Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time reverse transcription-PCR quantification of vascular endothelial growth factor splice variants.

Vascular endothelial growth factor (VEGF) is an endothelial cell–specific mitogen and a key regulator of angiogenesis in a variety of physiologic and pathologic processes (1). The human gene for VEGF resides on chromosome 6p21.3 and is organized into 8 exons (2)(3). Alternative exon splicing of the VEGF gene produces various splice variants (subscripts denote the number of amino acids after signal sequence cleavage): VEGF206, VEGF189, VEGF183, VEGF165, VEGF148, VEGF145, and VEGF121 (4)(5)(6)(7)(8). Exons 1–5 and 8 are preserved in all variants, whereas the presence or absence of exons 6a, 6b, and 7 distinguish variants. VEGF121 lacks these exons (4), VEGF165 contains the exon 7-encoded sequence (4), and VEGF148 has the same amino acid sequence as VEGF165 apart from a 35-bp–long deletion at the end of exon 7 (5). VEGF189 contains exons 6a and 7 (4), whereas in VEGF183 the final 18 bp of exon 6a are missing (6). VEGF145 contains exon 6a but lacks exon 7 (7). VEGF206 is the full-length form containing, in addition to exons 6a and 7, a 51-bp part from intron 3, exon 6b, neighboring exon 6a (8). VEGF isoforms differ in their heparin and heparan sulfate binding capacities as well as in their receptor affinities (9), but their exact biological roles remain unclear. Most VEGF-producing cells appear to preferentially express VEGF121, VEGF165, and VEGF189 (4). VEGF183 has a wide tissue distribution and may have not been detected earlier because of confusion with VEGF189 (6). VEGF145 is one of the main variants produced by several cell lines derived from carcinomas of the female reproductive system (7 …
Near Infrared Imaging and Photothermal Ablation of Vascular Inflammation Using Single-Walled Carbon Nanotubes

Background Macrophages are critical contributors to atherosclerosis. Single-walled carbon nanotubes (SWNTs) show promising properties for cellular imaging and thermal therapy, which may have application to vascular macrophages. Methods and Results In vitro uptake and photothermal destruction of mouse macrophage cells (RAW264.7) were performed with SWNTs (14.7 nmol/L) exposed to an 808-nm light source. SWNTs were taken up by 94±6% of macrophages, and light exposure induced 93±3% cell death. In vivo vascular macrophage uptake and ablation were then investigated in carotid-ligated FVB mice (n=33) after induction of hyperlipidemia and diabetes. Two weeks postligation, near-infrared fluorescence (NIRF) carotid imaging (n=12) was performed with SWNT-Cy5.5 (8 nmol of Cy5.5) given via the tail vein. Photothermal heating and macrophage apoptosis were evaluated on freshly excised carotid arteries (n=21). NIRF of SWNTs showed higher signal intensity in ligated carotids compared with sham, confirmed by both in situ and ex vivo NIRF imaging (P<0.05, ligation versus sham). Immunofluorescence staining showed colocalization of SWNT-Cy5.5 and macrophages in atherosclerotic lesions. Light (808 nm) exposure of freshly excised carotids showed heating and induction of macrophage apoptosis in ligated left carotid arteries with SWNTs, but not in control groups without SWNTs or without light exposure. Conclusions Carbon nanotubes accumulate in atherosclerotic macrophages in vivo and provide a multifunctional platform for imaging and photothermal therapy of vascular inflammation.
Glottal Source and Prosodic Prominence Modelling in HMM-based Speech Synthesis for the Blizzard Challenge 2009

This paper describes the CSTR entry for the Blizzard Challenge 2009. The work focused on modifying two parts of the Nitech 2005 HTS speech synthesis system to improve naturalness and contextual appropriateness. The first part incorporated an implementation of the Linjencrants-Fant (LF) glottal source model. The second part focused on improving synthesis of prosodic prominence including emphasis through context dependent phonemes. Emphasis was assigned to the synthesised test sentences based on a handful of theory based rules. The two parts (LF-model and prosodic prominence) were not combined and hence evaluated separately. The results on naturalness for the LF-model showed that it is not yet perceived as natural as the Benchmark HTS system for neutral speech. The results for the prosodic prominence modelling showed that it was perceived as contextually appropriate as the Benchmark HTS system, despite a low naturalness score. The Blizzard challenge evaluation has provided valuable information on the status of our work and continued work will begin with analysing why our modifications resulted in reduced naturalness compared to the Benchmark HTS system.
Schema transformation without database reorganization

