Miracle-dz/UniFAR-FTUs huggingface dataset:
Assembly of nuclear DNA‐encoded subunits into mitochondrial complex IV, and their preferential integration into supercomplex forms in patient mitochondria

Complex IV is the terminal enzyme of the mitochondrial respiratory chain. In humans, biogenesis of complex IV involves the coordinated assembly of 13 subunits encoded by both mitochondrial and nuclear genomes. The early stages of complex IV assembly involving mitochondrial DNA‐encoded subunits CO1 and CO2 have been well studied. However, the latter stages, during which many of the nuclear DNA‐encoded subunits are incorporated, are less well understood. Using in vitro import and assembly assays, we found that subunits Cox6a, Cox6b and Cox7a assembled into pre‐existing complex IV, while Cox4‐1 and Cox6c subunits assembled into subcomplexes that may represent rate‐limiting intermediates. We also found that Cox6a and Cox7a are incorporated into a novel intermediate complex of approximately 250 kDa, and that transition of subunits from this complex to the mature holoenzyme had stalled in the mitochondria of patients with isolated complex IV deficiency. A number of complex IV subunits were also found to integrate into supercomplexes containing combinations of complex I, dimeric complex III and complex IV. Subunit assembly into these supercomplexes was also observed in mitochondria of patients in whom monomeric complex IV was selectively reduced. We conclude that newly imported nuclear DNA‐encoded subunits can integrate into the complex IV holoenzyme and supercomplex forms by associating with pre‐existing subunits and intermediate assembly complexes.
Molecular Interaction between Lipoteichoic Acids and Lactobacillus delbrueckii Phages Depends on d-Alanyl and α-Glucose Substitution of Poly(Glycerophosphate) Backbones

ABSTRACT Lipoteichoic acids (LTAs) have been shown to act as bacterial counterparts to the receptor binding proteins of LL-H, LL-H host range mutant LL-H-a21, and JCL1032. Here we have used LTAs purified by hydrophobic interaction chromatography from different phage-resistant and -sensitive strains of Lactobacillus delbrueckii subsp. lactis. Nuclear magnetic resonance analyses revealed variation in the degree of α-glucosyl and d-alanyl substitution of the 1,3-linked poly(glycerophosphate) LTAs between the phage-sensitive and phage-resistant strains. Inactivation of phages was less effective if there was a high level of d-alanine residues in the LTA backbones. Prior incubation of the LTAs with α-glucose-specific lectin inhibited the LL-H phage inactivation. The overall level of decoration or the specific spatial combination of α-glucosyl-substituted, d-alanyl-substituted, and nonsubstituted glycerol residues may also affect phage adsorption.
Chile's Rapid Growth in the 1990s Good Policies, Good Luck, or Political Change?

Chile's average economic growth between 1990 and 1998 was above 7 percent per year, more than double than in previous decades, and higher than in any other Latin American country in the same period. This paper assesses empirically the main hypotheses suggested in the literature about the factors underlying this rapid growth: good economic policies, good luck in the external sector, and the country`s return to a democratic system of government. The statistical and quantitative results indicate that Chile's rapid growth during the 1990s was due to good policies and the improved political situation.
Association of a Chromosomal Rearrangement Event with Mouse Posterior Polymorphous Corneal Dystrophy and Alterations in Csrp2bp, Dzank1, and Ovol2 Gene Expression

We have previously described a mouse model of human posterior polymorphous corneal dystrophy (PPCD) and localized the causative mutation to a 6.2 Mbp region of chromosome 2, termed Ppcd1. We now show that the gene rearrangement linked to mouse Ppcd1 is a 3.9 Mbp chromosomal inversion flanked by 81 Kbp and 542 bp deletions. This recombination event leads to deletion of Csrp2bp Exons 8 through 11, Dzank1 Exons 20 and 21, and the pseudogene Znf133. In addition, we identified translocation of novel downstream sequences to positions adjacent to Csrp2bp Exon 7 and Dzank1 Exon 20. Twelve novel fusion transcripts involving Csrp2bp or Dzank1 linked to downstream sequences have been identified. Eight are expressed at detectable levels in PPCD1 but not wildtype eyes. Upregulation of two Csrp2bp fusion transcripts, as well as upregulation of the adjacent gene, Ovol2, was observed. Absence of the PPCD1 phenotype in animals haploinsufficient for Csrp2bp or both Csrp2bp and Dzank1 rules out haploinsufficiency of these genes as a cause of mouse PPCD1. Complementation experiments confirm that PPCD1 embryonic lethality is due to disruption of Csrp2bp expression. The ocular expression pattern of Csrp2bp is consistent with a role for this protein in corneal development and pathogenesis of PPCD1.
Seasonal differences in freezing stress resistance of needles of Pinus nigra and Pinus resinosa: evaluation of the electrolyte leakage method.

