Miracle-dz/UniFAR-FTUs huggingface dataset:
Spectral karyotyping combined with locus‐specific FISH simultaneously defines genes and chromosomes involved in chromosomal translocations

Genes that play roles in malignant transformation have often been found proximate to cancer‐associated chromosomal breakpoints. Identifying genes that flank chromosomal reconfigurations is thus essential for cancer cytogenetics. To simplify and expedite this identification, we have developed a novel approach, based on simultaneous spectral karyotyping and fluorescence in situ hybridization (FISH) which, in a single step, can identify gross chromosomal aberrations as well as detect the involvement of specific loci in these rearrangements. Signals for specifically queried genes (FISH probe) were easily detectable in metaphase cells, together with the signals from painted chromosomes (spectral karyotyping probes). The concentration and size of the FISH probes could cover a wide range and still be used successfully. Some of the nucleotide‐bound dyes used for the labeling, as Cy3, Spectrum Orange, Alexa 594, Texas Red, and Rhodamine 110, were particularly efficient. More than one gene can be queried in the same metaphase, because multiple FISH probes could be hybridized simultaneously. To demonstrate this technique, we applied it to the myeloma cell line Karpas 620, which has numerous chromosomal rearrangements. The approach that we present here will be particularly useful for the analysis of complex karyotypes and for testing hypotheses arising from cancer gene expression studies. Genes Chromosomes Cancer 27:418–423, 2000. Published 2000 Wiley‐Liss, Inc.
Building HVAC control systems - role of controls and optimization

As building systems become more integrated, one inherently introduces coupling between previously independent designs. Model-based controls and analysis tools are keys to identify problems and solution-paths early on. A model-based approach facilitates the developments of monitoring equipment, fault-tolerance, diagnosis and controls algorithms, that are critical in the operation of integrated system. This paper introduces a rich set of problems in controls and optimization related to commercial chilled water cooling plants and related systems. The problems range from opportunities in multivariable optimal control, dynamic resource allocation and control over networks. As an example, dither-based extremum seeking based controls is proposed as an online optimization algorithm for chilled water plant control
Analyze and simulation of linear antenna array fed with composite right/left-handed transmission line

A novel method which linear antenna array fed with composite right/left-handed transmission line (CRLH-TL) was presented. By utilizing the phase advance of left-handed transmission line (LH-TL) and the phase delay of right-handed transmission line (RH-TL), we can meet the requirement of radiation characteristic by adjust the length of LH-TL without changing the entire antenna array's size, so the flexibility of antenna design is improved. Phase characteristics of lossless CRLH-TL model were analyzed, and linear antenna array fed with CRLH-TL model was also established. The results show that comparing conventional linear antenna array design, it's more flexible by using the method mentioned in this paper, and it is applicable to practical microwave systems.
Investigation of a Single-Sideband Mixer Anomaly

Investigations into a higher than expected conversion loss phenomena in a single-sideband (SSB) balun-coupled mixer revealed an unusual feedthrough mechanism. The tests also showed the image frequency voltage to be short-circuited with a ring diode quad and open-circuited with a bridge diode quad.
SU 5416 and SU 5614 inhibit kinase activity of wild-type and mutant FLT 3 receptor tyrosine kinase

