Miracle-dz/UniFAR-FTUs huggingface dataset:
Heteroduplex substrates for bacteriophage lambda site‐specific recombination: cleavage and strand transfer products.

Lambda's Int protein acts as a specific topoisomerase at attachment sites, the DNA segments that are required for site‐specific recombination. Int cleaves each strand of an attachment site at a unique place and creates strand exchanges by joining broken ends from two different parents. To study the action of Int topoisomerase in more detail, heteroduplex attachment sites were made by annealing strands that are complementary except for a few base pairs that lie in the region between the points of top and bottom strand exchange in the attachment site core. These heteroduplexes appear to interact normally with Int and its accessory proteins IHF and Xis. Although the heteroduplex sites are specifically cleaved by Int topoisomerase, rejoining of the broken DNA is hindered by the lack of Watson‐‐Crick complementarity adjacent to the break. Because of this, heteroduplexes accumulate broken intermediates which are then processed in novel ways. We have used this feature to provide new information about functional differences between attachment sites, to investigate the way Xis protein controls directionality of site‐specific recombination, and to demonstrate that Int protein can join strands indiscriminately and can therefore generate recombinants with either of two genetic polarities.
Computational Studies of Subtilisin‐Catalyzed Transesterification of Sucrose: Importance of Entropic Effects.

Regioselective acylation of sugars at their hydroxy groups is currently of great importance for the food, chemical, and pharmaceutical industries. Enzymes are very useful for catalysis of these processes owing to their exquisite chemo-, stereo-, and regioselectivity, and subtilisins are among the most researched. One of these specific transformations is the transesterification of sucrose with fatty acid esters with a high selectivity for the 1 position (Figure 1; experimentally, 80 ± 90% of the products are the 1 -product while 2 ± 5% are minor species that are largely monoesters whose acylation positions could not be assigned; there is no available thermodynamic data on these reactions).
Ultrastructural observations on bronchial epithelial hyperplasia and squamous metaplasia

Alterations in rat bronchial epithelium produced by 3‐methylcholanthrene‐coated steel pellets and those resulting from uncoated steel pellets were studied by light and electron microscopy. Exposure to uncoated pellets resulted in increased cell interdigitations, moderate stratification and flattening, and incomplete loss of cilia and polarity. In contrast, carcinogen‐coated pellets produced complete loss of cilia and cell polarity and severe stratification. Increased cell interdigitations and desmosomal junctions as well as abundant cytoplasmic filaments, keratohyalin granules, and “membrane‐coating granules” were also observed. Thus, only contact with a carcinogen produced cells capable of keratin synthesis. We conclude that diagnoses such as basal cell hyperplasia, stratification and flattening, on the one hand, and squamous metaplasia, on the other, should be clearly differentiated. The diagnosis of squamous metaplasia should be made only in the presence of clear evidence of keratin synthesizing cells. Application of such criteria may result in more meaningful clinicopathologic correlations.
Single-Stage Frequency Quadrupler With SBD and Four-Octave LPF at 335 GHz

This paper presents designs of a single-stage quadrupler at 340 GHz based on Schottky varactors with 7 mW maximum output power. The Schottky diode model is invented to improve the accuracy of design, which considers the behaviors of current–voltage (<italic>I</italic>/<italic>V</italic>), capacitance–voltage (<italic>C</italic>/<italic>V </italic>), plasma resonance, self-heating effect, and skin effect of Schottky diodes under deep driven situation into consideration. Compact suspended microstrip resonators (CSMRs) are adopted as harmonic rejection structure with minimized length/width ratio and shorted idlers at both the second and third harmonics. The measurement results indicate that the CSMR low-pass filter has stopband bandwidth of more than four-octave, whose S12 <−10 dB within 140–385 GHz and S11 <−10 dB below 95 GHz. The measured quadrupler output power is above 1 mW at 322–345 GHz, and the measured peak efficiency achieves above 4.2% at 339.2 GHz with 100 mW driven power.
In situ analysis of heterogeneity in the lipid content of single green microalgae in alginate hydrogel microcapsules.

