Miracle-dz/UniFAR-FTUs huggingface dataset:
Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression

Eukaryotic cells rapidly reduce protein synthesis in response to various stress conditions. This can be achieved by the phosphorylation-mediated inactivation of a key translation initiation factor, eukaryotic initiation factor 2 (eIF2). However, the persistent translation of certain mRNAs is required for deployment of an adequate stress response. We carried out ribosome profiling of cultured human cells under conditions of severe stress induced with sodium arsenite. Although this led to a 5.4-fold general translational repression, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance to the inhibition. Nearly all resistant transcripts possess at least one efficiently translated upstream open reading frame (uORF) that represses translation of the main coding ORF under normal conditions. Site-specific mutagenesis of two identified stress resistant mRNAs (PPP1R15B and IFRD1) demonstrated that a single uORF is sufficient for eIF2-mediated translation control in both cases. Phylogenetic analysis suggests that at least two regulatory uORFs (namely, in SLC35A4 and MIEF1) encode functional protein products. DOI: http://dx.doi. org/10.7554/eLife.03971. 001
Wavelet-based combined signal filtering and prediction

We survey a number of applications of the wavelet transform in time series prediction. We show how multiresolution prediction can capture short-range and long-term dependencies with only a few parameters to be estimated. We then develop a new multiresolution methodology for combined noise filtering and prediction, based on an approach which is similar to the Kalman filter. Based on considerable experimental assessment, we demonstrate the powerfulness of this methodology.
Phenomenological study of charm photoproduction at HERA

We present predictions for single inclusive distributions of charmed mesons, relevant to the HERA experiments. Our results are based upon a computation that correctly incorporates mass effects up to the next-to-leading order level, and the resummation of transverse momentum logarithms up to next-to-leading-logarithmic level. We apply the same acceptance cuts as the H1 and Zeus experiments, and compare our results to their data. We perform a study of the sensitivity of our predictions on the charm mass, ? QCD, factorization scale, renormalization scale, and fragmentation parameters.
Leukocyte Cathepsin S Is a Potent Regulator of Both Cell and Matrix Turnover in Advanced Atherosclerosis

Objective—A dysbalance of proteases and their inhibitors is instrumental in remodeling of atherosclerotic plaques. One of the proteases implicated in matrix degradation is cathepsin-S (CatS). To address its role in advanced lesion composition, we generated chimeric LDLr−/− mice deficient in leukocyte CatS by transplantation with CatS−/−×LDLr−/− or with LDLr−/− bone marrow and administered a high-fat diet. Methods and Results—No difference in aortic root lesion size could be detected between CatS+/+ and CatS−/− chimeras. However, leukocyte CatS deficiency markedly changed plaque morphology and led to a dramatic reduction in necrotic core area by 77% and an abundance of large foam cells. Plaques of CatS−/− chimeras contained 17% more macrophages, 62% less SMCs, and 33% less intimal collagen. The latter two could be explained by a reduced number of elastic lamina fractures. Moreover, macrophage apoptosis was reduced by 60% with CatS deficiency. In vitro, CatS was found to be involved in cholesterol metabolism and in macrophage apoptosis in a collagen and fibronectin matrix. Conclusion—Leukocyte CatS deficiency results in considerably altered plaque morphology, with smaller necrotic cores, reduced apoptosis, and decreased SMC content and collagen deposition and may thus be critical in plaque stability.
Ameliorative Effect of Vitamin C on Alterations in Thyroid Hormones Concentrations Induced by Subchronic Coadministration of Chlorpyrifos and Lead in Wistar Rats

The present study evaluated the ameliorative effect of vitamin C on alteration in thyroid hormones induced by low-dose subchronic coadministration of chlorpyrifos (CPF) and lead (Pb). Forty Wistar rats were divided into 4 groups of 10 animals each. Groups I and II were administered soya oil (2 mL/kg) and vitamin C (100 mg/kg), respectively. Group III was coadministered CPF (4.25 mg/kg ~1/20th LD50) and Pb (250 mg/kg ~1/20th LD50), respectively. Group IV was pretreated with vitamin C (100 mg/kg) and then coadministered with CPF (4.25 mg/kg) and Pb (250 mg/kg), 30 min later. The regimens were administered by gavage for a period of 9 weeks. The marginal decrease in serum triiodothyronine and thyroxine and the significant increase in the concentrations of thyroid stimulating hormone and malonaldehyde in the group coadministered with CPF and Pb were ameliorated by vitamin C partly due to its antioxidant properties.
Comparing the Power of Robots