Internal tandem duplication (ITD) in the juxtamembrane portion of Fms-like tyrosine kinase 3 (FLT3), a type III receptor tyrosine kinase (RTK), is the most common molecular defect associated with acute myeloid leukemia (AML). The high prevalence of this activating mutation makes it a potential target for molecularly based therapy. Indolinone tyrosine kinase inhibitors have known activity against KIT, another member of the type III RTK family. Given the conserved homology between members of this family, we postulated that the activity of some KIT inhibitors would extend to FLT3. We used various leukemic cell lines (BaF3, MV 4-11, RS 4;11) to test the activity of indolinone compounds against the FLT3 kinase activity of both wild-type (WT) and ITD isoforms. Both SU5416 and SU5614 were capable of inhibiting autophosphorylation of ITD and WT FLT3 (SU5416 concentration that inhibits 50% [IC50], 100 nM; and SU5614 IC50 10 nM). FLT3-dependent activation of the downstream signaling proteins mitogen-activated protein kinase (MAPK) and signal transducer and activator of transcription 5 (STAT5) was also inhibited by treatment in the same concentration ranges. FLT3 inhibition by SU5416 and SU5614 resulted in reduced proliferation (IC50, 250 nM and 100 nM, respectively) and induction of apoptosis of FLT3 ITD-positive leukemic cell lines. Treatment of these cells with an alternative growth factor (granulocyte-macrophage colony-stimulating factor [GM-CSF]) restored MAPK signaling and cellular proliferation, demonstrating specificity of the observed inhibitory effects. We conclude that SU5416 and SU5614 are potent inhibitors of FLT3. Our finding that inhibition of FLT3 induces apoptosis of leukemic cells supports the feasibility of targeting FLT3 as a novel treatment strategy for AML. (Blood. 2002;100:2941-2949)
The measurement problem in consciousness research

Abstract States of sensory absorption may offer a means to disentangle perception from report. Interestingly, such states lead to an antagonistic relationship between perceptual and cognitive-access networks, suggesting that perceptual awareness does not depend on a read-out by high order cognitive-access mechanisms. Rather, it may emerge internally, through a cooperative coding dynamics, whereby each neuron simultaneously represents and reads-out the perceptual awareness state.
Fas-associated death domain (FADD) is a negative regulator of T-cell receptor–mediated necroptosis

Cell death is an important mechanism to limit uncontrolled T-cell expansion during immune responses. Given the role of death-receptor adapter protein Fas-associated death domain (FADD) in apoptosis, it is intriguing that T-cell receptor (TCR)–induced proliferation is blocked in FADD-defective T cells. Necroptosis is an alternate form of death that can be induced by death receptors and is linked to autophagy. It requires the death domain-containing kinase RIP1 and, in certain instances, RIP3. FADD and its apoptotic partner, Caspase-8, have also been implicated in necroptosis. To accurately assess the role of FADD in mature T-cell proliferation and death, we generated a conditional T-cell–specific FADD knockout mouse strain. The T cells of these mice develop normally, but lack FADD at the mature stage. FADD-deficient T cells respond poorly to TCR triggering, exhibit slow cell cycle entry, and fail to expand over time. We find that programmed necrosis occurs during the late stage of normal T-cell proliferation and that this process is greatly amplified in FADD-deficient T cells. Inhibition of necroptosis using an inhibitor of RIP1 kinase activity rescues the FADD knockout proliferative defect. However, TCR-induced necroptosis did not appear to require autophagy or involve RIP3. Consistent with their defective CD8 T-cell response, these mice succumb to Toxoplasma gondii infection more readily than wild-type mice. We conclude that FADD constitutes a mechanism to keep TCR-induced programmed necrotic signaling in check during early phases of T-cell clonal expansion.
UTD-type ray analysis of electromagnetic scattering from planar finite periodic structures

This paper presents the UTD-type solution for the electromagnetic scattering from a periodic structure, analogous to the conventional UTD solution for the scattering from electrically large scatterers. The solution was built up based on Kirchhoff approximation of equivalent currents from a unit cell, within which the structure can be arbitrary. This solution provides a convenient way to interpret the scattering mechanism in terms of ray optics. Theoretical illustration and numerical examples are presented to demonstrate its feasibility.
Mammalian cell cytotoxicity of diesel engine emission fractions