We argue for avoiding database reorganizations due to schema modification in object-oriented systems, since these are expensive operations and they conflict with reusing existing software components. We show that data independence, which is a neglected concept in object databases, helps to avoid reorganizations in case of capacity preserving and reducing schema transformations. We informally present a couple of examples to illustrate the idea of a schema transformation methodology that avoids database reorganization.
Progressing the global antimalarial portfolio: finding drugs which target multiple Plasmodium life stages

SUMMARY The number of novel antimalarial candidates entering preclinical development has seen an increase over the last several years. Most of these drug candidates were originally identified as hits coming from screening large chemical libraries specifically targeting the asexual blood stages of Plasmodium falciparum. Indeed, a large proportion of the current antimalarial arsenal has mainly targeted the asexual blood stage which is responsible for clinical symptoms of the disease. However, as part of the eradication agenda and to address resistance, any next-generation antimalarial should have additional activity on at least one other parasite life stage, i.e. gametocytocidal and/or tissue schizonticidal activity. We have applied this approach by screening compounds with intrinsic activity on asexual blood stages in assays against sexual and liver stages and identified two new antimalarial chemotypes with activity on multiple parasite life stages. This strategy can be expanded to identify other chemical classes of molecules with similar activity profiles for the next generation antimalarials. The following review summarizes the discovery of the spiroindolones and imidazolopiperazine classes of antimalarials developed by the NGBS consortium (Novartis Institute for Tropical Diseases, Genomic Institute of the Novartis Research Foundation, Biomedical Primate Research Center, and the Swiss Tropical and Public Health Institute) currently in clinical trials.
Prognostic Significance of POLE Proofreading Mutations in Endometrial Cancer

Background: Current risk stratification in endometrial cancer (EC) results in frequent over- and underuse of adjuvant therapy, and may be improved by novel biomarkers. We examined whether POLE proofreading mutations, recently reported in about 7% of ECs, predict prognosis. Methods: We performed targeted POLE sequencing in ECs from the PORTEC-1 and -2 trials (n = 788), and analyzed clinical outcome according to POLE status. We combined these results with those from three additional series (n = 628) by meta-analysis to generate multivariable-adjusted, pooled hazard ratios (HRs) for recurrence-free survival (RFS) and cancer-specific survival (CSS) of POLE-mutant ECs. All statistical tests were two-sided. Results: POLE mutations were detected in 48 of 788 (6.1%) ECs from PORTEC-1 and-2 and were associated with high tumor grade (P < .001). Women with POLE-mutant ECs had fewer recurrences (6.2% vs 14.1%) and EC deaths (2.3% vs 9.7%), though, in the total PORTEC cohort, differences in RFS and CSS were not statistically significant (multivariable-adjusted HR = 0.43, 95% CI = 0.13 to 1.37, P = .15; HR = 0.19, 95% CI = 0.03 to 1.44, P = .11 respectively). However, of 109 grade 3 tumors, 0 of 15 POLE-mutant ECs recurred, compared with 29 of 94 (30.9%) POLE wild-type cancers; reflected in statistically significantly greater RFS (multivariable-adjusted HR = 0.11, 95% CI = 0.001 to 0.84, P = .03). In the additional series, there were no EC-related events in any of 33 POLE-mutant ECs, resulting in a multivariable-adjusted, pooled HR of 0.33 for RFS (95% CI = 0.12 to 0.91, P = .03) and 0.26 for CSS (95% CI = 0.06 to 1.08, P = .06). Conclusion: POLE proofreading mutations predict favorable EC prognosis, independently of other clinicopathological variables, with the greatest effect seen in high-grade tumors. This novel biomarker may help to reduce overtreatment in EC.
The Role of Carboxydothermus hydrogenoformans in the Conversion of Calcium Phosphate from Amorphous to Crystalline State