Robots must complete their tasks in spite of unreliable actuators and limited, noisy sensing. In this paper, we consider the information requirements of such tasks. What sensing and actuation abilities are needed to complete a given task? Are some robot systems provably “more powerful”, in terms of the tasks that they can complete, than others? Can we find meaningful equivalence classes of robot systems? This line of research is inspired by the theory of computation, which has produced similar results for abstract computing machines. Our basic contribution is a dominance relation over robot systems that formalizes the idea that some robots are stronger than others. This comparison, which is based on how the robots progress through their information spaces, induces a partial order over the set of robot systems. We prove some basic properties of this partial order and show that it is directly related to the robots' ability to complete tasks. We give examples to demonstrate the theory, including a detailed analysis of a limited-sensing global localization problem.
Revision of Cannulated and Perforated Cement-Augmented Pedicle Screws: A Biomechanical Study in Human Cadavers

Study Design. Biomechanical investigation of primary and revised cement-augmented pedicle screws in comparison with unaugmented screws. Objective. To evaluate revision of cannulated pedicle screws and investigate cement-augmented and nonaugmented screws biomechanically, testing the torque of primary screws and axial pullout force of revised screws in cadaver vertebrae. Summary of Background Data. Cement augmentation increases the pullout force and stability of pedicle screws in vertebrae with low bone mineral density, but surgeons are concerned about complications during revision. Methods. Bone mineral density was measured using quantitative computed tomography (CT) in 23 osteoporotic thoracolumbar junction vertebrae from human cadavers. Cannulated pedicle screws, augmented with bone cement (on right) or unaugmented (left), were inserted into each vertebra. After CT control, extraction torque was measured and the pedicles were reinstrumented with larger-diameter screws. The right screws were augmented again, with another CT control, before pullout testing. Results. Mean vertebral bone density was 52.6 mg/cm3. No major screw malpositioning was observed on primary CTs. Cement leakage was observed anterolaterally and into the spinal canal. Mean maximal torque in augmented screws (1.2 Nm, SD: 0.6) differed significantly from nonaugmented screws (0.8 Nm, SD: 0.6). Screw removal did not lead to vertebral destruction. No relevant changes due to positioning or leakage were observed on CT after revision procedures compared with primary findings. Maximal pullout force in revised augmented screws (713.2 N, SD: 254.6) differed significantly compared with nonaugmented screws (554.0 N, SD: 296.5). Bone damage was observed in several vertebrae during pullout force testing in augmented screws. Conclusion. Revision of cement-augmented pedicle screws was feasible without bone destruction, and larger-diameter screws can be used in revision procedures. The pullout force after revision was significantly better in cement-augmented screws. During pullout testing, the cement-bone interface broke before the screw-cement interface in several vertebrae, fracturing the pedicles.
Extending The EU Single Market Eastwards: Sectoral Trade And Real Wage Effects

In this paper we address the question of the impact of permitting free migration in an enlarged trading bloc. We estimate two sectoral equations for trade flows and real wages of three regional blocs of the enlarged EU that we defined as North (wealthiest EU), South (Greece, Portugal and Spain) and East (acceding Central and Eastern European countries). We then use the estimated coefficients to compute potential trade flows and real wages for these three groups under the two alternative scenarios of an enlargement with and without free movement of labour. A fully-fledge Single Market allows the North, with good market access and human capital endowments, to consolidate its current hub position by attracting more firms and skilled workers. Thus its net exports of high scale economy, skill-intensive goods increase and so do overall real wages, though they decrease in low scale economies sectors. The South, with poor market access and human capital endowments, retains competitiveness in low scale economies, low skill-intensity sectors and sees an overall reduction in real wages, except in high scale economies, low skill-intensity sectors. The East, with poor market access but well endowed in human capital, has a marginal gain in trade terms but suffers a real wage loss. Moreover, skilled migration would cause a brain drain that, if of sufficiently large proportions, could have very damaging consequences in the long-term.
Effect of antilymphocytic and antithymocytic sera on the development of mouse lymphoma.