The relative toxicity of extracted and fractionated diesel engine emission material was assessed with two in vitro mammalian cell culture systems, continously maintained Balb/c 3T3 cells and freshly‐isolated baboon peripheral blood lymphocytes. Particulate emission material from a two‐stroke cycle and a four‐stroke cycle diesel engine was collected on filters and then solvent extracted. The neutral material was fractionated chromatographically after an initial chemical fractionation of the emission material into acidic, neutral and basic fractions. Balb/c 3T3 cells treated with chemically and chromatographically‐differentiated fractions from both the two‐stroke cycle and the four‐stroke cycle diesel engines had different toxicities on a concentration dependent (μg ml−1) basis. Fractions from the four‐stroke cycle engine showed greater toxicity than those from the two‐stroke cycle engine. Toxicity comparisons were made on the basis of cloning efficiency measurements (indicative of effects on reproductive integrity) 8 days after a 72 h treatment interval, and on the basis of DNA, RNA and protein precursor incorporation rates (biochemical indices) during or immediately after 72 h of treatment. The Balb/c 3T3 system results were supported by similar results obtained when freshly isolated baboon peripheral blood lymphocytes were mitogen (concanavilin A) stimulated in the presence of the various fractions. The results in the in vitro lymphocyte system indicate a potential for altered immune defense capability if the cells were to be exposed to the fractions in vivo.
Experimental and computer model of plaque formation in the artery

Atherosclerosis is a progressive disease characterized by inflammation, monocyte-macrophage migration, and lipid accumulation in the vascular wall. Atherosclerosis is initially characterized by endothelial dysfunction, which favors lipid and cell elements crossing inside blood vessel wall. In this study, two experiments are calculated numerically. The first is Cheng et al. 2006 experiment with cast model on the carotid artery and the second is our pig experiment on the left anterior descending coronary artery (LAD) after 2 months of high fat diet. Experimental model of plaque formation on pig LAD is simulated numerically using a specific animal data obtained from intravascular ultrasound (IVUS) and histological data. The 3D blood flow is governed by the Navier-Stokes equations, together with the continuity equation. Mass transfer within the blood lumen and through the arterial wall is coupled with the blood flow and is modeled by the convection-diffusion equation. LDL transport in lumen of the vessel is described by Kedem-Katchalsky equations. The inflammatory process is solved using three additional reaction-diffusion partial differential equations. Matching of IVUS and histological animal data is performed using 3D histological image reconstruction and 3D deformation of elastic body. Lipids concentration in the intimal area of the low shear stress was 16% and for oscillatory zone 10% which is in good agreement with experimental data. Computed concentration of macrophages for pig model indicates that there is a newly formed matter in the intima, especially in LAD 15 mm region below left main artery bifurcation where plaque 8% of the area intima thickness was found in the area of lowered shear stress. Matching of plaque location and progression in time between experimental and computer model shows a potential benefit for future prediction of this vascular decease using computer simulation.
The niche of higher plants: evidence for phylogenetic conservatism

A species' ecological niche depends on the species' adaptations to its present habitat, but also on the legacy from its ancestors. Most authors argue that such a phylogenetic niche conservatism is of minor importance, although no quantitative analyses across a major taxon is available. Higher plants from central Europe offer a unique opportunity for such an exercise, as the niche positions along various environmental gradients are available for most species. We quantified niche conservatism by two approaches. First, we used a phylogenetic tree and quantified the degree of retention of niches across the tree. Depending on the gradient, the values ranged from 0.43 to 0.22. This was significantly greater than the null expectation. Second, we used a taxonomy and quantified the amount of variance among species that could be explained at higher taxonomic levels. The values ranged from 25 to 72%. Again, this was significantly higher than the null expectation. Thus, both approaches indicated a clear niche conservatism. The distribution of conservatism across taxonomic levels differed considerably among environmental gradients. The differences among environmental gradients could be correlated with the palaeoenvironmental conditions during the radiation of the phylogenetic lineages. Thus, niche conservatism among extant plant species may reflect the opportunities of their ancestors during their diversification.
Imaging and staging of transitional cell carcinoma: part 1, lower urinary tract.