Microalgae, a group of microorganisms that grow using sunlight as the sole energy source and carbon dioxide as an only carbon source, have been considered as a feedstock of choice for the production of biofuels such as biodiesel. To explore the economic feasibility of such application, however, many technical hurdles must first be overcome; the selection and/or screening of competent species are some of the most important and yet challenging tasks. To greatly accelerate this rather slow and laborious step, we developed a droplet-based microfluidic system that uses alginate hydrogel microcapsules with a mean diameter of 26 μm, each of which is able to encapsulate a single microalgal cell. This novel device was successfully demonstrated using three microalgae species, namely, Chlorella vulgaris , Chlamydomonas sp. , and Botryococcus braunii . In situ analysis of the lipid content of individual microalgal cells by nondestructive fluorescence staining using BODIPY (4,4-difluoro-1,3,5,7,-tetramethyl-4-bora-3a,4a-diaza-s-indacene) was possible. In all cases, we confirmed that the lipid content of microalgal species in alginate hydrogel microcapsules was comparable to that of free-living cells. Stochastic heterogeneity in the lipid content was verified under a highly viable physiological condition, implying that other analyses were possible after the determination of lipid content. Furthermore, the designed microwell arrays enabled us to distinguish the BODIPY fluorescence response of a single live alga within the microcapsules.
Least squares parameter estimation methods for material decomposition with energy discriminating detectors.

PURPOSE Energy resolving detectors provide more than one spectral measurement in one image acquisition. The purpose of this study is to investigate, with simulation, the ability to decompose four materials using energy discriminating detectors and least squares minimization techniques. METHODS Three least squares parameter estimation decomposition techniques were investigated for four-material breast imaging tasks in the image domain. The first technique treats the voxel as if it consisted of fractions of all the materials. The second method assumes that a voxel primarily contains one material and divides the decomposition process into segmentation and quantification tasks. The third is similar to the second method but a calibration was used. The simulated computed tomography (CT) system consisted of an 80 kVp spectrum and a CdZnTe (CZT) detector that could resolve the x-ray spectrum into five energy bins. A postmortem breast specimen was imaged with flat panel CT to provide a model for the digital phantoms. Hydroxyapatite (HA) (50, 150, 250, 350, 450, and 550 mg/ml) and iodine (4, 12, 20, 28, 36, and 44 mg/ml) contrast elements were embedded into the glandular region of the phantoms. Calibration phantoms consisted of a 30/70 glandular-to-adipose tissue ratio with embedded HA (100, 200, 300, 400, and 500 mg/ml) and iodine (5, 15, 25, 35, and 45 mg/ml). The x-ray transport process was simulated where the Beer-Lambert law, Poisson process, and CZT absorption efficiency were applied. Qualitative and quantitative evaluations of the decomposition techniques were performed and compared. The effect of breast size was also investigated. RESULTS The first technique decomposed iodine adequately but failed for other materials. The second method separated the materials but was unable to quantify the materials. With the addition of a calibration, the third technique provided good separation and quantification of hydroxyapatite, iodine, glandular, and adipose tissues. Quantification with this technique was accurate with errors of 9.83% and 6.61% for HA and iodine, respectively. Calibration at one point (one breast size) showed increased errors as the mismatch in breast diameters between calibration and measurement increased. A four-point calibration successfully decomposed breast diameter spanning the entire range from 8 to 20 cm. For a 14 cm breast, errors were reduced from 5.44% to 1.75% and from 6.17% to 3.27% with the multipoint calibration for HA and iodine, respectively. CONCLUSIONS The results of the simulation study showed that a CT system based on CZT detectors in conjunction with least squares minimization technique can be used to decompose four materials. The calibrated least squares parameter estimation decomposition technique performed the best, separating and accurately quantifying the concentrations of hydroxyapatite and iodine.
The innervation of rainbow trout (Oncorhynchus mykiss) liver: protein gene product 9.5 and neuronal nitric oxide synthase immunoreactivities