Injections of antisera to lymphoid tissues of C3H/HeJ mice significantly increased the incidence of ( a ) lymphoma in normally resistant C3H/HeJ adult mice injected 4 times with Gross leukemia virus and ( b ) growth of allogeneic lymphomas in C3H/HeJ and AKR mice when compared to similarly treated animals injected with normal rabbit serum. The same antilymphoid cell sera were able to suppress sheep red blood cell hemagglutinin responses in parallel sets of mice. Immunosuppressive drugs, 6-mercaptopurine (100 mg/kg of diet) and azathioprine (100, 150, or 200 mg/kg of diets or 150 mg/kg mouse injected intraperitoneally), did not increase the incidence of lymphoma in C3H/HeJ adult mice receiving multiple injections of Gross leukemia virus or depress the hemagglutinin response to sheep red blood cells. There was a tendency towards prolongation of latent periods of spontaneous lymphoma in AKR mice and virus-induced lymphoma in C3H/HeJ mice injected with C3H/HeJ antithymocytic serum prior to development of lymphoma. Incidence and latent period of virus-accelerated lymphoma in AKR mice was not altered by administration of the antithymocytic serum during the latent period of lymphomagenesis.
LATTICES ACTING ON RIGHT-ANGLED HYPERBOLIC BUILDINGS

Let X be a right-angled hyperbolic building. We show that the lattices in Aut(X) share many properties with tree lattices. For example, we characterise the set of covolumes of uniform and of nonuniform lattices in Aut(X), and show that the group Aut(X) admits an infinite ascending tower of uniform and of nonuniform lattices. These results are proved by constructing a functor from graphs of groups to complexes of groups.
Emission of methane from plants

It has been proposed that plants are capable of producing methane by a novel and unidentified biochemical pathway. Emission of methane with an apparently biological origin was recorded from both whole plants and detached leaves. This was the first report of methanogenesis in an aerobic setting, and was estimated to account for 10–45 per cent of the global methane source. Here, we show that plants do not contain a known biochemical pathway to synthesize methane. However, under high UV stress conditions, there may be spontaneous breakdown of plant material, which releases methane. In addition, plants take up and transpire water containing dissolved methane, leading to the observation that methane is released. Together with a new analysis of global methane levels from satellite retrievals, we conclude that plants are not a major source of the global methane production.
Gene expression enhancement due to plasmid maintenance

Analysis of the chromosomic beta-galactosidase activity in strains of Escherichia coli with and without plasmids indicated that plasmid maintenance enhances gene expression. Cyclic AMP (cAMP) determinations confirmed that the gene enhancement observed in strains carrying plasmids was due to a small increase in the intracellular concentration of cAMP. Also, cells carrying plasmids displayed higher specific glucose uptake rates than did cells without plasmids. The increases in the expression of beta-galactosidase and the glucose uptake rate suggest a cAMP-mediated release of the glucose effect due to plasmid maintenance. Our results suggested that this effect is independent of the host and type and number of plasmids.
Hemodynamic Parameters during Laryngoscopic Procedures in the Office and in the Operating Room

Objective Previous research has shown that office-based laryngoscopic procedures can induce hemodynamic changes, including tachycardia and severe hypertension, calling into question the safety of these procedures. However, comparison between office and operating room (OR) procedures has not been carried out. Therefore, we prospectively measured hemodynamic variables in both settings to compare hemodynamic changes between office and OR procedures. Study Design Prospective cohort study. Setting Single academic center. Subjects and Methods Subjects undergoing office and OR laryngoscopic procedures were prospectively identified, and 92 OR and 70 office subjects were included. Heart rate and blood pressure were measured at established time points before, during, and after the procedures. Descriptive and comparative statistical analyses were conducted. Results Severe hemodynamic events, either tachycardia or severe hypertension (blood pressure >180 mm Hg systolic or >110 mm Hg diastolic), occurred significantly more frequently in OR than office procedures (41% vs 20%; P = .006). OR severe hemodynamic events occurred more commonly than previously reported rates in the office (41% vs 28%; P = .012). Regression analyses showed that the odds of having a severe hemodynamic event were 3.66 times higher in OR versus office procedures. Conclusion Severe hemodynamic events are more likely to occur in the OR than in the office during laryngologic procedures. While larger studies will be required to establish rates of dangerous cardiovascular events in laryngoscopic procedures, hemodynamic parameters indicate that office-based procedures have a safety benefit for procedures that can be conducted in either setting.
Stem Amaranth Yield in Response to Organic Manuring

