Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis of Chlorophyll-Binding Proteins in a Fully Segregated Δycf54 Strain of the Cyanobacterium Synechocystis PCC 6803

In the chlorophyll (Chl) biosynthesis pathway the formation of protochlorophyllide is catalyzed by Mg-protoporphyrin IX methyl ester (MgPME) cyclase. The Ycf54 protein was recently shown to form a complex with another component of the oxidative cyclase, Sll1214 (CycI), and partial inactivation of the ycf54 gene leads to Chl deficiency in cyanobacteria and plants. The exact function of the Ycf54 is not known, however, and further progress depends on construction and characterization of a mutant cyanobacterial strain with a fully inactivated ycf54 gene. Here, we report the complete deletion of the ycf54 gene in the cyanobacterium Synechocystis 6803; the resulting Δycf54 strain accumulates huge concentrations of the cyclase substrate MgPME together with another pigment, which we identified using nuclear magnetic resonance as 3-formyl MgPME. The detection of a small amount (~13%) of Chl in the Δycf54 mutant provides clear evidence that the Ycf54 protein is important, but not essential, for activity of the oxidative cyclase. The greatly reduced formation of protochlorophyllide in the Δycf54 strain provided an opportunity to use 35S protein labeling combined with 2D electrophoresis to examine the synthesis of all known Chl-binding protein complexes under drastically restricted de novo Chl biosynthesis. We show that although the Δycf54 strain synthesizes very limited amounts of photosystem I and the CP47 and CP43 subunits of photosystem II (PSII), the synthesis of PSII D1 and D2 subunits and their assembly into the reaction centre (RCII) assembly intermediate were not affected. Furthermore, the levels of other Chl complexes such as cytochrome b6f and the HliD– Chl synthase remained comparable to wild-type. These data demonstrate that the requirement for de novo Chl molecules differs completely for each Chl-binding protein. Chl traffic and recycling in the cyanobacterial cell as well as the function of Ycf54 are discussed.
On the complexity of asynchronous gossip

In this paper, we study the complexity of gossip in an asynchronous, message-passing fault-prone distributed system. In short, we show that an adaptive adversary can significantly hamper the spreading of a rumor, while an oblivious adversary cannot. This latter fact implies that there exist message-efficient asynchronous (randomized) consensus protocols, in the context of an oblivious adversary. In more detail, we summarize our results as follows. If the adversary is adaptive, we show that a randomized asynchronous gossip algorithm cannot terminate in fewer than O(f(d + delta)) time steps unless Omega(n+f2) messages are exchanged, where n is the total number of processes, f is the number of tolerated crash failures, d is the maximum communication delay for the specific execution in question, and delta is the bound on relative process speeds in the specific execution. The lower bound result is to be contrasted with deterministic synchronous gossip algorithms that, even against an adaptive adversary, require only O(polylog n) time steps and O(n polylog n) messages. In the case of an oblivious adversary, we present three different randomized, asynchronous algorithms that provide different trade-offs between time complexity and message complexity. The first algorithm is based on the epidemic paradigm, and completes in O(n / (n-f) log2 n (d + δ)) time steps using O(n log3 n (d + δ)) messages, with high probability. The second algorithm relies on more rapid dissemination of the rumors, yielding a constant-time (w.r.t. n) gossip protocol: for every constant epsilon < 1, and for f ≤ n/2, there is a variant with time complexity O((1 / ε)(d+δ)) and message complexity O((1/ε)n1+εlog n (d+δ)). The third algorithm solves a weaker version of the gossip problem in which each process receives at least a majority of the rumors. This algorithm achieves constant O(d+δ) time complexity and message complexity O(n7/4 log2 n). As an application of these message-efficient gossip protocols, we present three randomized consensus protocols. Our consensus algorithms derive from combining each of our gossip protocols with the Canetti-Rabin framework, resulting in message-efficient consensus algorithms. The resulting protocols have time and message-complexity asymptotically equal to our gossip protocols. We particularly highlight the third consensus protocol, a result that is interesting in its own right: the first asynchronous randomized consensus algorithm with strictly subquadradic message-complexity, i.e., O(n7/4 log2 n).
Experimental study on lossless compression of biometric iris data

