Miracle-dz/UniFAR-FTUs huggingface dataset:
Adverse effects of retinoic acid on embryo development and the selective expression of retinoic acid receptors in mouse blastocysts.

BACKGROUND All-trans retinoic acid (RA), the oxidative metabolite of vitamin A, is essential for normal development. In addition, high levels of RA are teratogenic in many species. We have previously shown that excess RA results in immediate effects on the preimplantation embryo and on blastocyst development. This study was conducted to clarify the long-term survival of mouse blastocyst and the effect of RA on gene expression. METHODS AND RESULTS Using an in vitro model, we identified the immediate adverse impact of RA on mouse blastocyst development. This involved an inhibition of cell proliferation and growth retardation. Using an in vivo model, we also identified the resorption of postimplanted blastocysts that had been treated with excess RA. Analysis of RA-mediated gene induction was also included. The retinoic acid receptors RARalpha and RARgamma were constitutively expressed in the blastocyst and the inner cell mass, whereas RARbeta was induced upon RA treatment. CONCLUSIONS This is the first evidence to show the impacts of RA on mouse blastocysts in vitro and any carry-over effects in the uterus. There is a retardation of early postimplantation blastocyst development and then subsequent blastocyst death. Our findings also show that there is some degree of selective induction of retinoic acid receptors when excess RA is administered to the blastocysts.
Black-Box Problem Diagnosis in Parallel File Systems

We focus on automatically diagnosing different performance problems in parallel file systems by identifying, gathering and analyzing OS-level, black-box performance metrics on every node in the cluster. Our peer-comparison diagnosis approach compares the statistical attributes of these metrics across I/O servers, to identify the faulty node. We develop a root-cause analysis procedure that further analyzes the affected metrics to pinpoint the faulty resource (storage or network), and demonstrate that this approach works commonly across stripe-based parallel file systems. We demonstrate our approach for realistic storage and network problems injected into three different file-system benchmarks (dd, IOzone, and Post-Mark), in both PVFS and Lustre clusters.
Molecular Basis for Class V β-Tubulin Effects on Microtubule Assembly and Paclitaxel Resistance*

Vertebrates produce at least seven distinct β-tubulin isotypes that coassemble into all cellular microtubules. The functional differences among these tubulin isoforms are largely unknown, but recent studies indicate that tubulin composition can affect microtubule properties and cellular microtubule-dependent behavior. One of the isotypes whose incorporation causes the largest change in microtubule assembly is β5-tubulin. Overexpression of this isotype can almost completely destroy the microtubule network, yet it appears to be required in smaller amounts for normal mitotic progression. Moderate levels of overexpression can also confer paclitaxel resistance. Experiments using chimeric constructs and site-directed mutagenesis now indicate that the hypervariable C-terminal region of β5 plays no role in these phenotypes. Instead, we demonstrate that two residues found in β5 (Ser-239 and Ser-365) are each sufficient to inhibit microtubule assembly and confer paclitaxel resistance when introduced into β1-tubulin; yet the single mutation of residue Ser-239 in β5 eliminates its ability to confer these phenotypes. Despite the high degree of conservation among β-tubulin isotypes, mutations affecting residue 365 demonstrate that amino acid substitutions can be context sensitive; i.e. an amino acid change in one isotype will not necessarily produce the same phenotype when introduced into a different isotype. Modeling studies indicate that residue Cys-239 of β1-tubulin is close to a highly conserved Cys-354 residue suggesting the possibility that disulfide formation could play a significant role in the stability of microtubules formed with β1- but not with β5-tubulin.
Measurement of Elastic Modulus of the Bovine Cornea by Means of Holographic Interferometry. Part 1. Method and Experiment

Holographic interferometry of the cornea of fresh, enucleated bovine eyes placed in air was used for determination of the elastic modulus of the central part of the cornea. The high sensitivity of the method enables measurement of the radial distension of the cornea even for intraocular pressure (IOP) changes equal to 5 Pa (0.05 mbar or ≈ 0.0375 mm Hg). The method of calculation of the tangent Young's modulus of the cornea Et, based on data obtained from double exposure as well as real-time holographic interferograms and on some geometrical data describing the form of the cornea are presented. The average value of Et amounting to 1.42·105 Pa was calculated from 2 interferograms of the same eye.
Interleukin-18-Mediated Microglia/Astrocyte Interaction in the Spinal Cord Enhances Neuropathic Pain Processing after Nerve Injury

