Miracle-dz/UniFAR-FTUs huggingface dataset:
A single amino acid change of translation termination factor eRF1 switches between bipotent and omnipotent stop-codon specificity†

In eukaryotes a single class-1 translation termination factor eRF1 decodes the three stop codons: UAA, UAG and UGA. Some ciliates, like Euplotes, have a variant code, and here eRF1s exhibit UAR-only specificity, whereas UGA is reassigned as a sense codon. Since eukaryote eRF1 stop-codon recognition is associated with its N-terminal domain, structural features should exist in the N domain of ciliate eRF1s that restrict their stop-codon specificity. Using an in vitro reconstituted eukaryotic translation system we demonstrate here that a chimeric eRF1 composed of the N domain of Euplotes aediculatus eRF1 fused to the MC domains of human eRF1 exhibits UAR-only specificity. Functional analysis of eRF1 chimeras constructed by swapping Euplotes N domain sequences with the cognate regions from human eRF1 as well as site-directed mutagenesis of human eRF1 highlighted the crucial role of the alanine residue in position 70 of E. aediculatus eRF1 in restricting UGA decoding. Switching the UAR-only specificity of E. aediculatus eRF1 to omnipotent mode is due to a single point mutation. Furthermore, we examined the influence of eRF3 on the ability of chimeric and mutant eRF1s to induce peptide release in response to different stop codons.
Ciclosporin A Tapering Monitored by NFAT-Regulated Gene Expression: A New Concept of Individual Immunosuppression

Background. The impact of long-term immunosuppression in renal transplant recipients with respect to safety and efficacy remains undetermined. Pharmacodynamic monitoring of the relative reduction of T-cell-specific gene expression in renal transplant recipients treated with cyclosporine A (CsA) was applied in this study. Methods. During the study, 20 stable renal transplant recipients with tapered CsA dose and 20 patients with stable CsA dose (matched for age, gender, CsA dose, time after transplantation) were compared for a median period of 18 months (range 6–44). CsA dose was tapered in two stages of 15% each, and the expression of the nuclear factor of activated T cells (NFAT)-regulated genes was determined by reverse-transcription polymerase chain reaction method at CsA trough level and 2 hr after oral uptake. Results. The initial residual gene expression at 2 hr after CsA intake increased from 6.31% (range 1.30–16.6) to 21.3% (range 6.58–31.8) in patients with CsA dosage reduction. In one patient, the residual gene expression increased more than 40% and resulted in a reversible Banff 1A rejection episode. Blood pressure was significantly lower after CsA dosage reduction (P<0.05). In the pair-matched control group NFAT-regulated gene expression was comparable before and after the follow-up period (7.45% [range 0.21–18.3] vs. 5.87% [range0.66–13.2]; P=NS). Estimated glomerular filtration rate was significantly worse in the control group (P<0.05). Conclusion. Our observation suggests that the measurement of the relative gene expression in CsA-treated patients is a promising tool to monitor the CsA dosage reduction in long-term renal transplant patients. An increase in residual expression of NFAT-regulated gene expression may result in an acute rejection episode.
Aspects of Biocompatibility of Two Different Dialysis Membranes: Cuprophane and Polysulfone

Intradialytic hypoxemia, leukopenia and coagulation system activation were monitored in 9 uremic patients during hemodialysis with cuprophane (Cu) and polysulfone (Psf) membranes, using the following parameters: polymorphonuclear count (PMN), elastase alpha-1 proteinase inhibitor (EI-α1PI) complex, platelet count, β-thromboglobulin (BTG), fibronectin (FN) and arterial oxygen tension (PaO2). Our results indicate that 1) intradialytic hypoxemia observed with both membranes does not seem to be exclusively related to the well-known membrane-dependent leukopenia; 2) platelet activation, as demonstrated by the plasma BTG increase, appears to be an exclusive cellulosic membrane-related phenomenon; 3) at the same time platelet activation seems to be the major factor responsible for high FN levels, the highest FN levels occurring concurrently with the lowest platelet count.
Lead (Pb) in Biota and Perceptions of Pb Exposure at a Recently Designated Superfund Beach Site in New Jersey