Two previously unknown modes of biomineralization observed in the presence of Carboxydothermus hydrogenoformans are presented. Following the addition of NaHCO3 and the formation of an amorphous calcium phosphate precipitate in a DSMZ medium inoculated with C. hydrogenoformans, two distinct crystalline solids were recovered after 15 and 30 days of incubation. The first of these solids occurred as micrometric clusters of blocky, angular crystals, which were associated with bacterial biofilm. The second solid occurred as 30–50 nm nanorods that were found scattered among the organic products of bacterial lysis. The biphasic mixture of solids was clearly dominated by the first phase. The X-ray diffractometry (XRD) peaks and Fourier transform infrared spectroscopy (FTIR) spectrum of this biphasic material consistently showed features characteristic of Mg-whitlockite. No organic content or protein could be identified by dissolving the solids. In both cases, the mode of biomineralization appears to be biologically induced rather than biologically controlled. Since Mg is known to be a strong inhibitor of the nucleation and growth of CaP, C. hydrogenoformans may act by providing sites that chelate Mg or form complexes with it, thus decreasing its activity as nucleation and crystal growth inhibitor. The synthesis of whitlockite and nano-HAP-like material by C. hydrogenoformans demonstrates the versatility of this organism also known for its ability to perform the water-gas shift reaction, and may have applications in bacterially mediated synthesis of CaP materials, as an environmentally friendly alternative process.
Strong Gravitational Lensing as a Probe of Gravity, Dark- Matter and Super-Massive Black Holes

Abstract Whereas considerable effort has been afforded in understanding the properties of galaxies, a full physical picture, connecting their baryonic and dark-matter content, supermassive black holes, and (metric) theories of gravity, is still ill-deﬁned. Strong gravitational lensing furnishes a powerful method to probe gravity in the central regions of galaxies. It can (1) provide a unique detection-channel of dark-matter substructure beyond the local galaxy group, (2) constrain dark-matter physics, complementary to direct-detection experiments, as well as metric theories of gravity, (3) probe central supermassive black holes, and (4) provide crucial insight into galaxy formation processes from the dark matter point of view, independently of the nature and state of dark matter. To seriously address the above questions, a considerable increase in the number of strong gravitational-lens systems is required. In the timeframe 2010-2020, a staged approach with radio (e.g. EVLA, e-MERLIN, LOFAR, SKA phase-I) and optical (e.g. LSST and JDEM) instruments can provide 10
Trying to Put the Puzzle Together: Age and Performance Level Modulate the Neural Response to Increasing Task Load within Left Rostral Prefrontal Cortex

Age-related working memory decline is associated with functional cerebral changes within prefrontal cortex (PFC). Kind and meaning of these changes are heavily discussed since they depend on performance level and task load. Hence, we investigated the effects of age, performance level, and load on spatial working memory retrieval-related brain activation in different subregions of the PFC. 19 younger (Y) and 21 older (O) adults who were further subdivided into high performers (HP) and low performers (LP) performed a modified version of the Corsi Block-Tapping test during fMRI. Brain data was analyzed by a 4 (groups: YHP, OHP, YLP, and OLP) × 3 (load levels: loads 4, 5, and 6) ANOVA. Results revealed significant group × load interaction effects within rostral dorsolateral and ventrolateral PFC. YHP showed a flexible neural upregulation with increasing load, whereas YLP reached a resource ceiling at a moderate load level. OHP showed a similar (though less intense) pattern as YHP and may have compensated age-effects at high task load. OLP showed neural inefficiency at low and no upregulation at higher load. Our findings highlight the relevance of age and performance level for load-dependent activation within rostral PFC. Results are discussed in the context of the compensation-related utilization of neural circuits hypothesis (CRUNCH) and functional PFC organization.
Simulated Driving Performance, Self-Reported Driving Behaviors, and Mental Health Symptoms in Adolescent Novice Drivers