Seasonal changes in freezing stress resistance of needles of red pine (Pinus resinosa Ait.) and Austrian pine (Pinus nigra Arnold) trees were measured by an electrolyte leakage method and by visual observation. During most of the year, freezing stress resistance determined by the two methods gave similar results. The electrolyte leakage method provided a good estimate of seasonal changes in freezing stress resistance except for red pine needles in their most winter-hardy state. To obtain a reliable estimate of freezing stress resistance in winter-hardy red pine needles it was necessary to combine the electrolyte leakage method with visual observations. When red pine needles survived exposure to -80 degrees C or lower, electrolyte leakage was never more than 30% even when the needles were exposed to a slow freeze-thaw stress of -196 degrees C. However, rapid freezing of red pine needles to -196 degrees C resulted in electrolyte leakage of over 80%. Red pine needles attained a much higher freezing stress resistance during the winter than Austrian pine. Red pine needles also acclimated and deacclimated faster than Austrian pine needles. An index of injury was developed based on the electrolyte leakage method ((R(2) + R(1))/2, where R(1) is the minimum % electrolyte leakage from noninjured tissue and R(2) is the maximum % electrolyte leakage at the highest injury) that reliably predicted freezing stress resistance of pine needles for most of the year. Important aspects for developing a successful index of injury for pine needles are: use of cut needles, vacuum infiltration and shaking during incubation in water.We conclude that: (1) during cold acclimation the cell wall properties of the pine needles changed and these changes, which appeared to differ in the two species, might explain the very low leakage of electrolytes from winter-hardy needles of red pine; (2) pine needles survive winter by developing the ability to tolerate extracellular ice formation, because after rapid freezing the needles were severely injured; and (3) red pine is adapted to a shorter growing season and colder winters than Austrian pine.
Natural history of progression after PSA elevation following radical prostatectomy.

CONTEXT In men who develop an elevated serum prostate-specific antigen level (PSA) after having undergone a radical prostatectomy, the natural history of progression to distant metastases and death due to prostate cancer is unknown. OBJECTIVE To characterize the time course of disease progression in men with biochemical recurrence after radical prostatectomy. DESIGN A retrospective review of a large surgical series with median (SD) follow-up of 5.3 (3.7) years (range, 0.5-15 years) between April 1982 and April 1997. SETTING An urban academic tertiary referral institution. PATIENTS A total of 1997 men undergoing radical prostatectomy, by a single surgeon, for clinically localized prostate cancer. None received neoadjuvant therapy, and none had received adjuvant hormonal therapy prior to documented distant metastases. MAIN OUTCOME MEASURES After surgery, men were followed up with PSA assays and digital rectal examinations every 3 months for the first year, semiannually for the second year, and annually thereafter. A detectable serum PSA level of at least 0.2 ng/mL was evidence of biochemical recurrence. Distant metastases were diagnosed by radionuclide bone scan, chest radiograph, or other body imaging, which was performed at the time of biochemical recurrence and annually thereafter. RESULTS The actuarial metastasis-free survival for all 1997 men was 82% (95% confidence interval, 76%-88%) at 15 years after surgery. Of the 1997 men, 315 (15%) developed biochemical PSA level elevation. Eleven of these underwent early hormone therapy after the recurrence and are not included in the study. Of the remaining 304 men, 103 (34%) developed metastatic disease within the study period. The median actuarial time to metastases was 8 years from the time of PSA level elevation. In survival analysis, time to biochemical progression (P<.001), Gleason score (P<.001), and PSA doubling time (P<.001) were predictive of the probability and time to the development of metastatic disease. An algorithm combining these parameters was constructed to stratify men into risk groups. Once men developed metastatic disease, the median actuarial time to death was 5 years. The time interval from surgery to the appearance of metastatic disease was predictive of time until death (P<.02). CONCLUSIONS Several clinical parameters help predict the outcomes of men with PSA elevation after radical prostatectomy. These data may be useful in the design of clinical trials, the identification of men for enrollment into experimental protocols, and counseling men regarding the timing of administration of adjuvant therapies.
Cytogenetic and molecular studies of variant Ph' translocations.

