Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles.

INTRODUCTION . 1 THE TRANSLATIONAL MACHINERY . 2 Structural Components of Ribosomes . 2 Ribosomal proteins . 2 Ribosomal ribonucleic acids (rRNAs). 3 Soluble Protein Factors Required for Initiation. 6 Initiator Transfer RNAs . 9 THE STRUCTURE OF MESSENGER RNA (mRNA). 12 mRNA Structure in Procaryotes . 12 Polycistronic mRNAs are the rule. 12 AUG is the usual, but not the only, initiator codon . 13 Sequence context around initiator codons . 13 mRNA Structure in Eucaryotes . 15 Monocistronic mRNAs are the rule . 15 AUG is the only initiator codon. 16 Post-transcriptional modifications . 16 Untranslated sequences at the 5' end . 17 Untranslated sequences at the 3' end. 19 Structure of Organedgr mRNAs . 20 Consequences of Pertilrbing mRNA S tructure . 20 THE INITIATION PROCESS . 20 Brief Overview . 20 Attempts to Tramnslate mRNAs in Heterologous Systems Suggest Dissimilarities in the Initiation Mechanisms . 22 Shine-Dalgarno Interaction Between mRNA and Small-Subunit Ribosomal RNA . 23 Role of mRNA-ribosomal RNA complementarity in eubacterial systems . 23 (i) Summary of the evidence . 23 (ii) Characteritics of the Shine-Dalgarno sequence in procaryotic mRNAs . 24 (iii) Is an exposed Shine-Dalgarno sequence, appropriately positioned upstream from an exposed initiator codon, sufficient to define a bacterial ribosome bnding site? 26 Can the Shin Dalgan o mechanism be extrapolated to other systems? 27 Eucaryotic tibosomes Probably Initiate via a S ning Mechanism . 28 Translational Control at the mRNA Level . o . 29 Alternative forms of mRNA. 29. -. o. 29 mRNA binding proteins. 30. 30 CONCLUSIONS AND PERSPECTIVES . 31 LITERATURE CITED. 31
Complete androgen insensitivity syndrome caused by a novel mutation in the ligand-binding domain of the androgen receptor: functional characterization.

Mutations in the X-linked androgen receptor (AR) gene cause the androgen insensitivity syndrome by impairing androgen-dependent male sexual differentiation to varying degrees. Complete androgen insensitivity (CAIS) yields an external female phenotype, whereas affected cases of partial androgen insensitivity have various ambiguities of the genitalia. Here we describe a 46,XY phenotypically female patient with all of the characteristics of CAIS, i.e. primary amenorrhea, no axillary or pubic hair, female external genitalia, no uterus, and undescended testes. Defects in testosterone and dihydrotestosterone synthesis were excluded. The molecular basis of the disease was clarified by means of direct sequencing of PCR-amplified exonic fragments of the AR gene. An A to C transition in exon 4 of the AR gene led to a novel missense His(689)Pro mutation in the ligand-binding domain of the AR protein. Functional studies demonstrated that the mutated AR is unable to efficiently bind its natural ligand dihydrotestosterone and to trans-activate known androgen response elements. Analysis of the structural consequences of the His(689)Pro substitution suggests that this mutation is likely to perturb the conformation of the second helix of the AR ligand-binding domain, which contains residues critical for androgen binding.
A Comparison of LORETA and the Borgiotti-Kaplan Beamformer in Simulated EEG Source Localization with a Realistic Head Model

An accurate and robust EEG source localization algorithm is an asset in the understanding, diagnosis, and treatment of some neurological disorders. Two inverse algorithms, LORETA and the Borgiotti-Kaplan beamformer (BK Beam) are used to localize a single dipole source from a simulated EEG within a realistic head model. Compared over a range of SNR values and source locations, the BK Beam exhibited superior localizing capabilities with less dispersion than LORETA.
Splanchnic microcirculatory changes during CO2 laparoscopy.

