Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiology and Outcomes of Invasive Candidiasis Due to Non-albicans Species of Candida in 2,496 Patients: Data from the Prospective Antifungal Therapy (PATH) Registry 2004–2008

This analysis describes the epidemiology and outcomes of invasive candidiasis caused by non-albicans species of Candida in patients enrolled in the Prospective Antifungal Therapy Alliance (PATH Alliance) registry from 2004 to 2008. A total of 2,496 patients with non-albicans species of Candida isolates were identified. The identified species were C. glabrata (46.4%), C. parapsilosis (24.7%), C. tropicalis (13.9%), C. krusei (5.5%), C. lusitaniae (1.6%), C. dubliniensis (1.5%) and C. guilliermondii (0.4%); 111 infections involved two or more species of Candida (4.4%). Non-albicans species accounted for more than 50% of all cases of invasive candidiasis in 15 of the 24 sites (62.5%) that contributed more than one case to the survey. Among solid organ transplant recipients, patients with non-transplant surgery, and patients with solid tumors, the most prevalent non-albicans species was C. glabrata at 63.7%, 48.0%, and 53.8%, respectively. In 1,883 patients receiving antifungal therapy on day 3, fluconazole (30.5%) and echinocandins (47.5%) were the most frequently administered monotherapies. Among the 15 reported species, 90-day survival was highest for patients infected with either C. parapsilosis (70.7%) or C. lusitaniae (74.5%) and lowest for patients infected with an unknown species (46.7%) or two or more species (53.2%). In conclusion, this study expands the current knowledge of the epidemiology and outcomes of invasive candidiasis caused by non-albicans species of Candida in North America. The variability in species distribution in these centers underscores the importance of local epidemiology in guiding the selection of antifungal therapy.
Toward iconic vibrotactile information display using floor surfaces

This paper presents our preliminary research on haptic displays integrated in floor surfaces. We emphasize potential roles for the latter as vibrotactile communication channels that might be seamlessly integrated in everyday environments. We describe the interactive floor component that is the platform for our research, and an application we have developed to support the design of vibrotactile icon sets for display with the device. The results of a preliminary evaluation of this display method are presented, and future directions for this research are described.
Clinical exome sequencing in early‐onset generalized dystonia and large‐scale resequencing follow‐up

Dystonia is clinically and genetically heterogeneous. Despite being a first‐line testing tool for heterogeneous inherited disorders, whole‐exome sequencing has not yet been evaluated in dystonia diagnostics. We set up a pilot study to address the yield of whole‐exome sequencing for early‐onset generalized dystonia, a disease subtype enriched for monogenic causation.
Comparative gene expression profiling of post-natal and post-pneumonectomy lung growth

Although increasing numbers of patients suffer from chronic destructive lung diseases, there are no effective therapeutic options apart from transplantation. Understanding the mechanisms of physiological and regenerative alveolar septation is prerequisite for the development of regenerative therapies for the lung. We compared lung gene expression in the phase of induction of post-natal and post-pneumonectomy alveolarisation to identify regulatory genes involved in both processes. We performed genome-wide microarray screenings of newborn and pneumonectomised mouse lungs 1 and 3 days after birth or surgery. Selected candidates were validated by real-time PCR, Western blot and in situ hybridisation. We found 58 genes to be regulated in both models with 40 candidates being changed likewise. Many of these genes participated in growth and differentiation processes. Additionally, immune system, structural molecules, respiratory chain, signal transduction and metabolism were involved. Some candidates were not yet linked to specific functions. The highest regulatory concordance was observed for various isoforms of (pro-)collagen molecules, elastin and the elastin-associated protein fibrillin1 being corporately upregulated. Our findings do not definitively support a common regulating mechanism for induction of post-natal and adult alveolarisation, but some candidates in the intersection of both models are promising for further investigations.
Filamentous structures in adherent Mycoplasma pneumoniae cells treated with nonionic detergents