We have explored the innervation of the rainbow trout (O. mykiss) liver using immunohistochemical procedures and light microscopy to detect in situ protein gene product 9.5 and neuronal nitric oxide synthase immunoreactivities (PGP‐IR and NOS‐IR). The results showed PGP‐IR nerve fibres running with the extralobular biliary duct (EBD), hepatic artery (EHA) and portal vein (EPV) that form the hepatic hilum, as well as following the spatial distribution of the intrahepatic blood vessel and biliary channels. These nerve fibres appear as single varicose processes, thin bundles, or thick bundles depending on their diameter and location in the wall of the blood vessel or biliary duct. No PGP‐IR fibres were detected in the liver parenchyma. NOS‐IR nerve fibres were located only in the vessels and ducts that form the hepatic hilum (EBD, EHA, EPV); in addition, NOS‐IR nerve cell bodies were found isolated or forming ganglionated plexuses in the peribiliary fibromuscular tissue of the EBD. No PGP‐IR ganglionated plexuses were detected in the EBD. The location of the general (PGP‐IR) and nitrergic (nNOS‐IR) intrinsic nerves of the trout liver suggest a conserved evolutionary role of the nervous control of hepatic blood flow and hepatobiliary activity.
Utility and pitfalls of immunohistochemistry in the differential diagnosis between epithelioid mesothelioma and poorly differentiated lung squamous cell carcinoma

The aims of this study were to clarify the usefulness of immunohistochemistry in the differential diagnosis of epithelioid mesothelioma with a solid growth pattern [solid epithelioid mesothelioma (SEM)] and poorly differentiated squamous cell carcinoma (PDSCC), and to confirm the validity of a specific type of antibody panel. Additionally, we aimed to clarify the pitfalls of immunohistochemical analyses.
PTP and LTP at a hippocampal mossy fiber-interneuron synapse

The mossy fiber-CA3 pyramidal neuron synapse is a main component of the hippocampal trisynaptic circuitry. Recent studies, however, suggested that inhibitory interneurons are the major targets of the mossy fiber system. To study the regulation of mossy fiber-interneuron excitation, we examined unitary and compound excitatory postsynaptic currents in dentate gyrus basket cells, evoked by paired recording between granule and basket cells or extracellular stimulation of mossy fiber collaterals. The application of an associative high-frequency stimulation paradigm induced posttetanic potentiation (PTP) followed by homosynaptic long-term potentiation (LTP). Analysis of numbers of failures, coefficient of variation, and paired-pulse modulation indicated that both PTP and LTP were expressed presynaptically. The Ca2+ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid (BAPTA) did not affect PTP or LTP at a concentration of 10 mM but attenuated LTP at a concentration of 30 mM. Both forskolin, an adenylyl cyclase activator, and phorbolester diacetate, a protein kinase C stimulator, lead to a long-lasting increase in excitatory postsynaptic current amplitude. H-89, a protein kinase A inhibitor, and bisindolylmaleimide, a protein kinase C antagonist, reduced PTP, whereas only bisindolylmaleimide reduced LTP. These results may suggest a differential contribution of protein kinase A and C pathways to mossy fiber-interneuron plasticity. Interneuron PTP and LTP may provide mechanisms to maintain the balance between synaptic excitation of interneurons and that of principal neurons in the dentate gyrus-CA3 network.
Historical and Material Approach to the Paintings at the Portugal National Library: Contributions to the History of Conservation and Restoration of Easel Painting in the 19th Century

There are in the National Library of Portugal (BNP) about fifty paintings from former convents, mainly portraits executed between the sixteenth and nineteenth centuries, which are hung in rooms and along corridors, far from the eyes of the public and simultaneously protected by recent conservation and restoration interventions. These paintings, of little artistic interest, are, however, individual cases for the study of conservation and restoration interventions made in the nineteenth century. The data obtained will contribute to the history of paintings restoration, in terms of its practical aspects (about materials and techniques used), that is still to be written in Portugal.Our research, which began in January 2011 and is predicted to end in December 2013, has been oriented by three complementary lines of action, with an interdisciplinary methodological base: the exploitation of the BNP's precious and unpublished documental archive; the assessment to the conservation status of the paintings and identi.
Desfronde y tasa de Descomposición foliar en rebollar-pinar de repoblación con distinto grado de clara