Field investigations are important tools for confirmation of the effectiveness of the organic manures on crop yield. As different N sources, this work presents a comparative study of the effects of urea, cow dung and poultry manure on plant height, stem length and diameter, leaf length, breadth and number accompanied with the fresh weight of plant, stem, leaf coupling stem leaf ratio and gross yield of stem amaranth (Amaranthus tricolor Var. BARI Data 1). With an imposition of eight treatments, a field study was conducted at the farm of BSMRAU campus, Gazipur during February-April, 2007 in a Randomized Complete Block Design (RCBD). Treatments were control and seven N sources namely, urea (107 kg N ha -1 ), cow dung (23.75 t ha -1 ), poultry manure (9.3 t ha -1 ), half cow dung and half urea, half poultry manure and half urea, three fourth cow dung and one fourth urea and three fourth poultry manure and one fourth urea, respectively with four replications ensuring the 107 kg N ha -1 supply from all sources of N used. Compared with cow dung and poultry manure, urea resulted in higher plant height, broader stem length and diameter, more fresh weight of plant, stem and leaf accompanied with maximum gross yield. However, data on the studied parameters varied significantly (p< 0.05). So cow dung and poultry manure applied at 23.75 t ha -1 and 9.3 t ha -1 , respectively were compatible to urea as N source for stem amaranth production. DOI: http://dx.doi. org/10.3329/jesnr.v6i2. 22082 J. Environ. Sci. & Natural Resources, 6(2): 19-23 2013
PCR Assay for Monitoring Trypanosoma cruzi Parasitemia in Childhood after Specific Chemotherapy

ABSTRACT Assessment of cure of Trypanosoma cruzi infection by antibody seroconversion usually involves several years of follow-up. Parasitological negativity is useless for cure assessment, since even untreated patients mostly show negative results; conversely, positive tests are of great value because they indicate treatment failure. Here, PCR was used to assess the rate of specific chemotherapy failure in a well-characterized Brazilian cohort of T. cruzi-seropositive children, who were enrolled in a field trial of benznidazole (Bz) efficacy. Paired blood samples from 111 children were taken at baseline and 36 months after treatment with either Bz (n = 58) or a placebo (n = 53). DNA extraction and PCR amplification were carried out as previously described, and hybridization was performed with all PCR products. At the end of follow-up, PCR was positive for 39.6% of the patients in the Bz group versus 64.2% in the placebo group (P = 0.01). Untreated patients had a 1.6-fold-higher chance of remaining positive by PCR than those in the Bz group (P < 0.05). We conclude that PCR is a useful tool for revealing therapeutic failure of T. cruzi infection on a short-term basis.
Human Antibodies that Recognize Novel Immunodominant Quaternary Epitopes on the HIV-1 Env Protein

