Miracle-dz/UniFAR-FTUs huggingface dataset:
Hoxa5/Cre transgenic mice: Novel tools for regional deletion along the anterior‐posterior axis

Summary: The Hoxa5 homeobox gene encodes a transcription factor that plays a critical role in specifying the identity of the cervico‐thoracic region along the anterior‐posterior embryo axis and in orchestrating organ morphogenesis. The loss of Hoxa5 function results in skeletal transformations, lethality at birth due to lung defects, and organ anomalies affecting the digestive tract, the mammary gland and the ovary. Study of Hoxa5 gene regulation has revealed the interplay of several control regions that direct Hoxa5 developmental expression. Enhancers targeting expression in the CNS, the paraxial and lateral plate mesoderm at the cervico‐thoracic level, and in the mesenchymal compartment of the respiratory and digestive tracts have been identified. Using these molecular tools, we have generated two Hoxa5/Cre transgenic mouse lines carrying different combinations of Hoxa5 regulatory enhancers and allowing site‐specific recombination in subsets of Hoxa5 expression sites as tested with the Rosa26/lacZ reporter mice. Further validation of the recombination efficiency of the Hoxa5/Cre transgenic lines was performed with mice carrying a Hoxa5 conditional allele. Hoxa5 deletion with the Hoxa5/Cre mouse lines recapitulates Hoxa5 mutant phenotypes, such as skeletal defects, neonatal lethality, and lung malformations. Hoxa5/Cre mouse lines provide novel genetic tools for gene function analysis in defined tissues along the anterior‐posterior axis. genesis 52:149–156. © 2013 Wiley Periodicals, Inc.
Problems of comorbidity in mortality after prostatectomy.

OBJECTIVE In recent studies of patients with benign prostatic hyperplasia (BPH), men undergoing transurethral resection of the prostate (TURP) had higher long-term mortality than men undergoing open prostatectomy. We tested the hypothesis that the higher mortality for patients undergoing TURP could have occurred if these patients were older and sicker at the time of surgery than patients undergoing open prostatectomy. DESIGN AND SETTING Retrospective cohort study at Yale-New Haven (Conn) Hospital. PATIENTS Two hundred fifty-two men who underwent TURP or open prostatectomy from 1979 through 1981 for the treatment of BPH. MAIN OUTCOME MEASURES Five-year mortality adjusted for age and severity of comorbid illness at the time of surgery. RESULTS The crude 5-year mortality rates were 17.5% (22 of 126 patients) for the TURP group and 13.5% (17 of 126 patients) for the open group. At the time of surgery, however, patients in the TURP group were sicker and older than patients in the open group. As the detail and quality of the assessment of comorbidity increased, the adjusted risk of TURP decreased. Improved classifications of comorbidity in three different forms of statistical analysis did not show an effect of type of prostatectomy on long-term mortality (Mantel-Haenszel relative risk, 1.03; 95% confidence interval, 0.57 to 1.87). CONCLUSIONS These results suggest that TURP does not increase long-term mortality after surgery for the treatment of BPH. Inadequate accounting for severity of illness may also affect other statistical "adjustments" used in research concerned with patient outcomes.
Steady-state visual evoked potential (SSVEP)-based communication: impact of harmonic frequency components

Brain–computer interfaces (BCIs) can be realized on the basis of steady-state evoked potentials (SSEPs). These types of brain signals resulting from repetitive stimulation have the same fundamental frequency as the stimulation but also include higher harmonics. This study investigated how the classification accuracy of a 4-class BCI system can be improved by incorporating visually evoked harmonic oscillations. The current study revealed that the use of three SSVEP harmonics yielded a significantly higher classification accuracy than was the case for one or two harmonics. During feedback experiments, the five subjects investigated reached a classification accuracy between 42.5% and 94.4%.
Delineating low‐count defective‐contour SPECT lung scans for PE diagnosis using adaptive dual exponential thresholding and active contours

