Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative and Continuous Analysis of ATP Release from Blood Platelets with Firefly Luciferase Luminescence

Summary An analytical method was devised to determine the entire course of the adenosine-triphosphate (ATP) release from blood platelets based on a continuous measurement of firefly luciferase luminescence. The equation of the release reaction was derived after due consideration of substrate (ATP) consumption and product (oxyluciferin) inhibition on the luciferase reaction as follows: C, = vt × (Km/Vmax) × (I + It/Ki) + It where Ct is the total concentration of the released ATP at time t, vt is the velocity of the luciferase reaction at time t and is directly measured, It is the concentration of oxyluciferin at time t, and Vmax, Km and Ki are constants. C, of the gel-filtered platelet suspension (GFP) could be determined by substituting vt and It as functions of t. The effects of albumin and temperature on the reaction were also studied.
Incorporating uncertainty as a Quality Measure in I-Vector Based Language Recognition

State-of-the-art language recognition systems involve modeling utterances with the i-vectors. However, the uncertainty of the i-vector extraction process represented by the i-vector posterior covariance is affected by various factors such as channel mismatch, background noise, incomplete transformations and duration variability. In this paper, we propose a new quality measure based on the i-vector posterior covariance and incorporate it into the recognition process to improve the recognition accuracy. The experimental results with LRE15 database and various duration conditions show a 2 . 9% relative improvement in terms of average performance cost as a result of incorporating the proposed quality measure in language recognition systems.
A simple modification in operative technique can reduce the incidence of nonanastomotic biliary strictures after orthotopic liver transplantation

Nonanastomotic strictures after liver transplantations are a source of significant morbidity, often necessitating retransplantation. The purpose of this study was twofold: first to identify features associated with the development of this lesion; second, to make technical modifications that will decrease the incidence of this problem. In the first part of this study, 15 of 131 patients were diagnosed with nonanastomotic biliary stricture. A stepwise logistic‐regression analaysis associated donor cold ischemie time and dopamine dose with the development of nonanastomotic biliary strictures. All these patients had arterial reconstruction after partial revascularization of the liver with portal venous blood. Because the bile duct receives its blood supply from only the hepatic artery, we hypothesized staged reconstruction of the vascular supply would promote the development of this lesion. In a second a part of this study, the stricture rate in 45 patients with simultaneous revascularization using both the hepatic artery and portal vein was compared with that in 83 patients from the first part of this study, initially revascularized with portal venous blood. All patients in the second study had grafts preserved using UW solution. Only 1 patient with simultaneous revascularization developed a nonanstomotic biliary stricture. Because we were unable to identify any significant complications related to this method of revascularization, we propose that the hepatic artery and portal vein should be released simultaneously, especially in patients receiving a graft with prolonged storage time. (Hepatology 1995;21:63–69).
Association Between Vascular Endothelial Growth Factor Gene Polymorphisms with Breast Cancer Risk in an Iranian Population

Breast cancer (BC) is one of the most causes of death in women worldwide. It affects Iranian female population approximately a decade earlier than those in other parts of the world. Previous studies have shown that vascular endothelial growth factor (VEGF) gene variants were associated with BC risk. The current study aimed to evaluate the impact of VEGF rs3025039 (+936C>T), rs2010963 (+405C>G), rs833061 (–460T>C), rs699947 (–2578C>A), and rs35569394 (18-bp I/D) polymorphisms on BC risk in an Iranian population in southeast of Iran. This case-control study was done on 250 BC patients and 215 healthy women. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or PCR was used to genotype the polymorphisms. Our findings showed that VEGF rs699947 variant increased the risk of BC (OR = 1.71, 95% CI = 1.15–2.54, P = 0.009, CA vs CC; OR = 2.12, 95% CI = 1.14–3.93, P = 0.021, AA vs CC; OR = 1.78, 95% CI = 1.22–2.60, P = 0.004, CA+AA vs CC; OR = 1.47, 95% CI = 1.12–1.92, P = 0.005, A vs C). The VEGF rs3025039, rs2010963, rs833061, and rs35569394 variants were not associated with risk/protection of BC. In conclusion, our results proposed that VEGF rs699947 polymorphism may increase the risk of BC development. Furthers studies with larger sample sizes and different ethnicities are necessary to confirm our findings.
Comparison of the Hypoxia PET Tracer 18F-EF5 to Immunohistochemical Marker EF5 in 3 Different Human Tumor Xenograft Models