The Raritan Bay Slag Site (New Jersey) was designated a Superfund site in 2009 because the seawall, jetties, and sediment contained lead (Pb). Our objective was to compare Pb and mercury (Hg) levels in biota and public perceptions of exposure at the Superfund and reference sites. Samples (algae, invertebrates, fish) were collected from the Raritan Bay Slag Site and reference sites and analyzed for Pb and Hg. Waterfront users were interviewed using a standard questionnaire. Levels of Pb in aquatic organisms were compared to ecological and human health safety standards. Lead levels were related to location, trophic level, and mobility. Lead levels in biota were highest at the western side of the West Jetty. Mean Pb levels were highest for algae (Fucus = 53,600 ± 6990 ng/g = ppb [wet weight], Ulva = 23,900 ± 2430 ppb), intermediate for grass shrimp (7270 ± 1300 ppb, 11,600 ± 3340 ppb), and lowest for fish (Atlantic silversides 218 ± 44 ppb). Within species, Pb levels varied significantly across the sampling sites. Lead levels in algae, sometimes ingested by individuals, were sufficiently high to exceed human safety levels. Mercury levels did not differ between the Superfund and reference sites. Despite the fence and warnings, people (1) used the Superfund and reference sites similarly, (2) had similar fish consumption rates, and (3) were not concerned about Pb, although most individuals knew the metal was present. The fish sampled posed no apparent risk for human consumers, but the algae did.
Self-adaptive software meets control theory: A preliminary approach supporting reliability requirements

This paper investigates a novel approach to derive self-adaptive software by automatically modifying the model of the application using a control-theoretical approach. Self adaptation is achieved at the model level to assure that the model—which lives alongside the application at run-time— continues to satisfy its reliability requirements, despite changes in the environment that might lead to a violation. We assume that the model is given in terms of a Discrete Time Markov Chain (DTMC). DTMCs can express reliability concerns by modeling possible failures through transitions to failure states. Reliability requirements may be expressed as reachability properties that constrain the probability to reach certain states, denoted as failure states.
Neurostimulation zur Behandlung von Epilepsien

Zusammenfassung Neurostimulationsverfahren wie die Vagus-Nerv-Stimulation (VNS), die direkte Hirnstimulation und die repetitive transkranielle Magnetstimulation (rTMS) eröffnen therapeutische Optionen für Patienten mit medikamentös therapieresistenten Epilepsien, die für einen epilepsiechirurgischen Eingriff nicht in Frage kommen oder bei denen eine solche Operation nicht zum Erfolg geführt hat. Mit der VNS können Responderraten (Anfallsreduktion > 50 %) von 30 bis 40% erzielt werden. Es besteht eine breite Wirksamkeit gegenüber allen Anfallstypen in allen Altersgruppen. Die antiepileptische Wirksamkeit nimmt über die ersten 18 bis 24 Monate kontinuierlich zu, um dann ein stabiles Plateau zu erreichen. Die VNS zeigt zudem einen positiven Effekt auf Stimmung, Gedächtnis und Lebensqualität. Bei der direkten Hirnstimulation kann einerseits eine direkte Stimulation der epileptogenen Zone und somit kortikaler Strukturen erfolgen, andererseits können auch tiefe Hirnstrukturen mit dem Ziel der Modifikation der Anfallsentstehung und/oder Ausbreitung stimuliert werden. Zudem kann die Stimulation entweder kontinuierlich oder responsiv, das heißt bei Auftreten eines Anfallsmusters im simultan mitregistrierten EEG erfolgen. Die tiefe Hirnstimulation befindet sich allerdings noch in einem experimentellen Stadium und sollte nur in spezialisierten Zentren angewendet werden. Kontrollierte Studien zum Einsatz der TMS bei therapieresistenten Epilepsien ergaben kontroverse Ergebnisse hinsichtlich der Wirksamkeit. Möglicherweise profitieren besonders Patienten mit neokortikalen Foci und Patienten mit fokalen kortikalen Dysplasien von der rTMS. Eine abschließende Empfehlung zu ihrem Einsatz bei Epilepsie kann derzeit noch nicht abgegeben werden.
Cancer-specific relationship awareness, relationship communication, and intimacy among couples coping with early-stage breast cancer