BACKGROUND Splanchnic macrocirculatory changes during high-pressure CO2 pneumoperitoneum include a decrease in mesenteric arterial blood flow, and decreased gastric perfusion with a drop in gastric pH in experimental studies. Microcirculatory changes in abdominal organs under clinical conditions with a low pressure CO2 pneumoperitoneum are unknown. STUDY DESIGN In 18 patients undergoing routine laparoscopy with a CO2 pneumoperitoneum (7 symptomatic cholecystolithiasis, 3 acute cholecystitis, and 8 acute appendicitis) gastric, duodenal, jejunal, colonic, hepatic, and peritoneal blood flow was measured with a custom-made laser Doppler flow probe at an intra-abdominal pressure of 0, 10, and 15 mm Hg. RESULTS Intra-abdominal pressure elevation from 10 mm Hg to 15 mm Hg significantly decreased the blood flow in the stomach by 40 percent to 54 percent, the jejunum by 32 percent, the colon by 44 percent, the liver by 39 percent, the parietal peritoneum by 60 percent, and the duodenum by 11 percent. Splanchnic blood flow decreased with operative time at a constant intra-arterial pressure (r = 0.88, p < 0.0001). CONCLUSIONS From our study, we concluded that laparoscopic procedures with a CO2 pneumoperitoneum should be performed at a pressure of 10 mm Hg or lower to avoid splanchnic microcirculatory disturbances.
Individual Driver Modeling via Optimal Selection of Steering Primitives

Abstract A shared lane keeping assistance system supports the driver in the steering task. In contrast to an autonomous system, the shared system works in parallel with the driver by applying an additional torque on the steering wheel. This means the system and the driver perform the steering task in cooperation. As the driver is still part of the control loop a driver model is required to predict the steering behavior of the actual driver. In this paper we introduce a new lateral steering model which is suited to characterize individual drivers. This model describes, in contrast to other models, the neuromuscular system, limbs and its control for a specific driver by using a set of dynamic primitives (so called movemes). These movemes build a gray-box model for the neuromuscular system. The steering wheel angle is the predicted output of the moveme model. In order to generate a steering angle trajectory suited for the desired maneuver, the steering model switches between these movemes. Therefore, the central component of the driver model is a framework which determines the optimal switching sequence of the movemes. For this task an optimal control strategy is introduced. The approach is validated using a simulation of an ISO-double lane change with movemes which were identified from a set of real driver trajectories. The results show that the steering trajectories of the driver model highly correspond with the recorded driver trajectories.
Recursive Spatial Multiplexing: Improving Unitary Precoding with Outdated Channel State Information

We propose a closed-loop multiple-input multiple-output (MIMO) architecture which incorporates unitary precoding and recursive spatial multiplexing. Both techniques take advantage of a feedback channel in a similar way for the transmission of data at high rates with limited signal processing complexity. Unitary precoding is effective in situations with accurate channel state information (CSI) at the transmitter end. In situations with outdated CSI due to time-variant channels, a linear signal reconstruction at the receiver end may result in severe noise amplification. Recursive multiplexing mitigates the noise enhancement by means of retransmissions of signal parts in critical subspaces. This significantly increases the ergodic capacity achieved by precoding based on outdated CSI, as shown for the cases of time-variant (4x4) and (8x8) MIMO channels.
Relationship of the structures of tannins to the binding activities with hemoglobin and methylene blue.

The determination of relative astringency (RA) and relative affinity to methylene blue (RMB), based on those of geraniin (RAG and RMBG), shows good reproducibility with small amounts of samples for the estimation of the tannin content of plant extracts, and has been applied to the evaluation of the basal activity of 84 tannins and related compounds. The values obtained for polyphenols of lower molecular weight, which are not regarded as tannins, were zero or almost zero. An increase of these two values of up to about 1.3-1.4 times with increase of molecular weight of polyphenols (particularly such increase due to galloylation) was observed for each type of tannin tested. The RMBG determination gives values somewhat larger than the RAG values for hydrolyzable tannins, and rather smaller than the RAG values for condensed tannins.
Pseudomonas aeruginosa dose response and bathing water infection