The availability of 18F-labeled and unlabeled 2-(2-nitro-1H-imidazol-1-yl)-N-(2,2,3,3,3-pentafluoropropyl)-acetamide (EF5) allows for a comparative assessment of tumor hypoxia by PET and immunohistochemistry; however, the combined use of these 2 approaches has not been fully assessed in vivo. The aim of this study was to evaluate 18F-EF5 tumor uptake versus EF5 binding and hypoxia as determined from immunohistochemistry at both macroscopic and microregional levels. Methods: Three tumor models—PC3, HCT116, and H460—were evaluated. Tumor-bearing animals were coinjected with 18F-EF5 and EF5 (30 mg/kg), and PET imaging was performed at 2.5 h after injection. After PET imaging and 2 min after Hoechst 33342 injection, the tumors were excised and evaluated for 18F-EF5 distribution by autoradiography and EF5 binding by immunohistochemistry. Additionally, the effects of nonradioactive EF5 (30 mg/kg) on the hypoxia-imaging characteristics of 18F-EF5 were evaluated by comparing the PET data for H460 tumors with those from animals injected with 18F-EF5 alone. Results: The uptake of 18F-EF5 in hypoxic tumor regions and the spatial relationship between 18F-EF5 uptake and EF5 binding varied among tumors. H460 tumors showed higher tumor-to-muscle contrast in PET imaging; however, the distribution and uptake of the tracer was less specific for hypoxia in H460 than in HCT116 and PC3 tumors. Correlation analyses revealed that the highest spatial correlation between 18F-EF5 uptake and EF5 binding was in PC3 tumors (r = 0.73 ± 0.02) followed by HCT116 (r = 0.60 ± 0.06) and H460 (r = 0.53 ± 0.10). Uptake and binding of 18F-EF5 and EF5 correlated negatively with Hoechst 33342 perfusion marker distribution in the 3 tumor models. Image contrast and heterogeneous uptake of 18F-EF5 in H460 tumors was significantly higher when the radiotracer was used alone versus in combination with unlabeled EF5 (tumor-to-muscle ratio of 2.51 ± 0.33 vs. 1.71 ± 0.17, P < 0.001). Conclusion: The uptake and hypoxia selectivity of 18F-EF5 varied among tumor models when animals also received nonradioactive EF5. Combined use of radioactive and nonradioactive EF5 for independent assessment of tumor hypoxia by PET and immunohistochemistry methods is promising; however, the EF5 drug concentrations that are required for immunohistochemistry assays may affect the uptake of 18F-EF5 in hypoxic cells in certain tumor types as observed in H460 in this study.
Induction of DNA strand breaks by ethylene oxide in human diploid fibroblasts

In vitro exposure of normal human diploid fibro‐blasts (strain VH‐10) to ethylene oxide (EtO) induced DNA strand breaks in the dose range of 2.5–30 mMh of EtO. Alkaline DNA unwinding (ADU), neutral filter elution (NFE), pulsed field gel electrophoresis (PFGE), and the comet assay were used to measure DNA single (SSBs) and double strand breaks (DSBs).
Effects of the Surrounding Matrix on Tree Recruitment in Amazonian Forest Fragments

Abstract: Little is known about how the surrounding modified matrix affects tree recruitment in fragmented forests. We contrasted effects of two different matrix types, Vismia‐ and Cecropia‐dominated regrowth, on recruitment of pioneer tree species in forest fragments in central Amazonia. Our analyses were based on 22, 1‐ha plots in seven experimental forest fragments ranging in size from 1 to 100 ha. By 13 to 17 years after fragmentation, the population density of pioneer trees was significantly higher in plots surrounded by Vismia regrowth than in plots surrounded by Cecropia regrowth, and the species composition and dominance of pioneers differed markedly between the two matrix types. Cecropia sciadophylla was the most abundant pioneer in fragments surrounded by Cecropia regrowth (constituting nearly 50% of all pioneer trees), whereas densities of species in Vismia‐surrounded fragments were distributed more evenly. Thus the surrounding matrix had a strong influence on patterns of tree recruitment in Amazonian forest fragments.
Length Analysis of Polymerase Chain Reaction Products: A Sensitive and Reliable Technique for the Detection of Mutations in KIT Exon 11 in Gastrointestinal Stromal Tumors