If couples can maintain normalcy and quality in their relationship during the cancer experience, they may experience greater relational intimacy. Cancer-specific relationship awareness, which is an attitude defined as partners focusing on the relationship and thinking about how they might maintain normalcy and cope with cancer as a couple or “team”, is one factor that may help couples achieve this goal. The main aim of this study was to evaluate the associations between cancer-specific relationship awareness, cancer-specific communication (i.e., talking about cancer’s impact on the relationship, disclosure, and responsiveness to partner disclosure), and relationship intimacy and evaluate whether relationship communication mediated the association between relationship awareness and intimacy. In the current study, a total of 254 women diagnosed with early-stage breast cancer and their partners were recruited. Participants completed measures of cancer-specific relationship awareness, relationship talk, self- and perceived partner-disclosure, perceived partner responsiveness, and relationship intimacy. Results indicated that patients and spouses who were higher in cancer-specific relationship awareness engaged in more relationship talk, reported higher levels of self-disclosure, and perceived that their partner disclosed more. Their partners reported that they were more responsive to disclosures. Relationship talk and perceived partner responsiveness mediated the association between cancer-specific relationship awareness and intimacy. Helping couples consider ways they can maintain relationship normalcy and quality during the cancer experience and framing coping with cancer as a “team” effort may facilitate better communication and ultimately enhance relationship intimacy.
Adaptive Deblocking of Images with DCT Compression

The discrete cosine transform (DCT) is widely used in image and video coding schemes. By applying the DCT to image blocks and quantizing the DCT coefficients, efficient image compression can be achieved. However, the quantization of the DCT coefficients introduces errors in the decompressed images, which appear as blocky artifacts. The blocky artifacts can be converted into “Gaussian-type” noise and removed via image denoising techniques. In this paper, an adaptive deblocking scheme has been developed to remove the blocky artifacts from images. Experimental results show that, with this adaptive approach, blocky artifacts have been successfully removed with improved peak signal-to-noise ratio (PSNR) values over the previous approach.
Clinical potential of intravascular ultrasound for physiological assessment of coronary stenosis: relationship between quantitative ultrasound tomography and pressure-derived fractional flow reserve.

BACKGROUND Little is known regarding intravascular ultrasound (IVUS) criteria to determine the functional severity of coronary stenosis. Recently, fractional flow reserve (FFR) has emerged as a lesion-specific index of the functional severity of a coronary stenosis that is independent of systemic hemodynamic variability. The present study was undertaken to determine the IVUS parameters for the physiological severity of coronary stenosis. METHODS AND RESULTS Fifty-one lesions in 42 patients were evaluated by means of quantitative coronary angiogram, IVUS, and intracoronary pressure measurements. The FFR was calculated as the ratio of the distal coronary pressure divided by the proximal coronary pressure under hyperemia. We considered a value of the FFR <0.75 as significant in determining inducible ischemia, according to the previous studies. The minimal luminal area (MLA) and the area stenosis were measured by IVUS. By regression analysis, the MLA showed a positive correlation with the FFR value (r(2)=0.62, P<0.0001). The area stenosis had a significant inverse correlation with the value of FFR (r(2)=0.60, P<0.0001). The IVUS thresholds that maximized the sensitivity and specificity were MLA <3.0 mm(2) (sensitivity, 83.0%; specificity, 92.3%) and area stenosis >0.6 (sensitivity, 92.0%; specificity, 88.5%). The combination of both criteria (MLA <3.0 mm(2) and area stenosis <0.6) without exception met a value of the FFR <0.75. CONCLUSIONS Anatomic parameters obtained by IVUS showed a significant correlation to the FFR values. The present study demonstrated that the combination of the MLA and area stenosis measured by IVUS can be an anatomic predictor for the physiological impact of coronary epicardial stenosis.
Characterization of a Conditional bosR Mutant in Borrelia burgdorferi

