Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of Aspergillus Ribosomal RNA Using Biotinylated Oligonucleotide Probes

Aspergillosis continues to be a devastating disease entity that results in significant mortality in immunosuppressed patients. Rapid diagnosis is often required to initiate appropriate therapy. Although the histopathologist may be able to visualize fungal organisms in tissue specimens, the histology of Aspergillus species may overlap with a variety of fungi, so diagnosis often relies on fungal cultures that can take weeks to complete. Recently, an in situ hybridization assay targeting Aspergillus 5S ribosomal RNA (rRNA) was reported. This assay proved to be useful when fungal cultures were negative or not performed but when fungi compatible with Aspergillus species were identified in tissue sections. That study was performed to compare the probe described in the previous study (5S-1 probe) with two other probes specific for Aspergillus. Two customly designed 21− and 23-base oligonucleotide probes complementary to 5S (5S-2 probe) and 18S (18S-1 probe) rRNA of Aspergillus were synthesized and labeled with multiple biotin moieties at the 3′ termini. By GenBank analysis, the sequence of the 18S-1 probe was shown to have 90% to 100% homology to Aspergillus fumigatus group. Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus parasiticus, Aspergillus tamarii, and Aspergillus glaucus group; the 5S-2 probe was homologous to Aspergillus flavus, Aspergillus niger, Aspergillus nidulans. Aspergillus awamori, and Aspergillus wentii. In situ hybridization was performed on 43 cases of Aspergillus infection including 41 localized aspergillomas in the lung, brain, sinonasal tract, and ear. and 2 cases of invasive aspergillosis involving pleura and soft tissue of the scapular region. The results were compared with those obtained using a previously reported 5S-1 probe. In situ hybridization was positive in 38. 38. and 40 cases with the 5S-1. 5S-2. and 18S-1 probes, respectively. The 18S-1 probe was most useful because of a wider detection spectrum. In situ hybridization for Aspergillus rRNA provides a useful means for rapidly and accurately identifying Aspergillus in tissues and may be useful if fungal organisms suggestive of Aspergillus species are present but if cultures are negative or have not been performed.
History and introduction to polygon models , polyominoes and polyhedra

*The genesis and history of self-avoiding polygons, polyominoes and polyhedra embedded in a regular space lattice is discussed, as is the related problem of tilings. We establish some basic notation and describe the connection with statistical mechanics. Throughout, our focus is to outline what is known and what remains unknown, and to discuss how the topic of the book is developed in the subsequent chapters.
Polymorphisms of the Interleukin-1&bgr; Gene Affect the Risk of Myocardial Infarction and Ischemic Stroke at Young Age and the Response of Mononuclear Cells to Stimulation In Vitro

Objectives— To investigate the role of interleukin-1&bgr; (IL-1&bgr;) gene polymorphisms as a link between inflammation, coagulation, and risk of ischemic vascular disease at young age. Methods and Results— A total of 406 patients with myocardial infarction (MI) at young age, frequency-matched for age, sex, and recruitment center, with 419 healthy population-based controls and 134 patients with ischemic stroke at young age, matched by age and sex, with 134 healthy population-based controls, were studied. Subjects carrying the TT genotype of the −511C/T IL-1&bgr; polymorphism showed a decreased risk of MI (odds ratio [OR], 0.36; 95% CI, 0.20 to 0.64) and stroke (OR, 0.32; 95% CI, 0.13 to 0.81) after adjustment for conventional risk factors. In both studies, the T allele showed a codominant effect (P=0.0020 in MI; P=0.021 in stroke). Mononuclear cells from volunteers carrying the T allele showed a decreased release of IL-1&bgr; and a decreased expression of tissue factor after stimulation with lipopolysaccharide compared with CC homozygotes. The presence of a monoclonal antibody against IL-1&bgr; during cell stimulation resulted in a marked reduction of tissue factor activity expression. Conclusions— −511C/T IL-1&bgr; gene polymorphism affects the risk of MI and ischemic stroke at young age and the response of mononuclear cells to inflammatory stimulation.
Deep venous thrombosis of the upper extremity. A review.