Gastrointestinal stromal tumors are the most common mesenchymal neoplasms of the digestive tract. These tumors express the c-kit receptor tyrosine kinase, and many have activating mutations in the juxtamembrane region coded by the exon 11 of KIT. Detection of these mutations has prognostic and therapeutic impact. The aim of the study was to compare a new detection method by length analysis of polymerase chain reaction products (LAPP) to direct sequencing. The detection of either deletion or insertion mutations within the exon 11 of KIT was performed on genomic DNA extracted from 40 paraffin-embedded samples from 38 patients. Double-strand direct sequencing revealed a mutation in 25 of 40 samples. In two additional samples, a mutation was suspected but could not be determined by sequencing. LAPP revealed a mutation in 27 samples, corresponding to the 25 determined and 2 suspected samples. One of these latter samples contained three different alleles. Mutations corresponded to either deletions (n = 24) or insertion (n = 1) and had the same size with sequencing and LAPP. Our results show that LAPP is as accurate and more sensitive than direct sequencing for the detection of deletion or insertion mutations of exon 11 of KIT in gastrointestinal stromal tumors.
The use of circulating cathodic antigen rapid test and serology for diagnosis of active Schistosoma mansoni infection in migrants in Italy, a non-endemic country: a cross sectional study

ABSTRACT Diagnosis of schistosomiasis in migrants coming from endemic areas can be difficult, especially in asymptomatic subjects. Light-intensity disease, in fact, may be missed due to the low sensitivity of the stool microscopy and serologic testing cannot distinguish between a resolved infection and an active infection in patients who have been infected and treated in the past, because specific antibodies can persist despite cure. We describe a cross-sectional study conducted on 82 migrants tested for Schistosoma mansoni on single blood (anti-schistosome antibodies, total IgE) and urine [point-of-care (POC) circulating-cathodic-antigen (CCA) test] samples. A positive POC-CCA test (active infection) resulted in two untreated patients with a positive serology while all patients (n = 66) with a past infection showed a negative POC-CCA test. POC-CCA urine test in combination with serology may be helpful in rapidly differentiate active from past S. mansoni infection in migrants coming from endemic areas.
Cervical Spine Lesions after Road Traffic Accidents: A systematic review

Study Design. A systematic critical literature review. Objectives. To determine whether occult pathoanatomical lesions in the cervical spine of road traffic fatalities exist and if they can be identified using optimal autopsy techniques. Summary of Background Data. Previous investigations have examined pathoanatomical conditions of the cervical spine of road traffic fatalities. However, different methods of investigation have been used, and results of studies are conflicting. Hence, potential pathoanatomical conditions in fatalities and survivors remain a controversial issue. Methods. Articles were retrieved searching the MEDLINE, Mantis, and Cochrane libraries. Studies examining the cervical spine of road traffic fatalities at autopsy were included and evaluated according to a set of quality criteria. For in-depth review, only studies using surface cryoplaning microtomy autopsy technique and a control group were included. Results. Twenty-seven articles of which three fulfilled the quality criteria were reviewed. In these studies, subtle pathoanatomical lesions were found in the cervical intervertebral discs, cartilaginous endplates, and the articular surfaces and capsules of the zygapophysial joints. The lesions were found exclusively in the traumatized patients and in none of the patients in the control group. Conclusions. Occult pathoanatomical lesions in the cervical intervertebral disc and zygapophysial joints after fatal road traffic trauma may exist. Present imaging methods, especially conventional radiography, do not visualize these subtle lesions; hence, underreporting of pathoanatomical lesions during standard autopsy is probably common. These findings may have clinical relevance in the management of road traffic trauma survivors with potentially similar pathoanatomy.
A comparison of methods to detect postural transitions using a single tri-axial accelerometer

