Miracle-dz/UniFAR-FTUs huggingface dataset:
Extra-hepatic expression of serum albumin mRNA in mouse retina

Purpose. In some mammals, serum albumin protein exists in the interphotoreceptor space (IPS), the space between photoreceptor cells and the retinal pigment epithelium. Serum albumin is synthesized largely in the liver, though low levels of extra-hepatic expression have been documented in several other tissues, including fetal rat kidney, pancreas, lung, and heart. The purpose of this study was to investigate whether serum albumin protein and mRNA are found in mouse retina. Methods. Using albumin rabbit antibodies and HRP goat anti-(rabbit IgG), we performed immunoassays on mouse IPS washes to detect the presence of serum albumin protein. Protein extracts from IPS washes were subjected to Affigel Blue chromatography. This resin has an affinity for serum albumin. Reverse transcription-polymerase chain reaction (RT-PCR) of retina total RNA was performed to search for albumin mRNA. Also, real-time reverse transcription polymerase chain reaction (RT-RT-PCR) was employed to look at the levels of expression in different age groups. Results. A constituent of the IPS washes specifically bound and eluted from Affigel Blue column, suggesting that the washes contained serum albumin. SDS PAGE revealed that the size of the constituent was 67 kDa, the size of serum albumin. This 67 kDa band reacted with mouse serum antibody. An RT-PCR amplified fragment of serum albumin mRNA from retina displayed the expected size. The sequence of this fragment is identical to authentic serum albumin cDNA sequence. RPE and choroid were negative for serum albumin mRNA. However, rd1 - /rd1 - retina was positive, suggesting that at least some serum albumin is synthesized in the inner layers of the retina. RT-RT-PCR showed that serum albumin mRNA levels in whole retina reached a maximum at about postnatal day 15 and gradually decreased to about one-sixth of maximum at 12 months age. Conclusions. Serum albumin protein and mRNA were found in mouse IPS and retina, suggesting that the protein is synthesized in the retina. The previously demonstrated ability of serum albumin to bind fatty acids and retinoids and its presence in the mouse IPS suggest a role for serum albumin in transporting retinoids in the retina or IPS, especially at young ages when concentrations appear greatest.
Software Cost Estimation Using Economic Production Models

One of the major difficulties in controlling software development project cost overruns and schedule delays has been developing practical and accurate software cost models. Software development could be modeled as an economic production process and we therefore propose a theoretical approach to software cost modeling. Specifically, we present the Minimum Software Cost Model (MSCM), derived from economic production theory and systems optimization. The MSCM model is compared with other widely used software cost models, such as COCOMO and SLIM, on the basis of goodness of fit and quality of estimation using software project data sets available in the literature. Judged by both criteria, the MSCM model is comparable to, if not better than, the SLIM, and significantly better than the rest of the models. In addition, the MSCM model provides some insights about the behavior of software development processes and environment, which could be used to formulate guidelines for better software project management polices and practices.
Learning Semantic Part-Based Models from Google Images

We propose a technique to train semantic part-based models of object classes from Google Images. Our models encompass the appearance of parts and their spatial arrangement on the object, specific to each viewpoint. We learn these rich models by collecting training instances for both parts and objects, and automatically connecting the two levels. Our framework works incrementally, by learning from easy examples first, and then gradually adapting to harder ones. A key benefit of this approach is that it requires no manual part location annotations. We evaluate our models on the challenging PASCAL-Part dataset [1] and show how their performance increases at every step of the learning, with the final models more than doubling the performance of directly training from images retrieved by querying for part names (from 12.9 to 27.2 AP). Moreover, we show that our part models can help object detection performance by enriching the R-CNN detector with parts.
The Influence of Pre- and Postoperative Fear Avoidance Beliefs on Postoperative Pain and Disability in Patients With Lumbar Spinal Stenosis: Analysis of the Lumbar Spinal Outcome Study (LSOS) Data