ABSTRACT Borrelia burgdorferi, the etiological agent of Lyme disease, adapts to unique host environments as a consequence of its complex life cycle that spans both arthropod and mammalian species. In this regard, B. burgdorferi must adapt to various environmental signals, pHs, temperatures, and O2 and CO2 levels to establish infectious foci. We hypothesize that the BosR protein functions as a global regulator that is required for both borrelial oxidative homeostasis and pathogenesis. To assess the role of BosR in B. burgdorferi, we constructed an IPTG (isopropyl-β-d-thiogalactopyranoside)-regulated bosR strain. The selective decrease of bosR resulted in a change in growth when cells were cultured either anaerobically or microaerobically; however, a distinct growth defect was observed for anaerobically grown B. burgdorferi relative to the growth attenuation observed for microaerobically grown B. burgdorferi. B. burgdorferi cells in which BosR levels were reduced were more sensitive to hydrogen peroxide and produced lower levels of NapA (Dps) and SodA, proteins involved in the oxidative stress response. In addition, the levels of OspC and DbpA were also induced coincident with increased BosR levels, suggesting that BosR interfaces with the RpoS regulatory cascade, which is known to modulate virulence gene expression in B. burgdorferi. Taken together, these results indicate that BosR is involved in the resistance of B. burgdorferi to oxidative stressors and affects the expression of genes, either directly or indirectly, whose products are important in borrelial pathogenesis.
MedAssist: Automated Medication Kit

Owing to people's busy schedule and their forgetfulness or age-related loss of memory, many a times they miss their medication dosage meant to be taken at a specific time. Apart from forgetfulness, sometimes the patients (specifically in the case of elderly and blind patients) are unable to read the names written on the medicine packets which may lead to intake of wrong medicines. These factors lead to medication non-adherence, resulting in negative consequences for the patient. This is a critical problem for medical researchers as it hampers treatment success [1]. This paper proposes the design of an automated system which reminds people (majorly the elderly people living in the rural areas) of their medication schedule and also bypasses the need to memorize medicine details and its intake schedule.
Handbook of Intelligent Control: Neural, Fuzzy, and Adaptive Approaches

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A Genetic Framework for Grain Size and Shape Variation in Wheat[C][W]

Using large-scale quantitative analysis, this work reveals that grain shape and size are independent traits in both modern and primitive wheat and are under the control of distinct genetic components. Moreover, the phenotypic diversity in grain morphology found in modern commercial wheat is the result of a recent and severe bottleneck. Grain morphology in wheat (Triticum aestivum) has been selected and manipulated even in very early agrarian societies and remains a major breeding target. We undertook a large-scale quantitative analysis to determine the genetic basis of the phenotypic diversity in wheat grain morphology. A high-throughput method was used to capture grain size and shape variation in multiple mapping populations, elite varieties, and a broad collection of ancestral wheat species. This analysis reveals that grain size and shape are largely independent traits in both primitive wheat and in modern varieties. This phenotypic structure was retained across the mapping populations studied, suggesting that these traits are under the control of a limited number of discrete genetic components. We identified the underlying genes as quantitative trait loci that are distinct for grain size and shape and are largely shared between the different mapping populations. Moreover, our results show a significant reduction of phenotypic variation in grain shape in the modern germplasm pool compared with the ancestral wheat species, probably as a result of a relatively recent bottleneck. Therefore, this study provides the genetic underpinnings of an emerging phenotypic model where wheat domestication has transformed a long thin primitive grain to a wider and shorter modern grain.
Burden and transmission of zoonotic foodborne disease in a rural community in Mexico.

