Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Diffusion of Green Fluorescent Protein in the Mitochondrial Matrix

Abstract. It is thought that the high protein density in the mitochondrial matrix results in severely restricted solute diffusion and metabolite channeling from one enzyme to another without free aqueous-phase diffusion. To test this hypothesis, we measured the diffusion of green fluorescent protein (GFP) expressed in the mitochondrial matrix of fibroblast, liver, skeletal muscle, and epithelial cell lines. Spot photobleaching of GFP with a 100× objective (0.8-μm spot diam) gave half-times for fluorescence recovery of 15–19 ms with >90% of the GFP mobile. As predicted for aqueous-phase diffusion in a confined compartment, fluorescence recovery was slowed or abolished by increased laser spot size or bleach time, and by paraformaldehyde fixation. Quantitative analysis of bleach data using a mathematical model of matrix diffusion gave GFP diffusion coefficients of 2–3 × 10−7 cm2/s, only three to fourfold less than that for GFP diffusion in water. In contrast, little recovery was found for bleaching of GFP in fusion with subunits of the fatty acid β-oxidation multienzyme complex that are normally present in the matrix. Measurement of the rotation of unconjugated GFP by time-resolved anisotropy gave a rotational correlation time of 23.3 ± 1 ns, similar to that of 20 ns for GFP rotation in water. A rapid rotational correlation time of 325 ps was also found for a small fluorescent probe (BCECF, ∼0.5 kD) in the matrix of isolated liver mitochondria. The rapid and unrestricted diffusion of solutes in the mitochondrial matrix suggests that metabolite channeling may not be required to overcome diffusive barriers. We propose that the clustering of matrix enzymes in membrane-associated complexes might serve to establish a relatively uncrowded aqueous space in which solutes can freely diffuse.
Are click-through data adequate for learning web search rankings?

Learning-to-rank algorithms, which can automatically adapt ranking functions in web search, require a large volume of training data. A traditional way of generating training examples is to employ human experts to judge the relevance of documents. Unfortunately, it is difficult, time-consuming and costly. In this paper, we study the problem of exploiting click-through data for learning web search rankings that can be collected at much lower cost. We extract pairwise relevance preferences from a large-scale aggregated click-through dataset, compare these preferences with explicit human judgments, and use them as training examples to learn ranking functions. We find click-through data are useful and effective in learning ranking functions. A straightforward use of aggregated click-through data can outperform human judgments. We demonstrate that the strategies are only slightly affected by fraudulent clicks. We also reveal that the pairs which are very reliable, e.g., the pairs consisting of documents with large click frequency differences, are not sufficient for learning.
Therapy and Long-Term Prophylaxis of Vaccinia Virus Respiratory Infections in Mice with an Adenovirus-Vectored Interferon Alpha (mDEF201)

An adenovirus 5 vector encoding for mouse interferon alpha, subtype 5 (mDEF201) was evaluated for efficacy against lethal vaccinia virus (WR strain) respiratory infections in mice. mDEF201 was administered as a single intranasal treatment either prophylactically or therapeutically at doses of 106 to 108 plaque forming units/mouse. When the prophylactic treatment was given at 56 days prior to infection, it protected 90% of animals from death (100% protection for treatments given between 1–49 days pre-infection), with minimal weight loss occurring during infection. Surviving animals re-challenged with virus 22 days after the primary infection were protected from death, indicating that mDEF201 did not compromise the immune response against the initial infection. Post-exposure therapy was given between 6–24 h after vaccinia virus exposure and protection was afforded by a 108 dose of mDEF201 given at 24 h, whereas a 107 dose was effective up to 12 h. Comparisons were made of the ability of mDEF201, given either 28 or 1 day prior to infection, to inhibit tissue virus titers and lung infection parameters. Lung, liver, and spleen virus titers were inhibited to nearly the same extent by either treatment, as were lung weights and lung hemorrhage scores (indicators of pneumonitis). Lung virus titers were significantly (>100-fold) lower than in the placebo group, and the other infection parameters in mDEF201 treated mice were nearly at baseline. In contrast, viral titers and lung infection parameters were high in the placebo group on day 5 of the infection. These results demonstrate the long-acting prophylactic and treatment capacity of mDEF201 to combat vaccinia virus infections.
Taeaniamaliponensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater.