Mycoplasma pneumoniae cells adhering to glass or Parlodion-coated grids were extracted with Triton X-100. The extracted cells showed a cytoskeleton consisting of a rodlike tip structure and a filamentous network in the cytoplasm. The tip structure was up to 300 nm long and approximately 40 nm wide ending at the distal end in a bleb-like structure, and seemed to consist of filaments arranged in parallel, 4.8 +/- 0.5 nm wide. In the cytoplasm the filaments formed an irregular lattice. Similar filaments were found in platinum replicated critical- point dried extracted cells. An actinlike nature of the filaments is suggested by some of their properties, but the degree of homology with respect to eucaryotic actin is still unknown. The filaments were sensitive to protease treatment but stable in high molar KCl solutions. They were apparently destroyed by incubation in high molar KI solution, leaving only some parts of the tip structure. Formaldehyde-fixed M. pneumoniae cells treated with Triton X-100 bound rhodamine-labeled phalloidin specifically. Furthermore, they could be stained with antiactin antibodies. Binding of myosin subfragment 1 to the filaments was not observed.
An efficient solution to the five-point relative pose problem

An efficient algorithmic solution to the classical five-point relative pose problem is presented. The problem is to find the possible solutions for relative camera pose between two calibrated views given five corresponding points. The algorithm consists of computing the coefficients of a tenth degree polynomial in closed form and, subsequently, finding its roots. It is the first algorithm well-suited for numerical implementation that also corresponds to the inherent complexity of the problem. We investigate the numerical precision of the algorithm. We also study its performance under noise in minimal as well as overdetermined cases. The performance is compared to that of the well-known 8 and 7-point methods and a 6-point scheme. The algorithm is used in a robust hypothesize-and-test framework to estimate structure and motion in real-time with low delay. The real-time system uses solely visual input and has been demonstrated at major conferences.
Effects of homogeneous and inhomogeneous static magnetic fields combined with gamma radiation on DNA and DNA repair

The aim of this study was to reveal whether static magnetic fields (SMFs) influence the repair of radiation‐damaged DNA on leukocytes or has any effect on DNA. After 4 Gy of 60Co‐γ irradiation, some of the samples were exposed to inhomogeneous SMFs with a lateral magnetic flux density gradient of 47.7, 1.2, or 0.3 T/m by 10 mm lateral periodicity, while other samples were exposed to homogeneous SMF of 159.2 ± 13.4 mT magnetic flux density for a time period of 0.5 min, 1, 2, 4, 6, 18, 20, or 24 h. Another set of samples was exposed to the aforementioned SMFs before gamma irradiation. The following three groups were examined: (i) exposed to SMF only, (ii) exposed to SMF following irradiation by 60Co‐γ, and (iii) exposed to SMF before 60Co‐γ irradiation. The analysis of the DNA damage was made by single‐cell gel electrophoresis technique (comet assay). Statistically significant differences were found at 1 h (iSMF), 4 h (hSMF), and 18 h (hSMF) if samples were exposed to only SMF, compared to control. When the SMF exposure followed the 60Co‐γ irradiation, statistically significant differences were found at 1 h (iSMF) and 4 h (hSMF). If exposure to SMF preceded 60Co‐γ irradiation, no statistically significant difference was found compared to 4 Gy gamma‐irradiated group. Bioelectromagnetics 31:488–494, 2010. © 2010 Wiley‐Liss, Inc.
Does polycythemia affect interleukin‐6 response pattern in early postnatal period?

Introduction: Neonatal polycythemia may result in increased cytokine production. We aimed to investigate whether polycythemia and partial exchange transfusion (PET) affect interleukin‐6 (IL‐6) response pattern in early neonatal period. Methods: Ninety‐four newborns, 57 with polycythemia (Group 1) and 37 as control group (Group 2) were enrolled in the study. PET was performed at 4–6 hr following birth in the first group. Blood levels of IL‐6 were measured at 2–4 hr following birth; measurements were repeated at 6 and 24 hr after PET in newborns with polycythemia and at similar hours in Group 2. In Group 1, two patients (3.5%) who were diagnosed with proven sepsis excluded from the study. Results: Both initial and the last IL‐6 levels were higher in Group 1 (21.7; 5.5–190 pg/ml and 18.3; 2.7–92.4 pg/ml) than those of the controls (8.4; 0.2–47.8 pg/ml and 8.6; 2.0–21.0 pg/ml) (P=0.001 for both comparisons). In Group 1, IL‐6 levels increased at 6 hr after PET and decreased thereafter. IL‐6 showed the same pattern in the control group. IL‐6 levels were higher than >70pg/ml in two (3.6%), seven (12.7%), and two (3.6%) subjects during three evaluation steps, respectively. Neither clinical nor proven sepsis was subsequently detected in any of these subjects. IL‐6 levels were within the acceptable values in Group 2. Conclusion: IL‐6 levels seem to be high in newborns with polycythemia during the first days of life, although they rarely exceed maximum acceptable levels. The pattern of IL‐6 response might be taken into account to optimize its use in the diagnosis of early‐onset neonatal sepsis. J. Clin. Lab. Anal. 24:340–347, 2010. © 2010 Wiley‐Liss, Inc.
Heart disease and work