El desfronde representa un factor clave en el funcionamiento de los ecosistemas forestales. Por un lado representa el mayor aporte de nutrientes en sistemas naturales y, por otro, su acumulacion en el suelo constituye un banco de elementos esenciales que, por descomposicion y mineralizacion, se integran en el suelo y en los ciclos biogeoquimicos. Este trabajo analiza el efecto de la clara en la produccion de desfronde, la eficiencia en el uso del nitrogeno y en la tasa de descomposicion de la hojarasca en una masa mixta de Pinus pinaster Ait. procedente de repoblacion sobre una masa natural de Quercus pyrenaica Wild. El sitio experimental esta situado en los Montes de Toledo y consta de tres tratamientos: control, clara moderada y clara fuerte con tres replicas en un diseno de cuadrado latino. Los datos de desfronde proceden de recogida mensual en cestos y separacion en fracciones para el calculo de la materia seca. El nitrogeno se analizo en muestras compuestas cada tres meses. Para el estudio de la tasa de descomposicion se utilizaron bolsas con mezcla de aciculas y hojas, recolectandose y analizandose tambien cada tres meses. Los resultados muestran picos de desfronde en los meses de verano y en el otono. La mayor produccion de desfronde se observa en las parcelas testigo. La aplicacion de las claras no supone grandes diferencias ni en el desfronde ni en la eficencia en el uso del nitrogeno. Por el contrario las claras ralentizan la tasa de descomposicion de las hojas de rebollo.
Remating and sperm displacement in a natural population of Drosophila buzzatii inferred from mother–offspring analysis of microsatellite loci

Prospects for estimation of parameters of models of sperm competition from field data have improved recently with the development of methods that employ multilocus genotype data from brood‐structured samples. Sperm competition in Drosophila buzzatii is of special interest because it is possible to directly observe the breeding behaviour of this species in its natural habitat of rotting cactus. Previous laboratory experiments showed that this species exhibits an unusual pattern of frequent remating and sperm partitioning. This paper reports the first attempt to estimate the frequency of female remating and sperm competition in natural populations of D. buzzatii. For the Australian population studied, the mean remating frequency was lower (α = 2.12–2.20) than previously estimated in laboratory experiments with the same population, whereas mean sperm displacement (β = 0.69–0.71) fell within the limits of previous laboratory results. The evolution of the D. buzzatii mating system is discussed.
Economic Growth, Financial Development, and Income Inequality

ABSTRACT The central objective of our article is to empirically examine the relationship between financial development and income inequality. Theoretically, there are grounds for both a positive and negative relationship between the two variables. Our main finding is that financial development contributes to lower inequality up to a point, but as financial development proceeds further, it contributes to higher inequality. We also find that when the ratio of primary schooling to total schooling increases and law and order improves, financial development becomes more effective in reducing inequality. Finally, we find that financial inclusion is particularly effective in lowering income inequality.
Lower Limb Interjoint Postural Coordination One Year after First-Time Lateral Ankle Sprain.

INTRODUCTION Longitudinal analyses of participants with a history of lateral ankle sprain are lacking. This investigation combined measures of lower limb interjoint coordination and stabilometry to evaluate static unipedal stance with the eyes open (condition 1) and closed (condition 2) in a group of participants with chronic ankle instability (CAI) compared to lateral ankle sprain "copers" (both recruited 12 months after sustaining an acute first-time lateral ankle sprain) and a group of noninjured controls. METHODS Twenty-eight participants with CAI, 42 lateral ankle sprain "copers," and 20 noninjured controls completed three 20-s single-limb stance trials in conditions 1 and 2. An adjusted coefficient of multiple determination statistic was used to compare stance limb three-dimensional kinematic data for similarity to establish patterns of interjoint coordination. The fractal dimension of the stance limb center of pressure path was also calculated. RESULTS Between-group analyses revealed that participants with CAI displayed notable increases in ankle-hip linked coordination compared with both lateral ankle sprain "copers" (-0.52 (1.05) vs 0.28 (0.9), P = 0.007) and controls (-0.52 (1.05) vs 0.63 (0.64), P = 0.006) in condition 1 and compared with controls only (0.62 (1.92) vs 0.1 (1.0) P = 0.002) in condition 2. Participants with CAI also exhibited a decrease in the fractal dimension of the center-of-pressure path during condition 2 compared with both controls and lateral ankle sprain "copers. " CONCLUSIONS Participants with CAI present with a hip-dominant strategy of eyes-open and eyes-closed static unipedal stance. This coincided with reduced complexity of the stance limb center of pressure path in the eyes-closed condition.
Clinical testing of accommodative facility: Part 1. A critical appraisal of the literature.

