Miracle-dz/UniFAR-FTUs huggingface dataset:
Synbindin, a Novel Syndecan-2–Binding Protein in Neuronal Dendritic Spines

Dendritic spines are small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. We previously showed that the cell-surface heparan sulfate proteoglycan syndecan-2 induces spine formation upon transfection into hippocampal neurons. This effect requires the COOH-terminal EFYA sequence of syndecan-2, suggesting that cytoplasmic molecules interacting with this sequence play a critical role in spine morphogenesis. Here, we report a novel protein that binds to the EFYA motif of syndecan-2. This protein, named synbindin, is expressed by neurons in a pattern similar to that of syndecan-2, and colocalizes with syndecan-2 in the spines of cultured hippocampal neurons. In transfected hippocampal neurons, synbindin undergoes syndecan-2–dependent clustering. Synbindin is structurally related to yeast proteins known to be involved in vesicle transport. Immunoelectron microscopy localized synbindin on postsynaptic membranes and intracellular vesicles within dendrites, suggesting a role in postsynaptic membrane trafficking. Synbindin coimmunoprecipitates with syndecan-2 from synaptic membrane fractions. Our results show that synbindin is a physiological syndecan-2 ligand on dendritic spines. We suggest that syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin.
Welfare Leakage and Immigration Policy

This paper analyzes the interaction between the welfare state and immigra- tion policy. We establish a negative relationship between the number of dependents and the extent of the welfare state due to the leakage of benefits. We also explain the determination of immigration policy as the outcome of a lobbying game between domestic interest groups and the government. Our results indicate that there is evi- dence for welfare leakage and for lobbying as a determinant of immigration policy. In our baseline specification, a 10 percentage points increase in the share of dependents leads to a 7-10 percentage point decrease in the labor tax rate. Furthermore, an increase by 10 percentage points in union density leads to a decrease of one percentage point in the share of immigrants in the population. In the context of EU enlargement and the ensuing migration flows, our model predicts a reduction in the size of the welfare state in the old member countries. (JEL H5, J1, J61)
DNA Sequence-Based Subtyping and Evolutionary Analysis of Selected Salmonella enterica Serotypes

ABSTRACT While serotyping and phage typing have been used widely to characterize Salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining Salmonella transmission, ecology, and evolution. A set of 25 Salmonella enterica isolates, representing five clinically relevant serotypes (serotypes Agona, Heidelberg, Schwarzengrund, Typhimurium, and Typhimurium var. Copenhagen) was initially used to develop a multilocus sequence typing (MLST) scheme for Salmonella targeting seven housekeeping and virulence genes (panB, fimA, aceK, mdh, icdA, manB, and spaN). A total of eight MLST types were found among the 25 isolates sequenced. A good correlation between MLST types and Salmonella serotypes was observed; only one serotype Typhimurium var. Copenhagen isolate displayed an MLST type otherwise typical for serotype Typhimurium isolates. Since manB, fimA, and mdh allowed for the highest subtype discrimination among the initial 25 isolates, we chose these three genes to perform DNA sequencing of an additional 41 Salmonella isolates representing a larger diversity of serotypes. This “three-gene sequence typing scheme” allowed discrimination of 25 sequence types (STs) among a total of 66 isolates; STs correlated well with serotypes and allowed within-serotype differentiation for 9 of the 12 serotypes characterized. Phylogenetic analyses showed that serotypes Kentucky and Newport could each be separated into two distinct, statistically well supported evolutionary lineages. Our results show that a three-gene sequence typing scheme allows for accurate serotype prediction and for limited subtype discrimination among clinically relevant serotypes of Salmonella. Three-gene sequence typing also supports the notion that Salmonella serotypes represent both monophyletic and polyphyletic lineages.
Phonetic and phonological errors in children with high functioning autism and Asperger syndrome

This study involved a qualitative analysis of speech errors in children with autism spectrum disorders (ASDs). Participants were 69 children aged 5–13 years; 30 had high functioning autism and 39 had Asperger syndrome. On a standardized test of articulation, the minority (12%) of participants presented with standard scores below the normal range, indicating a speech delay/disorder. Although all the other children had standard scores within the normal range, a sizeable proportion (33% of those with normal standard scores) presented with a small number of errors. Overall 41% of the group produced at least some speech errors. The speech of children with ASD was characterized by mainly developmental phonological processes (gliding, cluster reduction and final consonant deletion most frequently), but non-developmental error types (such as phoneme specific nasal emission and initial consonant deletion) were found both in children identified as performing below the normal range in the standardized speech test and in those who performed within the normal range. Non-developmental distortions occurred relatively frequently in the children with ASD and previous studies of adolescents and adults with ASDs shows similar errors, suggesting that they do not resolve over time. Whether or not speech disorders are related specifically to ASD, their presence adds an additional communication and social barrier and should be diagnosed and treated as early as possible in individual children.
Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