OBJECTIVE Transitional cell carcinoma (TCC) of the bladder is one of the most common malignancies affecting the genitourinary tract and is characterized by multifocality and a high incidence of recurrence. Radiologists play an important role in the staging and surveillance of this malignancy. In this article, we discuss the epidemiology, pathologic characteristics, and patterns of tumor spread of bladder carcinomas. We illustrate and focus on the role of imaging in the diagnosis, staging, and surveillance of TCC. CONCLUSION The hallmark of TCC is multiplicity and recurrence. Cystoscopy is the method of choice for evaluation of the primary tumor in patients with bladder carcinoma. Imaging acts as an adjunct to accurately stage disease in these patients. Nearly 2-4% of patients with bladder cancer develop upper tract TCC. Hence, surveillance of the upper tract, in which imaging plays a central role, is an important component in the management of TCC. As in every other cancer, we face some limitations in nodal staging of TCC, particularly when the nodes are not enlarged. Development and validation of newer scanning techniques and MR contrast agents may help address some of these limitations in the future.
Letter: Interaction between two factors that influence vowel duration.

It is well known that stressed vowels are shorter before voiceless consonants than before voiced, and that stressed vowels are shorter before an unstressed syllable in a bisyllabic word than in a monsyllabic word. A set of test materials was designed to study the interaction between these two rules. Results suggest that vowels become strongly incompressible beyond a certain amount of shortening and that vowel duration modification rules should have the form Do = k (Di − Dmin)+Dmin, where Di is the input duration to the rule, Do is the output duration of the rule, Dmin is the minimum duration for the vowel, and the scale factor k is greater than zero and depends on the particular rule. The data indicate that Dmin is about 45% of the inherent duration of a given vowel.
Preference for information about an uncertain but unavoidable outcome.

Abstract : (Predictive strategies and the need to confirm them: some notes on pathological types of decision. 'Psychological Reports,' 15:99-105 (1964)). The study was designed to examine the effects on search of type of outcome (whether positive or negative), and to monitor the affective state of subjects in an attempt to clarify the basis for overtly noninstrumental search behavior. The study had three objectives: (a) to extend to the human level the analysis of the effects of uncertain and unavoidable outcomes on information search where, to date, only Pervin's paired comparison preference data are available; (b) to assess the differential effects of type of outcome (shock, monetary reward) on search; and in particular (c) to measure possible changes in the affective or arousal state of subjects in response to information. (Author)
Early-stage hepatocellular carcinoma in patients with cirrhosis: long-term results of percutaneous image-guided radiofrequency ablation.

PURPOSE To perform a prospective, intention-to-treat clinical trial to determine the long-term survival rates of patients with hepatic cirrhosis and early-stage hepatocellular carcinoma (HCC) in whom percutaneous image-guided radiofrequency (RF) ablation was used as the sole first-line anticancer treatment. MATERIALS AND METHODS The study was performed with approval of the ethics committee, and written informed consent was obtained for all patients. From June 1, 1996, to January 1, 2003, 206 patients (143 men, 63 women; age range, 51-81 years; mean age, 67 years +/- 7) who were excluded from surgery and who had Child class A or B cirrhosis with either a single HCC less than or equal to 5 cm in diameter or multiple (as many as three) HCCs less than or equal to 3 cm in diameter each were enrolled. RF ablation was performed in 187 (91%) of 206 patients; 19 (9%) were excluded from RF treatment because of unfavorable tumor location. Follow-up ranged from 3 to 78 months (mean, 24 months +/- 21) and included measurement of alpha-fetoprotein level, ultrasonography at 3-month intervals, and spiral computed tomography at 6-month intervals. Patients were observed for recurrence of the treated tumor and for the emergence of new HCC tumors. Survival probabilities were estimated with the Kaplan-Meier method, and differences between survival curves were evaluated with the log-rank test. RESULTS At the end of the study, 145 patients were alive, and 61 were dead. In the intention-to-treat analysis, overall survival rates were 97% at 1 year, 67% at 3 years, and 41% at 5 years. Median survival was 49 months. In the 187 patients treated with RF ablation, overall survival rates were 97% at 1 year, 71% at 3 years, and 48% at 5 years. Median survival was 57 months. The difference between the two survival curves was not statistically significant (P=.5094). Survival of patients treated with RF ablation was dependent on Child class (P=.0006) and tumor multiplicity (P=.0133). Patients who had Child class A cirrhosis with solitary HCC (n=116) had 1-, 3-, and 5-year survival rates of 100%, 89% and 61%; median survival was 65 months. The 1-, 3-, and 5-year recurrence rates were 14%, 49%, and 81% for the emergence of new tumors and 4%, 10%, and 10% for local tumor progression. CONCLUSION RF ablation is an effective first-line treatment for cirrhotic patients with early-stage HCC who were excluded from surgery.
Differences in Quality of Life and Compliance with Diet in Children with Celiac Disease in Slovak Republic