Background Risky driving behaviors contribute to adolescent injury, disability, and death, yet little is known about how mental health factors are associated with adolescent driving behaviors. Objectives The purpose of the research was to determine the association of risky driving behaviors and mental health symptoms in novice adolescent drivers. Methods We recruited a convenience sample (n = 60) of adolescents to complete an assessment of driving performance errors in a high-fidelity simulator (Simulated Driving Assessment [SDA] Error Score) and a self-report measure of risky driving (Behavior of Young Novice Drivers Survey [BYNDS]). Participants also completed a mental health assessment of self-reported symptoms of depression (Center for Epidemiologic Studies-Depression Scale) and attention-deficit/hyperactivity disorder (ADHD; inattention and hyperactivity–impulsivity), conduct disorder, and oppositional defiant disorder (Conners-3 self-report and parent report). We evaluated the cross-sectional relationships between SDA Error Score, BYNDS, and mental health survey data with descriptive statistics, bivariate correlations, and linear regression. Results In linear regression models, higher self-reported inattentive ADHD T-scores were associated with higher SDA Error Score (model adjusted R2 = .20). Higher self-reported T-scores of hyperactive–impulsive ADHD and conduct disorder were associated with higher BYNDS total scores (model adjusted R2 = .32). Parent report measures were not associated with adolescent BYNDS total score or SDA Error Score. Discussion These data highlight the association of risky driving with adolescent symptoms of inattention, hyperactivity, and conduct disorder. The early stage of independent driving is an important time for addressing the relationship between driving performance and mental health conditions.
An efficient algorithm for approximate betweenness centrality computation

Betweenness centrality is an important centrality measure widely used in social network analysis, route planning etc. However, even for mid-size networks, it is practically intractable to compute exact betweenness scores. In this paper, we propose a generic randomized framework for unbiased approximation of betweenness centrality. The proposed framework can be adapted with different sampling techniques and give diverse methods. We discuss the conditions a promising sampling technique should satisfy to minimize the approximation error and present a sampling method partially satisfying the conditions. We perform extensive experiments and show the high efficiency and accuracy of the proposed method.
Fuzzy clustering algorithm based on PSO in body shape analysis

Mass customization is a new manufacturing trend in which mass-market products are quickly modified one at a time based on customers' needs. Body scanners will play a critical role in mass customization because they enable retailers to rapidly collect three-dimensional (3D) data for each consumer. In this article, we discuss how to deal with the three-dimensional (3D) data based on fuzzy particle swarm optimization clustering algorithm. The results show it's an effective method.
Real-Time HDR Image Based Lighting

This report presents the work done on the final project for the course of Image Based Rendering. A real-time application has been implemented with the purpose of demonstrating the capabilities of nowadays GPU’s power within the scope of Image Based Rendering and Lighting. The built application has a full High Dynamic Range (HDR) pipeline and it deals with issues like tone mapping, automatic scene exposure, vignette effect and blooming (to increase the high dynamic effect). Furthermore, some materials were used to demonstrate the potentiality of Image Based Lighting.
Spermine Alleviates Acute Liver Injury by Inhibiting Liver-Resident Macrophage Pro-Inflammatory Response Through ATG5-Dependent Autophagy