RNA Structural Principles Revealed The thermodynamic principles that link RNA primary and secondary structure are well understood, but the relation to tertiary structure is unclear. To gain insight, Bailor et al. (p. 202) analyzed all available three-dimensional structures of an important RNA motif, the two-way junction, and found that flanking helices sample only a small percentage of possible interhelical orientations. They identified a set of general rules for the relative orientation of helices as a function of the size of the interconnecting junction. The results also rationalize how ligands stabilize specific conformations. Understanding the topological constraints that define RNA global conformation and dynamic adaptation provides guiding principles for rational manipulation of RNA structure. Topological constraints imposed by the secondary structure determine the global conformation ensemble sampled by RNA. Thermodynamic rules that link RNA sequences to secondary structure are well established, but the link between secondary structure and three-dimensional global conformation remains poorly understood. We constructed comprehensive three-dimensional maps depicting the orientation of A-form helices across RNA junctions in the Protein Data Bank and rationalized our findings with modeling and nuclear magnetic resonance spectroscopy. We show that the secondary structures of junctions encode readily computable topological constraints that accurately predict the three-dimensional orientation of helices across all two-way junctions. Our results suggest that RNA global conformation is largely defined by topological constraints encoded at the secondary structural level and that tertiary contacts and intermolecular interactions serve to stabilize specific conformers within the topologically allowed ensemble.
Chronos-ung Nominalizations of Verbs of Saying in German Events and Propositions

-ung nominalizations of verbs of saying in German can be interpreted as events or propositions. There are context partners of such nominals which disambiguate the reading or suggest preferences. We consider a specific ambiguous constellation which is very frequent in German, where the nominal is the internal argument of a PP with nach. We detail the semantic representations of corresponding sentence types in the framework of Discourse Representation Theory and conclude from this an explanation of why some context partners suggest the one reading and some the other. The findings are currently used in corpus analyses to test the relevance and coverage of the stipulated criteria and to optimize preference weights statistically. This shows a way to avoid deep semantic evaluation with respect to disambiguation and to replace it by a combination of shallow semantic interpretation (based upon selectional restrictions and semantic hierarchies) and data driven methods. We present some of the results.
Effect of floating toes on knee and trunk acceleration during walking: a preliminary study

[Purpose] This study investigated the effect of floating toes on knee and trunk acceleration during walking in experimental setting. [Subjects and Methods] Twelve healthy volunteers walked barefoot at a preferred speed along a linear pathway under 2 conditions: normal gait (control) condition and floating toes (FT) condition. In the latter, weight bearing by the toes was avoided using kinesiology tape applied along the toe extensors. Accelerations of the knee (Kn) and lumbar spine (Lx) were assessed using triaxial accelerometers mounted on the right fibular head and the spinous process of L3. Acceleration vectors were oriented such that the anterior, right, and cranial deviations were positive along the anteroposterior, lateral, and vertical axes, respectively. The root mean squares (RMSs; anteroposterior, RMSap; lateral, RMSl; vertical, RMSv) were calculated, and the mean values of 3 trials in each condition were determined. Differences between the conditions were assessed using the Wilcoxon signed-rank test. [Results] LxRMSap and LxRMSv were larger in the FT condition than in the control condition. KnRMSv tended to be higher in the FT condition than in the control condition. [Conclusion] Floating toes increase acceleration and might create mechanical stress on the lower back and knee during walking.
Modelling the response of stable water isotopes in Greenland precipitation to orbital configurations of the previous interglacial

The relation between δ 18O of precipitation and temperature has been used in numerous studies to reconstruct past temperatures at ice core sites in Greenland and Antarctica. During the past two decades, it has become clear that the slope between δ 18O and temperature varies in both space and time. Here, we use a general circulation model driven by changes in orbital parameters to investigate the Greenland δ 18O–temperature relation for the previous interglacial, the Eemian. In our analysis, we focus on changes in the moisture source regions, and the results underline the importance of taking the seasonality of climate change into account. The orbitally driven experiments show that continental evaporation over North America increases during summer in the warm parts of the Eemian, while marine evaporation decreases. This likely flattens the Greenland δ 18O response to temperature during summer. Since the main climate change in the experiments occurs during summer this adds to a limited response of δ 18O, which is more strongly tied to temperature during winter than during summer. A south–west to north–east gradient in the δ 18O–temperature slope is also evident for Greenland, with low slopes in the south–west and steeper slopes in the north–east. This probably reflects the proportion of continental moisture and Arctic moisture arriving in Greenland, with more continental moisture in the south–west and less in the north–east, and vice versa for the Arctic moisture.
Opportunities and challenges for better than worst-case design