Study Design. Prospective multicenter cohort study. Objective. To evaluate the effect of pre- and postoperatively assessed fear avoidance beliefs (FAB) on pain and disability in patients with degenerative lumbar spinal stenosis (LSS) after decompression surgery. Summary of Background Data. To the present, the influence of pre- and postoperative FAB on the prognosis after surgery for LLS is still unclear. Methods. Patients of the Swiss Lumbar Stenosis Outcome Study (LSOS) with confirmed LSS undergoing first-time decompression without fusion were enrolled in this study. The main outcome of this study was minimal clinically important difference (MCID) in spinal stenosis measure symptoms (pain) and function (disability) after 12 months. To analyze the influence of pre- and postoperatively assessed FAB on pain and disability we built simple and multiple logistic regression models. Results. In this analysis of 234 patients undergoing decompression surgery for symptomatic degenerative LSS we found baseline FAB measured by the FAB physical activity subscale (FABQ-P) not to be associated with pain (OR 0.95; 95% CI: 0.55–1.67) and disability (OR 1.11; 95% CI: 0.64–1.92) at 12 months’ follow-up. In the final multiple logistic regression models patients with high FABQ-P at 6 months (OR 0.46; 95% CI: 0.24–0.91) and high persistent FABQ-P at baseline and 6 months (OR 0.34, 95% CI: 0.16–0.73) were less likely to report a MCID for spinal stenosis measure symptoms at 12 months. Our analysis found a similar trend for disability; however, the results were not statistically significant. Conclusion. In elderly patients undergoing decompression surgery for symptomatic degenerative LSS preoperative fear avoidance beliefs were not a prognostic indicator for the outcome. Patients with FAB at 6 months and persistent FAB were less likely to experience clinically relevant improvement in pain at 12 months. Studies should address the importance of persistent postoperative FAB. Level of Evidence: 3
The biomechanical effectiveness of prophylactic vertebroplasty: a dynamic cadaveric study.

OBJECT The purpose of the study was to investigate the segmental effects of prophylactic vertebroplasty under increasingly demanding loading conditions and to assess the effect of altered cement properties on the construct biomechanics. METHODS Twelve human cadaveric 3-vertebral functional spinal units (T12-L2) were prepared such that the intact L-1 vertebra was prophylactically augmented with cements of differing elastic moduli (100, 50, 25, and 12.5% modulus of the base cement). These specimens were subjected to quasistatic subfailure compression pre- and postaugmentation to 50% of the predicted failure strength and then cyclic loading in a fatigue rig (115,000 cycles) to characterize the high-stress, short-cycle fatigue properties of the construct. Loading was increased incrementally in proportion to body weight to a maximum of 3.5 x body weight. Quantitative computed tomography assessment was conducted pre- and postaugmentation and following cyclic testing to assess vertebral condition, cement placement, and fracture classification. RESULTS Adjacent and periaugmentation fractures were induced in the prophylactically augmented segments. However, it appeared that these fractures mainly occurred when the specimens were subjected to loads beyond those that may commonly occur during most normal physiological activities. CONCLUSIONS Lowering the elastic modulus of the cement appeared to have no significant effect on the frequency or severity of the induced fracture within the vertebral segment.
Slc4a11 Gene Disruption in Mice

NaBC1 (the SLC4A11 gene) belongs to the SLC4 family of sodium-coupled bicarbonate (carbonate) transporter proteins and functions as an electrogenic sodium borate cotransporter. Mutations in SLC4A11 cause either corneal abnormalities (corneal hereditary dystrophy type 2) or a combined auditory and visual impairment (Harboyan syndrome). The role of NaBC1 in sensory systems is poorly understood, given the difficulty of studying patients with NaBC1 mutations. We report our findings in Slc4a11−/− mice generated to investigate the role of NaBC1 in sensorineural systems. In wild-type mice, specific NaBC1 immunoreactivity was detected in fibrocytes of the spiral ligament, from the basal to the apical portion of the cochlea. NaBC1 immunoreactivity was present in the vestibular labyrinth, in stromal cells underneath the non-immunoreactive sensory epithelia of the macula utricle, sacule, and crista ampullaris, and the membranous vestibular labyrinth was collapsed. Both auditory brain response and vestibular evoked potential waveforms were significantly abnormal in Slc4a11−/− mice. In the cornea, NaBC1 was highly expressed in the endothelial cell layer with less staining in epithelial cells. However, unlike humans, the corneal phenotype was mild with a normal slit lamp evaluation. Corneal endothelial cells were morphologically normal; however, both the absolute height of the corneal basal epithelial cells and the relative basal epithelial cell/total corneal thickness were significantly increased in Slc4a11−/− mice. Our results demonstrate for the first time the importance of NaBC1 in the audio-vestibular system and provide support for the hypothesis that SLC4A11 should be considered a potential candidate gene in patients with isolated sensorineural vestibular hearing abnormalities.
Test Method Evaluation Experiments & Data

