL)-17-producing T helper (Th17) cells. The therapeutic activity of lithium required functional IFN-γ-signaling, but not the receptor for type I IFN (IFNAR). Inhibitor/s of GSK3 attenuated IFN-γ dependent activation of the transcription factor STAT1 in naïve T cells as well as in encephalitogenic T cells and Th1 cells. The inhibition of STAT1 activation was associated with reduced IFN-γ production and decreased expansion of encephalitogenic Th1 cells. Furthermore, lithium treatment induced Il27 expression within the spinal cords of mice with EAE. In contrast, such treatment of Ifngr−/− mice did not induce Il27 and was associated with lack of therapeutic response. Our study reveals a novel mechanism for the efficacy of GSK3 targeting in EAE, through the IFN-γ-STAT1 axis that is independent IFNAR-STAT1 axis. Overall our findings set the framework for the use of GSK3 inhibitors as therapeutic agents in autoimmune neuroinflammation.
Urodynamic Investigation: A Valid Tool to Define Normal Lower Urinary Tract Function?

Objectives To evaluate whether urodynamic investigation (UDI), the gold standard to assess refractory lower urinary tract symptoms (LUTS), is appropriate to select healthy volunteers with apparent normal lower urinary tract function as control subjects for comparative studies. Subjects and Methods 42 healthy subjects (22 women, mean age 32±10 years; 20 men, mean age 37±12 years) without LUTS were included into this prospective single-centre cohort study. All subjects recorded a 3-day bladder diary, completed validated questionnaires regarding LUTS, and underwent neuro-urological assessment as well as free uroflowmetry. Same session repeat UDI was performed according to “Good Urodynamic Practice” recommended by the International Continence Society, but using an air-charged instead of a water-filled catheter, and evaluated by a blinded investigator. Results All 3-day bladder diaries, LUTS questionnaires, neuro-urological assessments and free uroflowmetries were within normal limits. Overall (either during the first or second UDI), same session repeat UDI revealed pathological findings in 71% (30/42): Detrusor overactivity was detected in 14% (3/22) and 30% (6/20), post void residual >100mL in 14% (3/22) and 25% (5/20), bladder outlet obstruction in 9% (2/22) and 20% (4/20) and detrusor sphincter dyssynergia in 77% (17/22) and 65% (13/20) of our women and men, respectively. Repeatability of detrusor overactivity (κ = 0.78, 95% CI: 0.54–1.02) and detrusor sphincter dyssynergia (κ = 0.77, 95% CI: 0.55–0.98) showed substantial agreement between both UDIs. All other assessed urodynamic parameters had wide 95% limits of agreement for differences in the parameters indicating poor repeatability. Conclusions More than 70% of our healthy subjects showed pathological urodynamic findings. Although UDI is the gold standard to assess refractory LUTS, it seems not to be applicable in healthy subjects to define normal lower urinary tract function. Therefore, we do not recommend using UDI to select healthy control subjects.
Buckling of thin metal shells

List of contributors. Preface 1. Buckling of thin shells: an overview 2. Cylindrical shells under axial compression 3. Cylindrical shells above local supports 4. Settlement beneath cylindrical shells 5. Cylindrical shells under uniform external pressure 6. Cylindrical shells under non-uniform external pressure 7. Cantilever cylindrical shells under wind loading 8. Cylindrical shells under torsion and transverse shear 9. Cylindrical shells under static and cyclic shear 10. Cylindrical shells under combined loading 11. Stiffened cylindrical shells 12. Large diameter fabricated steel tubes 13. Shell junctions 14. Rings at shell junctions 15. A probabilistic design approach for shell structures
The Rate-Controlled Constrained-Equilibrium Approach to Far-From-Local-Equilibrium Thermodynamics

The Rate-Controlled Constrained-Equilibrium (RCCE) method for the description of the time-dependent behavior of dynamical systems in non-equilibrium states is a general, effective, physically based method for model order reduction that was originally developed in the framework of thermodynamics and chemical kinetics. A generalized mathematical formulation is presented here that allows including nonlinear constraints in non-local equilibrium systems characterized by the existence of a non-increasing Lyapunov functional under the system’s internal dynamics. The generalized formulation of RCCE enables to clarify the essentials of the method and the built-in general feature of thermodynamic consistency in the chemical kinetics context. In this paper, we work out the details of the method in a generalized mathematical-physics framework, but for definiteness we detail its well-known implementation in the traditional chemical kinetics framework. We detail proofs and spell out explicit functional dependences so as to bring out and clarify each underlying assumption of the method. In the standard context of chemical kinetics of ideal gas mixtures, we discuss the relations between the validity of the detailed balance condition off-equilibrium and the thermodynamic consistency of the method. We also discuss two examples of RCCE gas-phase combustion calculations to emphasize the constraint-dependent performance of the RCCE method.
Problem Representations in Multitasking : a Cognitive Bottleneck ?