Numerous broadly neutralizing antibodies (Abs) target epitopes that are formed or enhanced during mature HIV envelope formation (i.e. quaternary epitopes). Generally, it is thought that Env epitopes that induce broadly neutralizing Abs are difficult to access and poorly immunogenic because of the characteristic oligomerization, conformational flexibility, sequence diversity and extensive glycosylation of Env protein. To enhance for isolation of quaternary epitope-targeting Abs (QtAbs), we previously used HIV virus-like particles (VLPs) to bind B cells from long-term non-progressor subjects to identify a panel of monoclonal Abs. When expressed as recombinant full-length Abs, a subset of these novel Abs exhibited the binding profiles of QtAbs, as they either failed to bind to monomeric Env protein or showed much higher affinity for Env trimers and VLPs. These QtAbs represented a significant proportion of the B-cell response identified with VLPs. The Ab genes of these clones were highly mutated, but they did not neutralize common HIV strains. We sought to further define the epitopes targeted by these QtAbs. Competition-binding and mapping studies revealed these Abs targeted four separate epitopes; they also failed to compete for binding by Abs to known major neutralizing epitopes. Detailed epitope mapping studies revealed that two of the four epitopes were located in the gp41 subunit of Env. These QtAbs bound pre-fusion forms of antigen and showed differential binding kinetics depending on whether oligomers were produced as recombinant gp140 trimers or as full-length Env incorporated into VLPs. Antigenic regions within gp41 present unexpectedly diverse structural epitopes, including these QtAb epitopes, which may be targeted by the naturally occurring Ab response to HIV infection.
Journal of Translational Medicine Toll like Receptor-3 Ligand Poly-iclc Promotes the Efficacy of Peripheral Vaccinations with Tumor Antigen-derived Peptide Epitopes in Murine Cns Tumor Models

Background: Toll-like receptor (TLR)3 ligands serve as natural inducers of pro-inflammatory cytokines capable of promoting Type-1 adaptive immunity, and TLR3 is abundantly expressed by cells within the central nervous system (CNS). To improve the efficacy of vaccine strategies directed against CNS tumors, we evaluated whether administration of a TLR3 ligand, polyinosinic-polycytidylic (poly-IC) stabilized with poly-lysine and carboxymethylcellulose (poly-ICLC) would enhance the anti-CNS tumor effectiveness of tumor peptide-based vaccinations.
Weaning induces an increase in the number of specific cytokine-secreting intestinal lymphocytes in mice.

Intestinal immunity differs from systemic immunity in several aspects and is frequently studied separately. In this work we have analysed the frequency of mononuclear cells spontaneously secreting the cytokines IL-2, IL-4, IL-5, IL-6, IL-10, interferon gamma (IFN-gamma) and tumour necrosis factor (TNF-alpha), in Peyer's patches and lamina propria of small intestine in mice by enzyme linked immunosorbent spot (ELISPOT) during 1 month after weaning. We have found a high percentage of spontaneous Th(1)as well as Th(2)cytokine-secreting lymphocytes in both populations, Peyer's patches and lamina propria. An increase in the number of the lymphocytes secreting most of the studied cytokines, at 1 and 2 weeks after weaning, was also observed. These results suggest that the increase in the number of cytokine secreting lymphocytes may be one of the potential mechanisms involved in the development of the intestinal immune system at weaning.
Using Ground Clutter to Adjust Relative Radar Calibration at Kwajalein, RMI

The ground radar situated on Kwajalein Atoll in the Republic of the Marshall Islands serves an important role in providing reflectivity measurements for comparison with rain gauge data collected and analyzed by the Tropical Rainfall Measuring Mission (TRMM) Ground Validation (GV) group at NASA Goddard Space Flight Center (GSFC) as well as satellite data obtained from TRMM. Radar calibration is a major source of uncertainty in radar rainfall estimation. Almost thirty years ago, Rinehart (1978) described a method for performing radar calibration checks using individual ground targets. GV staff attempted to perform an analysis using a single target, a tower situated on the island of Ebeye. The results of this single target procedure proved too noisy and a broader solution utilizing the entire clutter field at Kwajalein was sought.
Electric field stimulation of excitable tissue

The authors consider the determination of conditions when an excitable membrane can be considered linear and steady-state. The following topics are dealt with: threshold for a space-clamped fiber; threshold for a fiber stimulated by a point current source; subthreshold response; passive vs. active response; defibrillation stimulus-response time-constant; the transient intracellular current; the transient transmembrane potential due to junctional resistance.
Haar features for FACS AU recognition

We examined the effectiveness of using Haar features and the Adaboost boosting algorithm for FACS action unit (AU) recognition. We evaluated both recognition accuracy and processing time of this new approach compared to the state-of-the-art method of classifying Gabor responses with support vector machines. Empirical results on the Cohn-Kanade facial expression database showed that the Haar+Adaboost method yields AU recognition rates comparable to those of the Gabor+SVM method but operates at least two orders of magnitude more quickly