A Gram-strain-negative, rod-shaped, non-motile bacterial strain, designated MM-8T, was isolated from seawater in the Korean peninsula. Strain MM-8T was found to grow optimally at pH 7.0-8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MM-8T falls within the clade comprising members of the genera Actibacter, Lutimonas and Namhaeicolain the family Flavobacteriaceae. Strain MM-8T exhibited 16S rRNA gene sequence similarity values of 94.4-96.9 % with respect to the type strains of members of the genera Actibacter, Lutimonas and Namhaeicola. Strain MM-8T was found to contain MK-6 (90.0 %) and MK-7 (10.0 %) as the predominant menaquinones and iso-C15 : 0 (32.4 % ), iso-C15 : 1 G (11.4 %) and iso-C15 : 0 3-OH (10.1 %) as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain MM-8T was determined to be 40.7 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrate that strain MM-8T is distinguishable from the type strains of type species of the genera Actibacter, Lutimonas and Namhaeicola. On the basis of the data presented, strain MM-8T is considered to represent a novel genus and species, for which the name Taeania maliponensis gen. nov., sp. nov. is proposed. The type strain is MM-8T (=KCTC 52209T=NBRC 112238T).
Processing Pronouns without Antecedents: Evidence from Event-related Brain Potentials

Pronouns that do not have explicit antecedents typically cause processing problems. We investigate a specific example in which this may not be the case, as in At the interview, they asked really difficult questions, where the plural pronoun they has no explicit antecedent, yet is intuitively easy to process. Some unspecified but constrained set of individuals (the interview panel or the company) can be inferred as the referent, but it is not crucial to determine specifically which entities are being referred to. We propose that this contrasts with the processing of singular pronouns (he or she), for which it is necessary to determine a specific referent. We used event-related brain potentials to investigate how readers process the pronoun (they vs. he/she) in these cases. Sentences were placed in a context that either did or did not contain an explicit antecedent for the pronoun. There were two key findings. Firstly, when there was no explicit antecedent, a larger fronto-central positivity was observed 750 msec after pronoun onset for he/she than they, possibly reflecting the additional difficulty involved in establishing a referent for he/she than for they when no explicit referent is available. Secondly, there was a larger N400-like deflection evoked by he/she than they, regardless of whether there was an explicit antecedent for the pronoun. We suggest that this is due to the singular pronouns bringing about a greater integration effort than the plural pronoun. This observation adds to a growing body of research revealing fundamental differences in the way these pronouns are handled by the language processor.
Homer1a drives homeostatic scaling-down of excitatory synapses during sleep

Synapse remodeling during sleep General activity and information processing while an animal is awake drive synapse strengthening. This is counterbalanced by weakening of synapses during sleep (see the Perspective by Acsády). De Vivo et al. used serial scanning electron microscopy to reconstruct axon-spine interface and spine head volume in the mouse brain. They observed a substantial decrease in interface size after sleep. The largest relative changes occurred among weak synapses, whereas strong ones remained stable. Diering et al. found that synapses undergo changes in synaptic glutamate receptors during the sleep-wake cycle, driven by the immediate early gene Homer1a. In awake animals, Homer1a accumulates in neurons but is excluded from synapses by high levels of noradrenaline. At the onset of sleep, noradrenaline levels decline, allowing Homer1a to move to excitatory synapses and drive synapse weakening. Science, this issue p. 457, p. 507; see also p. 511 Excitatory synapses are globally weakened during sleep. Sleep is an essential process that supports learning and memory by acting on synapses through poorly understood molecular mechanisms. Using biochemistry, proteomics, and imaging in mice, we find that during sleep, synapses undergo widespread alterations in composition and signaling, including weakening of synapses through removal and dephosphorylation of synaptic AMPA-type glutamate receptors. These changes are driven by the immediate early gene Homer1a and signaling from group I metabotropic glutamate receptors mGluR1/5. Homer1a serves as a molecular integrator of arousal and sleep need via the wake- and sleep-promoting neuromodulators, noradrenaline and adenosine, respectively. Our data suggest that homeostatic scaling-down, a global form of synaptic plasticity, is active during sleep to remodel synapses and participates in the consolidation of contextual memory.
Interaction Mismatch Discovery Based Transformation from BPMN to BPEL

