Miracle-dz/UniFAR-FTUs huggingface dataset:
In‐depth protein profiling of the postsynaptic density from mouse hippocampus using data‐independent acquisition proteomics

Located at neuronal terminals, the postsynaptic density (PSD) is a highly complex network of cytoskeletal scaffolding and signaling proteins responsible for the transduction and modulation of glutamatergic signaling between neurons. Using ion‐mobility enhanced data‐independent label‐free LC‐MS/MS, we established a reference proteome of crude synaptosomes, synaptic junctions, and PSD derived from mouse hippocampus including TOP3‐based absolute quantification values for identified proteins. The final dataset across all fractions comprised 49 491 peptides corresponding to 4558 protein groups. Of these, 2102 protein groups were identified in highly purified PSD in at least two biological replicates. Identified proteins play pivotal roles in neurological and synaptic processes providing a rich resource for studies on hippocampal PSD function as well as on the pathogenesis of neuropsychiatric disorders. All MS data have been deposited in the ProteomeXchange with identifier PXD000590 (http://proteomecentral.proteomexchange.org/dataset/PXD000590).
Stackelberg Game for Bandwidth Allocation in Cloud-Based Wireless Live-Streaming Social Networks

Multimedia social networks have been introduced as a new technology to enrich people's lives through enhanced multimedia distribution. On the other hand, a media cloud system can perform multimedia processing and storage, and provide heterogeneous multimedia services. However, the challenges still remain for end users (e.g., mobile devices and PCs) to receive multimedia streaming from the cloud system with satisfied quality-of-service (QoS). To address these challenges, an efficient multimedia distribution approach taking advantage of live-streaming social networks is innovated in this paper to deliver the media services from the cloud to both desktop and wireless end users. Our approach allows bandwidth limited mobile users to acquire live multimedia streaming from desktop users, directly based on their social relationships rather than from the cloud. When a number of mobile users compete for limited bandwidth access with the desktop users, a bandwidth allocation problem must be solved to meet all users' QoS requirements in the live-streaming social network. We formulate the problem as a two-stage Stackelberg game, in which both desktop users and mobile users target at maximizing their utilities. In our study, a noncooperative game is used to model the competition among the desktop users in terms of shared bandwidth and price in the first stage of the game. The second stage of the game models the behavior of a mobile user selecting the desktop users by an evolutionary game. In addition, a case study is conducted following the general Stackelberg game formulation, where the existence of a unique Nash equilibrium is proved. Based on our game modeling, we design protocols for both desktop and mobile users and evaluate them with numerical examples.
Prime-Boost Immunization Schedules Based on Influenza Virus and Vaccinia Virus Vectors Potentiate Cellular Immune Responses against Human Immunodeficiency Virus Env Protein Systemically and in the Genitorectal Draining Lymph Nodes

ABSTRACT Vaccines that elicit systemic and mucosal immune responses should be the choice to control human immunodeficiency virus (HIV) infections. We have previously shown that prime-boost immunizations with influenza virus Env and vaccinia virus (VV) WR Env recombinants induced an enhanced systemic CD8+ T-cell response against HIV-1 Env antigen. In this report, we analyzed in BALB/c mice after priming with influenza virus Env the ability of two VV recombinants expressing HIV-1 Env B (VV WR Env and the highly attenuated modified VV Ankara [MVA] Env) to boost cellular immune responses in the spleen and in the lymph nodes draining the genital and rectal tracts. Groups of mice were primed by the intranasal route with 104 PFU of influenza virus Env and boosted 14 days later by the intraperitoneal or intranasal route with 107 PFU of MVA Env or VV WR Env, while the control group received two immunizations with influenza virus Env. We found that the combined immunization (Flu/VV) increased more than 60 times the number of gamma interferon-specific CD8+ T cells compared to the Flu/Flu scheme. Significantly, boosting with MVA Env by the intraperitoneal route induced a response 1.25 or 2.5 times (spleen or genital lymph nodes) higher with respect to that found after the boost with VV WR Env. Mice with an enhanced CD8+ T-cell response also had an increased Th1/Th2 ratio, evaluated by the cytokine pattern secreted following in vitro restimulation with gp160 protein and by the specific immunoglobulin G2a (IgG2a)/IgG1 ratio in serum. By the intranasal route recombinant WR Env booster gave a more efficient immune response (10 and 1.3 times in spleen and genital lymph nodes, respectively) than recombinant MVA Env. However, the scheme influenza virus Env/MVA Env increased four times the response in the spleen, giving a low but significant response in the genital lymph nodes compared with a single intranasal immunization with MVA Env. These results demonstrate that the combination Flu/MVA in prime-booster immunization regimens is an effective vaccination approach to generate cellular immune responses to HIV antigens at sites critical for protective responses.
Phenylalanine transfer across the isolated perfused human placenta: an experimental and modeling investigation