SUMMARY Pseudomonas aeruginosa is the opportunistic pathogen mostly implicated in folliculitis and acute otitis externa in pools and hot tubs. Nevertheless, infection risks remain poorly quantified. This paper reviews disease aetiologies and bacterial skin colonization science to advance dose-response theory development. Three model forms are identified for predicting disease likelihood from pathogen density. Two are based on Furumoto & Mickey's exponential ‘single-hit’ model and predict infection likelihood and severity (lesions/m2), respectively. ‘Third-generation’, mechanistic, dose-response algorithm development is additionally scoped. The proposed formulation integrates dispersion, epidermal interaction, and follicle invasion. The review also details uncertainties needing consideration which pertain to water quality, outbreaks, exposure time, infection sites, biofilms, cerumen, environmental factors (e.g. skin saturation, hydrodynamics), and whether P. aeruginosa is endogenous or exogenous. The review's findings are used to propose a conceptual infection model and identify research priorities including pool dose-response modelling, epidermis ecology and infection likelihood-based hygiene management.
Cooperativity in sandpiles: statistics of bridge geometries

Bridges form dynamically in granular media as a result of spatiotemporal inhomogeneities. We classify bridges as linear and complex, and analyse their geometrical characteristics. In particular, we find that the length distribution of linear bridges is exponential. We then turn to the analysis of the orientational distribution of linear bridges and find that, in three dimensions, they are vertically diffusive but horizontally superdiffusive; thus, when they exist, long linear bridges form 'domes'. Our results are in good accord with Monte Carlo simulations of bridge structure; we make predictions for quantities that are experimentally accessible, and suggest that bridges are very closely related to force chains.
Functional runtime systems within the lambda-sigma calculus

We define a weak λ-calculus, λσw, as a subsystem of the full λ-calculus with explicit substitutions λσ[uArr ]. We claim that λσw could be the archetypal output language of functional compilers, just as the λ-calculus is their universal input language. Furthermore, λσ[uArr ] could be the adequate theory to establish the correctness of functional compilers. Here we illustrate these claims by proving the correctness of four simplified compilers and runtime systems modelled as abstract machines. The four machines we prove are the Krivine machine, the SECD, the FAM and the CAM. Thus, we give the first formal proofs of Cardelli's FAM and of its compiler.
The Same, but Different: Enterprise Systems Adoption Lifecycles in Transition Economies

We investigated differences in enterprise systems adoption lifecycles in transition economies when compared to developed economies. For that purpose, we collected data from experienced practitioners who participated in enterprise systems adoption lifecycles in transition and developed economies. Then we contrasted the findings with the normative literature. We identify similarities and variations in lifecycle phases and the actors involved in the process. This helps to better understand this phenomenon and extend the body of knowledge.
Ezrin/Radixin/Moesin Proteins Are Phosphorylated by TNF-α and Modulate Permeability Increases in Human Pulmonary Microvascular Endothelial Cells1

Endothelial cells (ECs) respond to TNF-α by altering their F-actin cytoskeleton and junctional permeability through mechanisms that include protein kinase C (PKC) and p38 MAPK. Ezrin, radixin, and moesin (ERM) regulate many cell processes that often require a conformational change of these proteins as a result of phosphorylation on a conserved threonine residue near the C terminus. This study tested the hypothesis that ERM proteins are phosphorylated on this critical threonine residue through TNF-α-induced activation of PKC and p38 and modulate permeability increases in pulmonary microvascular ECs. TNF-α induced ERM phosphorylation on the threonine residue that required activation of p38, PKC isoforms, and phosphatidylinositol-4-phosphate 5-kinase Iα, a major enzyme generating phosphatidylinositol 4,5-bisphosphate, and phosphorylated ERM were prominently localized at the EC periphery. TNF-α-induced ERM phosphorylation was accompanied by cytoskeletal changes, paracellular gap formation, and increased permeability to fluxes of dextran and albumin. These changes required activation of p38 and PKC and were completely prevented by inhibition of ERM protein expression using small interfering RNA. Thus, ERM proteins are phosphorylated through p38 and PKC-dependent mechanisms and modulate TNF-α-induced increases in endothelial permeability. Phosphorylation of ERM likely plays important roles in EC responses to TNF-α by modulating the F-actin cytoskeleton, adhesion molecules, and signaling events.
Men's circumcision status and women's risk of HIV acquisition in Zimbabwe and Uganda

