Miracle-dz/UniFAR-FTUs huggingface dataset:
A Molecular Gram Stain Using Broad Range PCR and Pyrosequencing Technology: A Potentially Useful Tool for Diagnosing Orthopaedic Infections

The bacteria associated with orthopaedic infections are usually common gram-positive and gram-negative bacteria. This fundamental grouping of bacteria is a necessary first step in the selection of appropriate antibiotics. Since polymerase chain reaction (PCR) is more rapid and may be more sensitive than culture, we developed a postamplification pyrosequencing method to subcategorize bacteria based on a few nucleotide polymorphisms in the 16S rRNA gene. We validated this method using well-characterized strains of bacteria and applied it to specimens from spinal surgery cases with suspected infections. Lysates of 114 bacteria including 75 species were created following standard cultivation to obtain DNA. The DNA was amplified by a broad-range real-time PCR. The amplicons were evaluated by pyrosequencing and were classified as gram-positive, gram-negative, or acid-fast bacilli based on the first three to five nucleotides sequenced. In addition, clinical cases of suspected infection were obtained from spinal surgery. The results of the “molecular Gram stain” were compared with the results of traditional Gram stain and culture. The lysates of 107 (93.9%) of the bacteria extracts tested were appropriately categorized as gram-positive and gram-negative or as acid-fast bacilli on the basis of this assay. The sensitivity and specificity of this assay were 100% and 97.4% for gram-positive and 88.3% and 100% for gram-negative isolates. All of the five clinical samples were appropriately categorized as containing gram-positive or gram-negative bacteria with this assay. This study demonstrates that high sensitivity and specificity of a molecular gram stain may be achieved using broad-range real-time PCR and pyrosequencing.
Modeling time series volatility using fuzzy rule systems

Summary form only given. A special class of volatility models based on Takagi-Sugeno fuzzy rules is presented in the paper. The corresponding identification problem is stated and techniques for constructing and estimating fuzzy rules by observation data are thoroughly described. A comparison between models of proposed class and traditional ARCH-/GARCH-models is made for a sample data produced by a non-linear model. A question of using fuzzy rule systems for modeling time-varying volatility of real-life time series is briefly discussed.
A Study on Immersion and Presence of a Portable Hand Haptic System for Immersive Virtual Reality

This paper proposes a portable hand haptic system using Leap Motion as a haptic interface that can be used in various virtual reality (VR) applications. The proposed hand haptic system was designed as an Arduino-based sensor architecture to enable a variety of tactile senses at low cost, and is also equipped with a portable wristband. As a haptic system designed for tactile feedback, the proposed system first identifies the left and right hands and then sends tactile senses (vibration and heat) to each fingertip (thumb and index finger). It is incorporated into a wearable band-type system, making its use easy and convenient. Next, hand motion is accurately captured using the sensor of the hand tracking system and is used for virtual object control, thus achieving interaction that enhances immersion. A VR application was designed with the purpose of testing the immersion and presence aspects of the proposed system. Lastly, technical and statistical tests were carried out to assess whether the proposed haptic system can provide a new immersive presence to users. According to the results of the presence questionnaire and the simulator sickness questionnaire, we confirmed that the proposed hand haptic system, in comparison to the existing interaction that uses only the hand tracking system, provided greater presence and a more immersive environment in the virtual reality.
Pseudomonas aeruginosa Exotoxin Y Is a Promiscuous Cyclase That Increases Endothelial Tau Phosphorylation and Permeability*