Membrane transporters are considered essential for placental amino acid transfer, but the contribution of other factors, such as blood flow and metabolism, is poorly defined. In this study we combine experimental and modeling approaches to understand the determinants of [14C]phenylalanine transfer across the isolated perfused human placenta. Transfer of [14C]phenylalanine across the isolated perfused human placenta was determined at different maternal and fetal flow rates. Maternal flow rate was set at 10, 14, and 18 ml/min for 1 h each. At each maternal flow rate, fetal flow rates were set at 3, 6, and 9 ml/min for 20 min each. Appearance of [14C]phenylalanine was measured in the maternal and fetal venous exudates. Computational modeling of phenylalanine transfer was undertaken to allow comparison of the experimental data with predicted phenylalanine uptake and transfer under different initial assumptions. Placental uptake (mol/min) of [14C]phenylalanine increased with maternal, but not fetal, flow. Delivery (mol/min) of [14C]phenylalanine to the fetal circulation was not associated with fetal or maternal flow. The absence of a relationship between placental phenylalanine uptake and net flux of phenylalanine to the fetal circulation suggests that factors other than flow or transporter-mediated uptake are important determinants of phenylalanine transfer. These observations could be explained by tight regulation of free amino acid levels within the placenta or properties of the facilitated transporters mediating phenylalanine transport. We suggest that amino acid metabolism, primarily incorporation into protein, is controlling free amino acid levels and, thus, placental transfer.
Families by Choice and the Management of Low Income Through Social Supports

Processes of individualization have transformed families in late modernity. Although families may be more opportunistically created, they still face challenges of economic insecurity. In this article, we explore through in-depth qualitative interviews how families by choice manage low income through the instrumental and expressive supports that they give and receive. Two central themes organize our analysis: “defining/doing family” and “generationing. ” Coupling the individualization thesis with a life course perspective, we find that families by choice, which can include both kin and nonkin relations, are created as a result of shared life events and daily needs. Families by choice are then sustained through intergenerational practices and relations. Importantly, we add to the growing body of literature that illustrates that both innovation and convention characterize contemporary family life for low-income people.
Analysis of Numerical Errors in Large Eddy Simulation

We consider the question of "numerical errors" in large eddy simulation. It is often claimed that straightforward discretization and solution using centered methods of models for large eddy motion can simulate the motion of turbulent flows with complexity independent of the Reynolds number and dependence only on the resolution ``$\delta$'' of the eddies sought. This report considers this question analytically: Is it possible to prove error estimates for discretizations of actually used large eddy models whose error constants depend only on $\delta$ but not Re? We consider the most common, simplest, and most mathematically tractable model and the most mathematically clear discretization. In two cases, we prove such an error estimate and try to explain why our technique of proof fails in the most general case. Our analysis aims to assume as little time regularity on the true solution as possible.
Undiagnosed and Uncontrolled Chronic Conditions in China: Could Social Health Insurance Consolidation Make a Change?

Policy makers in China are considering consolidating the country’s fragmented health insurance programs. This system consists of three components. The Urban Employee Basic Medical Insurance (UEBMI) covers formal employees, the New Cooperative Medical Scheme (NCMS) covers rural residents, and the Urban Resident Basic Medical Insurance (URBMI) covers urban residents. Consolidation could, in theory, create a more efficient health system that is better able to address noncommunicable diseases. Using national survey data during 2011 to 2013, I found that 44% to 76% cases of hypertension, diabetes, and dyslipidemia went undiagnosed among Chinese adults aged 45 and older. I found that the UEBMI enrollees had a greater number of health checks and 10% higher rates of diagnosis. Assuming that this level of efficiency would be possible under an integrated system, I conducted microsimulation analyses to project future benefits. Such consolidation could result in 46.2 million new diagnoses, and 30.0 million of these cases would be controlled.
TALE-PvuII Fusion Proteins – Novel Tools for Gene Targeting

Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity.
Skull of a 5,300-year-old mummy: reproduction and investigation with CT-guided stereolithography.