Many techniques have been proposed to transform BPMN into BPEL. The transformation for single BPMN process is studied well. But multiple BPMN processes often suffer from mismatch issues. This paper aims to better transform multiple BPMN processes containing interaction mismatches. The challenges for such trans-formation are: 1) ensuring transformed BPEL processes compatible 2) ensuring transformation interaction-preserved, which means keeping interactions those do not cause transformed processes mismatch preserved and transformed. In the paper, interaction mismatches are classified into two categories: static and runtime interaction mismatch. Both of them can be discovered by our approach based on interaction control-flow relations. For better transformation, discovered mismatch interactions are minimized and only the minimized result will not be transformed. A case study is given to illustrate the approach. The transformation also provides general support for transforming cross-organizational business processes into executable processes.
Long-term objective results of proximal phalanx fracture treatment.

BACKGROUND Proximal phalanx fractures are common. In this study, our preferred methods regarding the treatment of proximal phalanx fractures and their long-term objective results are presented. METHODS Between October 2001 and March 2010, in the Plastic Reconstructive and Aesthetic Surgery Department of Düzce Medical Faculty, we treated 23 patients with 32 proximal phalanx fractures. Stable fractures (n=5) were treated with splints, while unstable fractures (n=27) were stabilized with 1.0 mm percutaneous intramedullary Kirschner wires following open reduction. RESULTS At follow-ups, ranging from 3 months to 9 years, patients were evaluated with radiologic efficiency, range of motion (ROM), total active movements (TAM), and grip power of the digit. TAM scores of 20 fingers were perfect (≥220° for D2-5, ≥150° for D1), for 7 fingers were good (180- 220° for D2-5, 120-150° for D1), and for 5 fingers were either moderate or poor. No difference was observed between grip strength of broken fingers and that of healthy fingers. As a major complication, non-union occurred in one finger. CONCLUSION We concluded that Kirschner wire fixation is a reliable and simple method of treating unstable proximal phalangeal fractures, and excellent long-term results can be obtained in suitable cases. In stable proximal phalanx fractures, splints provide sufficient treatment.
The Rod cGMP-phosphodiesterase β-Subunit Promoter Is a Specific Target for Sp4 and Is Not Activated by Other Sp Proteins or CRX*

The β-subunit of cGMP-phosphodiesterase (β-PDE) is a key protein in phototransduction expressed exclusively in rod photoreceptors. It is necessary for visual function and for structural integrity of the retina. β-PDE promoter deletions showed that the −45/−23 region containing a consensus Crx-response element (CRE) was necessary for low level transcriptional activity. Overexpressed Crx modestly transactivated this promoter in 293 human embryonic kidney cells; however, mutation of CRE had no significant effect on transcription either in transfected Y79 retinoblastoma cells or Xenopus embryonic heads. Thus, Crx is unlikely to be a critical β-PDE transcriptional regulator in vivo. Interestingly, although the β/GC element (−59/−49) binds multiple Sp transcription factors in vitro, only Sp4, but not Sp1 or Sp3, significantly enhancedβ-PDE promoter activity. Thus, the Sp4-mediated differential activation of the β-PDE transcription defines the first specific Sp4 target gene reported to date and implies the importance of Sp4 for retinal function. Further extensive mutagenesis of the β-PDE upstream sequences showed no additional regulatory elements. Although this promoter lacks a canonical TATA box or Inr element, it has the (T/A)-rich β/TA sequence located within the −45/−23 region. We found that it binds purified TBP and TFIIB in gel mobility shift assays with cooperative enhancement of binding affinity.
Proinflammatory S100 Proteins Regulate the Accumulation of Myeloid-Derived Suppressor Cells1