Background: ExoY induces inter-endothelial gaps, although the mechanisms by which this occurs are poorly understood. Results: ExoY synthesized cAMP and cGMP, which caused endothelial Tau hyperphosphorylation, accumulation of insoluble Tau, inter-endothelial cell gaps, and increased permeability. Conclusion: ExoY is a promiscuous cyclase and an edema factor. Significance: Acute Pseudomonas infections cause a pathophysiological sequela in endothelium previously recognized only in chronic neurodegenerative diseases. Exotoxin Y (ExoY) is a type III secretion system effector found in ∼ 90% of the Pseudomonas aeruginosa isolates. Although it is known that ExoY causes inter-endothelial gaps and vascular leak, the mechanisms by which this occurs are poorly understood. Using both a bacteria-delivered and a codon-optimized conditionally expressed ExoY, we report that this toxin is a dual soluble adenylyl and guanylyl cyclase that results in intracellular cAMP and cGMP accumulation. The enzymatic activity of ExoY caused phosphorylation of endothelial Tau serine 214, accumulation of insoluble Tau, inter-endothelial cell gap formation, and increased macromolecular permeability. To discern whether the cAMP or cGMP signal was responsible for Tau phosphorylation and barrier disruption, pulmonary microvascular endothelial cells were engineered for the conditional expression of either wild-type guanylyl cyclase, which synthesizes cGMP, or a mutated guanylyl cyclase, which synthesizes cAMP. Sodium nitroprusside stimulation of the cGMP-generating cyclase resulted in transient Tau serine 214 phosphorylation and gap formation, whereas stimulation of the cAMP-generating cyclase induced a robust increase in Tau serine 214 phosphorylation, gap formation, and macromolecular permeability. These results indicate that the cAMP signal is the dominant stimulus for Tau phosphorylation. Hence, ExoY is a promiscuous cyclase and edema factor that uses cAMP and, to some extent, cGMP to induce the hyperphosphorylation and insolubility of endothelial Tau. Because hyperphosphorylated and insoluble Tau are hallmarks in neurodegenerative tauopathies such as Alzheimer disease, acute Pseudomonas infections cause a pathophysiological sequela in endothelium previously recognized only in chronic neurodegenerative diseases.
A telephone call reminder to improve outpatient attendance in patients referred from the emergency department: a randomised controlled trial.

BACKGROUND Poor compliance with attendance at outpatient clinic appointments in patients referred from emergency departments (EDs) is a major problem in public hospitals. AIMS To determine whether the intervention of a telephone call within three days of ED attendance would improve: 1. the proportion of patients making recommended outpatient appointments; and 2. the proportion of patients attending scheduled appointments. To characterise reasons for non-attendance at appointments made by patients referred from the ED. METHODS A randomised controlled trial was undertaken of 400 patients recommended to make outpatient appointments during attendance at The Royal Melbourne Hospital ED in July-August 1999. INTERVENTION a telephone call one to three days after attendance to remind the patient about the appointment (and its importance for medical follow-up) if one had been made and to offer to make an appointment if one had not been made. OUTCOME MEASURES 1. making the recommended appointment; 2. attendance at the scheduled appointment; and 3. reasons for non-attendance at scheduled appointments. RESULTS The telephone intervention improved attendance at scheduled appointments from 54.4% to 70.7% (p=0.002). The proportion of patients making appointments was not significantly affected. The commonest reasons given for non-attendance were: attended general practitioner (13%), attended private specialist (6.6%), inpatient in hospital at time of appointment (6.6%), too busy or inconvenient (5.3%), claimed to have attended (5.3%) and did not differ by intervention. CONCLUSIONS A significant improvement in the proportion of patients attending outpatients appointments can be made by a simple reminder telephone call one to three days after attendance at the ED.
Food Insecurity Among American Indians and Alaska Natives: A National Profile Using the Current Population Survey–Food Security Supplement

ABSTRACT Food insecurity increases the risk for obesity, diabetes, hypertension, and cancer—conditions highly prevalent among American Indians and Alaska Natives (AI/ANs). Using the Current Population Survey Food Security Supplement, we analyzed the food insecurity trends of AI/ANs compared to other racial and ethnic groups in the United States from 2000 to 2010. From 2000 to 2010, 25% of AI/ANs remained consistently food insecure and AI/ANs were twice as likely to be food insecure compared to whites. Urban AI/ANs were more likely to experience food insecurity than rural AI/ANs. Our findings highlight the need for national and tribal policies that expand food assistance programs; promote and support increased access to healthy foods and community food security, in both rural and urban areas; and reduce the burden of diet-related disparities on low-income and racial/ethnic minority populations.
A compression technique for the boundary integral equation reduced from Helmholtz equation