including acute lymphoblastic leukemias (ALL) and non-Hodgkin’s lymphomas. Recently, a novel gene (BCL9), was cloned from a t(1;14)(q21;q23) in a cell line CEMO-1 derived from a pre-B ALL.6 Whether or not this novel gene is rearranged with the TEL gene in this translocation requires further elucidation. The limits between MDS and myeloproliferative syndromes as well as truly acute non-lymphoblastic leukemias with myelodysplasia seem to be indistinct7 and new entities could be defined provided that nonrandom chromosomal abnormalities can be demonstrated in these patients.
Understanding the social context of the Schelling segregation model

A recent article [Vinkovic D, Kirman A (2006) Proc Natl Acad Sci USA 103:19261–19265] showing that the Schelling model has a physical analogue extends our understanding of the model. However, prior research has already outlined a mathematical basis for the Schelling model and simulations based on it have already enhanced our understanding of the social dynamics that underlie the model, something that the physical analogue does not address. Research in social science has provided a formal basis for the segregative outcomes resulting from the residential selection process and simulations have replicated relevant spatial outcomes under different specifications of the residential dynamics. New and increasingly detailed survey data on preferences demonstrates the embeddedness of the Schelling selection process in the social behaviors of choosing alternative residential compositions. It also demonstrates that, in the multicultural context, seemingly mild preferences for living with similar neighbors carry the potential to be strong determinants for own race selectivity and residential segregation.
Correlated topic model for image annotation

For the task of image annotation, traditional methods based on probabilistic topic model, such as correspondence Latent Dirichlet Allocation (corrLDA) [1], assumes that image is a mixture of latent topics. However, this kind of models is unable to directly model correlation between topics since topic proportions of an image are generated independently. Our model, called correspondence Correlated Topic Model (corrCTM), extends Correlated Topic Model (CTM) [2] from natural language processing to capture topic correlation from covariance structure of more flexible model distribution. Unlike previous LDA based models, topic proportions are correlated with each other in proposed corrCTM. And the topic correlation propagates from image features to annotation words through a generative process, and finally correspondence between images and words could be generated. We derive an approximate inference and estimation algorithm based on variational method. We examine the performance of our model on two benchmark image datasets, show improved performance over corrLDA for both annotation and modeling word correlation.
Characterization of Silicon Mach-Zehnder Modulator in 20-Gbps NRZ-BPSK Transmission

SUMMARY 20-Gbps non return-to-zero (NRZ) — binary phase shift keying (BPSK) using the silicon Mach-Zehnder modulator is demonstrated and characterized. Measurement of a constellation diagram confirms successful modulation of 20-Gbps BPSK with the silicon modulator. Transmission performance is characterized in the measurement of bit-error-rate in accumulated dispersion range from −347 ps/nm to +334 ps/nm using SMF and a dispersion compensating fiber module. Optical signal-to-noise ratio required for bit-error-rate of 10 −3 is 10.1 dB at back-to-back condition. It is 1.2-dB difference from simulated value. Obtained dispersion tolerance less than 2-dB power penalty for bit-error-rate of 10−3 is −220 ps/nm to +230 ps/nm. The symmetric dispersion tolerance indicates chirp-free modulation. Frequency chirp inherent in the modulation mechanism of the silicon MZM is also discussed with the simulation. The effect caused by the frequency chirp is limited to 3% shift in the chromatic dispersion range of 2 dB power penalty for BER 10 −3 . T he effect inherent in the silicon
No 975 , November 2004 On Decision Procedures for Set-Valued Fields