Interleukin (IL)-18 is an important regulator of innate and acquired immune responses. Here we show that both the IL-18 and IL-18 receptor (IL-18R), which are induced in spinal dorsal horn, are crucial for tactile allodynia after nerve injury. Nerve injury induced a striking increase in IL-18 and IL-18R expression in the dorsal horn, and IL-18 and IL-18R were upregulated in hyperactive microglia and astrocytes, respectively. The functional inhibition of IL-18 signaling pathways suppressed injury-induced tactile allodynia and decreased the phosphorylation of nuclear factor κB in spinal astrocytes and the induction of astroglial markers. Conversely, intrathecal injection of IL-18 induced behavioral, morphological, and biochemical changes similar to those observed after nerve injury. Our results indicate that IL-18-mediated microglia/astrocyte interactions in the spinal cord have a substantial role in the generation of tactile allodynia. Thus, blocking IL-18 signaling in glial cells might provide a fruitful strategy for treating neuropathic pain.
Sites phosphorylated in bovine cardiac troponin T and I. Characterization by 31P-NMR spectroscopy and phosphorylation by protein kinases.

Bovine cardiac troponin isolated in a highly phosphorylated form shows four 31P-NMR signals [Beier, N. , Jaquet, K. , Schnackerz, K. & Heilmeyer, L.M. G. Jr (1988) Eur. J. Biochem. 176, 327-334]. Troponin I, which contains phosphate covalently linked to serine-23 and/or -24 [Swiderek, K. , Jaquet, K. , Meyer, H. E. & Heilmeyer, L. M. G. Jr (1988) Eur. J. Biochem. 176, 335-342], shows three resonances. Mg2(+)-saturation of holotroponin shifts these troponin I resonances to higher fields. Direct binding of Mg2+ to the phosphate groups can be excluded. Both these serine residues of troponin I, 23 and 24, are substrates for cAMP- and cGMP-dependent protein kinases as well as for protein kinase C. Isolated bovine cardiac troponin T contains 1.5 mol phosphoserine/mol protein, indicating that minimally two serine residues are phosphorylated. One phosphoserine residue is located at the N-terminus. An additional phosphoserine is located in the C-terminal cyanogen bromide fragment, CN4, which contains covalently bound phosphate. Protein kinase C phosphorylates serine-194, thus demonstrating exposure of this residue on the surface of holotoponin.
A Generic Architecture for the Conversion of Document Collections into Semantically Annotated Digital Archives

Mass digitization of document collections with further processing and semantic annotation is an increasing activity among libraries and archives at large for preservation, browsing and navigation, and search purposes. In this paper we propose a software architecture for the process of converting high volumes of document collections to semantically annotated digital libraries. The proposed architecture recognizes two sources of knowledge in the conversion pipeline, namely document images and humans. The Image Analysis module and the Correction and Validation module cover the initial conversion stages. In the former information is automatically extracted from document images. The latter involves human intervention at a technical level to define workflows and to validate the image processing results. The second stage, represented by the Knowledge Capture modules requires information specific to the particular knowledge domain and generally calls for expert practitioners. These two principal conversion stages are coupled with a Knowledge Management module which provides the means to organise the extracted and acquired knowledge. In terms of data propagation, the architecture follows a bottom-up process, starting with document image units, called terms, and progressively building meaningful concepts and their relationships. In the second part of the paper we describe a real scenario with historical document archives implemented according to the proposed architecture.
The effectiveness of mass media in changing HIV/AIDS-related behaviour among young people in developing countries.