Applying the trigonometric wavelets and the multiscale Galerkin method, we investigate the numerical solution of the boundary integral equation reduced from the exterior Dirichlet problem of Helmholtz equation by the potential theory. Consequently, we obtain a matrix compression strategy, which leads us to a fast algorithm. Our truncated treatment is simple, the computational complexity and the condition number of the truncated coefficient matrix are bounded by a constant. Furthermore, the entries of the stiffness matrix can be evaluated from the Fourier coefficients of the kernel of the boundary integral equation. Examples given for demonstrating our numerical method shorten the runtime obviously.
Measurements and Analysis of an In-Car UWB Channel

Car manufacturers have been showing great interest in setting up ultra-wideband (UWB) systems due to the offered high data rates. In this paper, the fundamental features of the in-car UWB channel in terms of large-scale and small-scale parameters are investigated. These values are based on measurement data collected with a vector network analyzer (VNA) in the frequency band of 3-8 GHz. With the aid of the measurements, simple preliminary empirical models have been derived describing both, path loss as well as small-scale features of the channel. The results are shown for LOS and NLOS situations as well as for an empty car and a car occupied with persons.
Mortality among employees at a petrochemical research facility.

BACKGROUND This retrospective follow-up study evaluated mortality during 1970-1996 among 6,956 employees at a petrochemical research facility in Illinois. METHODS Standardized mortality ratios (SMRs) compared employees' mortality rates with those of the Illinois general population. Poisson regression procedures estimated rate ratios for various subject subgroups compared to other facility employees. RESULTS Subjects had 267 observed/524 expected deaths (SMR = 51) from all causes combined and a large deficit of deaths from all cancers (76/136, SMR = 56) and from most other major diseases. Other results included fewer than expected brain cancers (1/4.0, SMR = 25) and a slight increase in colorectal cancer (20/14, SMR = 139) that was concentrated in white male scientists employed for one of the three main companies at the facility (SMR = 295, RR = 2.6). CONCLUSIONS The deficit of brain cancer deaths contrasts with an excess incidence seen in a companion study. Subjects' generally favorable mortality experience probably reflects socioeconomic advantages of employees relative to the Illinois general population.
Expansion of CD 4 + CD 25-GITR + regulatory T-cell subset in the peripheral blood of patients with primary Sjögren ’ s syndrome : correlation with disease activity

Regulatory T cells (TREG) represent a Tcell subtype with functional suppressive activity that is a key factor in modulating immune response and, therefore, in the development of autoimmunity. There is much evidence to confirm a central role for this cell subset in the pathogenesis of systemic autoimmune or chronic inflammatory diseases given the anomalies in their number or alterations in their function in patients with these pathologies. There is further evidence to suggest that effector T cells activated in these pathologies are resistant, at least in part, to the action of T REG cells. The particular phenotypic characteristic of T REG cells that has allowed them to be isolated, first in mouse and subsequently in humans, is the high expression of a receptor molecule on their surface, known as CD25 (IL2Rα). This is associated with the intracellular expression of the transcription factor forkhead winged helix (Fox)P3 (1, 2). FoxP3, previously known as JM2, was initially identified as the gene the mutations of which were associated with a murine autoimmune syndrome, the Corresponding author: Prof. Roberto Gerli SSD di Reumatologia Via Enrico dal Pozzo, Padiglione X 06122 Perugia, Italy E-mail: gerlir@unipg.it summary Objectives: CD4CD25 regulatory T cells (T REG ) represent a suppressive T-cell subset that plays a key role in the modulation of immune responses and eventually in the prevention of autoimmunity. There is growing evidence that patients with autoimmune and inflammatory chronic diseases show an impairment of T REG cells or activated effector T cells unresponsive to T REG . Glucocorticoid-induced TNFR-related protein (GITR) is a widely accepted marker of murine T REG cells, but little is known of its role in humans. The aim of the present study was to investigate the characteristics of different subsets of T REG cells in Sjögren’s syndrome and the potential role of GITR as a marker of human T REG cells. Methods: Fifteen patients with primary Sjogren’s syndrome (SS) and 10 sexand age-matched normal controls (NC) were enrolled in the study. CD4 T cells were separated from peripheral blood by magnetic cell sorting (negative selection). Cell phenotype was analyzed by flow-cytometry using primary and secondary antibodies. Disease activity was assessed using the EULAR Sjögren’s syndrome disease activity index (ESSDAI). Results: Although the proportion of circulating CD25GITR subset was similar in SS patients and normal controls, an expansion of the CD25GITR cell population was observed in the peripheral blood of SS patients. Interestingly, this expansion was greater in patients with inactive rather than active disease. Conclusions: The number of CD4CD25GITR cells increases in SS as compared to normal controls. Furthermore, the fact that the expansion of this cell subset is mainly observed in patients with inactive disease suggests that these cells may play a role in counteracting inflammatory response.
Extracting Electron-Ion Differential Scattering Cross Sections for Partially Aligned Molecules by Laser-induced Rescattering Photoelectron Spectroscopy