To develop an automated lung delineation method that greatly improves the accuracy of contour extraction in SPECT lung scans with low maximum count, total counts, and/or defective contour edges, by combining deformable contour and planar image processing techniques with our existing adaptive dual exponential thresholding method. Two datasets consisting of 90 Monte Carlo simulations and 35 SPECT scans of real patients both with low maximum/total counts were used as the basis of this study. After preliminary contour extraction using dual exponential thresholding, a deformable contour algorithm was applied, combined with edge enhancement using image processing techniques such as Gaussian transformation and Sobel edge detection. Both quantitative validation via statistical measures and qualitative verification by an experienced practitioner were implemented to evaluate the method. An average of 83% congruency was achieved for 45 simulations with maximum count values below 31. This is a significant 33% improvement on the results of our previous study using dual exponential thresholding alone. Overall congruence averaged 95% for the entire simulation dataset. With the set of 35 actual SPECT scans with relatively low maximum/total counts, congruency again averaged near 95% with a few outliers ranging between 75 and 90%. We have successfully combined active contour with adaptive dual exponential thresholding to delineate lung contours accurately for SPECT scans with low maximum/total counts and/or defective contours due to various cardiopulmonary disorders. © 2010 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 20, 149–154, 2010
Seasonal survival and expectation of infective life of Culicoides spp. (Diptera: Ceratopogonidae) in Israel, with implications for bluetongue virus transmission and a comparison of the parous rate in C. imicola from Israel and Zimbabwe.

The vectorial potential of Culicoides imicola, Culicoides obsoletus, and Culicoides oxystoma with respect to bluetongue virus (BTV) in Israel in 1981–1982 was evaluated based upon their respective mean periods between blood meals, their estimated survival rates between blood meals, and their expectation of infective life. Culicoides imicola was identified as the species with the highest vectorial potential because of its seasonality, presence throughout the entire year, survival rate, and expectation of infective life. This species may serve as an overwintering agent for BTV. By the same criteria, C. obsoletus was ranked 2nd in vectorial potential. Its survival rate and expectation of infective life were more limited than in C. imicola, but it also appeared capable of serving as an overwintering agent for BTV. Culicoides oxystoma was ranked 3rd because of its small numbers, presence only from August to December, limited peak survival rate, and brief period of expected infective life. However, for a limited period the last 2 variables for the 3 species tested were highest in C. oxystoma . During the bluetongue season the mean period between blood meals is 3.3 to 4.6 days for C. imicola, 3.5 to 5.0 days for C. oxystoma, and 4.0 to 4.9 days for C. obsoletus . Comparison between C. imicola from Bet-Dagan, Israel, and C. imicola from Mt Hampden, Zimbabwe, shows that in both countries the parous rate in this species peaks from midsummer to the onset of winter, a period corresponding to the bluetongue season.
Nucleotide Sequence of a cDNA for Catalase from Arabidopsis thaliana.

The study of germination and early seedling growth is experimentally attractive in Arabidopsis thaliana because a large collection of mutants with altered germination profiles are available (5). However, to fully understand the process of germination in higher plants also requires the development of molecular markers sensitive to both environmental and genetic signals that govern this process. In oil seed plants such as Arabidopsis, catalase (EC 1.11.1.6) is very suitable as a germination marker because this enzyme scavenges H202 produced during the early /3-oxidation of storage lipids in the seed (8). Using an antibody raised against a glyoxysomal specific catalase from pumpkin (9), we screened a leaf-specific Xgtl 1 cDNA library. Two positive clones containing partial cDNAs were isolated from among 100,000 plaques and subsequently sequenced (Table I). One clone that showed 75% identity at the protein level to the Zea maize Cat2 gene (1) was used to screen an Arabidopsis Xgtl0 cDNA library to find a full-length cDNA. Two positives were selected based on their size (1.8
Tumor necrosis factor-alpha and lipopolysaccharide induce apoptotic cell death in bovine glomerular endothelial cells.