Understanding the effectiveness of their production tests is a critical task for IC suppliers. Numerous trends suggesting that conventionally applied test methods must change to meet future needs will make the task even more critical – and difficult – in the future. This paper presents characterization and diagnostic data and ideas aimed at helping IC suppliers understand test effectiveness.
Crucial Role for Phylogenetically Conserved Cytoplasmic Loop 3 in ABCC4 Protein Expression*

Background: The role of cytoplasmic loops (CL) in ABCC4 expression at the plasma membrane is unknown. Results: A conserved amino acid substitution in the CL3 of ABCC4 reduced expression and impaired membrane localization. Conclusion: An α-helical domain in CL3 appears crucial for proper ABCC4 plasma membrane localization. Significance: These findings reveal ABCC4 membrane localization requires a conserved domain in CL3. The ABC transporter ABCC4 is recognized as an ATP-dependent exporter of endogenous substances as well as an increasing variety of anionic chemotherapeutics. A loss-of-function variant of zebrafish Abcc4 was identified with a single amino acid substitution in the cytoplasmic loop T804M. Because this substituted amino acid is highly conserved among ABCC4 orthologs and is located in cytoplasmic loop 3 (CL3), we investigated the impact of this mutation on human and zebrafish Abcc4 expression. We demonstrate that zebrafish Abcc4 T804M or human ABCC4 T796M exhibit substantially reduced expression, coupled with impaired plasma membrane localization. To understand the molecular basis for the localization defect, we developed a homology model of zebrafish Abcc4. The homology model suggested that the bulky methionine substitution disrupted side-chain contacts. Molecular dynamic simulations of a fragment of human or zebrafish CL3 containing a methionine substitution indicated altered helicity coupled with reduced thermal stability. Trifluoroethanol challenge coupled with circular dichroism revealed that the methionine substitution disrupted the ability of this fragment of CL3 to readily form an α-helix. Furthermore, expression and plasma membrane localization of these mutant ABCC4/Abcc4 proteins are mostly rescued by growing cells at subphysiological temperatures. Because the cystic fibrosis transmembrane conductance regulator (ABCC7) is closely related to ABCC4, we extended this by engineering certain pathogenic CFTR-CL3 mutations, and we showed they destabilized human and zebrafish ABCC4. Altogether, our studies provide the first evidence for a conserved domain in CL3 of ABCC4 that is crucial in ensuring its proper plasma membrane localization.
Cascading cis-Cleavage on Transcript from trans-Acting siRNA-Producing Locus 3

The production of small RNAs (sRNAs) from phased positions set by microRNA-directed cleavage of trans-acting-siRNA-producing locus (TAS) transcript has been characterized extensively; however, the production of sRNAs from non-phased positions remains unknown. We report three cis-cleavages that occurred in TAS3 transcripts in Vitis vinifera, by combining high-throughput sRNA deep sequencing information with evolutional conservation and genome-wide RNA degradome analysis. The three cis-cleavages can be deciphered to generate an orderly cleavage cascade, and can also produce distinct phasing patterns. Each of the patterns, either upstream or downstream of the cis-cleaved position, had a set of sRNAs arranged in 21-nucleotide increments. Part of the cascading cis-cleavages was also conserved in Arabidopsis thaliana. Our results will enhance the understanding of the production of sRNAs from non-phased positions that are not set by microRNA-directed cleavage.
Evidence for successful implementation of exposure and response prevention in a naturalistic group format for pediatric OCD