BACKGROUND The foodborne transmission and human health impact of Salmonella and Campylobacter infections have rarely been evaluated at the population level in highly endemic settings. METHODS A prospective 15-month cohort study of 127 infants and 119 elderly people was combined with animal and food surveillance to determine the incidence and severity of Salmonella and Campylobacter gastroenteritis in a comparatively prosperous rural community in Mexico. RESULTS Salmonella and Campylobacter were isolated in up to 75% and 57%, respectively, of raw retail meat and in up to 4.5% of ready-to-eat foods. Rates of acute gastroenteritis of any etiology in infants and elderly people were, respectively, 2.1 and 0.7 episodes per person per year. The annual incidence density rate of Salmonella gastroenteritis was 17.8 per 100 infants and 7.9 per 100 elderly people; the rate of Campylobacter gastroenteritis was 11.7 per 100 infants and 0 per 100 elderly people. Pulsed-field gel electrophoresis analysis yielded multiple clusters of human, meat, and/or animal Salmonella and Campylobacter isolates with indistinguishable patterns. On average, gastroenteritis episodes with these pathogens lasted 3 days in infants and 2 days in elderly people. Medical attention was sought in 44% of diarrheal episodes in infants and in 26% of diarrheal episodes in elderly people; none required hospitalization. Infants with multidrug-resistant Salmonella gastroenteritis had a higher frequency of bloody stools and medical visits (50% vs 11%; odds ratio, 8.5; P = .04) than those with more susceptible strains. CONCLUSIONS In this relatively advantaged Mexican rural community, the human health impact of a food chain heavily contaminated with Salmonella and Campylobacter was of low magnitude.
Multidimensional Scaling, Tree-Fitting, and Clustering

American mathematical psychologists have developed computer-based methods for constructing representations of the psychological structure of a set of stimuli on the basis of pairwise measures of similarity or confusability. Applications to perceptual and semantic data illustrate how complementary aspects of the underlying psychological structure are revealed by different types of representations, including multidimensional spatial configurations and nondimensional tree-structures or clusterings.
Pleomorphic adenoma: A diagnostic pitfall in the diagnosis of salivary gland lesions on FNAC: Case reports with review of the literature

Fine needle aspiration cytology (FNAC) is commonly being used with increasing frequency for the pre-operative evaluation of salivary gland lesions. However, it has areas of considerable interpretational difficulties. The most frequent problems involve variations in the expected cytology of pleomorphic adenoma (PA). Salivary gland FNACs performed at Pt. JNM Medical College, Raipur, Chhattisgarh, during July 2006 to June 2007 were reviewed, and we report four cases of interesting diagnostic dilemma. As PA is the most common salivary gland neoplasm, it should always be considered and ruled out as the first differential in the diagnosis of salivary gland FNACs. In order to avoid diagnostic pitfalls, we emphasize a diagnostic approach based on the mandatory presence of all three elements of PA, i.e. 3-dimensional cohesive clusters of ductal cells, background of singly lying plasmacytoid myoepithelial cells and dense fibrillary brightly metachromatic stroma with partially obscured entrapped myoepithelial cells. To document the same, we advocate liberal use of repeat aspirations with multiple sampling performed from different parts of the tumor. Some differential diagnostic problems, e.g. carcinoma ex PA, may still however remain insolvable by cytologic means.
Prognostic significance of received relative dose intensity in non-Hodgkin's lymphoma patients: application to LNH-87 protocol. The GELA. (Groupe d'Etude des Lymphomes de l'Adulte).

BACKGROUND To evaluate the effects of chemotherapy dose intensity (DI) on outcome in patients with aggressive lymphoma, the received relative DI (received RDI) is usually calculated using Hryniuk's model. We applied this model to a selected patient subgroup included in the LNH87 protocol (LNH87-2 protocol), who had been treated with the ACVB induction regimen. PATIENTS AND METHODS Patients aged < 55 who had at least one of the following prognostic factors: performance status (PS) > or = 2, number of extranodal sites > or = 2, tumor burden > or = 10 cm, bone marrow or central nervous system involvement, and Burkitt's or lymphoblastic histologic subtype, were included in this study. Actual DI was calculated using the definition of DI as mg/m2/week previously described by Hryniuk. RESULTS Eighty-seven of the 311 patients included in the study (28%) presented a RDI below 70% of the theoretical DI. We demonstrated a decreased response rate (65% vs. 79%, p = 0.01) and shorter overall 2-year survival (61% vs. 72%, p = 0.02) in patients receiving a DI < 70%. This difference was still significant when the multiparametric analysis was used (p = 0.004). CONCLUSION Results obtained when this model was applied to aggressive lymphoma patients included in the LNH-87 protocol led to the demonstration of a strong relationship between received RDI and survival.