Heart disease is common both in the population at large but also in the population of working age. It is estimated that heart disease, including stroke and high blood pressure, is responsible for more costs than any other disease or injury. The cost in occupational terms of cardiovascular disease (CVD) is, however, harder to quantify but is likely to be similarly high. Heart disease can claim the ultimate cost as the most common cause of death. CVD is the main cause of death in the UK, accounting for over 245 000 deaths per year. The main forms of CVD are coronary heart disease (CHD) and stroke. Death before retirement age is commonly attributed to CVD, accounting for 36% of premature deaths in men and 27% of premature deaths in women. CHD is responsible for 120 000 deaths a year in the UK and is responsible for 23% of deaths before the age of 65 years in men and 13% in women. Significant advances in acute medical care have, however, brought reductions in mortality from CHD over the last 10 years or more. Morbidity rates have not seen that same fall; in fact, rates have risen, especially in older individuals over the last 20 years. Two million people in the UK suffer from angina, 680 000 people have heart failure, and 270 000 will suffer a heart attack each year—highlighting the significance of CVD as a cause of morbidity. A recent study of self reported work related illness in 2001–21 shows that record numbers of workers feel that they have an illness that was caused by or made worse by their work, equating to 2.3 million people and 33 million working days lost. These figures show a prevalence estimate for CVD caused or made worse by work of 80 000 …
The Effects of Item Parceling on Goodness-of-Fit and Parameter Estimate Bias in Structural Equation Modeling

Two simulation studies were conducted to investigate the effects of the practice of item parceling. In Study 1, unidimensional sets of normally and nonnormally distributed item-level data were categorized into 2-, 3-, and 4-item parcels. Analyses revealed that the use of item parcels resulted in better fitting solutions, as measured by the root mean squared error of approximation (RMSEA), comparative fit index (CFI), and chi-square test, when items had a unidimensional structure. Parceled solutions also resulted in less bias in estimates of structural parameters under these conditions than did solutions based on the individual items. In Study 2 the issue of whether the use of item parceling could mask a known multidimensional factor structure among a set of items was investigated. Results indicated that certain types of item parceling can obfuscate a multidimensional factor structure in such a way that acceptable values of fit indexes are found for a misspecified solution. In addition, parceling under these conditions was found to result in bias in the estimates of structural parameters. Although parceling can ameliorate the effects of coarsely categorized and nonnormally distributed item-level data when the items are unidimensional, the use of parceling with items that are multidimensional or for which the factor structure is unknown cannot be recommended.
Individual assignment test reveals differential restriction to dispersal between two salmonids despite no increase of genetic differences with distance

In many species genes move over limited distances, such that genetic differences among populations or individuals are expected to increase as a function of geographical distance. In other species, however, genes may move any distance over a single generation time, such that no increase of genetic differences is expected to occur with distance. Patterns of gene dispersal have been assessed typically using this theoretical property. In this study, this classical approach based on a Mantel test was compared to a new method using individual assignment to reveal contrasts in dispersal patterns between 15 populations of brook charr Salvelinus fontinalis and 10 populations of Atlantic salmon Salmo salar sampled in eastern Canada, where both species co‐occur naturally. Based on the Mantel test, we found evidence for neither an increase of genetic differences with distance in either species nor a significant contrast between them. The individual‐based method, in contrast, revealed that individual assignment in both species was non random, being significantly biased toward geographically proximate locations. Furthermore, brook charr were on average assigned to a closer river than were salmon, according to a priori expectations based on the dispersal behaviour of the two species. We thus propose that individual assignment methods might be a promising and more powerful alternative to Mantel tests when isolation by distance cannot be postulated a priori.
Model for Immune Responses to Mycobacterium avium Subspecies paratuberculosis in Cattle