Most multitasking models make use of executive processes to assign resources to tasks (Kieras et al., 2000). An alternative is to have no executive, but constrain individual processes so that they share resources in a plausible way. Salvucci and Taatgen (under revision) in their theory of threaded cognition have shown how peripheral resources and declarative memory are shared between processes without an executive. In this paper we will extend this work by showing how two tasks share a resource to store the problem representation in a dual-task paradigm where either task sometimes needs a problem representation and sometimes not. Threaded cognition predicts extra interference when both tasks need a problem representation, which is what we found in the experiment.
Analysis of temperature distribution in composite plates during thermal fatigue

The paper discusses the character of the self-heating temperature distribution during thermal fatigue of laminated composite cantilever plate in the stress relaxation mode. The temperature distributions and their evolution were acquired on the own-designed test rig using infrared camera. The thermograms were compared with force and velocity of displacement measurements and dynamic properties of the investigated composite in order to evaluate characteristic distributions of a temperature for various phases of fatigue: the initiation of the self-heating, thermomechanical degradation, initiation and propagation of cracks etc. Basing on obtained results the correlation between self-heating temperature, stress relaxation and dynamic properties was presented. The characteristic temperature distributions were justified basing on plate theories.
Astral microtubules are not required for anaphase B in Saccharomyces cerevisiae

tub2-401 is a cold-sensitive allele of TUB2, the sole gene encoding beta-tubulin in the yeast, Saccharomyces cerevisiae. At 18 degrees C, tub2-401 cells are able to assemble spindle microtubules but lack astral microtubules. Under these conditions, movement of the spindle to the bud neck is blocked. However, spindle elongation and chromosome separation are unimpeded and occur entirely within the mother cell. Subsequent cytokinesis produces one cell with two nuclei and one cell without a nucleus. The anucleate daughter can not bud. The binucleate daughter proceeds through another cell cycle to produce a cell with four nuclei and another anucleate cell. With additional time in the cold, the number of nuclei in the nucleated cells continues to increase and the percentage of anucleate cells in the population rises. The results indicate that astral microtubules are needed to position the spindle in the bud neck but are not required for spindle elongation at anaphase B. In addition, cell cycle progression does not depend on the location or orientation of the spindle.
Topic-Based Coherence Modeling for Statistical Machine Translation

Coherence that ties sentences of a text into a meaningfully connected structure is of great importance to text generation and translation. In this paper, we propose topic-based coherence models to produce coherence for document translation, in terms of the continuity of sentence topics in a text. We automatically extract a coherence chain for each source text to be translated. Based on the extracted source coherence chain, we adopt a maximum entropy classifier to predict the target coherence chain that defines a linear topic structure for the target document. We build two topic-based coherence models on the predicted target coherence chain: 1) a word level coherence model that helps the decoder select coherent word translations and 2) a phrase level coherence model that guides the decoder to select coherent phrase translations. We integrate the two models into a state-of-the-art phrase-based machine translation system. Experiments on large-scale training data show that our coherence models achieve substantial improvements over both the baseline and models that are built on either document topics or sentence topics obtained under the assumption of direct topic correspondence between the source and target side. Additionally, further evaluations on translation outputs suggest that target translations generated by our coherence models are more coherent and similar to reference translations than those generated by the baseline.
Terahertz Plasmonic Structure With Enhanced Sensing Capabilities

We have designed, fabricated, and experimentally verified a highly sensitive plasmonic sensing device in the terahertz frequency range. For a proof of concept of the sensing phenomenon, we have chosen the so-called fishnet structure based on circular hole array insensitive to the polarization of the incident wave. We employ the localized resonance associated with the cutoff frequency (electric plasma frequency) of the hole array to investigate its sensing capability. A thin-film overlayer deposited on the surface of the metallic apertures causes an amplitude modulation and a shift in the resonant frequency of the terahertz transmission. The frequency shift and the amplitude modulation were investigated as a function of the refractive index and the thickness of the overlayer for determining the sensing potential of the proposed structure. Measurements carried out using terahertz time-domain spectroscopy show good agreement with the numerical predictions. The results we obtained indicate that the proposed device could be very promising for enhancing the sensing capabilities of the refractive index changes involved in bio-applications, for instance.
Transfer Region of pO113 from Enterohemorrhagic Escherichia coli: Similarity with R64 and Identification of a Novel Plasmid-Encoded Autotransporter, EpeA