PURPOSE In September 1991, a mummified corpse was discovered soon after it was released by the receding ice of the Similaun glacier in the Tyrolean Alps. This body proved to be an astonishingly well-preserved man from the late Neolithic Age or early Bronze Age. To preserve the fragile mummy, scientific investigations were required to be as noninvasive and nondestructive as possible. MATERIALS AND METHODS A radiologic investigation that included conventional radiography, digital radiography, and whole-body computed tomography (CT) was performed from the CT data, the skull was duplicated by means of stereolithography. RESULTS The copy of the prehistoric skull was validated by means of comparison of measurements obtained from the original CT images and from external physical measurements of the intact head of the mummy. CONCLUSION The CT images, radiologic findings, and duplicated skull are expected to provide anthropologists and other interested scientists relatively accurate information without the need to handle the mummy, to expose it to the considerable risks of repeated partial thawing, or to perform invasive exploratory studies such as autopsy.
A comparison of three methods for measure of Time to Contact

Time to contact (TTC) is a biologically inspired method for obstacle detection and reactive control of motion that does not require scene reconstruction or 3D depth estimation. Estimating TTC is difficult because it requires a stable and reliable estimate of the rate of change of distance between image features. In this paper we propose a new method to measure time to contact, active contour affine scale (ACAS). We experimentally and analytically compare ACAS with two other recently proposed methods: scale invariant ridge segments (SIRS), and image brightness derivatives (IBD). Our results show that ACAS provides a more accurate estimation of TTC when the image flow may be approximated by an affine transformation, while SIRS provides an estimate that is generally valid, but may not always be as accurate as ACAS, and IBD systematically over-estimate time to contact.
Adaptive Dropout Rates for Learning with Corrupted Features

Feature noising is an effective mechanism on reducing the risk of overfitting. To avoid an explosive searching space, existing work typically assumes that all features share a single noise level, which is often cross-validated. In this paper, we present a Bayesian feature noising model that flexibly allows for dimension-specific or group-specific noise levels, and we derive a learning algorithm that adaptively updates these noise levels. Our adaptive rule is simple and interpretable, by drawing a direct connection to the fitness of each individual feature or feature group. Empirical results on various datasets demonstrate the effectiveness on avoiding extensive tuning and sometimes improving the performance due to its flexibility.
Explaining Delinquent Involvement: a Consideration of Suppressor Effects

Delinquency research is characterized by empirical models which generally afford low degrees of explanatory power. While the small R2s which characterize the discipline may be attributed, in part, to methodological and theoretical problems, part of the explanation for the insufficiency of our models may lie in a failure to consider the statistical issue of suppression. Utilizing data from the first two waves of the Youth in Transition study, an empirical example is offered in an attempt to demonstrate the importance of considering suppressor effects in delinquency research. Beginning with a bivariate correlation between social class and delinquency that is effectively zero, multivariate analyses are conducted in order to determine whether attachment to school serves as a suppressor in this relationship. The results of the analyses reveal that social class is, in fact, related to delinquent involvement but that the relationship is apparent only when controlling for the attachment variables. Ramifications of this finding are discussed and an explanation of how to recognize suppressor effects is offered.
Time-frequency principal components of speech: application to speaker identification

In this paper, we propose a formalism, called vector ﬁltering of spectral trajectories, which allows to integrate under a common formalism a lot of speech parameterization approaches. We then propose a new ﬁltering in this framework, called time-frequency principal components (TFPC) of speech. We apply this new ﬁltering in the framework of speaker identiﬁcation, using a subset of the POLYCOST database. The results show an improvement of roughly 20 % compared to the use of the classical cepstral coefﬁcients augmented by their (cid:1) coefﬁcients.
Feedback from plant species change amplifies CO2 enhancement of grassland productivity

Dynamic global vegetation models simulate feedbacks of vegetation change on ecosystem processes, but direct, experimental evidence for feedbacks that result from atmospheric CO2 enrichment is rare. We hypothesized that feedbacks from species change would amplify the initial CO2 stimulation of aboveground net primary productivity (ANPP) of tallgrass prairie communities. Communities of perennial forb and C4 grass species were grown for 5 years along a field CO2 gradient (250–500 μL L−1) in central Texas USA on each of three soil types, including upland and lowland clay soils and a sandy soil. CO2 enrichment increased community ANPP by 0–117% among years and soils and increased the contribution of the tallgrass species Sorghastrum nutans (Indian grass) to community ANPP on each of the three soil types. CO2‐induced changes in ANPP and Sorghastrum abundance were linked. The slope of ANPP‐CO2 regressions increased between initial and final years on the two clay soils because of a positive feedback from the increase in Sorghastrum fraction. This feedback accounted for 30–60% of the CO2‐mediated increase in ANPP on the upland and lowland clay soils during the final 3 years and 1 year of the experiment, respectively. By contrast, species change had little influence on the ANPP‐CO2 response on the sandy soil, possibly because Sorghastrum increased largely at the expense of a functionally similar C4 grass species. By favoring a mesic C4 tall grass, CO2 enrichment approximately doubled the initial enhancement of community ANPP on two clay soils. The CO2‐stimulation of grassland productivity may be significantly underestimated if feedbacks from plant community change are not considered.
History of Education in Modern and Contemporary Europe: New Sources and Lines of Research