An important feature of object-oriented programming languages is the ability to dynamically instantiate user-defined container data structures such as lists, trees, and hash tables. Programs implement such data structures using references to dynamically allocated objects, which allows data structures to store unbounded numbers of objects, but makes reasoning about programs more difficult. Reasoning about object-oriented programs with complex data structures is simplified if data structure operations are specified in terms of abstract sets of objects associated with each data structure. For example, an insertion into a data structure in this approach becomes simply an insertion into a dynamically changing set-valued field of an object, as opposed to a manipulation of a dynamically linked structure linked to the object. In this paper we explore reasoning techniques for programs that manipulate data structures specified using set-valued abstract fields associated with container objects. We compare the expressive power and the complexity of specification languages based on 1) decidable prefix vocabulary classes of first-order logic, 2) twovariable logic with counting, and 3) Nelson-Oppen combinations of multisorted theories. Such specification logics can be used for verification of object-oriented programs with supplied invariants. Moreover, by selecting an appropriate subset of properties expressible in such logic, the decision procedures for these logics yield automated computation of lattice operations in abstract interpretation domain, as well as automated computation of abstract program semantics.
Energy router interface model based on bidirectional flow control for intelligent park

The new generation intelligent park is demanded for the flexible utilization mode of distributed renewable energy, energy storage equipment and the various characteristic load access. However, the energy router is correspondingly responsible for energy routing and dynamic control. Its uniform interface supports the plug and play of distributed power, energy storage and load of the intelligent park. In our paper, the new energy network architecture are firstly presented. Then, the function structure and the bidirectional flow control strategy of these energy routers are designed to satisfy the energy routing demands. The bidirectional flow control among users and a variety of distributed power, energy storage equipment is achieved by implementing our energy exchange scheme of the energy routing interface design. Meanwhile, we put the energy router interface design into the practical operation in local energy internet, construct the application system based on the energy internet technology with Cell in intelligent park, and ultimately make the collaborative operation and green resource sharing in intelligent system.
A cache based algorithm to predict HDL modules faults

Verification is the most challenging and time consuming stage in the integrated circuit development cycle. As designs complexities double every two years, novel verification methodologies are needed. We propose an algorithm that dynamically builds and updates an HDL module error proneness list. This list can be used to assist the development team to allocate resources during verification stage. The algorithm is build up using the idea that problematic modules usually hide many uncovered errors. Thus, our algorithm caches the most frequently modified and fixed modules. In an academic experiment composed by 17 modules, using a cache of size 3, we were able to correctly predict almost 80% of the faults occurrences.
Requirements for Endothelin type-A receptors and Endothelin-1 signaling in the facial ectoderm for the patterning of skeletogenic neural crest cells in zebrafish

Genetic studies in mice and zebrafish have revealed conserved requirements for Endothelin 1 (Edn1) signaling in craniofacial development. Edn1 acts through its cognate type-A receptor (Ednra) to promote ventral skeletal fates and lower-jaw formation. Here, we describe the isolation and characterization of two zebrafish ednra genes - ednra1 and ednra2 - both of which are expressed in skeletal progenitors in the embryonic neural crest. We show that they play partially redundant roles in lower-jaw formation and development of the jaw joint. Knockdown of Ednra1 leads to fusions between upper- and lower-jaw cartilages, whereas the combined loss of Ednra1 and Ednra2 eliminates the lower jaw, similar to edn1-/- mutants. edn1 is expressed in pharyngeal arch ectoderm, mesoderm and endoderm. Tissue-mosaic studies indicate that, among these tissues, a crucial source of Edn1 is the surface ectoderm. This ectoderm also expresses ednrA1 in an edn1-dependent manner, suggesting that edn1 autoregulates its own expression. Collectively, our results indicate that Edn1 from the pharyngeal ectoderm signals through Ednra proteins to direct early dorsoventral patterning of the skeletogenic neural crest.
Fabrication of Modified Transport Fluconazole Transdermal Spray Containing Ethyl Cellulose and Eudragit® RS100 as Film Formers