We extract large-angle elastic differential cross sections (DCSs) for electrons scattering from partially aligned O+2 and CO+2 molecules using rescattering photoelectrons generated by infrared laser pulses. The extracted DCSs are in good agreement with those calculated theoretically, demonstrating that accurate DCSs for electron-ion scattering can be extracted from the laser-induced rescattering spectra.
Validation of a Numerical Model for the Prediction of the Annoyance Condition at the Operator Station of Construction Machines

It is well-known that the reduction of noise levels is not strictly linked to the reduction of noise annoyance. Even earthmoving machine manufacturers are facing the problem of customer complaints concerning the noise quality of their machines with increasing frequency. Unfortunately, all the studies geared to the understanding of the relationship between multidimensional characteristics of noise signals and the auditory perception of annoyance require repeated sessions of jury listening tests, which are time-consuming. In this respect, an annoyance prediction model was developed for compact loaders to assess the annoyance sensation perceived by operators at their workplaces without repeating the full sound quality assessment but using objective parameters only. This paper aims at verifying the feasibility of the developed annoyance prediction model when applied to other kinds of earthmoving machines. For this purpose, an experimental investigation was performed on five earthmoving machines, different in type, dimension, and engine mechanical power, and the annoyance predicted by the numerical model was compared to the annoyance given by subjective listening tests. The results were evaluated by means of the squared value of the correlation coefficient, R2, and they confirm the possible applicability of the model to other kinds of machines.
Fitting range of the BAHA Cordelle

The performance of the most powerful Bone-Anchored Hearing Aid (BAHA) currently available, the BAHA Cordelle, was evaluated in 25 patients with severe to profound mixed hearing loss. Patients showed bone conduction thresholds at 500, 1000 and 2000 Hz, ranged between 30 and 70 dB HL, and an additional air-bone gap of about at least 30 dB. With the BAHA Cordelle, free-field thresholds improve relative to bone-conduction thresholds with 1.5, 5.0, 17.8, and 4.3 dB at 500, 1000, 2000, and 4000 Hz, respectively, with substantial inter-individual variability. The differences in unaided air conduction thresholds and aided free-field thresholds amount to 45.3, 45.8, 47.5, and 43.5 dB at 500, 1000, 2000, and 4000 Hz, respectively. Speech perception, measured both with monosyllables of the consonant-vowel-consonant type and with bisyllables, showed highly similar results. The fitting range of a (linear) hearing aid is determined by its gain characteristics. Requiring aided speech reception thresholds at or better than 65 dB SPL results in an upper limit of the fitting range of the BAHA Cordelle for bone-conduction thresholds of 51, 56, 67, and 58 dB HL at 500, 1000, 2000, and 4000 Hz, respectively. The dynamic range provided by the BAHA Cordelle was estimated from loudness growth functions at 500, 1500, and 3000 Hz employing 7-point categorical scaling. On average, aided loudness growth functions exhibit normal slopes but they level off at input levels of about 80, 70, 65 dB SPL for 500, 1500, and 3000 Hz stimuli, respectively. Measurements with a skull simulator demonstrated that the levelling-off reflects saturation of the output of the Cordelle. The relatively low saturation levels of the device suggest that increasing maximum output levels may be a worthwhile consideration for candidates with more profound sensorineural loss.
Migration of iron-labeled KHYG-1 natural killer cells to subcutaneous tumors in nude mice, as detected by magnetic resonance imaging.