Infection of ruminant species with the facultative intracellular bacterium Mycobacterium avium subsp. paratuberculosis causes a fatal granulomatous enteritis known as Johne's disease or paratuberculosis. In cattle, Johne's disease is responsible for significant losses to the U.S. dairy industry (an
The Carnian Pluvial Episode and the origin of dinosaurs

We present new evidence for a major inflection point in the history of tetrapods on land, a jump in the diversification of archosauromorphs, primarily dinosaurs, at 232–230 Ma. This corresponds to a long-noted changeover in Triassic terrestrial tetrapod faunas from those dominated by synapsids, many of them holdovers from the Permian, to those dominated by dinosaurs. The dinosaur explosion is shown here to correspond in timing to the Carnian Pluvial Episode (CPE), dated at 232 Ma, a time of increased rainfall and perturbation of oceans and atmospheres, followed by substantial aridification. The rock record through the CPE confirms that this event shared many characters with other mass extinctions driven by eruption of large igneous provinces, in this case the Wrangellia flood basalts of the west coast of North America. If this was a catastrophic extinction event, then the environmental perturbations of the CPE explain the sharp disappearance of various terrestrial tetrapods, and the subsequent sharp rise of dinosaurs and perhaps other clades too, especially those that constitute much of the modern terrestrial faunas, such as lissamphibians, turtles, crocodiles, lizards and mammals. Supplementary material: The sampled tetrapod faunas, geological ages, and details of the R code method and results are available at https://doi.org/10.6084/m9.figshare. c.4111439
Necropsy study of endomyocardial fibrosis and rheumatic heart disease in Uganda 1950-1965.

Endomyocardial fibrosis is a relatively common form of heart disease in Uganda (Davies, 1948; Shaper and Williams, 1960) and accounts for some 10 per cent of heart disease seen at necropsy in Kampala (Davies, 1961). It is characterized in the established condition by fibrosis in the endocardium and subjacent myocardium affecting particularly the inflow tract and the apex of one or both ventricles. The aetiology of this disorder is not known, and hypotheses have been put forward in attempts to incriminate virus or filarial infections, plantain diets, and rheumatic heart disease. The disorder has also been described in West Africa, Ceylon, South India, and Central Africa, and wellauthenticated cases have been seen in Europeans resident in tropical areas (Brockington, Olsen, and Goodwin, 1967). Mulago Hospital, Kampala, is situated in Buganda, the largest province of Uganda, and about half the patients admitted to the hospital belong to the local Ganda tribe (Fig. 1). There is also a large immigrant population in Buganda, coming in particular from Rwanda and Burundi (herein referred to as 'Rwandans') and from the Western Province of Uganda (Kigezi, Ankole, Toro, and Bunyoro districts). An analysis of the tribal origins of cases of endomyocardial fibrosis coming to necropsy at Mulago Hospital in the period 19501961 showed a preponderance of this condition among those groups immigrant to Buganda, in particular those originating from Rwanda and Burundi. The condition was far less common than expected among the indigenous Ganda people (Shaper and Coles, 1965). This analysis of the tribal origins of subjects with endomyocardial fibrosis has now been extended to cover the period 1950-1965, and a similar analysis
An Exact Enumeration of Distance-Hereditary Graphs

Distance-hereditary graphs form an important class of graphs, from the theoretical point of view, due to the fact that they are the totally decomposable graphs for the split-decomposition. The previous best enumerative result for these graphs is from Nakano et al. (J. Comp. Sci. Tech., 2007), who have proven that the number of distance-hereditary graphs on $n$ vertices is bounded by ${2^{\lceil 3.59n\rceil}}$. In this paper, using classical tools of enumerative combinatorics, we improve on this result by providing an exact enumeration of distance-hereditary graphs, which allows to show that the number of distance-hereditary graphs on $n$ vertices is tightly bounded by ${(7.24975\ldots)^n}$---opening the perspective such graphs could be encoded on $3n$ bits. We also provide the exact enumeration and asymptotics of an important subclass, the 3-leaf power graphs. Our work illustrates the power of revisiting graph decomposition results through the framework of analytic combinatorics.
Role of the Major Glutamate Transporter GLT1 in Nucleus Accumbens Core Versus Shell in Cue-Induced Cocaine-Seeking Behavior