UNLABELLED Upper extremity deep venous thrombosis (UEDVT) occurs either spontaneously, as a consequence of strenuous upper limb activity (also known as the Paget-Schroetter syndrome) or secondary to an underlying cause. Primary and secondary UEDVT differs in long-term sequelae and mortality. This review will focus on the clinical presentation, risk factors, diagnosis, and treatment strategies of UEDVT. In the period from January to October 2012 an electronic literature search was performed in the PubMed/MEDLINE database, and 27 publications were included. CLINICAL PRESENTATION swelling, pain and functional impairment are typical symptoms of UEDVT, although completely asymptomatic cases have been described. However life-threatening, massive pulmonary embolism (PE) can also be a sign of UEDVT. RISK FACTORS for the primary condition anatomical abnormalities (Thoracic Outlet Syndrome, TOS) may dispose to the condition. Malignancy and therapeutic interventions are major risk factors for the secondary deep vein thrombosis in combination with the patient's characteristics, comorbidities and prior history of deep vein thrombosis. COMPLICATIONS recurrent deep venous thrombosis, pulmonary embolism and Post Thrombotic Syndrome (PTS) are the major complications after UEDVT. PTS is a chronic condition leading to significant functional disability and impaired quality of life. DIAGNOSIS compression ultrasonography is noninvasive and the most frequently used objective test with a high accuracy in experienced hands. Treatment modalities and strategies: the treatment modalities include anticoagulation therapy, catheter-directed thrombolysis, surgical decompression, percutaneous transluminal angioplasty and stenting and they may be combined. However, the optimal treatment and timing of treatment remains controversial. Early diagnosis and treatment is essential to prevent PTS in primary UEDVT; however, there is no consensus on which treatment is the best. Anticoagulation is still considered the treatment of choice for at least 3-6 months, until Randomized Controlled Trials may have demonstrated otherwise.
Model Reduction Using Multiple Time Scales in Stochastic Gene Regulatory Networks

Abstract : Gene network dynamics often involves processes that take place on widely differing time scales -- from the order of nanoseconds to the order of several days. Multiple time scales in mathematical models often lead to serious computational difficulties, such as numerical stiffness in the case of differential equations or excessively redundant Monte Carlo simulations in the case of stochastic processes. We present a method that takes advantage of multiple time scales and dramatically reduces the computational time for a broad class of problems arising in stochastic gene regulatory networks. We illustrate the efficiency of our method in two gene network examples, which describe two substantially different biological processes -- cellular heat shock response and expression of the pap gene in Escherichia coli bacteria.
Highly‐Efficient, Flexible Piezoelectric PZT Thin Film Nanogenerator on Plastic Substrates

A highly-efficient, flexible piezoelectric PZT thin film nanogenerator is demonstrated using a laser lift-off (LLO) process. The PZT thin film nanogenerator harvests the highest output performance of ∼200 V and ∼150 μA·cm(-2) from regular bending motions. Furthermore, power sources generated from a PZT thin film nanogenerator, driven by slight human finger bending motions, successfully operate over 100 LEDs.
Clustered Sorting R-Tree: An Index for Multi-Dimensional Spatial Objects

We propose new R-tree construction techniques (CSR-tree) for spatial databases. The main ideal of this algorithm is to make the spatial objects that near to each other in spatial space in nearest leaf nodes, and to reduce the overlap among the spatial objects' rectangles. Given a collection of multi-dimensional spatial objects with rectangles, we cluster them to k groups by distance relativity, sort all the spatial objects in the i-th (iepsi[1,k]) group, and then sort all the groups by the group center points, and build the R-tree bottom-up at last. We proposed and implemented several variations and performed experiments on synthetic 3D data. The experimental results show that the CSR-tree outperforms the previously R-tree methods in query efficiency and space utilization.
SIR-Network Model and Its Application to Dengue Fever

The SIR-network model, introduced in [S. Boatto et al., SIR-Network Model for Epidemics Dynamics in a City, in preparation] and [L. Stolerman, Spreading of an Epidemic over a City: A Model on Networks, Master's thesis, 2012 (in Portuguese)], deals with the propagation of disease epidemics in highly populated cities. The nodes, or vertices, are the city's neighborhoods, in which the local populations are assumed to be well-mixed. The directed edges represent the fractions of people moving from their neighborhoods of residence to those of daily activities. First, we present some fundamental properties of the basic reproduction number ($R_o$) for this model. In particular, we focus on how $R_o$ depends upon the geometry and the heterogeneity (different infection rates in each vertex) of the network. This allows us to conclude whether an epidemic outbreak can be expected or not. Second, we submit the SIR-network model to data fitting, using data collected during the 2008 Rio de Janeiro dengue fever epidemic. Important conclusions are drawn from the fitted parameters, and we show that improved results are found when a time-dependent infection parameter is introduced.
Uniformly fast evaluation of holonomic functions