The progressive trend of fabrication technologies towards the nanometer regime has created a number of new physical design challenges for computer architects. Design complexity, uncertainty in environmental and fabrication conditions, and single-event upsets all conspire to compromise system correctness and reliability. Recently, researchers have begun to advocate a new design strategy called better than worst-case design that couples a complex core component with a simple reliable checker mechanism. By delegating the responsibility for correctness and reliability of the design to the checker, it becomes possible to build probably correct designs that effectively address the challenges of deep submicron design. In this paper, we present the concepts of better than worst-case design and highlight two exemplary designs: the DIVA checker and Razor logic. We show how this approach to system implementation relaxes design constraints on core components, which reduces the effects of physical design challenges and creates opportunities to optimize performance and power characteristics. We demonstrate the advantages of relaxed design constraints for the core components by applying typical case optimization (TCO) techniques to an adder circuit. Finally, we discuss the challenges and opportunities posed to CAD tools in the context of better than worst-case design. In particular, we describe the additional support required for analyzing run time characteristics of designs and the many opportunities which are created to incorporate typical-case optimizations into synthesis and verification.
Nurse Staffing and Patient Outcomes in Inpatient Rehabilitation Settings

&NA; In rehabilitation nursing, the patient classification systems or acuity models and nurse‐staffing ratios are not supported by empirical evidence. Moreover, there are no studies published characterizing nursing hours per patient day, proportion of RN staff, and impact of agency nurses in inpatient rehabilitation settings. The purpose of this prospective observational study was to describe rehabilitation nurse staffing patterns, to validate the impact of rehabilitation nursing on patient outcomes, and to test whether existing patient measures on severity and outcomes in rehabilitation could be used as a proxy for burden of care to predict rehabilitation nurse staffing ceilings and daily nurse staffing requirements. A total of 54 rehabilitation facilities in the United States, stratified by geography, were randomly selected to participate in the study.
Similarity in Information Retrieval

One of the key problems in the Information Retrieval (IR) is a similarity measure. IR systems that can model human performance often make use of similarity judgments that are non-metric; but when the triangle inequality is not obeyed, most existing IR techniques are not applicable. We define similarity as epsilon-k-ball in this paper and we focused on algorithms which use this similarity measure.
Reinforcement Belief Revision

The capability of revising its beliefs upon new information in a rational and efficient way is crucial for an intelligent agent. The classical work in belief revision focuses on idealized models and is not concerned with computational aspects. In particular, many researchers are interested in the logical properties (e.g. the AGM postulates) that a rational revision operator should possess. For the implementation of belief revision, however, one has to consider that any realistic agent is a finite being and that calculations take time. In this article, we introduce a new operation for revising beliefs which we call reinforcement belief revision. The computational model for this operation allows us to assess it in terms of time and space consumption. Moreover, the operation is proved equivalent to a (semantical) model based on the concept of possible worlds, which facilitates showing that reinforcement belief revision satisfies all desirable rationality postulates.
Investigating Endocytic Pathways to the Endoplasmic Reticulum and to the Cytosol Using SNAP‐Trap

Cholera toxin enters cells via an unusual pathway that involves trafficking through endosomes to the endoplasmic reticulum (ER). Whether the toxin induces its own pathway or travels along a physiological retrograde route is not known. To study its trafficking, we labeled cholera toxin B (CTB) or endogenous plasma membrane proteins with a small chemical compound, benzylguanine, which covalently reacts with the protein SNAP‐tag. Using ER‐targeted SNAP‐tag as reporter, we found that transport of CTB to the ER depends on dynamin‐2 and syntaxin 5. Plasma membrane proteins and a fluid‐phase marker added to the medium were also transported to the ER. This flux was not affected by exposing cells to CTB but was inhibited by depleting syntaxin 5 and increased by depleting dynamin‐2. As a control for confined intracellular localization of ER‐targeted SNAP‐tag we used adenovirus‐5, which traffics to endosomes and then escapes into the cytosol. The virus did not react with ER‐targeted SNAP but with cytosolic SNAP. Together, our results establish a new method (SNAP‐trap) to study trafficking of different cargo to the ER and the cytosol and provide evidence for the existence of a constitutive pathway from the cell surface to the ER.
Tetracarbonylbis(η5-cyclopentadienyl)bis(diphenylphosphine)dimolybdenum(Mo—Mo) hexane solvate

The title compound, [Mo2(C5H5)2(C12H11P)2(CO)4]·C6H14, is a centrosymmetric Mo complex in which two Mo atoms are connected by an Mo—Mo bond [3.2072 (12) Å]. Each Mo atom is coordinated by an η5-cyclopentadienyl ligand, two carbonyl ligands and a diphenylphosphine ligand in a piano-stool fashion.
Simple method for determination of cocaine and main metabolites in urine by CE coupled to MS