Relapse to cocaine-seeking behavior requires an increase in nucleus accumbens (NAc) core glutamate transmission. Decreased expression of glutamate type I transporter (GLT1), which is responsible for >90% of glutamate clearance, occurs in the core of rats withdrawn from cocaine self-administration, while treatment with ceftriaxone, a β-lactam antibiotic previously shown to increase GLT1 expression and function in rodents, upregulates GLT1 and attenuates cue-induced cocaine reinstatement. Here, we tested the effects of increasing GLT1 expression on cue-induced cocaine seeking in rats exposed to either limited (2 h/d) or extended (6 h/d) cocaine access followed by short (2 d) or long (45 d) withdrawal periods. Treatment with ceftriaxone (200 mg/kg, i.p.) upregulated core GLT1 expression and attenuated cue-induced cocaine-seeking behavior only in rats exposed to long withdrawal periods, with a greater effect in the extended-access condition. Pearson's correlation revealed GLT1 expression in core to be inversely correlated with cue-induced cocaine-seeking behavior. To localize the effects of GLT1 upregulation within NAc, we tested the hypothesis that blockade of GLT1 in NAc core, but not shell, would reverse the ceftriaxone-mediated effect. Rats withdrawn from cocaine self-administration were treated with the same dose of ceftriaxone followed by intracore or intrashell infusions of one of two GLT1 blockers, dihydrokainic acid (500 μm) or dl-threo-β-benzyloxyaspartate (250 μm), or saline. Our results reveal that the ceftriaxone-mediated attenuation of cue-induced cocaine reinstatement is reversed by GLT1 blockade in core, but not shell, and further implicate core GLT1 as a potential therapeutic target for cocaine relapse.
The Anderson Model of Localization: A Challenge for Modern Eigenvalue Methods

We present a comparative study of the application of modern eigenvalue algorithms to an eigenvalue problem arising in quantum physics, namely, the computation of a few interior eigenvalues and their associated eigenvectors for the large, sparse, real, symmetric, and indefinite matrices of the Anderson model of localization. We compare the Lanczos algorithm in the 1987 implementation of Cullum and Willoughby with the implicitly restarted Arnoldi method coupled with polynomial and several shift-and-invert convergence accelerators as well as with a sparse hybrid tridiagonalization method. We demonstrate that for our problem the Lanczos implementation is faster and more memory efficient than the other approaches. This seemingly innocuous problem presents a major challenge for all modern eigenvalue algorithms.
Alteration in Intracellular Zn2+ Homeostasis as a Result of TRPM2 Channel Activation Contributes to ROS-Induced Hippocampal Neuronal Death

Transient receptor potential melastatin-related 2 (TRPM2) channel, a molecular sensor for reactive oxygen species (ROS), plays an important role in cognitive dysfunction associated with post-ischemia brain damage thought to result from ROS-induced TRPM2-dependent neuronal death during reperfusion. Emerging evidence further suggests that an alteration in the Zn2+ homeostasis is critical in ROS-induced TRPM2-dependent neuronal death. Here we applied genetic and pharmacological interventions to define the role of TRPM2 channel in ROS-induced neuronal death and explore the mechanisms contributing in the alteration in intracellular Zn2+ homeostasis in mouse hippocampal neurons. Exposure of neurons to 30–300 μM H2O2 for 2–24 h caused concentration/duration-dependent neuronal death, which was significantly suppressed, but not completely prevented, by TRPM2-knockout (TRPM2-KO) and pharmacological inhibition of the TRPM2 channel. H2O2-induced neuronal death was also attenuated by treatment with TPEN acting as a Zn2+ selective chelator. Single cell imaging demonstrated that H2O2 evoked a prominent increase in the intracellular Zn2+ concentration, which was completely prevented by TPEN as well as TRPM2-KO and inhibition of the TRPM2 channel. Furthermore, H2O2 induced lysosomal Zn2+ release and lysosomal dysfunction, and subsequent mitochondrial Zn2+ accumulation that provokes mitochondrial dysfunction and ROS generation. These H2O2-induced lysosomal/mitochondrial effects were prevented by TRPM2-KO or TPEN. Taken together, our results provide evidence to show that a dynamic alteration in the intracellular Zn2+ homeostasis as a result of activation of the TRPM2 channel contributes to ROS-induced hippocampal neuronal death.