OBJECTIVES To review the strength of the evidence for the effects of three types of mass media interventions (radio only, radio with supporting media, or radio and television with supporting media) on HIV/AIDS-related behaviour among young people in developing countries and to assess whether these interventions reach the threshold of evidence needed to recommend widespread implementation. METHODS We conducted a systematic review of studies that evaluated mass media interventions and were published or released between 1990 and 2004. Studies were included if they evaluated a mass media campaign that had the main objective of providing information about HIV/AIDS or sexual health. To be eligible for inclusion studies had to use a pre-intervention versus post-intervention design or an intervention versus control design or analyse cross-sectional data comparing those who had been exposed to the campaign with those who had not been exposed. Studies also had to comprehensively report quantitative data for most outcomes. FINDINGS Of the 15 programmes identified, 11 were from Africa, 2 from Latin America, 1 from Asia, and 1 from multiple countries. One programme used radio only, six used radio with supporting media, and eight others used television and radio with supporting media. The data support the effectiveness of mass media interventions to increase the knowledge of HIV transmission, to improve self-efficacy in condom use, to influence some social norms, to increase the amount of interpersonal communication, to increase condom use and to boost awareness of health providers. Fewer significant effects were found for improving self-efficacy in terms of abstinence, delaying the age of first sexual experience or decreasing the number of sexual partners. CONCLUSIONS We found that mass media programmes can influence HIV-related outcomes among young people, although not on every variable or in every campaign. Campaigns that include television require the highest threshold of evidence, yet they also yield the strongest evidence of effects. This suggests that comprehensive mass media programmes are valuable.
Once daily high dose tigecycline - pharmacokinetic/pharmacodynamic based dosing for optimal clinical effectiveness: dosing matters, revisited

ABSTRACT Introduction: Tigecycline has emerged as first line therapy for serious systemic infections due to important pathogens (except P. aeruginosa and Proteus sp.), including multi-drug resistant (MDR) and Gram negative bacilli (GNB), including carbapenem resistant Enterobacteriae. Tigecycline has a ‘low resistance potential,’ is protective against C. difficile, and is often the only antibiotic effective against MDR GNB, e.g., Klebsiella sp. Areas covered: Standard dose tigecycline therapy has been used for intra-abdominal infections, complicated skin/skin structure infections (cSSSIs), and CAP. Clinical experience with once daily high dose tigecycline (HDT), i.e., 200 – 400 mg (IV) x 1, then 100 – 200 mg (IV) q24 h, is reviewed. Optimal tigecycline efficacy is dependent on PK/PD based dosing. Suboptimal outcomes have been due to inappropriate use or suboptimal dosing. Expert commentary: Tigecycline’s spectrum against nearly all important pathogens (including MSSA/MRSA, VSE/VRE, B. fragilis, C. difficile, MDR and GNB) assures tigecycline a critical place in the antibiotic armamentarium. Dosed optimally, HDT can be a cornerstone of antibiotic stewardship programs in preventing C. difficile, treating MDR GNB pathogens, and in preventing resistance. Properly used and optimally dosed, once daily HDT should be considered preferred therapy for severe systemic infections and those due to MDR GNB pathogens.
Identification of cytochrome P-450 1 A ( CYPlA ) genes from two teleost fish , toadfish ( Opsanus tau ) and scup ( Stenotomus chrysops ) , and phylogenetic analysis of CYPlA genes

Cytochrome P-450-mediated responses to environmental challenges are well known in diverse animal taxa, but the evolution of the complex gene superfamily coding for these enzymes is poorly understood. Here we report a phylogenetic analysis of the cytochrome P-450 IA (CYP1A) genes including two new sequences determined from teleost fish, toadfish (Opsanus tau) and scup (Stenotomus chrysops). Degenerate PCR primers were used to amplify a 1.2 kbp fragment from liver cDNA. The toadfish PCR product was used as a probe to identify a full-length CYPIA clone from a toadfish liver cDNA library. The entire coding region of the scup CYPIA was obtained by rapid amplification of cDNA ends (RACE) using specific primers based on the sequence of the partial PCR product. The predicted protein sequences for toadfish and scup CYP1A shared 78 % and 83 %
A hybrid OPEN model technique for accurate device characterization