Liver-resident macrophages (Kupffer cells, KCs) and autophagy play critical roles in the pathogenesis of toxin-induced liver injury. Recent evidence indicates that autophagy can regulate macrophage M1/M2 polarization under different inflammatory conditions. Polyamines, including putrescine, spermidine, and spermine (SPM), are polycations with anti-oxidative, anti-aging, and cell autophagy induction properties. This study aimed to determine the mechanisms by which SPM protects against thioacetamide (TAA)-induced acute liver injury in a mouse model. Pretreatment with SPM significantly alleviated liver injury and reduced intrahepatic inflammation in TAA-induced liver injury compared to controls. SPM markedly inhibited M1 polarization, but promoted M2 polarization of KCs obtained from TAA-exposed livers, as evidenced by decreased IL-1β and iNOS gene induction but increased Arg-1 and Mrc-1 gene induction accompanied by decreased STAT1 activation and increased STAT6 activation. Furthermore, pretreatment with SPM enhanced autophagy, as revealed by increased LC3B-II levels, decreased p62 protein expression, and increased ATG5 protein expression in TAA-treated KCs. Knockdown of ATG5 in SPM-pretreated KCs by siRNA resulted in a significant increase in pro-inflammatory TNF-α and IL-6 secretion and decreased anti-inflammatory IL-10 secretion after TAA treatment, while no significant changes were observed in cytokine production in the TAA treatment alone. Additionally, the effect of SPM on regulation of KC M1/M2 polarization was abolished by ATG5 knockdown in TAA-exposed KCs. Finally, in vivo ATG5 knockdown in KCs abrogated the protective effect of SPM against TAA-induced acute liver injury. Our results indicate that SPM-mediated autophagy inhibits M1 polarization, while promoting M2 polarization of KCs in TAA-treated livers via upregulation of ATG5 expression, leading to attenuated liver injury. This study provides a novel target for the prevention of acute liver injury.
Engine Compartment UWB Channel Model for Intravehicular Wireless Sensor Networks

Intravehicular wireless sensor network (IVWSN) is a cutting edge research topic that delivers cost reduction, assembly, and maintenance efficiency by removing the wiring harnesses within the vehicle and enables the integration of new sensors into the locations inside a vehicle where cable connection is not possible. Providing energy efficiency through the low-duty-cycle operation and high reliability by exploiting the large bandwidth, ultrawideband (UWB) has been determined to be the most appropriate technology for IVWSNs. We investigate the UWB channel model for IVWSNs within the engine compartment of a vehicle by collecting an extensive amount of data for 19 × 19 links for different types and conditions of the vehicle. These include a Fiat Linea with engine off, Fiat Linea with engine on, and Peugeot Bipper with engine off. The path-loss exponent is estimated to be around 3.5 without exhibiting much variation when the engine is turned on and for different types of vehicles. The power variation around the expected path loss has lognormal distribution with zero mean and standard deviation in the range of [5.5, 6.3] dB for different types of vehicles with almost no variation when the engine of the same vehicle is turned on. The clustering phenomenon in the power delay profile (PDP) is well represented by a modified Saleh-Valenzuela (SV) model. The interarrival times of the clusters are modeled using a Weibull distribution. The cluster-amplitude and ray-amplitude decay functions are represented with a dual-slope linear model with breakpoint around 26.6 and 5.5 ns, respectively. The parameters of the Weibull distribution and these dual-slope linear models do not vary significantly for different types and conditions of the vehicle. The variations of the observed PDPs around the SV model is well modeled by independent normal random variables with zero mean and with a variance independent of the delay bin, and the type and condition of the vehicle. We propose a simulation model for the UWB channel within the engine compartment based on these findings and validate it by comparing the received energy and root mean square (RMS) delay spread of the generated and observed PDPs.
Complementary Tracking and Two-Handed Interaction for Remote 3 D Medical Consultation with a PDA

We report here on applying a complementary tracking and twohanded interaction paradigm to remote medical consultation using a mobile hand-held device. The basic idea is to track the relative pose between the mobile device and an integrated but detachable “patient surrogate” such as the device cover, enabling 6 DOF visualization of streaming vision-based 3D reconstructions of a remote patient. The two-handed device/target paradigm is complementary in that it enables 6 DOF user interaction with applications on the device, while making the tracking problem tractable.
The IDP framework for declarative problem solving

The IDP framework is a declarative problem solving paradigm, in which the computational task is to expand a given finite interpretation of a set of symbols into a model of a given ID-logic theory, a classical logic theory extended with inductive definitions. This framework has been proposed as a general approach for solving finite domain problems. In this paper, we introduce a typed version of the IDP-language, illustrate the use of the framework through some prototypical examples and discuss theoretical and methodological aspects. We also compare the framework to SAT and ASP. Finally, we report on an implementation of IDP.