BACKGROUND The glomerular endothelial cell is a specialized microvascular cell type involved in the regulation of glomerular ultrafiltration. During gram-negative sepsis, glomerulonephritis, and acute renal failure, bacterial lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-alpha) may cause severe cell damage. Our aim was to study and compare the direct effects of TNF-alpha and LPS on the induction of apoptosis in bovine glomerular endothelial cells. METHODS Primary bovine glomerular endothelial cells were stimulated with TNF-alpha or LPS, and apoptotic cell death was investigated by DNA fragmentation analysis, morphological studies, measurement of cytochrome c efflux and mitochondrial permeability transition, Bak, Bad, Bax, Bcl-2, Bcl-xL protein expression, and caspase-3-like protease activity. RESULTS TNF-alpha, as well as LPS, elicited apoptotic cell death both time and concentration dependently. Along with DNA ladder formation, we detected the formation of 50 kbp high molecular weight DNA fragments, nuclear condensation, and mitochondrial permeability transition. Concerning all parameters, LPS signaling proved to be more rapid than TNF-alpha. Mechanistically, TNF-alpha-induced cell death was preceded by an efflux of mitochondrial cytochrome c into the cytosol and, subsequently, by a marked increase in the proapoptotic protein Bak and a decrease in the anti-apoptotic Bcl-xL protein content. Comparable but more pronounced effects were seen with LPS. Later, caspase-3-like protease activity was first detectable after 10 hours and was continuously increased up to 24 hours in both TNF-alpha- and LPS-stimulated cells. Correspondingly, we detected an extended cleavage of the nuclear enzyme poly(ADP-ribose) polymerase. Caspase inhibitors Z-Asp-CH2-DCB and Z-VAD-fmk blocked both TNF-alpha- and LPS-induced apoptosis in a comparable manner. Only Z-Asp-CH2-DCB was able to block apoptotic cell death completely. CONCLUSION Both bacterial LPS and TNF-alpha potently induced apoptotic cell death in glomerular endothelial cells. Direct endotoxin-induced apoptosis may therefore be relevant in the progression of acute renal failure, which is a frequent complication of gram-negative sepsis.
Picomolar detection of carcinoembryonic antigen in whole blood using microfluidics and surface‐enhanced Raman spectroscopy

Carcinoembryonic antigen (CEA) is a wide‐spectrum biomarker. Clinically, we generally use serum sample to detect CEA, which needs to be centrifuged to pretreat the raw blood sample. In this study, we realized direct CEA detection in raw blood samples exploiting microfluidics. The LOD was as low as 10−12 M.
Alcohol accounts for a high proportion of premature mortality in central and eastern Europe.

BACKGROUND There is a west-east mortality gradient in Europe, more pronounced in men. The objective of this article was to quantify the contribution of alcohol use to the gap in premature adult mortality between three old (France, Sweden and United Kingdom) and four new (Czech Republic, Hungary, Lithuania and Poland) European Union (EU) member states for the year 2002. Russia was added as an external comparator. METHODS Exposure data were taken from surveys and per capita consumption records from the World Health Organization (WHO) Global Alcohol Database. Mortality data were taken from the WHO databank. The risk relationships were taken from published meta-analyses and from the WHO Comparative Risk Assessment project. Alcohol exposure and relative risk information was combined to derive alcohol-attributable fractions for relevant causes of premature mortality. RESULTS Alcohol consumption was responsible for 14.6% of all premature adult mortality in the eight countries, 17.3% in men and 8.0% in women. This proportion was clearly higher in the new EU member states and Russia compared with the comparison countries from the old EU. For men, Russia with 29.0 alcohol-attributable premature deaths per 10,000 population had a more than 10-fold higher rate compared with Sweden (2.7 deaths/10,000). For women, the ratio between Hungary (5.0 alcohol-attributable deaths/10,000) and Russia (4.7 deaths/10,000) compared with Sweden (0.5 deaths/10,000) was almost as high, but the rates were much lower. The Czech Republic and Poland showed proportionally less alcohol-attributable premature mortality than the other new EU member states or Russia for both genders, which, however, was still higher than in any of the old EU member states. CONCLUSIONS Alcohol is a strong contributor to the health gap between western and central and eastern Europe, with both average volume of consumption and patterns of drinking contributing to burden of disease and injury. Alcohol also contributes substantially to male-female differences in mortality and life expectancy. However, there are feasible and cost-effective measures to reduce alcohol-related burden that should be implemented in central and eastern Europe.
Downregulation of the c‐MYC target gene, peroxiredoxin III, contributes to arsenic trioxide‐induced apoptosis in acute promyelocytic leukemia