The present investigation was undertaken to fabricate modified transport fluconazole transdermal spray using ethyl cellulose and Eudragit® RS100 as film-forming polymers. Eudragit® RS100 (X1) and ethyl cellulose (X2) were selected as independent variables in 32 full factorial design, whereas drug transport in first hour (Y1) and the time required for 50% drug transport (Y2) were selected as dependent variables. Eutectic blend of camphor and menthol was used as permeation enhancer cum solvent for film-forming polymers. The pH, viscosity, volume of solution delivered upon each actuation, spray angle, ex–in vivo physical evaluation and in vitro drug transport of the formulated products were evaluated. The optimized batch B16 containing 5.25% w/w ethyl cellulose and 10.6% w/w Eudragit® RS100 was formulated by overlapping the contour plots of Y1 and Y2. The pH, viscosity, volume of solution sprayed upon each actuation and spray angle of the batch B16 was 6.3, 52.9 cPs, 0.24 ml and 82.6° respectively. The film of optimized batch was flexible and dermal-adhesive. The responses Y1 and Y2 of batch B16 were 7.91 μg/ml and 347 min respectively. The kinetics of drug transport was best explained by the Korsmeyer and Peppas model. The eutectic mixture consisting of equal parts of camphor and menthol showed improved drug permeation through shed snake skin. Short-term stability study demonstrated insignificant changes in performance characteristics.
The Moving Tablet of the Eye: The Origins of Modern Eye Movement Research

1. Informing contemporary research 1.1 Introduction 1.2 Scanning the way the eyes move 1.3 Modern eye movement measuring techniques 1.4 The moving tablet of the eye 2. Origins of eye movement research 2.1 Introduction 2.2 Binocular eye movements 2.3 Oculomotor anatomy and physiology 2.4 Internal motions of the eye 2.5 External motions of the eye 2.6 Afterimages 2.7 William Charles Wells 2.8 Erasmus Darwin's 'Zoonomia' 3. Nystagmus 3.1 Introduction 3.2 Visual vertigo 3.3 Wells on vertigo 3.4 Darwin on vertigo 3.5 Wells and Darwin 3.6 Purkinje and Flourens 3.7 Mach, Breuer and Crum Brown 3.8 James and Barany 3.9 Griffith and Dodge 4. Saccades and fixations 4.1 Introduction 4.2 Fixations 4.3 Saccades 4.4 Did Javal discover saccades? 4.5 Developments from Dodge 5. Visual motion illusions and eye movements 5.1 Introduction 5.2 Induced motion 5.3 Motion aftereffect 5.4 Visual vertigo 5.5 Autokinetic motion 5.6 Stroboscopic motion 5.7 Vection 5.8 Eye movements and visual motion 6. Perceptual stability and eye movements 6.1 Introduction 6.2 Stability during eye movements 6.3 Stability and saccades 6.4 Stability and fixation 7. Summary and conclusions 7.1 Introduction 7.2 Emergence of methods for measuring eye movements 7.3 Eye movement and eye position 7.4 Normal and abnormal eye movements 7.5 Sleep and wakefulness 7.6 Developmental trends 7.7 Perceptual and cognitive processes 7.8 Moving tablets - literature on eye movements
RepDroid: An Automated Tool for Android Application Repackaging Detection

In recent years, with the explosive growth of mobile smart phones, the number of Android applications (apps) increases rapidly. Attackers usually leverage the popularity of Android apps by inserting malwares, modifying the original apps, repackaging and releasing them for their own illegal purposes. To avoid repackaged apps from being detected, they usually use sorts of obfuscation and encryption tools. As a result, it's important to detect which apps are repackaged. People often intuitively judge whether two apps are a repackaged pair by executing them and observing their runtime user interface (UI) traces. Hence, we propose layout group graph (LGG) built from UI trances to model those UI behaviors and use LGG as the birthmark of Android apps for identification. Based on LGG, we also implement a dynamic repackaging detection tool, RepDroid. Since our method does not require the apps' source code, it is resilient to app obfuscation and encryption. We conducted an experiment with two data sets. The first set contains 98 pairs of repackaged apps. The original apps and repackaged ones are compared and we can detect all of these repackaged pairs. The second set contains 125 commercial apps. We compared them pair-wisely and the false positive rate was 0.08%.
Conjunction as composition

Partial specifications written in many different specification languages can be composed if they are all given semantics in the same domain, or alternatively, all translated into a common style of predicate logic. The common semantic domain must be very general, the particular semantics assigned to each specification language must be conducive to composition, and there must be some means of communication that enables specifications to build on one another. The criteria for success are that a wide variety of specification languages should be accommodated, there should be no restrictions on where boundaries between languages can be placed, and intuitive expectations of the specifier should be met.