The impact of using different lossless compression algorithms when compressing biometric iris sample data from several public iris databases is investigated. In particular, we relate the application of dedicated lossless image codecs like lossless JPEG, JPEG-LS, PNG, and GIF, lossless variants of lossy codecs like JPEG2000, JPEG XR, and SPIHT, and a few general purpose compression schemes to rectilinear iris imagery. The results are discussed in the light of the recent ISO/IEC FDIS 19794-6 and ANSI/NIST-ITL 1-2011 standards and the IREX recommendations.
NONPARAMETRIC IDENTIFICATION OF PHARMACOKINETIC POPULATION MODELS VIA GAUSSIAN PROCESSES

Abstract Population models are used to describe the behaviour of different subjects belonging to a population and play an important role in drug pharmacokinetics. A nonparametric identification scheme is proposed in which both the average population response and the individual ones are modelled as Gaussian stochastic processes. Assuming that the average curve is an integrated Wiener process, it is shown that its estimate is a cubic spline. An Empirical Bayes (EB) algorithm for estimating both the typical and the individual curves is worked out. The model is tested on xenobiotics pharmacokinetic data.
On the Growth Rate of Non-Enzymatic Molecular Replicators

It is well known that non-enzymatic template directed molecular replicators X + nO ---> 2X exhibit parabolic growth d[X]/dt = k [X]^{1/2}. Here, we analyze the dependence of the effective replication rate constant k on hybridization energies, temperature, strand length, and sequence composition. First we derive analytical criteria for the replication rate k based on simple thermodynamic arguments. Second we present a Brownian dynamics model for oligonucleotides that allows us to simulate their diffusion and hybridization behavior. The simulation is used to generate and analyze the effect of strand length, temperature, and to some extent sequence composition, on the hybridization rates and the resulting optimal overall rate constant k. Combining the two approaches allows us to semi-analytically depict a fitness landscape for template directed replicators. The results indicate a clear replication advantage for longer strands at low temperatures.
The Ovarian Reserve of Primordial Follicles and the Dynamic Reserve of Antral Growing Follicles: What Is the Link?1

ABSTRACT The growing follicles develop from a reserve of primordial follicles constituted early in life. From this pre-established reserve, a second ovarian reserve is formed, which consists of gonadotropin-responsive small antral growing follicles and is a dynamic reserve for ovulation. Its size, evaluated by direct antral follicular count or endocrine markers, determines the success of assisted reproductive technologies in humans and embryo production biotechnologies in animals. Strong evidence indicates that these two reserves are functionally related. The size of both reserves appears to be highly variable between individuals of similar age, but the equilibrium size of the dynamic reserve in adults seems to be specific to each individual. The dynamics of both follicular reserves appears to result from the fine tuning of regulations involving two main pathways, the phosphatase and tensin homolog (PTEN)/phosphatidylinositol-3 kinase (PI3K)/3-phosphoinositide-dependent protein kinase-1 (PDPK1)/v-akt murine thymoma viral oncogene homolog 1 (AKT1) and the bone morphogenetic protein (BMP)/anti-Müllerian hormone (AMH)/SMAD signaling pathways. Mutations in genes encoding the ligands, receptors, or signaling effectors of these pathways can accelerate or modulate the exhaustion rate of the ovarian reserves, causing premature ovarian insufficiency (POI) or increase in reproductive longevity, respectively. With female aging, the decline in primordial follicle numbers parallels the decrease in the size of the dynamic reserve of small antral follicles and the deterioration of oocyte quality. Recent progress in our knowledge of signaling pathways and their environmental and hormonal control during adult and fetal life opens new perspectives to improve the management of the ovarian reserves.
Management of NSAID induced gastrointestinal disturbance.