In a series of previous articles, we have given ecient algorithms for the evaluation of holonomic functions over the algebraic numbers and for the computation of their limits at singularities. The focus of these articles was mainly on the ecient evaluation at a xed point. In the present note, we will show that there exist uniformly ecient algorithms for evaluating holonomic functions. The main technical diculty is to maintain uniform eciency near irregular singularities. We will introduce a variant of accelerato-summation for this purpose that we call expedito-summation.
Chinese medicinal compound delisheng has satisfactory anti-tumor activity, and is associated with up-regulation of endostatin in human hepatocellular carcinoma cell line HepG2 in three-dimensional culture.

AIM To investigate the multicellular resistance of human hepatocellular carcinoma HepG2 cells in three-dimensional culture to delisheng, 5-fluorouracil and adriamycin, and the possible molecular mechanisms of delisheng. METHODS Human hepatocellular carcinoma HepG2 cells were cultured with a liquid overlay technique. After the formation of multicellular spheroids, morphology was analyzed by phase contrast microscopy, scanning electron microscopy and transmission electron microscopy. Sensitivity of HepG2 cells to delisheng, 5-fluorouracil and adriamycin was investigated by MTT assay in multicelluar spheroids and monolayers. Vascular endothelial growth factor (VEGF) and endostatin expression were analyzed in multicellular spheroids treated with delisheng, 5-fluorouracil, adriamycin and negative control PBS, with immunohistochemical staining. RESULTS Multicellular spheroids exhibited structural characteristics somewhat different to those in monolayers. The cells in three-dimensional cell culture turned out to be less sensitive to delisheng, 5-fluorouracil and adriamycin than the cells cultured in monolayer. This showed that delisheng had a satisfactory cells inhibition ratio compared to 5-fluorouracil and adriamycin. Immunohistochemical staining showed that VEGF and endostatin expression was positive during growth as multicellular spheroids, and endostatin expression in spheroids with treatment of delisheng was higher than that with 5-fluorouracil, adriamycin and PBS (139.35 +/- 7.83, 159.23 +/- 10.34, 162.83 +/- 3.47 and 148.48 +/- 11.06, P < 0.05). CONCLUSION Chinese medicine compound delisheng has satisfactory anti-tumor activity in HepG2 cells in three-dimensional culture, and the effects are associated with up-regulation of endostatin.
Prospective randomised study of intensive insulin treatment on long term survival after acute myocardial infarction in patients with diabetes mellitus

Abstract Objectives: To test the hypothesis that intensive metabolic treatment with insulin-glucose infusion followed by multidose insulin treatment in patients with diabetes mellitus and acute myocardial infarction improves the prognosis. Design: Patients with diabetes mellitus and acute myocardial infarction were randomly allocated standard treatment plus insulin-glucose infusion for at least 24 hours followed by multidose insulin treatment or standard treatment (controls). Subjects: 620 patients were recruited, of whom 306 received intensive insulin treatment and 314 served as controls. Main outcome measure: Long term all cause mortality. Results: The mean (range) follow up was 3.4 (1.6-5.6) years. There were 102 (33%) deaths in the treatment group compared with 138 (44%) deaths in the control group (relative risk (95% confidence interval) 0.72 (0.55 to 0.92); P=0.011). The effect was most pronounced among the predefined group that included 272 patients without previous insulin treatment and at a low cardiovascular risk (0.49 (0.30 to 0.80); P=0.004). Conclusion: Insulin-glucose infusion followed by intensive subcutaneous insulin in diabetic patients with acute myocardial infarction improves long term survival, and the effect seen at one year continues for at least 3.5 years, with an absolute reduction in mortality of 11%. This means that one life was saved for nine treated patients. The effect was most apparent in patients who had not previously received insulin treatment and who were at a low cardiovascular risk. Key messages Diabetes mellitus is common among patients with acute myocardial infarction Diabetic patients with myocardial infarction have a poor short and long term prognosis Poor metabolic control is common among diabetic patients with myocardial infarction Improved metabolic control by means of acute insulin-glucose infusion followed by long term intensive insulin treatment improves long term prognosis among these patients
Bovine trypanosomosis and its fly vectors in three selected settlement areas of Hawa-Gelan district, western Ethiopia.