BACKGROUND AIMS A novel cell line of cytotoxic natural killer (NK) cells, KHYG-1, was examined in vivo for immunotherapy against prostate cancer. The feasibility of using magnetic resonance imaging (MRI) tracking to monitor the fate of injected NK cells following intravenous (i.v.), intraperitoneal (i.p.) and subcutaneous (s.c.) administration was assessed. METHODS PC-3M human prostate cancer cells were injected s.c. into the flank of nude mice (day 0). KHYG-1 NK cells were labeled with an iron oxide contrast agent and injected s.c. , i.v. or i.p. on day 8. Mice were imaged by MRI on days 7, 9 and 12. Tumor sections were examined with fluorescence microscopy and immunohistologic staining for NK cells. RESULTS NK cells were detected in the tumors by histology after all three administration routes. NK cells and fluorescence from the iron label were co-localized. Signal loss was seen in the areas around the tumors and between the tumor lobes in the s.c. group. CONCLUSIONS We are the first to label this cell line of NK cells with an iron oxide contrast agent. Accumulation of NK cells was visualized by MRI after s.c. injection but not after i.v. and i.p. injection.
Character Value in Kampong Sala Legend and its Relevancy as Teaching Materials at School

The research is aimed at preserving the story of Kota Sala Legend. It used qualitative approach. The data were derived from caretakers, the elderly, the artists from Surakarta Palace, and the public figures, as well as from books and articles by using documentation and interview techniques. The data were analyzed by using qualitative descriptive method into several steps as the following: (1) Conducting interview and observing the documents, (2) Collecting and arranging the data into a complete story, (3) Analyzing its character values, and (4) Analyzing its relevance as a teaching material. The results indicate that (1) the oral tradition of Kampong Sala Legend can be documented into a pictorial story book in three languages: Javanese, Indonesian, and English; (2) The story consists of character values such as religious, honest, discipline, hard-working, creative, solicitous, and responsible; (3) The story is very relevantly used as teaching materials at school especially in the subject of Bahasa Jawa and Bahasa Indonesia.
APPLICATIONS OF DENDROCHRONOLOGY IN NORTHWESTERN MEXICO

Although dendrochronological methods have the potential to provide precise calendar dates, they are virtually absent in Mesoamerican archaeological research. This absence is due to several long-standing, but erroneous, assumptions: that tree rings in this region do not reflect annual growth and environmental variability, that an adequate number of samples do not exist, and that tree-ring measurements cannot be useful without modern trees to link prehispanic chronologies. In this article we present data from the sites of La Quemada and Los Pilarillos, located in the Malpaso Valley, Zacatecas, to demonstrate that suitable archaeologically derived samples of dendrochronologically useful species do exist, that the samples from these sites are measurable and cross-datable, and that the tree rings can yield precise calendar dates using a method that “wiggle-matches” radiocarbon dates on tree-ring sequences. The work demonstrates the potential of these methods to address chronological, and, in the future, climatic questions, which have so far eluded archaeological work in the region. Los métodos dendrocronológicos tienen el potencial de proporcionar fechas de calendario precisas, sin embargo son escasamente utilizados en las investigaciones arqueológicas Mesoamericanas. Esto se debe a la existencia de varios supuestos de larga permanencia, pero erróneos tales como: que los anillos de los árboles en esta región no reflejan el crecimiento anual y la variabilidad medioambiental, que no existe un número adecuado de muestras, y que las mediciones de los anillos de los árboles no pueden ser útiles sin la existencia de árboles modernos para vincular las curvas prehispánico. En este artículo, se presentan datos de los sitios de La Quemada y Los Pilarillos, localizados en el Valle de Malpaso, Zacatecas, para demostrar que existen muestras arqueológicas dendrocronológicamente adecuadas, medibles, que se pueden “cross-date”, y que se pueden obtener fechas precisas usando un método llamado “calibración de radiocarbono de secuencias definidas” (radiocarbon wiggle-matching). El trabajo pone en evidencia el potencial de estos métodos para abordar cuestiones cronológicas, y en el futuro, también climáticas, las cuales hasta la fecha han eludido el trabajo arqueológico en la región.