James Albisetti is certainly right when stressing that “attempting to establish an agenda for one's own research is often challenging; trying to do so for a broad swath of one's field is even more so. ” One might add that discussing the research agenda of other historians is equally difficult in light of the peculiarities of the lines of investigations which reflect specific research interests, sometimes consolidated over years or even decades. Specialization legitimates a historian's competence and guarantees the completeness or relevance of the sources used, the methodological rigor, the reliability and consistency of the reconstruction carried out, and, finally, the effectiveness of critical evaluations and judgments formulated.
An efficient AdaBoost tracking algorithm based on the particle framework

Object tracking is a classic problem in the computer vision field. Its main purpose is to get the locations, the motion parameters, the trajectories and other information of the objects from the videos. An Adaboost tracking algorithm based on the particle framework is proposed in this paper. Due to the existence of high noises in the training samples, the difficulty of the AdaBoost training and the possibility of the unsuccessful tracking would be increased to some extent. So we use the random distributed particles to avoid the tracking falling into the local optimum. And by combining some weak classifiers with weights, the strong classifier of the Adaboost is used to update the training template on line. The experiments results show that our algorithm improves the tracking accuracy significantly compared to the original AdaBoost tracking.
Revisiting the relationship between document length and relevance

The scope hypothesis in Information Retrieval (IR) states that a relationship exists between document length and relevance, such that the likelihood of relevance increases with document length. A number of empirical studies have provided statistical evidence supporting the scope hypothesis. However, these studies make the implicit assumption that modern test collections are complete (i.e. all documents are assessed for relevance). As a consequence the observed evidence is misleading. In this paper we perform a deeper analysis of document length and relevance taking into account that test collections are incomplete. We first demonstrate that previous evidence supporting the scope hypothesis was an artefact of the test collection, where there is a bias towards longer documents in the pooling process. We evaluate whether this length bias affects system comparison when using incomplete test collections. The results indicate that test collections are problematic when considering MAP as a measure of effectiveness but are relatively robust when using bpref. The implications of the study indicate that retrieval models should not be tuned to favour longer documents, and that designers of new test collections should take measures against length bias during the pooling process in order to create more reliable and robust test collections.
A novel splice site mutation of CDHR1 in a consanguineous Israeli Christian Arab family segregating autosomal recessive cone-rod dystrophy

Purpose To investigate the genetic basis for autosomal recessive cone-rod dystrophy in a consanguineous Israeli Christian Arab family. Methods Patients underwent a detailed ophthalmic examination, including funduscopy, electroretinography (ERG), visual field testing, and optical coherence tomography. Genome-wide homozygosity mapping using a single nucleotide polymorphism array was performed to identify homozygous regions shared between the two affected individuals. Mutation screening of the underlying gene was performed with direct sequencing. In silico analysis was used to predict the effect of the mutation on splicing. Results The family included two affected individuals. Clinical findings included progressive deterioration of visual acuity, photophobia, defective color vision, loss of central visual fields, pigmentary deposits localized mainly in the peripheral retina, a thinned and atrophic macular region, retinal vessel attenuation, absent ERG cone responses, and reduced ERG rod responses. Homozygosity mapping revealed several homozygous intervals shared among the affected individuals. One, a 12Mb interval on chromosome 10, included the CDHR1 gene. Direct sequencing revealed a single base transversion, c.1485+2T>G, located in the conserved donor splice site of Intron 13. This mutation cosegregated with the disease in the family, and was not detected in 208 Israeli Christian Arab control chromosomes. In silico analysis predicted that this mutation eliminates the Intron 13 donor splice site. Conclusions Only three distinct pathogenic mutations of CDHR1 have been reported to date in patients with autosomal recessive retinal degeneration. Here we report a novel splice site mutation of CDHR1, c.1485+2T>G, underlying autosomal recessive cone-rod dystrophy in a consanguineous Israeli Christian Arab family. This report expands the spectrum of pathogenic mutations of the CDHR1 gene.