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) is a prominent, food-borne cause of diarrhea, bloody diarrhea, and the hemolytic uremic syndrome in industrialized countries. Most strains of EHEC carry the locus for enterocyte effacement (LEE) pathogenicity island, but a proportion of isolates from patients with severe disease do not carry LEE and very little is known about virulence factors in these organisms. LEE-negative strains of EHEC typically express Shiga toxin 2 and carry a large plasmid that encodes the production of EHEC hemolysin. In this study, we determined the nucleotide sequence of the transfer region of pO113, the large hemolysin plasmid from LEE-negative EHEC O113:H21 (EH41). This 63.9-kb region showed a high degree of similarity with the transfer region of R64, and pO113 was capable of self-transmission at low frequencies. Unlike R64 and the related dot/icm system of Legionella pneumophila, however, pO113 was unable to mobilize RSF1010. In addition, the pO113 transfer region encoded a novel high-molecular-weight serine protease autotransporter of Enterobacteriaceae (SPATE) protein, termed EpeA. Like other SPATEs, EpeA exhibited protease activity and mucinase activity, but expression was not associated with a cytopathic effect on epithelial cells. Analysis of a second high-molecular-weight secreted protein revealed that pO113 also encodes EspP, a cytopathic SPATE identified previously in EHEC O157:H7. The nucleotide sequences encoding the predicted β-domains of espP and epeA were identical and also shared significant homology with a third SPATE protein, EspI. Both espP and epeA were detected in several LEE-negative clinical isolates of EHEC and thus may contribute to the pathogenesis of this subset of EHEC.
Phylogeny-Based Rapid Identification of Mycoplasmas and Ureaplasmas from Urethritis Patients

ABSTRACT Some strains of mycoplasmas and ureaplasmas (family Mycoplasmataceae) are associated with nongonococcal urethritis (NGU) or other genitourinary infections. We have developed a rapid and reliable method of identifying the presence and prevalence of mycoplasmas and ureaplasmas in men with NGU. This method is based on the amplification of a part of the 16S rRNA gene by PCR and phylogenetic analysis. A portion of the 16S rRNA gene from 15 prototype strains was amplified with a set of common primers, and their nucleotides were sequenced. The nucleotide sequence of the V4 and V5 regions was analyzed by the neighbor-joining method. The 15 prototype strains were grouped into three distinct clusters, allowing us to clearly segregate the strains into distinct lineages. To determine the prevalence of these pathogens among patients with NGU, this protocol was tested with 148 urine samples. Amplifications were observed for 42 samples, and their nucleotide sequences were analyzed along with those of the 15 prototype strains. The phylogenetic tree thus constructed indicated that 15 of the 42 formed a cluster with Mycoplasma genitalium. Among the remaining specimens, 2 formed a cluster with Mycoplasma hominis, 19 with Ureaplasma urealyticum, and 5 with Ureaplasma parvum; the remaining sample contained both M. genitalium and U. urealyticum. This phylogeny-based identification of mycoplasmas and ureaplasmas provides not only a powerful tool for rapid diagnosis but also the basis for etiological studies of these pathogens.
Recognizing Mathematical Expressions Using Tree Transformation

We describe a robust and efficient system for recognizing typeset and handwritten mathematical notation. From a list of symbols with bounding boxes the system analyzes an expression in three successive passes. The Layout Pass constructs a Baseline Structure Tree (BST) describing the two-dimensional arrangement of input symbols. Reading order and operator dominance are used to allow efficient recognition of symbol layout even when symbols deviate greatly from their ideal positions. Next, the Lexical Pass produces a Lexed BST from the initial BST by grouping tokens comprised of multiple input symbols; these include decimal numbers, function names, and symbols comprised of nonoverlapping primitives such as "=". The Lexical Pass also labels vertical structures such as fractions and accents. The Lexed BST is translated into L/sup A/T/sub E/X. Additional processing, necessary for producing output for symbolic algebra systems, is carried out in the Expression Analysis Pass. The Lexed BST is translated into an Operator Tree, which describes the order and scope of operations in the input expression. The tree manipulations used in each pass are represented compactly using tree transformations. The compiler-like architecture of the system allows robust handling of unexpected input, increases the scalability of the system, and provides the groundwork for handling dialects of mathematical notation.
Static Specification Mining Using Automata-Based Abstractions

We present a novel approach to client-side mining of temporal API specifications based on static analysis. Specifically, we present an interprocedural analysis over a combined domain that abstracts both aliasing and event sequences for individual objects. The analysis uses a new family of automata-based abstractions to represent unbounded event sequences, designed to disambiguate distinct usage patterns and merge similar usage patterns. Additionally, our approach includes an algorithm that summarizes abstract traces based on automata clusters, and effectively rules out spurious behaviors. We show experimental results mining specifications from a number of Java clients and APIs. The results indicate that effective static analysis for client-side mining requires fairly precise treatment of aliasing and abstract event sequences. Based on the results, we conclude that static client-side specification mining shows promise as a complement or alternative to dynamic approaches.
Notch2, but not Notch1, is required for proximal fate acquisition in the mammalian nephron