From the 'Department of Rheumatology, Nottingham City Hospital; the 2Division of Gastroenterology, McMaster University Medical Centre, Hamilton, Ontario, Canada; the 3Queens Medical Centre, Nottingham; the 4Academic Department of Medicine, Royal Free Hospital, London; the 5Department of Gastroenterology, Glasgow Royal Infirmary; the 6Centre for Rheumatic Diseases, Glasgow Roval Infirmary; and the 7Department of Rheumatology, Royal Cornwall Hospital, Truro
Syllable Weight, Stress Patterns and Nativisation

This paper looks at stress assignation for unknown foreign words read aloud by Scottish subjects. The syllable structure and syllable weight of the written words is examined, to determine where stress is most likely to be placed according to English stress rules, and the stress rules for the languages of origin of the words are also described. The stress patterns in the spoken responses are then analysed to determine the innuence of syllable weight (both written and spoken), and the perceived language of origin of the word. Applicability of the ndings to a wider context is discussed.
Optimal Power Allocation for Distributed Detection in Wireless Sensor Networks

In distributed detection systems with wireless sensor networks, communication between sensors and a fusion center is not perfect due to interference and limited communication power of the sensors to combat noise. The problem of optimizing detection performance with imperfect communication between the sensors and the fusion center over wireless channels brings a new challenge to distributed detection. In this paper, a distributed detection system infrastructure is provided, and a multiaccess channel model is included to account for imperfect communication between the sensors and the fusion center. The J-divergence between the distributions of the detection statistic under different hypotheses is used as a performance criterion in order to provide a tractable analysis. Optimizing the performance (in terms of the J-divergence) under a total communication power constraint on the sensors is studied, and the corresponding optimal power allocation scheme is provided. It is interesting to see that, for the case with orthogonal channels, the power allocation can be solved by a weighted water-filling algorithm. Numerical results are used to illustrate the solution.
The Basin and Range Province

A fuel injection nozzle for internal combustion engines includes a nozzle holder. A pressure channel leads, in sections, to a nozzle pressure chamber, along a spring chamber and passes eccentrically in the nozzle holder. The pressure channel has a connecting bore passing radially to the longitudinal axis of the nozzle holder. A drain channel of the spring chamber passes in the vicinity of a pressure channel connection bore in a longitudinal direction of the nozzle holder. An intersection is provided between the pressure channel and the drain channel. A pressure socket is arranged in the connecting bore for separating the pressure channel and the drain channel. An end portion of the socket protrudes into the nozzle holder axially before and after the intersection. Sealing members are provided in each side of the intersection, and a recess means having a surface and defining a passageway for leak channel traverse flow is provided in the intersection.
Influence of hypotensive drugs on lipopolysaccharide ( LPS )-induced serum concentrations of tumor necrosis factor alpha ( TNF-) , interleukin ( IL )-1 , IL-6 in spontaneously hypertensive rats ( SHR )

A growing body of evidence suggests that some drugs used in cardiovascular diseases may modulate the level of proinflammatory cytokines. Therefore, we have investigated whether propranolol, doxazosin, amlodipine and indapamide can influence lipopolysaccharide (LPS)-induced serum concentrations of tumor necrosis factor alpha (TNF), interleukin (IL)-1 and IL-6 in spontaneously hypertensive rats (SHR). The animals were divided into five groups as follows: SHR + MET (control rats receiving 1% solution of methylcellulose), SHR + PROP (rats receiving propranolol – 40 mg/kg), SHR + DOX (rats receiving doxazosin – 10 mg/kg), SHR + AML (rats receiving amlodipine – 25 mg/kg) and SHR + IND (rats receiving indapamide – 1.5 mg/kg). Solution of methylcellulose (1%) and hypotensive drugs were administered by a gavage once a day for 21 days. Arterial blood pressure was measured in conscious rats, using the tail-cuff method. Serum TNF, IL-1 and IL-6 concentrations were measured with enzyme-linked immunosorbent assay kits. Additionally, total cholesterol and high density lipoproteins (HDL) cholesterol were evaluated. Propranolol and amlodipine significantly decreased LPS-stimulated TNFlevel after 21 days of administration in SHR. Three-week administration of propranolol, amlodipine and indapamide lowered IL-1 serum concentration after LPS stimulation. Doxazosin caused a significant increase of the IL-6 serum concentration in SHR. The results were accompanied by a statistically significant decrease in systolic, diastolic and medium blood pressure after 21 days of administration for propranolol and amlodipine. Indapamide lowered diastolic and medium blood pressure while doxazosin only diastolic blood pressure after 21 days. Hypotensive drugs showed no effect on lipid level. The present data indicate that hypotensive drugs possess additional properties, beyond their most commonly known mechanism of action. The elucidation of interactions between hypotensive drugs and cytokines could be of great importance in cardiovascular diseases (e.g. atherosclerosis).
Performance of the compensation comparison method for retinal straylight measurement: effect of patient’s age on repeatability