A hybrid OPEN model, which consists of equivalent circuit model and behavior transmission line (TL) model, is proposed to accurately extract device characteristics. The proposed method requires only one OPEN dummy structure so the silicon occupation area is efficiently reduced. The other benefit is it avoids the errors, which is occurred while performing the classical de-embedding procedure. A Ka-band CPW filter is fabricated in 130 nm RF CMOS technique to prove this method is efficient up to 67 GHz.
Secure encryption with digital signature approach for Short Message Service

As Short Message Service (SMS) is now widely used as business tool, its security has become a major concern for business organizations and customers. However, their security is a critical issue cumbering their application and development. This paper analyses the most popular digital signature algorithms such as DSA, RSA and ECDSA and compared these algorithms. These signature algorithms were implemented in Java with various different key sizes set. Experimental comparison results of the three signature algorithms were presented and analysed. The results show that ECDSA is more suitable to generate the signature and RSA is more suitable to verify the signature on mobile devices. The experimental results are presented to show the effectiveness of each algorithm and to choose the most suitable algorithm for SMS digital signature. Next, we propose a new algorithm for digital signature based on ECDSA. At the end, conclusion and future extension of this work is discussed.
III. Electrophysiological Studies of Face Processing in Williams Syndrome

Williams Syndrome (WMS) is a genetically based disorder characterized by pronounced variability in performance across different domains of cognitive functioning. This study examined brain activity linked to face-processing abilities, which are typically spared in individuals with WMS. Subjects watched photographic pairs of upright or inverted faces and indicated if the second face matched or did not match the first face. Results from a previous study with normal adults showed dramatic differences in the timing and distribution of ERP effects linked to recognition of upright and inverted faces. In normal adults, upright faces elicited ERP differences to matched vs. mismatched faces at approximately 320 msec (N320) after the onset of the second stimulus. This N320 effect was largest over anterior regions of the right hemisphere. In contrast, the mismatch/match effect for inverted faces consisted of a large positive component between 400 and 1000 msec (P500) that was largest over parietal regions and was symmetrical. In contrast to normal adults, WMS subjects showed an N320-mismatch effect for both upright and inverted faces. Additionally, the WMS subjects did not display the N320 right-hemisphere asymmetry observed in the normal adults. WMS subjects also displayed an abnormally small negativity at 100 msec (N100) and an abnormally large negativity at 200 msec (N200) to both upright and inverted faces. This ERP pattern was observed in all subjects with WMS but was not observed in the normal controls. These results may be linked to increased attention to faces in subjects with WMS and might be specific to the disorder. These results were consistent with our ERP studies of language processing in WMS, which suggested abnormal cerebral specialization for spared cognitive functions in individuals with WMS.
Expression of the peripheral-type benzodiazepine receptor and apoptosis induction in hepatic stellate cells.

BACKGROUND AND AIMS Hepatic stellate cell (HSC) transformation and proliferation play an important role in liver fibrogenesis, and HSC apoptosis may be involved in the termination of this response. METHODS Expression of the peripheral benzodiazepine receptor (PBR) and PBR-ligand-induced apoptosis were studied in cultured rat liver HSC. RESULTS Transformation of HSC led to a transient expression of PBR at the messenger RNA and protein level, which was maximal after about 3 and 7 days of culture, respectively, and declined thereafter. Immunoreactive PBR showed a punctate staining and colocalized with mitochondrial manganese-dependent superoxide dismutase and adenine nucleotide translocator 1. The selective PBR ligands 1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3-isoquinolinecarboxamide (PK11195) and 4' chlorodiazepam (Ro5-4864), but not the centrally acting benzodiazepine ligand clonazepam, induced dose-dependent apoptosis in HSC. The apoptotic potency of PK11195 paralleled the level of PBR expression. PK11195 induced dephosphorylation of protein kinase B/Akt and Bad and a downregulation of Bcl-2. Collapse of the mitochondrial membrane potential preceeded PBR-ligand-induced apoptosis. No apoptosis was induced by PK11195 in parenchymal cells, despite the presence of PBR, and PK11195 had no effect in these cells on Bad phosphorylation and Bcl-2 expression. CONCLUSIONS Transformation of HSC leads to a transient expression of PBR and renders the cells sensitive to PBR-ligand-induced apoptosis, involving protein kinase B/Akt and Bad-dependent mechanisms.
Quantity adjustments in the regional labour markets of EU candidate countries