A cross-sectional study aimed at investigating the species diversity of fly vectors and estimating the prevalence of bovine trypanosomosis was carried out from October 2009 to May 2010 in selected settlement areas of the Hawa-Gelan district in the western Wollega zone of Ethiopia. Standard methods of sampling and identification were employed for both entomological and parasitological examination. Three species of the genus Glossina (Glossina pallidipes, Glossina morsitans submorsitans and Glossina fuscipes) and two genera of biting flies (Stomoxys and Tabanus) were caught and identified. The overall apparent density of Glossina species caught was 10.5 flies per trap per day, with a higher proportion of female flies (57.2%). Out of a total 389 cattle examined, 42 (10.8%; 95% CI: 7.89% - 14.3%) were found infected with trypanosomes. Three trypanosome species were detected in the study area, namely Trypanosoma congolense (54.8%), Trypanosoma brucei (23.8%) and Trypanosoma vivax (21.4%). The prevalence of trypanosomosis was found to be significantly (p < 0.05) higher in cattle with poor body condition. There was an association between mean packed cell volume (PCV) and the occurrence of parasitaemia (χ2 = 49.5, p < 0.05). About 95.2% of cattle that were positive for trypanosomes had a PCV less than the lower limit for cattle. Considering the current result, bovine trypanosomosis seems to be a serious constraint for agricultural activities in the settlement areas of the Hawa-Gelan district and seems to be associated with the presence of Glossina species. Therefore, application of control methods through community involvement to reduce the Glossina species infestation level is likely to increase animal productivity.
Involvement of p38 mitogen‐activated protein kinase in lipopolysaccharide‐induced iNOS and COX‐2 expression in J774 macrophages

Both the nitrite and prostaglandin E2 (PGE2) release caused by lipopolysaccharide (LPS) in J774 macrophages are inhibited by SB 203580, a specific p38 mitogen‐activated protein kinase (MAPK) inhibitor, in a concentration‐dependent manner. The 50% inhibitory concentration (IC50) for nitrite and PGE2 responses was 1 μm and 0·5 μm, respectively. Inhibition was marked following simultaneous treatment with SB 203580 and LPS, and was much reduced when SB 203580 was added 6 hr after LPS treatment. In parallel, LPS induction of inducible NO synthase (iNOS) and cyclo‐oxygenase‐2 (COX‐2) proteins and their steady‐state levels of mRNA were reduced by SB 203580. LPS activation of nuclear factor‐kappa B (NF‐κB), activator protein‐1 (AP‐1) and p38 MAPK was also inhibited by SB 203580. These results suggest a crucial role of p38 MAPK in regulation of the transcriptional level of endotoxin LPS‐induced iNOS and COX‐2 protein expression.
Diffuse distribution of sulforhodamine‐labeled neurons during serotonin‐evoked locomotion in the neonatal rat thoracolumbar spinal cord