Arsenic trioxide (ATO) induces differentiation and apoptosis in acute promyelocytic leukemia (APL). Several reports indicate that in APL cells apoptosis occurs mainly by a mechanism that involves the inhibition of glutathione peroxidase, one of the enzymes that regulates mitochondrial levels of H2O2. Peroxiredoxin (Prx) III, a c‐MYC target gene, is also a mitochondria‐specific H2O2‐scavenger enzyme. We studied here the role of Prx III during ATO‐induced apoptosis in APL‐derived NB4 cells, since these cells express high levels of Prx III. The protein and mRNA levels of Prx III decreased during ATO‐induced apoptosis of NB4 cells. The downregulation of Prx III occurred before reactive oxygen species accumulation, reduction in the mitochondrial membrane potential and apoptosis. Depletion of Prx III enhanced mitochondrial‐dependent apoptosis events. In contrast, overexpression of Prx III led to reduced levels of ATO‐induced apoptosis. c‐MYC was also downregulated in ATO‐treated NB4 cells. Furthermore, depletion of c‐MYC also reduced the Prx‐III expression levels. Finally chromatin immunoprecipitation and luciferase reporter assays confirmed that downregulation of Prx‐III was caused by the reduction of c‐MYC levels during ATO‐induced apoptosis of NB4 cells. These findings demonstrate a novel apoptotic‐response pathway whereby downregulation of Prx‐III potentiates ATO‐induced apoptosis in APL cells. © 2009 UICC
Hetero-mark, a benchmark suite for CPU-GPU collaborative computing

Graphics Processing Units (GPUs) can easily outperform CPUs in processing large-scale data parallel workloads, but are considered weak in processing serialized tasks and communicating with other devices. Pursuing a CPU-GPU collaborative computing model which takes advantage of both devices could provide an important breakthrough in realizing the full performance potential of heterogeneous computing. In recent years platform vendors and runtime systems have added new features such as unified memory space and dynamic parallelism, providing a path to CPU-GPU coordination and necessary programming infrastructure to support future heterogeneous applications. As the rate of adoption of CPU-GPU collaborative computing continues to increase, it becomes increasingly important to formalize CPU-GPU collaborative programming paradigms and understand the impact of this emerging model on overall application performance. We propose the Hetero-Mark to help heterogeneous system programmers understand CPU-GPU collaborative computing and to provide guidance to computer architects in order to enhance the design of the runtime and the driver. We summarize seven common CPU-GPU collaborative computing programming patterns and include at least one benchmark for each pattern in the suite. We also characterize different workloads in Hetero- Mark to analyze execution metrics specific to CPU-GPU collaborative computing, including CPU and GPU performance, CPU-GPU communication latency and memory transfer latency.
Surfactant improves oxygenation in infants and children with pneumonia and acute respiratory distress syndrome

Aim: Pneumonia in childhood may be associated with surfactant dysfunction and severe acute respiratory distress syndrome (ARDS). The aim of this study was to investigate the effects of surfactant treatment on oxygenation in 8 infants (age range: 1 mo to 13 y) with severe respiratory failure owing to viral, bacterial or Pneumocystis Carinii pneumonia. Methods and results: Instillation of a modified porcine surfactant (Curosurf®) improved gas exchange immediately. Median paO2/FiO2 increased from 66 to 140mmHg (8.8–18.7 kPa; p < 0.01) within 1 h of surfactant treatment. Seven of the 8 patients received multiple surfactant doses. Four patients (50%) died 3–62 d after surfactant treatment. However, 6 patients (75%) were immunodeficient, so that the observed mortality rate was mainly due to the underlying disease.
Ideas on collision detection in vehicles using WSN

As traffic and population is increasing, it’s monitoring and automation is finding a scope for development and it is emerging as a lucrative field for research and development. Intelligent transportation systems (ITS) are advanced applications which aim to provide innovative services relating to different modes of transport and traffic management and enable various users to be better informed and make safer, more coordinated, and 'smarter' use of transport networks. Realizing its enormous potential in automation, this review work was built around ITS and its applications. As ITS majorly involves the Wireless Sensor Networks, it was also explored to some extent. Various architectures were explored and compared to deduce the strengths and weaknesses of proposed solution.
Evaluation of a disease management program for COPD using propensity matched control group.