Celiac disease is chronic disease with immune disorder which is connected with the allergy reaction on molecule of gluten and prolamine. Celiac disease is expressed in persons with genetic susceptibility. The aim of the study was to follow adherence to gluten-free diet. We designed cross-sectional study where was recruited 125 volunteers, children at age 9 - 15 years old, with diagnosis of celiac diseases confirmed by European Society for Pediatric Gastroenterology Hepatology and Nutrition criteria. The data were collected in 2012-2013. In the selected group of celiac children were 78 girls and 47 boys. Compliance with diet is statistically significantly higher among girls comparing to boys. It means that girls adhered diet better than boys. Also younger group of children have a little bit higher compliance with gluten-free diet comparing to older group, but OR was not statistically significant. Our outputs didn't confirm fact that duration of disease is important factor which may influence the compliance with gluten-free diet, but more close is a relationship in diet compliance in children with shorter duration of disease.
Linguistically guided anticipatory eye movements in scene viewing

The present study replicated the well-known demonstration by Altmann and Kamide (1999) that listeners make linguistically guided anticipatory eye movements, but used photographs of scenes rather than clip-art arrays as the visual stimuli. When listeners heard a verb for which a particular object in a visual scene was the likely theme, they made earlier looks to this object (e.g., looks to a cake upon hearing The boy will eat …) than when they heard a control verb (The boy will move …). New data analyses assessed whether these anticipatory effects are due to a linguistic effect on the targeting of saccades (i.e., the where parameter of eye movement control), the duration of fixations (i.e., the when parameter), or both. Participants made fewer fixations before reaching the target object when the verb was selectionally restricting (e.g., will eat). However, verb type had no effect on the duration of individual eye fixations. These results suggest an important constraint on the linkage between spoken language processing and eye movement control: Linguistic input may influence only the decision of where to move the eyes, not the decision of when to move them.
Experimental results of the pulsed digital oscillator for MEMS in undersampling conditions

This paper describes experimental work and results showing that the PDO, a set of sigma-delta based oscillator structures for MEMS recently introduced by the authors, can also maintain a good oscillation behaviour for sampling frequencies under the Nyquist limit. So, it can work in undersampling conditions and an extension of the use of this kind of structures to higher frequency applications becomes possible.
Placebo-controlled trial of gabapentin in patients with amyotrophic lateral sclerosis. WALS Study Group. Western Amyotrophic Lateral Sclerosis Study Group.

We designed a phase II trial to evaluate the efficacy of gabapentin in slowing the rate of decline in muscle strength of patients with amyotrophic lateral sclerosis (ALS) and to assess safety and tolerability. Gabapentin (800 mg) or placebo was administered t.i. d. in a randomized, double-blinded, placebo-controlled, trial for 6 months. We enrolled 152 patients at eight sites in the United States. The primary outcome measure was the slope of the arm megascore, the average maximum voluntary isometric strength from eight arm muscles standardized against a reference ALS population. A secondary outcome measure was forced vital capacity. Slopes of arm megascores for patients on gabapentin were compared with slopes of those taking placebo using a two-way ANOVA. We observed a nonstatistically significant trend (p = 0.057-0.08) toward slower decline of arm strength in patients taking gabapentin compared with those taking placebo (mean difference 24%, median 37%). We observed no treatment effect on forced vital capacity. Gabapentin was well tolerated by patients with ALS. These results suggest that further studies of gabapentin in ALS are warranted.