Chronic inflammation is a complex process that promotes carcinogenesis and tumor progression; however, the mechanisms by which specific inflammatory mediators contribute to tumor growth remain unclear. We and others recently demonstrated that the inflammatory mediators IL-1β, IL-6, and PGE2 induce accumulation of myeloid-derived suppressor cells (MDSC) in tumor-bearing individuals. MDSC impair tumor immunity and thereby facilitate carcinogenesis and tumor progression by inhibiting T and NK cell activation, and by polarizing immunity toward a tumor-promoting type 2 phenotype. We now show that this population of immature myeloid cells induced by a given tumor share a common phenotype regardless of their in vivo location (bone marrow, spleen, blood, or tumor site), and that Gr1highCD11bhighF4/80−CD80+IL4Rα+/−Arginase+ MDSC are induced by the proinflammatory proteins S100A8/A9. S100A8/A9 proteins bind to carboxylated N-glycans expressed on the receptor for advanced glycation end-products and other cell surface glycoprotein receptors on MDSC, signal through the NF-κB pathway, and promote MDSC migration. MDSC also synthesize and secrete S100A8/A9 proteins that accumulate in the serum of tumor-bearing mice, and in vivo blocking of S100A8/A9 binding to MDSC using an anti-carboxylated glycan Ab reduces MDSC levels in blood and secondary lymphoid organs in mice with metastatic disease. Therefore, the S100 family of inflammatory mediators serves as an autocrine feedback loop that sustains accumulation of MDSC. Since S100A8/A9 activation of MDSC is through the NF-κB signaling pathway, drugs that target this pathway may reduce MDSC levels and be useful therapeutic agents in conjunction with active immunotherapy in cancer patients.
Fast mapping in late-talking toddlers

ABSTRACT This study investigated fast mapping in late-talking (LT) toddlers and toddlers with normal language (NL) development matched on age, nonverbal cognition, and maternal education. The fast-mapping task included novel object labels and familiar words. The LT group scored significantly lower than the NL group on novel word comprehension and production, as well as familiar word production. For both groups, fast-mapping performance was associated with concurrent language ability and later language outcomes. A post hoc analysis of phonotactic probability (PP) and neighborhood density (ND) suggested that the majority of NL toddlers displayed optimal learning of the nonword with low PP/ND. The LT group did not display the same sensitivity to PP/ND characteristics as the NL group.
FPGA-Based Communications Receivers for Smart Antenna Array Embedded Systems

Field-programmable gate arrays (FPGAs) are drawing ever increasing interest from designers of embedded wireless communications systems. They outpace digital signal processors (DSPs), through hardware execution of a wide range of parallelizable communications transceiver algorithms, at a fraction of the design and implementation effort and cost required for application-specific integrated circuits (ASICs). In our study, we employ an Altera Stratix FPGA development board, along with the DSP Builder software tool which acts as a high-level interface to the powerful Quartus II environment. We compare single- and multibranch FPGA-based receiver designs in terms of error rate performance and power consumption. We exploit FPGA operational flexibility and algorithm parallelism to design eigenmode-monitoring receivers that can adapt to variations in wireless channel statistics, for high-performing, inexpensive, smart antenna array embedded systems.
Deceit and indefeasible knowledge: the case of dubitatio