BACKGROUND Disease management programs (DMPs) have proliferated recently as a means of improving the quality and efficiency of care for patients with chronic illness. These programs include education about disease, optimization of evidence-based medications, information and support from case managers, and institution of self-management principles. Chronic obstructive pulmonary disease (COPD) is a major cause of morbidity and mortality in Singapore and worldwide. DMP aims to reduce mortality, hospitalizations, and average length of stay in such patients. This study assesses the outcomes of the DMP, comparing the propensity score matched DMP patients with controls. METHODS DMP patients were compared with the controls, who were COPD patients fulfilling the DMP's inclusion criteria but not included in the program. Control patients were identified from Operations Data Store (ODS) database. The outcomes of interest were average length of stay, number of days admitted to hospital per 100 person days, readmission, and mortality rates per person year. The risk of death and readmission was estimated using Cox, and competing risk regression respectively. Propensity score was estimated to identify the predictors of DMP enrolment. DMP patients and controls were matched on their propensity score. RESULTS There were 170 matched DMP patients and control patients having 287 and 207 hospitalizations respectively. Program patient had lower mortality than the controls (0.12 vs. 0.27 per person year); cumulative 1-year survival was 91% among program patient and 76% among the control patients. Readmission, and hospital days per 100 person-days was higher for the program patients (0.36 vs. 0.17 per person year), and (2.19 vs. 1.88 per person year) respectively. CONCLUSIONS Participation in "DMP" was associated with lower all-cause mortality when compared to the controls. This survival gain in the program patients was paradoxically associated with an increase in readmission rate and total hospital days.
Recognition of Smac‐mimetic compounds by the BIR domain of cIAP1

Inhibitor of apoptosis proteins (IAPs) are negative regulators of apoptosis. As IAPs are overexpressed in many tumors, where they confer chemoresistance, small molecules inactivating IAPs have been proposed as anticancer agents. Accordingly, a number of IAP‐binding pro‐apoptotic compounds that mimic the sequence corresponding to the N‐terminal tetrapeptide of Smac/DIABLO, the natural endogenous IAPs inhibitor, have been developed. Here, we report the crystal structures of the BIR3 domain of cIAP1 in complex with Smac037, a Smac‐mimetic known to bind potently to the XIAP‐BIR3 domain and to induce degradation of cIAP1, and in complex with the novel Smac‐mimetic compound Smac066. Thermal stability and fluorescence polarization assays show the stabilizing effect and the high affinity of both Smac037 and Smac066 for cIAP1‐ and cIAP2‐BIR3 domains.
Visual and haptic angle perception in the matching task.

Forty subjects reproduced angles of 30-150 deg from a series of comparison angles presented in ascending and descending orders. Magnitude of error was significantly lower for the visual-visual group than for the haptic-haptic, visualhaptic, and haptic-visual groups. The results suggest that haptic percepts of angle are smaller in magnitude than those for vision and that performance differences between modalities reflect both the nature of form discrimination and the nature of the matching task itself.
A Combined Model To Predict the Functionality of the Bacteriocin-Producing Lactobacillus sakei Strain CTC 494

ABSTRACT The use of bacteriocin-producing lactic acid bacteria for improved food fermentation processes seems promising. However, lack of fundamental knowledge about the functionality of bacteriocin-producing strains under food fermentation conditions hampers their industrial use. Predictive microbiology or a mathematical estimation of microbial behavior in food ecosystems may help to overcome this problem. In this study, a combined model was developed that was able to estimate, from a given initial situation of temperature, pH, and nutrient availability, the growth and self-inhibition dynamics of a bacteriocin-producing Lactobacillus sakei CTC 494 culture in (modified) MRS broth. Moreover, the drop in pH induced by lactic acid production and the bacteriocin activity toward Listeria as an indicator organism were modeled. Self-inhibition was due to the depletion of nutrients as well as to the production of lactic acid. Lactic acid production resulted in a pH drop, an accumulation of toxic undissociated lactic acid molecules, and a shift in the dissociation degree of the growth-inhibiting buffer components. The model was validated experimentally.