Objective:To assess whether male circumcision of the primary sex partner is associated with women's risk of HIV. Design:Data were analyzed from 4417 Ugandan and Zimbabwean women participating in a prospective study of hormonal contraception and HIV acquisition. Most were recruited from family planning clinics; some in Uganda were referred from higher-risk settings such as sexually transmitted disease clinics. Methods:Using Cox proportional hazards models, time to HIV acquisition was compared for women with circumcised or uncircumcised primary partners. Possible misclassification of male circumcision was assessed using sensitivity analysis. Results:At baseline, 74% reported uncircumcised primary partners, 22% had circumcised partners and 4% had partners of unknown circumcision status. Median follow-up was 23 months, during which 210 women acquired HIV (167, 34, and 9 women whose primary partners were uncircumcised, circumcised, or of unknown circumcision status, respectively). Although unadjusted analyses indicated that women with circumcised partners had lower HIV risk than those with uncircumcised partners, the protective effect disappeared after adjustment for other risk factors [hazard ratio (HR), 1.03; 95% confidence interval (CI), 0.69–1.53]. Subgroup analyses suggested a non-significant protective effect of male circumcision on HIV acquisition among Ugandan women referred from higher-risk settings: adjusted HR 0.16 (95% CI, 0.02–1.25) but little effect in Ugandans (HR, 1.33; 95% CI, 0.72–2.47) or Zimbabweans (HR, 1.12; 95% CI, 0.65–1.91) from family planning clinics. Conclusions:After adjustment, male circumcision was not significantly associated with women's HIV risk. The potential protection offered by male circumcision for women recruited from high-risk settings warrants further investigation.
β-N-Methylamino-l-alanine (BMAA) Toxicity Is Gender and Exposure-Age Dependent in Rats

Cyanobacterial β-N-methylamino-l-alanine (BMAA) has been suggested as a causative or contributory factor in the development of several neurodegenerative diseases. However, no BMAA animal model has adequately shown clinical or behavioral symptoms that correspond to those seen in either Alzheimer’s Disease (AD), Amyotrophic Lateral Sclerosis (ALS) or Parkinson’s Disease (PD). We present here the first data that show that when neonatal rats were exposed to BMAA on postnatal days 3, 4 and 5, but not on gestational day 14 or postnatally on days 7 or 10, several AD and/or PD-related behavioral, locomotor and cognitive deficits developed. Male rats exhibited severe unilateral hindlimb splay while whole body tremors could be observed in exposed female rats. BMAA-exposed rats failed to identify and discriminate a learned odor, an early non-motor symptom of PD, and exhibited decreased locomotor activity, decreased exploration and increased anxiety in the open field test. Alterations were also observed in the rats’ natural passive defense mechanism, and potential memory deficits and changes to the rat’s natural height avoidance behavior could be observed as early as PND 30. Spatial learning, short-term working, reference and long-term memory were also impaired in 90-day-old rats that had been exposed to a single dose of BMAA on PND 3–7. These data suggest that BMAA is a developmental neurotoxin, with specific target areas in the brain and spinal cord.
A novel phytochemical, digoxigenin-3-O-rutin in the amelioration of isoproterenol-induced myocardial infarction in rat: a comparison with digoxin.

INTRODUCTION The commonly used cardiac glycoside, digoxin (DIG), has a narrow therapeutic window. Although some investigations were made to counteract its toxic effects, no alternate phytochemical is available till date that is more potent and safer than DIG. AIMS Our main aim was to isolate a novel cardenolide from the seeds of Trigonella foenum graceium and to evaluate its relative potential in comparison to that of DIG. EXPERIMENTAL DESIGN In one experiment effects of the isolated compound at 2.5, 5.0, and 10 mg/kg (p.o.) were evaluated in isoproterenol (ISO)-induced cardiovascular problems in rats. As the test drug (TDR) reversed most of the ISO-induced changes, it was subjected to the phytochemical analyses and was identified as digoxigenin-3-O-rutin. In another experiment effects of DIG and rutin (Rtn) were compared with those of TDR or DIG alone. The hydroxyl radical scavenging activity was also measured by electron spin resonance (EPR). RESULTS digoxigenin-3-O-rutin at 10 mg/kg markedly reduced the ISO-induced increase in cardiac lipid peroxidation and in the levels of serum creatinine phosphokinase-MB, glutamate oxaloacetate transaminase, glutamate pyruvate transaminase, lactate dehydrogenase, and creatinine. It also reversed the ISO-induced changes in the cardiac histomorphology. Interestingly TDR appeared to be more effective than DIG alone or DIG and Rtn in combination. CONCLUSION The newly isolated digoxigenin-3-O-rutin appears to be more potent and safe than digoxin. Its higher efficacy could be due to its structural specificity and might have been mediated through its better free radical scavenging action.
Patterns of medication use by chronic and episodic headache sufferers in the general population: Results from the frequent headache epidemiology study