The current trend in knowledge revision in the Dynamic Epistemic Logic tradition focuses on the addition of new knowledge, rather than the possibility of losing knowledge. Yet there are natural situations, such as an agent who does not want another agent to know that she knows a certain piece of information, where there is a need to be able to model the retraction of a proposition from a knowledge base. One situation where this is systematically required is the variant of the medieval theory of obligationes known as dubitatio, where one of the agents in the dialogue is obliged to hold the initial proposition, the dubitatum, as doubtful, regardless of what other propositions she may concede or deny during the disputation. In this paper, we use dubitatio as a motivation for studying deceitful agents, and we discuss various ways that an agent can move from a model where f is known to one where f is not known.
Experimental inbreeding reduces seed production and germination independent of fragmentation of populations of

We studied effects of inbreeding on the early fitness measures seed production and germination in Swertia perennis L. (Gentianaceae), a locally abundant specialist of fen grasslands, which have been greatly fragmented in Switzerland. We further tested whether such effects differed between populations of different size and isolation. We studied effects of free pollination, hand-outcrossing and hand-selfing on 160 plants in 16 populations in large, in small barely isolated, and in small isolated habitat islands. We found a distinct gradient in experimental outcomes from free pollination to hand-outcrossing to hand-selfing. Compared with free pollination, selfing reduced the number of seeds per capsule by 22% (P < 0.01), the seed/ovule ratio by 26% (P < 0.001), seed mass by 25% (P < 0.001) and germination percentage by 23% (P < 0.05). The outcome of hand-outcrossing was intermediate for all traits. The reduction in early fitness components after selfing is most likely due to inbreeding depression. Higher seed production and germination after free pollination than after hand-outcrossing may be due to a larger number of pollen donors involved in free pollination or due to higher quality of free pollen because of lower relatedness of parent plants. Moreover, the fact that seed production was highest after free pollination indicates that S. perennis is not pollen limited. Pollination treatment effects did not differ between different island types. Hence, there are no indications that early inbreeding depression was purged from more strongly fragmented populations. Wir untersuchten die Auswirkungen von Inzucht auf die fruhen Fitnessmerkmale Samenproduktion und Keimung bei der lokal haufigen Swertia perennis L. (Gentianaceae), einer Pflanze der in der Schweiz stark fragmentierten Flachmoore. Um zu untersuchen, ob sich solche Auswirkungen in verschieden grosen und unterschiedlich isolierten Populationen unterscheiden, verglichen wir die Auswirkungen von freier Bestaubung, Handfremdbestaubung und Handselbstbestaubung fur 160 Pflanzen in 16 Populationen in grosen, in kleinen wenig isolierten und in kleinen isolierten Habitatinseln. Wir fanden einen ausgepragten Gradienten von freier Bestaubung uber Fremdbestaubung von Hand zu Handselbstbestaubung: Im Vergleich zu freier Bestaubung war nach Selbstbestaubung die Anzahl Samen pro Kapsel um 22% (P < 0.01), der Samenansatz um 26% (P < 0.001), die Samenmasse um 25% (P < 0.001) und der Keimungserfolg um 23% (P < 0.05) herabgesetzt. Die Resultate der Handfremdbestaubung waren fur alle Mase intermediar. Die Herabsetzung von Merkmalen fruher Fitness von S. perennis nach Selbstbestaubung ist hochstwahrscheinlich eine Folge von Inzuchtdepression. Der im Vergleich zu Handfremdbestaubung nach freier Bestaubung hohere Fortpflanzungserfolg und die hohere Keimung konnten durch eine grosere Anzahl zu freier Bestaubung beitragende Pollenspender oder durch geringere Verwandtschaft der in freier
Revisiting Context-based Projection Methods for Term-Translation Spotting in Comparable Corpora

Context-based projection methods for identifying the translation of terms in comparable corpora has attracted a lot of attention in the community, e.g. (Fung, 1998; Rapp, 1999). Surprisingly, none of those works have systematically investigated the impact of the many parameters controlling their approach. The present study aims at doing just this. As a test-case, we address the task of translating terms of the medical domain by exploiting pages mined from Wikipedia. One interesting outcome of this study is that significant gains can be obtained by using an association measure that is rarely used in practice.