Background: Although exposure and response prevention (ERP) is an effective treatment for youth with obsessive–compulsive disorder (OCD), the majority of studies, randomized clinical trials of individual therapy, find variability in treatment response. We evaluated the potential role of individual differences in OCD presentation, comorbid disorders, age, and gender on treatment effects. Moreover, we examined these potential effects in a group format in a naturalistic, clinic‐based sample of patients. Methods: Pediatric patients with a DSM‐IV diagnosis of OCD (n=41) were treated with ERP in an intensive outpatient community‐based program. OCD, mood, and anxiety symptom severity was measured at baseline, during treatment, and at discharge. Trajectories and predictors of treatment outcome were measured using linear growth models. Results: We found that group‐based ERP was effective in reducing pediatric OCD symptom severity in a naturalistic treatment setting irrespective of age or gender. Furthermore, ERP was found to be effective at reducing depressive symptoms but not other anxiety symptoms. We also found inter‐individual variability in the discharge levels of contamination, symmetry, and intrusive sexual thoughts and in the rate of severity reduction of intrusive sexual thoughts. Conclusion: Group‐based ERP is an effective treatment for children and adolescents with OCD. Several factors, including symptom dimensions and comorbid psychopathology, are associated with treatment response and outcome in this pediatric population. Depression and Anxiety, 2011. © 2011 Wiley‐Liss, Inc.
Regulation of the intracellular free calcium concentration in acutely dissociated neurones from rat nucleus basalis.

1. Neurones were acutely dissociated from the rat nucleus basalis. Whole‐cell patch clamp recordings of calcium currents (ICa) and fura‐2 microfluorimetric recordings of intracellular free Ca2+ concentration ([Ca2+]i) were made simultaneously. 2. Depolarization from ‐60 to 0 mV elicited ICa and a gradual increase in [Ca2+]i. After repolarization, ICa terminated in 0.7 ms, and [Ca2+]i recovered to control exponentially (1‐5 s). 3. Both ICa and the transient [Ca2+]i increase in response to step depolarizations, were abolished in Ca2+ free extracellular solution and in Cd(2+)‐containing solution. 4. Depolarizations from ‐90 mV to membrane potentials less negative than ‐40 mV induced ICa and an increase in [Ca2+]i. Depolarization to 0 mV elicited the maximum ICa, and produced the largest increase in [Ca2+]i. There was a parallel relationship between the [Ca2+]i increase and the magnitude of the ICa. 5. The [Ca2+]i increase was associated with an increase in total Ca2+ influx when the duration of the step depolarization was varied. The relationship between the total Ca2+ influx and the peak of [Ca2+]i transient reached an asymptote as total Ca2+ influx exceeded 200 pC. A similar finding was made when more than thirty action potentials were used in increasing [Ca2+]i. 6. The process of the [Ca2+]i recovery was slowed down by lowering the temperature, by an intracellular dialysis with vanadate, by extracellular application of a mitochondrial inhibitor, carbonyl cyanide m‐chlorophenyl‐hydrazone (CCCP), and by Na(+)‐free external solution. It was unaffected by membrane potential (‐50 to ‐130 mV). 7. When pipette solution contained a high concentration of fura‐2 (200 microM), the [Ca2+]i increase per 1 pC of Ca2+ influx decreased, and the [Ca2+]i recovery was slowed. 8. The results indicate that the ICa through voltage‐dependent Ca2+ channels elevates [Ca2+]i. The neurones possess a large capacity for Ca2+ buffering, and the recovery of [Ca2+]i requires both the Ca2+ pump and membrane Na(+)‐Ca2+ exchange.
eGraphSearch: Effective Keyword Search in Graphs