In this work, a simple method for the simultaneous determination of cocaine (COC) and five COC metabolites (benzoylecgonine, cocaethylene (CET), anhydroecgonine, anhydroecgonine methyl ester and ecgonine methyl ester) in human urine using CE coupled to MS via electrospray ionization (CE‐ESI‐MS) was developed and validated. Formic acid at 1 mol/L concentration was used as electrolyte whereas formic acid at 0.05 mol/L concentration in 1:1 methanol:water composed the coaxial sheath liquid at the ESI nozzle. The developed method presented good linearity in the dynamic range from 250 ng/mL to 5000 ng/mL (coefficient of determination greater than 0.98 for all compounds). LODs (signal‐to‐noise ratio of 3) were 100 ng/mL for COC and CET and 250 ng/mL for the other studied metabolites whereas LOQ's (signal‐to‐noise ratio of 10) were 250 ng/mL for COC and CET and 500 ng/mL for all other compounds. Intra‐day precision and recovery tests estimated at three different concentration levels (500, 1500 and 5000 ng/mL) provided RSD lower than 10% (except anhydroecgonine, 18% RSD) and recoveries from 83–109% for all analytes. The method was successfully applied to real cases. For the positive urine samples, the presence of COC and its metabolites was further confirmed by MS/MS experiments.
Re-sequencing Expands Our Understanding of the Phenotypic Impact of Variants at GWAS Loci

Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20–30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic traits, we conducted re-sequencing studies in >6,000 members of a Finnish population cohort (The Northern Finland Birth Cohort of 1966 [NFBC]) and a type 2 diabetes case-control sample (The Finland-United States Investigation of NIDDM Genetics [FUSION] study). By sequencing the coding sequence and 5′ and 3′ untranslated regions of 78 genes at 17 GWAS loci associated with one or more of six metabolic traits (serum levels of fasting HDL-C, LDL-C, total cholesterol, triglycerides, plasma glucose, and insulin), and conducting both single-variant and gene-level association tests, we obtained a more complete understanding of phenotype-genotype associations at eight of these loci. At all eight of these loci, the identification of new associations provides significant evidence for multiple genetic signals to one or more phenotypes, and at two loci, in the genes ABCA1 and CETP, we found significant gene-level evidence of association to non-synonymous variants with MAF<1%. Additionally, two potentially deleterious variants that demonstrated significant associations (rs138726309, a missense variant in G6PC2, and rs28933094, a missense variant in LIPC) were considerably more common in these Finnish samples than in European reference populations, supporting our prior hypothesis that deleterious variants could attain high frequencies in this isolated population, likely due to the effects of population bottlenecks. Our results highlight the value of large, well-phenotyped samples for rare-variant association analysis, and the challenge of evaluating the phenotypic impact of such variants.
Effect of increasing the fat content but not the energy load of a meal on gastro-oesophageal reflux and lower oesophageal sphincter motor function

Background—Although fatty foods are commonly considered detrimental in patients with reflux disease, no objective data exist that substantiate this belief. Aims—To investigate the effect of fat on gastro-oesophageal reflux and lower oesophageal sphincter (LOS) motor activity. Subjects—Thirteen healthy subjects and 14 patients with reflux disease. Methods—Oesophageal pH, LOS, and oesophageal pressures were recorded for 180 minutes after a high fat (52% fat) and a balanced (24% fat) meal (both 3.18 MJ) on two different occasions. Eight controls and seven patients were studied in the recumbent position and the others in the sitting position. Results—The percentage of time at pH less than 4 and the rate of reflux episodes were higher (p<0.01) in the patients than in the healthy subjects (mean 14.1% versus 1.7% and 4.4/h versus 0.8/h respectively), as was the percentage of transient LOS relaxations associated with reflux (62% versus 32%, p<0.01). The high fat meal did not increase the rate of reflux episodes nor exposure to oesophageal acid in either group regardless of body posture.The rate of transient LOS relaxations, their association with reflux, and basal LOS pressure were also unaffected. Conclusions—Increasing fat intake does not affect gastro-oesophageal reflux or oesophagogastric competence for at least three hours after a meal.
Analysis of a reconfigurable network processor

In this paper an analysis of a dynamically reconfigurable processor is presented. The network processor incorporates a processor and a number of coprocessors that can be connected to the processor either directly or using a shared bus. The analysis investigates the configuration (in terms of co-processor distributions and interface), formulates the throughput that meets the network demands and the constraints of the platform (area, bus bandwidth, etc.) and takes into account the reconfiguration overhead. To find the configuration that meets the constraints, the platform is formulated into integer linear programming equations. Furthermore, the results of two case studies are presented, for a soft- and a hard-IP core processor, that uses three flows with different processing requirements (IP forward, encryption and media processing). In each case the number and the type of co-processors is shown in terms of the network distribution and the average packet size. Finally, the mapping of the framework in the Xilinx FPGA platform is discussed