The fluorescent dye sulforhodamine‐101 undergoes synaptic activity‐dependent endocytotic uptake and consequent retrograde transport in presynaptic neurons. We used sulforhodamine to identify thoracolumbar spinal premotor neurons (T11‐L6) activated during serotonin (5‐HT) ‐induced hindlimb locomotor‐like activity in the in vitro neonatal rat spinal cord preparation. Sulforhodamine labeling required locomotor‐like activity because few neurons were labeled unless bath applied 5‐HT recruited the locomotor rhythm. In contrast, N‐methyl‐D‐aspartate (NMDA; 5 μM) profoundly increased spinal neuronal labeling irrespective of locomotor activity. The contribution of false‐positive activity labeling during locomotion induced by application of NMDA with 5‐HT (Kjærulff et al. [1994] J Physiol (Lond). 478:265–273) necessitated the present re‐mapping of sulforhodamine‐labeled neurons. During 5‐HT–evoked locomotion, the sulforhodamine‐labeled neurons were diffusely scattered within the spinal cord with predominant labeling in lamina VII. Motor nuclei (lamina IX) and superficial laminae (I‐II) were typically devoid of labeled cells in the isolated spinal cord. However, unilateral labeling of motoneurons was achieved when the ipsilateral hindlimb remained attached, suggesting that uptake in motoneurons requires an intact neuromuscular junction. The rostrocaudal incidence and distribution of labeled neurons was uniform in spinal segments L1‐L5, with reduced numbers observed in thoracic and L6 spinal segments. Mean total cell labeling was less than 400 per spinal segment, suggesting recruitment from a very small fraction of the neurons contained within the spinal cord (calculated at < 0.1%). These results are consistent with the limited transfer of locomotor‐related synaptic activity (Raastad et al. [1996] Neuron 17:729–738) and severe synaptic fatigue (Lev‐Tov and Pinco [1992] J Physiol. 447:149–169; Pinco and Lev‐Tov [1993] J Neurophysiol. 70:1151–1158; Fleoter and Lev‐Tov [1993] J Neurophysiol. 70:2241–2250) observed in the neonatal rat spinal cord. J. Comp. Neurol. 423:590–602, 2000. © 2000 Wiley‐Liss, Inc.
A real-time robot arm collision avoidance system

A data structure and update algorithm are presented for a prototype real-time collision avoidance safety system simulating a multirobot workspace. The data structure is a variant of the octree, which serves as a spatial index. The authors use the N-objects octree, which indexes a collection of 3D primitive solids. These primitives make up the two seven-degree-of-freedom robot arms and workspace modeled by the system. Octree nodes containing mor than a predetermined number N of primitives are decomposed. This rule keeps the octree small, as the entire world model for the application can be implemented using a few dozen primitives. As robot arms move, the octree is updated to reflect their changed positions. Modification to the octree is rarely required. Incidents in which one robot arm comes too close to another arm or an object are reported. Cycle time for interpreting current arm joint angles, updating the octree to reflect new positions, and detecting/reporting imminent collisions averages 30 ns on an Intel 80386 processor running at 20 MHz. >
Interleukin 17A Promotes Lymphocytes Adhesion and Induces CCL2 and CXCL1 Release from Brain Endothelial Cells

The nature of the interaction between Th17 cells and the blood–brain barrier (BBB) is critical for the development of autoimmune inflammation in the central nervous system (CNS). Tumor necrosis factor alpha (TNF-α) or interleukin 17 (IL-17) stimulation is known to enhance the adherence of Th17 cells to the brain endothelium. The brain endothelial cells (bEnd.3) express Vascular cell adhesion molecule 1 (VCAM-1), the receptor responsible for inflammatory cell adhesion, which binds very late antigen 4 (VLA-4) on migrating effector lymphocytes at the early stage of brain inflammation. The present study examines the effect of the pro-inflammatory cytokines TNF-α and IL-17 on the adherence of Th17 cells to bEnd.3. The bEnd.3 cells were found to increase production of CCL2 and CXCL1 after stimulation by pro-inflammatory cytokines, while CCL2, CCL5, CCL20 and IL17 induced Th17 cell migration through a bEnd.3 monolayer. This observation may suggest potential therapeutic targets for the prevention of autoimmune neuroinflammation development in the CNS.
Syncope in a Previously Healthy Young Adult: Undiagnosed Aortic Stenosis, Dilation and Coarctation Requiring Emergent Surgery

Aortic stenosis is a valvular heart disease that needs particular attention; due to the fact that asymptomatic patients may go undiagnosed for periods of time long enough to cause severe morbidity. On the other hand, aortic stenosis frequently is accompanied with other cardiac pathologies, such as a post-stenotic dilation, and coarctation. Imputed as a possible causative factor for sudden cardiac death, among other, aortic stenosis is a common finding in the setting of a bicuspid valve. We present the case of a previously young adult that suffered an episode of syncope during a football game. Exertion and sport activities are well-known situations that might provoke an abrupt manifestation of the latent valvular pathology. We dealt with an aortic stenosis of severe grade, accompanied with dilation and coarctation of aorta, in an individual with bicuspid aortic valve. A major heart surgery intervention was performed, with replacement of the valve, correction of the dilated arch and removal of the coarcted segment. Close follow-ups and monitoring are warranted even in asymptomatic patients, when the stenosis is uncovered as an incidental finding, during routine checkups.