Though symptomatic medication overuse is believed to play a role in progression from episodic headaches (EH) to chronic daily headaches (CDH), population-based data on this topic are limited. Our objective was to describe patterns of medication use among CDH and EH sufferers in a general population sample. We compared medications used to treat headache in CDH cases and EH controls identified from a large population-based computer-assisted telephone interview survey. CDH began within 5 years of the computer-assisted telephone interview. Questions on medication use focused on treatment prior to the onset of CDH for cases and on an equivalent period in the past for controls. We asked about the likelihood of treating, time waiting to treat, number of different medications used, first, second and third most frequently used headache pain medication, and total treatment days. Questions were also asked about the use of medication for non-headache pain. Current treatment patterns and past treatment patterns were assessed. Likelihood of use of specific medications was compared between CDH cases and EH controls after adjusting for age, sex, primary headache type and number of medications taken to treat pain. Our sample consists of 206 CDH cases and 507 EH controls. CDH subjects were more likely than EH controls to use over-the-counter/caffeine combination products, triptans, opioid compounds and ‘other’ prescription pain medications. Use of aspirin was protective. After adjustment, aspirin and ibuprofen were (negatively) associated with CDH [OR = 0.5 (0.3–0.9), OR = 0.7 (0.5–1.0)] and opioids remained positively associated with CDH [OR = 2.3 (1.3–3.9)]. For past use, CDH was positively associated with over-the-counter/caffeine combination products and opioid compounds and was negatively associated with use of aspirin. Only ibuprofen remained (negatively) associated with CDH after adjustment [OR = 0.6 (0.4–0.9)]. After adjusting for demographic factors, primary headache type and number of medications taken, CDH sufferers are more likely to use opioid-combination analgesics, and less likely to use aspirin or ibuprofen, than EH sufferers.
Amino acids augment muscle protein synthesis in neonatal pigs during acute endotoxemia by stimulating mTOR-dependent translation initiation.

In skeletal muscle of adults, sepsis reduces protein synthesis by depressing translation initiation and induces resistance to branched-chain amino acid stimulation. Normal neonates maintain a high basal muscle protein synthesis rate that is sensitive to amino acid stimulation. In the present study, we determined the effect of amino acids on protein synthesis in skeletal muscle and other tissues in septic neonates. Overnight-fasted neonatal pigs were infused with endotoxin (LPS, 0 and 10 microg.kg(-1). h(-1)), whereas glucose and insulin were maintained at fasting levels; amino acids were clamped at fasting or fed levels. In the presence of fasting insulin and amino acids, LPS reduced protein synthesis in longissimus dorsi (LD) and gastrocnemius muscles and increased protein synthesis in the diaphragm, but had no effect in masseter and heart muscles. Increasing amino acids to fed levels accelerated muscle protein synthesis in LD, gastrocnemius, masseter, and diaphragm. LPS stimulated protein synthesis in liver, lung, spleen, pancreas, and kidney in fasted animals. Raising amino acids to fed levels increased protein synthesis in liver of controls, but not LPS-treated animals. The increase in muscle protein synthesis in response to amino acids was associated with increased mTOR, 4E-BP1, and S6K1 phosphorylation and eIF4G-eIF4E association in control and LPS-infused animals. These findings suggest that amino acids stimulate skeletal muscle protein synthesis during acute endotoxemia via mTOR-dependent ribosomal assembly despite reduced basal protein synthesis rates in neonatal pigs. However, provision of amino acids does not further enhance the LPS-induced increase in liver protein synthesis.