In a node-labeled graph, keyword search finds subtrees of the graph whose nodes contain all of the query keywords. This provides a way to query graph databases that neither requires mastery of a query language such as SPARQL, nor a deep knowledge of the database schema. We demonstrate eGraphSearch, a new system for effective keyword search in graph databases. Previous work ranks answer trees using combinations of structural and content-based metrics, such as path length between keywords or relevance of the labels in the answer tree to the query keywords. However, different nodes in the graph might have different importance, which affects the utility of the answer. In the proposed system, we implemented two new ways to rank keyword search results over graphs: the first one takes node importance into account while the second one is a bi-objective optimization of edge weights and node importance. In the demonstration, participants will execute keyword queries against several popular graph datasets.
The D1 Dopamine Receptor Is Constitutively Phosphorylated by G Protein-Coupled Receptor Kinase 4

G protein-coupled receptor (GPCR) kinases (GRKs) phosphorylate agonist-activated GPCRs, initiating their homologous desensitization. In this article, we present data showing that GRK4 constitutively phosphorylates the D1 receptor in the absence of agonist activation. This constitutive phosphorylation is mediated exclusively by the α isoform of GRK4; the β, γ, and δ isoforms are ineffective in this regard. Mutational analysis reveals that the constitutive phosphorylation mediated by GRK4α is restricted to the distal region of the carboxyl terminus of the receptor, specifically to residues Thr428 and Ser431. Phosphorylation of the D1 receptor by GRK4α results in a decrease in cAMP accumulation, an increase in receptor internalization, and a decrease in total receptor number—all of which are abolished in a D1 receptor mutant containing T428V and S431A. The increase in internalized D1 receptors induced by GRK4α phosphorylation is due to enhanced receptor internalization rather than retarded trafficking of newly synthesized receptors to the cell surface. The constitutive phosphorylation of the D1 receptor by GRK4α does not alter agonist-induced desensitization of the receptor because dopamine pretreatment produced a similar decrease in cAMP accumulation in control cells versus cells expressing GRK4α. These observations shift the attenuation of D1 receptor signaling from a purely agonist-driven process to one that is additionally modulated by the complement of kinases that are coexpressed in the same cell. Furthermore, our data provide direct evidence that, in contrast to current dogma, GRKs can (at least in some instances) constitutively phosphorylate GPCRs in the absence of agonist activation resulting in constitutive desensitization.
Perceptual quality prediction on authentically distorted images using a bag of features approach

Current top-performing blind perceptual image quality prediction models are generally trained on legacy databases of human quality opinion scores on synthetically distorted images. Therefore, they learn image features that effectively predict human visual quality judgments of inauthentic and usually isolated (single) distortions. However, real-world images usually contain complex composite mixtures of multiple distortions. We study the perceptually relevant natural scene statistics of such authentically distorted images in different color spaces and transform domains. We propose a “bag of feature maps” approach that avoids assumptions about the type of distortion(s) contained in an image and instead focuses on capturing consistencies—or departures therefrom—of the statistics of real-world images. Using a large database of authentically distorted images, human opinions of them, and bags of features computed on them, we train a regressor to conduct image quality prediction. We demonstrate the competence of the features toward improving automatic perceptual quality prediction by testing a learned algorithm using them on a benchmark legacy database as well as on a newly introduced distortion-realistic resource called the LIVE In the Wild Image Quality Challenge Database. We extensively evaluate the perceptual quality prediction model and algorithm and show that it is able to achieve good-quality prediction power that is better than other leading models.
A stochastic analogue of Aubry-Mather theory

In this paper, we discuss a stochastic analogue of Aubry-Mather theory in which a deterministic control problem is replaced by a controlled diffusion. We prove the existence of a minimizing measure (Mather measure) and discuss its main properties using viscosity solutions of Hamilton-Jacobi equations. Then we prove regularity estimates on viscosity solutions of the Hamilton-Jacobi equation using the Mather measure. Finally, we apply these results to prove asymptotic estimates on the trajectories of controlled diffusions and study the convergence of Mather measures as the rate of diffusion vanishes.