Two algorithms for evaluating postural transitions (PTs) in cohorts of 40 healthy younger and 40 older adults are described and evaluated. The time of sit-to-stand (SiSt) and stand-to-sit (StSi) transitions and their duration were measured with two tri-axial accelerometers, one on the chest and one on the lower back. Each algorithm was optimized for these sensor placements. The first algorithm for sensor placement on the chest used a scalar product and vertical velocity estimates. The second algorithm for sensor placement on the lower back used a vector magnitude and a discrete wavelet transform. Both algorithms performed excellently in PT classification for younger and older adults (>86%). However, the chest based sensor and algorithm were better for estimating transition duration (TD) with ICCs to video analysis ranging from 0.678 to 0.969.
The nature of small-airway obstruction in chronic obstructive pulmonary disease.

BACKGROUND Chronic obstructive pulmonary disease (COPD) is a major public health problem associated with long-term exposure to toxic gases and particles. We examined the evolution of the pathological effects of airway obstruction in patients with COPD. METHODS The small airways were assessed in surgically resected lung tissue from 159 patients--39 with stage 0 (at risk), 39 with stage 1, 22 with stage 2, 16 with stage 3, and 43 with stage 4 (very severe) COPD, according to the classification of the Global Initiative for Chronic Obstructive Lung Disease (GOLD). RESULTS The progression of COPD was strongly associated with an increase in the volume of tissue in the wall (P<0.001) and the accumulation of inflammatory mucous exudates in the lumen (P<0.001) of the small airways. The percentage of the airways that contained polymorphonuclear neutrophils (P<0.001), macrophages (P<0.001), CD4 cells (P=0.02), CD8 cells (P=0.038), B cells (P<0.001), and lymphoid aggregates containing follicles (P=0.003) and the absolute volume of B cells (P=0.03) and CD8 cells (P=0.02) also increased as COPD progressed. CONCLUSIONS Progression of COPD is associated with the accumulation of inflammatory mucous exudates in the lumen and infiltration of the wall by innate and adaptive inflammatory immune cells that form lymphoid follicles. These changes are coupled to a repair or remodeling process that thickens the walls of these airways.
Monocytes Immunoselected via the Novel Monocyte Specific Molecule, CD300e, Differentiate Into Active Migratory Dendritic Cells

Monocytes, immunoselected using MMRI-1, a monoclonal antibody specific for CD300e, were used to generate dendritic cells (DC). These CD300e immunoselected monocyte-derived DC (MoDC) were compared phenotypically and functionally to CD14 immunoselected MoDC. CD300e and CD14 immunoselected mature MoDC expressed similar levels of the DC marker, CD83 and costimulatory molecules, CD80, CD86, and CD40. Both preparations took up soluble antigen with similar efficiency by pinocytosis and receptor mediated uptake. The CD300e and CD14 immunoselected MoDC also induced comparable CD4+ T lymphocyte allogeneic responses and recall responses to tetanus toxoid. Similar magnitude CD8+ T lymphocyte responses to the naive antigen, MART-1 and the recall antigen, FMP, were induced by both MoDC preparations. Cytokine secretion by each type of MoDC preparation was similar; each secreted interleukin-12, tumor necrosis factor-α, and low levels of interferon-γ but in most cases no interleukin-10. Migration studies confirmed that both types of MoDC migrated towards the chemokine, CCL21 although CD300e immunoselected showed greater migration. Overall, the CD14 immunoselected MoDC had higher spontaneous background migration, compared with the CD300e immunoselected MoDC. Differential signaling from the antibodies used to immunoselect the monocytes may account for the slight differences in migratory capacity. These data identify the CD300e antigen as another monocyte-specific marker that can be used to purify monocytes for differentiation into functionally active MoDC.
Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes.