Aim: The assessment of repeatability and reproducibility of retinal straylight measurements with the C-Quant straylight meter (Oculus AG, Germany) and the effect of patient’s age on the instrument performance are tested with a series of experiments. Methods: First, 20 eyes from 20 subjects (mean age 26.9 (SD 2.7) years, mean refractive error −1.34 (2.72) D) were examined with the C-Quant straylightmeter, taking 10 consecutive readings. Five subjects were also examined on five consecutive days to assess reproducibility. Additionally, repeated measures of straylight from 84 subjects of ages ranging from 19 to 86 years (mean (SD): 42.4 (24.0) years) were retrospectively analysed to assess the effect of patient’s age on repeatability. Results: The results failed to show significant differences between the readings taken within the same session (mean (0.07), p>0.05) or between sessions (mean (0.05), p>0.05). Variability of intrasession measurements was not significant for subjects of different age (p = 0.094). Conclusion: It may be concluded that the C-Quant straylightmeter is repeatable and reliable for the assessment of retinal straylight in human eyes. Age of the patient does not decrease repeatability, even though they feel more insecure about their ability to perform the test.
Raman spectroscopic investigation of chondroitinase ABC treatment after spinal cord injury in an organotypic model

This study investigated (1) the ability of an organotypic model of spinal cord injury (SCI) to recapitulate significant pathobiological events of in vivo SCI from a Raman spectroscopic perspective, and (2) the Raman spectroscopic effects of chondroitinase ABC (cABC) treatment on said model of SCI. Tissue from mouse spinal cords was excised, sectioned, and placed into culture, before being systematically injured to induce trauma. Cultures with and without cABC treatment were assessed using Raman spectroscopy at varying times post-injury. We demonstrate that Raman spectral phenomena characteristic of SCI can be observed using an organotypic model. By comparing these phenomena with well-known cellular mechanisms of SCI, we hypothesize their correlation with apoptosis, demyelination, and upregulation of endogenous biochemicals, such as chondroitin sulfate proteoglycans (CSPGs), among others. Furthermore, we demonstrate for the first time that Raman spectral phenomena are discernable during cABC treatment of SCI. Observed spectral variations correlate to the enzymatic degradation of CSPGs, protein compositional changes, and remyelination. Multivariate regression modeling confirms changes in lipid and chondroitin sulfate concentration during SCI and its cABC treatment, and provides a semi-quantitative measure of these changes. Overall, these data establish Raman spectroscopy as a viable resource for monitoring cABC treatment of SCI. RAMAN SPECTROSCOPIC INVESTIGATION OF CHONDROITINASE ABC TREATMENT AFTER SPINAL CORD INJURY IN AN ORGANOTYPIC MODEL
Improving Hybrid Vehicle Fuel Efficiency Using Inverse Reinforcement Learning

Deciding what mix of engine and battery power to use is critical to hybrid vehicles' fuel efficiency. Current solutions consider several factors such as the charge of the battery and how efficient the engine operates at a given speed. Previous research has shown that by taking into account the future power requirements of the vehicle, a more efficient balance of engine vs. battery power can be attained. In this paper, we utilize a probabilistic driving route prediction system, trained using Inverse Reinforcement Learning, to optimize the hybrid control policy. Our approach considers routes that the driver is likely to be taking, computing an optimal mix of engine and battery power. This approach has the potential to increase vehicle power efficiency while not requiring any hardware modification or change in driver behavior. Our method outperforms a standard hybrid control policy, yielding an average of 1.22% fuel savings.
TRPA1‐mediated responses in trigeminal sensory neurons: interaction between TRPA1 and TRPV1