BACKGROUND Accommodative facility testing is used in clinical care to assess functioning of the ocular accommodative system. The current clinical standard (binocular assessment using +/- 2.00 D lenses at 40 cm with a vectographic suppression check) was first described nearly 20 years ago as part of the last comprehensive review of the literature. The standard accommodative facility test imposes a variable requirement on patients of different ages who have a wide range of accommodative amplitudes. METHOD In this article, we critically reviewthe present body of literature on accommodative facility testing, with emphasis on the relation between symptoms, accommodative amplitude, and the results found during accommodative facility testing. RESULT We include discussion of the five broad categories of accommodative facility studies: (11 recommendations for testing criteria; (2) normative data investigations; (3) reliability and variability assessment; (4) relation between accommodative facility and symptoms; and (5) other relationships (e.g., effect of test parameters on accommodative facility). CONCLUSION Given the substantial variation in demand when testing patients of different ages (amplitudes), it is not surprising that a significant variation in responses has been reported in the clinical accommodative facility literature. Future clinical investigation of accommodative facility would benefit from a systematic investigation into the relationship between age and amplitude. The presence or absence of symptoms needs to be considered so that results of testing can be analyzed in relation to the severity of binocular vision-related symptoms.
A model‐free approach to eliminate autocorrelation when testing for process capability

There is an increasing use of on‐line data acquisition systems in industry. This usually leads to autocorrelated data and implies that the assumption of independent observations has to be re‐examined. Most decision procedures for capability analysis assume independent data. In this article we present a new way of performing capability analysis when data are autocorrelated. This method is based on what can be called the ‘iterative skipping’ strategy. In that, by skipping a pre‐determined number of observations, e.g. considering every fifth observation, the data set is divided into subsamples for which the independence assumption may be valid. For each such subsample of the data we estimate a capability index. Then traditional tests, assuming independence, can be performed based on each estimated capability index from the subsamples. By combining the information from each test statistic based on the subsamples in a suitable way, a new and efficient decision procedure is obtained. We discuss different ways of combining the information from these individual tests. A main appeal of our proposed method is that no time‐series model is needed. Copyright © 2007 John Wiley & Sons, Ltd.
The Yeast Pdr15p ATP-binding Cassette (ABC) Protein Is a General Stress Response Factor Implicated in Cellular Detoxification*

ATP-binding cassette (ABC) transporters play important roles in drug efflux, but some may also function in cellular detoxification. The Pdr15p ABC protein is the closest homologue of the multidrug efflux transporter Pdr5p, which mediates pleiotropic drug resistance to hundreds of unrelated compounds. In this study, we show that the plasma membrane protein Pdr15p displays limited drug transport capacity, mediating chloramphenicol and detergent tolerance. Interestingly, Pdr15p becomes most abundant when cells exit the exponential growth phase, whereas its closest homologue, Pdr5p, disappears after exponential growth. Furthermore, in contrast to Pdr5p, Pdr15p is strongly induced by various stress conditions including heat shock, low pH, weak acids, or high osmolarity. PDR15 induction bypasses the Pdr1p/Pdr3p regulators but requires the general stress regulator Msn2p, which directly decorates the stress response elements in the PDR15 promoter. Remarkably, however, Pdr15p induction bypasses upstream components of the high osmolarity glycerol (HOG) pathway including the Hog1p and Pbs2p kinases as well as the dedicated HOG cell surface sensors. Our data provide evidence for a novel upstream branch of the general stress response pathway activating Msn2p. In addition, the results demonstrate a cross-talk between stress response and the pleiotropic drug resistance network.