AIMS Protein hydroxylases are oxygen- and α-ketoglutarate-dependent enzymes that catalyse hydroxylation of amino acids such as proline, thus linking oxygen and metabolism to enzymatic activity. Prolyl hydroxylation is a dynamic post-translational modification that regulates protein stability and protein-protein interactions; however, the extent of this modification is largely uncharacterized. The goals of this study are to investigate the biological consequences of prolyl hydroxylation and to identify new targets that undergo prolyl hydroxylation in human cardiomyocytes. METHODS AND RESULTS We used human induced pluripotent stem cell-derived cardiomyocytes in combination with pulse-chase amino acid labelling and proteomics to analyse the effects of prolyl hydroxylation on protein degradation and synthesis. We identified 167 proteins that exhibit differences in degradation with inhibition of prolyl hydroxylation by dimethyloxalylglycine (DMOG); 164 were stabilized. Proteins involved in RNA splicing such as serine/arginine-rich splicing factor 2 (SRSF2) and splicing factor and proline- and glutamine-rich (SFPQ) were stabilized with DMOG. DMOG also decreased protein translation of cytoskeletal and sarcomeric proteins such as α-cardiac actin. We searched the mass spectrometry data for proline hydroxylation and identified 134 high confidence peptides mapping to 78 unique proteins. We identified SRSF2, SFPQ, α-cardiac actin, and cardiac titin as prolyl hydroxylated. We identified 29 prolyl hydroxylated proteins that showed a significant difference in either protein degradation or synthesis. Additionally, we performed next-generation RNA sequencing and showed that the observed decrease in protein synthesis was not due to changes in mRNA levels. Because RNA splicing factors were prolyl hydroxylated, we investigated splicing ± inhibition of prolyl hydroxylation and detected 369 alternative splicing events, with a preponderance of exon skipping. CONCLUSIONS This study provides the first extensive characterization of the cardiac prolyl hydroxylome and demonstrates that inhibition of α-ketoglutarate hydroxylases alters protein stability, translation, and splicing.
Terrain-based landing site selection and path planning for fixed-wing UAVs

UAVs are used in several remote applications. While performing a mission, electro-mechanical faults can occur which requires the UAVs to land quickly and safely. Landing in emergency conditions is a time critical problem, where, the UAV needs to find a landing site and plan a path to the selected site that satisfies some safety criterion in a given time. In this paper, we use terrain information from digital elevation maps to find a list of potential landing sites, selecting a site from the list and determine a path to the selected site in a given time. We use two any time path planners - RRT and PSO for path planning in limited time and compare their performance. Simulation results are presented to validate our approach and an analysis on the effect of path cost, computational time and site selection is presented.
Quantitative differences in CD45 expression unmask functions for CD45 in B-cell development, tolerance, and survival

The receptor-like tyrosine phosphatase CD45 positively regulates antigen receptor signaling by dephosphorylating the inhibitory tyrosine of the src family kinases. CD45-deficient mice fail to fully unmask the role of CD45 in B cells because of the expression of a partially redundant tyrosine phosphatase, CD148. However, mice that are doubly deficient in CD45 and CD148 exhibit a very early block in B-cell development, thereby obscuring later roles for CD45. To overcome these limitations, here we take advantage of an allelic series of mice in which CD45 expression is titrated broadly (0–180%). Although high expression of CD45 inhibits T-cell receptor (TCR) signaling, we show that CD45 plays a purely positive regulatory role during B-cell receptor (BCR) signaling. In concert with exaggerated BCR signaling, increasing CD45 expression drives enhanced receptor editing in the bone marrow and profound loss of follicular and marginal zone B cells in the spleen. In the context of the IgHEL/sHEL model of B-cell tolerance, such high CD45 expression transforms anergy into deletion. Unexpectedly, elimination of the autoantigen sHEL in this model system in order to block clonal deletion fails to rescue survival of mature B cells. Rather, high CD45 expression reduces B-cell activating factor receptor (BAFFR) expression and inhibits B-cell activating factor (BAFF)–induced B-cell survival in a cell-intrinsic manner. Taken together, our findings reveal how CD45 function diverges in T cells and B cells, as well as how autoreactive B cells are censored as they transit development.