The transient receptor potential (TRP)A1 channel is involved in the transduction of inflammation‐induced noxious stimuli from the periphery. Previous studies have characterized the properties of TRPA1 in heterologous expression systems. However, there is little information on the properties of TRPA1‐mediated currents in sensory neurons. A capsaicin‐sensitive subset of rat and mouse trigeminal ganglion sensory neurons was activated with TRPA1‐specific agonists, mustard oil and the cannabinoid WIN55,212. Mustard oil‐ and WIN55,212‐gated currents exhibited marked variability in their kinetics of activation and acute desensitization. TRPA1‐mediated responses in neurons also possess a characteristic voltage dependency with profound outward rectification that is influenced by extracellular Ca2+ and the type and concentration of TRPA1‐specific agonists. Examination of TRPA1‐mediated responses in TRPA1‐containing cells indicated that the features of neuronal TRPA1 are not duplicated in cells expressing only TRPA1 and, instead, can be restored only when TRPA1 and TRPV1 channels are coexpressed. In summary, our results suggest that TRPA1‐mediated responses in sensory neurons have distinct characteristics that can be accounted for by the coexpression of the TRPV1 and TRPA1 channels.
Errors in the medication process: frequency, type, and potential clinical consequences.

OBJECTIVE To investigate the frequency, type, and consequences of medication errors in more stages of the medication process, including discharge summaries. DESIGN A cross-sectional study using three methods to detect errors in the medication process: direct observations, unannounced control visits, and chart reviews. With the exception of errors in discharge summaries all potential medication error consequences were evaluated by physicians and pharmacists. SETTING A randomly selected medical and surgical department at Aarhus University Hospital, Denmark. STUDY PARTICIPANTS Eligible in-hospital patients aged 18 or over (n = 64), physicians prescribing drugs and nurses dispensing and administering drugs. MAIN OUTCOME MEASURES Frequency, type, and potential clinical consequences of all detected errors compared with the total number of opportunities for error. RESULTS We detected a total of 1065 errors in 2467 opportunities for errors (43%). In worst case scenario 20-30% of all evaluated medication errors were assessed as potential adverse drug events. In each stage the frequency of medication errors were-ordering: 167/433 (39%), transcription: 310/558 (56%), dispensing: 22/538 (4%), administration: 166/412 (41%), and finally discharge summaries: 401/526 (76%). The most common types of error throughout the medication process were: lack of drug form, unordered drug, omission of drug/dose, and lack of identity control. CONCLUSION There is a need for quality improvement, as almost 50% of all errors in doses and prescriptions in the medication process were caused by missing actions. We assume that the number of errors could be reduced by simple changes of existing procedures or by implementing automated technologies in the medication process.
Elevated levels of serum uric acid, creatinine or urea in preeclamptic women

Background: Hypertensive disorders of human pregnancy, such as preeclampsia, complicate a sizeable percentage of all pregnancies, needing its early indication and warning. Aim of the Study: To measure and compare serum uric acid, serum creatinine and serum urea in preeclamptic and normotensive groups. Materials and Methods: This is a cross-sectional, hospital based study involving 105 age – matched women of South India (devoid of diabetes, urinary tract infections, renal or liver disorders), all in their third trimester singleton pregnancy, at the Obstetrics and Gynecology Department of Sri Ramachandra Medical College and Hospital, Chennai, India during the period of December 2008 to July 2009. The data were collected following standard procedures and statistical analysis was done using unpaired t – test. Results: The levels of serum uric acid and serum creatinine, expressed in mg/ dL were significantly elevated in preeclamptics respectively (5.29 ± 0.84 and 0.72 ± 0.387) when compared to normotensives (3.86 ± 0.92 and 0.58 ± 0.283). There was a statistically insignificant and small increase in serum urea level in preeclamptics (28.07 ± 4.97) compared to normotensives (26.46 ± 3.55). There was a lack of any correlation between the positive differences in the values of each parameter with the extent of corresponding raised blood pressure. Conclusions: the elevated values of uncorrelated serum uric acid, serum creatinine or serum urea thus precludes them to be useful for consideration as consistent predictive indicator(s) for preeclampsia or pregnancy related hypertension.
Perception and Attention for Visualization

Perception and Attention for Visualization By STEVE HAROZ B.S. (Clemson University) 2004 DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Computer Science in the OFFICE OF GRADUATE STUDIES of the UNIVERSITY OF CALIFORNIA DAVIS Approved: David Whitney, Chair Michael Neff Ken Joy Committee in Charge i