The Notch pathway regulates cell fate determination in numerous developmental processes. Here we report that Notch2 acts non-redundantly to control the processes of nephron segmentation through an Rbp-J-dependent process. Notch1 and Notch2 are detected in the early renal vesicle. Genetic analysis reveals that only Notch2 is required for the differentiation of proximal nephron structures (podocytes and proximal convoluted tubules) despite the presence of activated Notch1 in the nuclei of putative proximal progenitors. The inability of endogenous Notch1 to compensate for Notch2 deficiency may reflect sub-threshold Notch1 levels in the nucleus. In line with this view, forced expression of a γ-secretase-independent form of Notch1 intracellular domain drives the specification of proximal fates where all endogenous, ligand-dependent Notch signaling is blocked by aγ -secretase inhibitor. These results establish distinct (non-redundant), instructive roles for Notch receptors in nephron segmentation.
Deciphering magnetospheric cross‐field currents

A single near‐tail magnetic field line can be part of a variety of cross‐field current systems, making the interpretation of such currents difficult. It is shown that global, coupled‐model simulation results from the 22 October 1999 storm include a field line crossing downtail at L = 8 during the main phase that contains partial ring current, symmetric ring current, and tail current simultaneously. Such field lines with multiple currents are common in the near‐Earth tail. Another time from the same event showed two closely‐spaced field lines (L = 6.0 and 6.5) with completely different current systems on them (one entirely symmetric ring current and the other entirely tail current). It is shown that, for this storm from this simulation, the tail current inner edge systematically shifts inward then outward during the storm main phase and that most of the Dst perturbation is from the ring current (both partial and symmetric). Caution is advised when analyzing observational or numerical cross‐field currents and when making conclusions about which type of current system dominates the distortion of the near‐Earth magnetosphere.
Microstructures and Interfaces in Concrete after 15 Years of Exposure in Tidal Environment

Detailed investigations on the properties of concrete specimens after long-term exposure to a marine environment are very scarce in the technical literature. In this paper, a detailed study of microstructure and aggregate-matrix and steel-matrix interfaces in concrete specimens after 15 years of exposure to a tidal environment was conducted. Cement types were ordinary portland, slag cements, and fly ash cement. The results of this research will be useful in understanding the changes in microstructure and interfacial conditions after a long-term exposure, and comparing them with the short-term laboratory test results.
Poor Performance of Current Prognostic Scores for Early Risk of Recurrence After Minor Stroke

Background and Purpose— The ABCD2 score predicts the early risk of stroke after transient ischemic attack. The early risk of recurrence after minor stroke is as high but the only validated prognostic scores for use in minor stroke predict long-term risk of recurrence: the Essen Stroke Risk Score and the Stroke Prognosis Instrument II. Methods— We determined the prognostic value of the ABCD2 score, Essen Stroke Risk Score, and Stroke Prognosis Instrument II in a prospective population-based study in Oxfordshire, UK, of all incident and recurrent stroke (Oxford Vascular Study). Minor stroke was defined as an National Institutes of Health Stroke Scale score ≤5 at the time of first assessment. The 90-day risks of recurrent stroke were determined in relation to each score. Areas under the receiver operator curves indicated predictive value. Results— Of 1247 first events in the study period, 488 were transient ischemic attacks, 520 were minor strokes, and 239 were major strokes. The ABCD2 score was modestly predictive (area under the receiver operator curve, 0.64; 0.53 to 0.74; P=0.03) of recurrence at 7 days after minor stroke and at 90 days (0.62; 0.54 to 0.70; P=0.004). Neither Essen Stroke Risk Score (0.50; 0.42 to 0.59; P=0.95) nor Stroke Prognosis Instrument II (0.48; 0.39 to 0.60; P=0.92) were predictive of 7-day or 90-day risk of recurrent stroke. Of the traditional vascular risk factors, etiologic classification (Trial of ORG 10172 in Acute Stroke Treatment) and variables in the ABCD2 score, only blood pressure >140/90 mm Hg (hazard ratio, 2.75; 1.18 to 6.38; P=0.02) and large artery disease (hazard ratio, 2.21; 1.00 to 4.88; P=0.05) were predictive of 90-day risk. Conclusions— The predictive power of the ABCD2 score is modest in patients with minor stroke, and neither the Essen Stroke Risk Score nor the Stroke Prognosis Instrument II predicts early recurrence. More reliable early risk prediction after minor stroke is required.