The article comprises an analysis of the adjustment of regional labour markets of former (and present) EU candidate countries to asymmetric shocks. As in EU member states, a substantial part of the adjustment to changes in employment in candidate countries is carried by participation decisions, and migration plays a small role. Candidate countries, however, have experienced larger region-specific shocks to labour demand than member states, and these shocks lead to higher long-run changes in employment. Furthermore, adjustment mechanisms partly explain high regional unemployment. High unemployment regions exhibit a lower capability to absorb region-specific shocks through mechanisms other than higher unemployment. Copyright RSAI 2005.
Affective Speech Recognition

Speech, as a medium of interaction, carries two different streams of information. Whereas one stream carries explicit messages, the other one contains implicit information about speakers themselves. Affective speech recognition is a set of theories and tools that intend to automate unfolding the part of the implicit stream that has to do with humans emotion. Application of affective speech recognition is to human computer interaction; a machine that is able to recognize humans emotion could engage the user in a more effective interaction. This thesis proposes a set of analyses and methodologies that advance automatic recognition of affect from speech. The proposed solution spans two dimensions of the problem: speech signal processing, and statistical learning. At the speech signal processing dimension, extraction of speech low-level descriptors is discussed, and a set of descriptors that exploit the spectrum of the signal are proposed, which have shown to be particularly practical for capturing affective qualities of speech. Moreover, considering the non-stationary property of the speech signal, further proposed is a measure of dynamicity that captures that property of speech by quantifying changes of the signal over time. Furthermore, based on the proposed set of low-level descriptors, it is shown that individual human beings are different in conveying emotions, and that parts of the spectrum that hold the affective information are different from one person to another. Therefore, the concept of emotion profile is proposed that formalizes those differences by taking into account different factors such as cultural and gender-specific differences, as well as those distinctions that have to do with individual human beings. At the statistical learning dimension, variable selection is performed to identify speech features that are most imperative to extracting affective information. In doing so, low-level descriptors are distinguished from statistical functionals, therefore, effectiveness of each of the two are studied dependently and independently. The major importance of variable selection as a standalone component of a solution is to real-time application of affective speech recognition. Although thousands of speech features are commonly used to tackle this problem in theory, extracting that many features in a real-time manner is unrealistic, especially for mobile applications. Results of the conducted investigations show that the required number of speech features is far less than the number that is commonly used in the literature of the problem. At the core of an affective speech recognition solution is a statistical model that uses speech features to recognize emotions. Such a model comes with a set of parameters that are estimated through a learning process. Proposed in this thesis is a learning algorithm, developed based on the notion of Hilbert-Schmidt independence criterion and named max-dependence regression, that maximizes the dependence between predicted and actual values of affective qualities. Pearson’s
Axisymmetric magnetic fields in stars: relative strengths of poloidal and toroidal components

In this third paper in a series on stable magnetic equilibria in stars, I look at the stability of axisymmetric field configurations and, in particular, the relative strengths of the toroidal and poloidal components. Both toroidal and poloidal fields are unstable on their own, and stability is achieved by adding the two together in some ratio. I use Tayler's stability conditions for toroidal fields and other analytic tools to predict the range of stable ratios and then check these predictions by running numerical simulations. If the energy in the poloidal component as a fraction of the total magnetic energy is written as E p /E, it is found that the stability condition is a(E/U) < Ep/E ≤ 0.8 where E/U is the ratio of magnetic to gravitational energy in the star and a is some dimensionless factor whose value is of order 10 in a main-sequence star and of order 10 3 in a neutron star. In other words, whilst the poloidal component cannot be significantly stronger than the toroidal, the toroidal field can be very much stronger than the poloidal-given that in realistic stars we expect E/U < 10- 6 . The implications of this result are discussed in various contexts such as the emission of gravitational waves by neutron stars, free precession and a 'hidden' energy source for magnetars.