Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic Integration and the Plasticity of Integration in an Amphicarpic Annual

In annual plants, including amphicarpic annuals, variation in light availability can evoke phenotypic plasticity in multiple traits. We examined plasticity to light availability of vegetative and reproductive performance traits in Amphicarpaea bracteata (Fabaceae) by developing and evaluating three path‐analysis models using data from a greenhouse study. To assess whether light availability altered the phenotypic integration of these performance traits, we examined the models’ fit to data collected within a high‐ or a low‐light treatment. We also examined whether a single model or alternate models were required to fit data from the two contrasting light treatments. Using our path‐analysis approach, we also made comparisons among three population types: shade‐ and sun‐native populations of the widespread variety A. bracteata var. bracteata and sun‐native populations of the variety A. bracteata var. comosa. Although each type of population was somewhat distinctive in patterns of integration and in the plasticity of integration, patterns did not correspond to contrasting ecological affinity, i.e., shade‐ and sun‐native population types or to genetic relatedness of the two varieties. Counter to the prediction that selection regimes involving variation in one or more environmental factor favor intermediate levels of integration, phenotypic integration in A. bracteata was very flexible, with plasticity occurring in a trait‐by‐trait manner. In particular, there was an inverse relationship between aerial and subterranean reproductive modes in low but not high light. Previous studies of amphicarpic annuals have not observed this type of environment‐specific life history trade‐off.
The Role of Bacterial Biofilm in Adverse Soft-Tissue Filler Reactions: A Combined Laboratory and Clinical Study

Background: The development of chronic nodules and granulomatous inflammation after filler injections has been attributed to bacterial biofilm infection. The authors aimed to investigate the relationship between filler and bacterial biofilm using a combined in vitro and in vivo study. Methods: In vitro assays to investigate the ability of filler materials to support the growth of Staphylococcus epidermidis biofilm and the effect of multiple needle passes through a biofilm-contaminated surface were designed. Analysis of clinical biopsy specimens from patients presenting with chronic granulomas following filler administration using a number of laboratory tests for biofilm was performed. Results: All fillers (i.e., hyaluronic acid, polyacrylamide gel, and poly-L-lactic acid) supported the growth of S. epidermidis biofilm in vitro. Multiple needle passes through a biofilm-contaminated surface resulted in significantly increased contamination of filler material by a factor of 10,000 (p < 0.001). Six clinical samples from five patients all demonstrated bacterial biofilm. The mean number of bacteria was found to be 2.2 × 107 bacteria/mg tissue (range, 5.6 × 105 to 3.7 × 107 bacteria/mg tissue). Microbiome analysis detected a predominance of Pseudomonas, Staphylococcus, and Propionibacterium as present in these samples. Conclusions: Filler material can support the growth of bacterial biofilm in vitro. Multiple needle passes can significantly increase the risk of filler contamination. Biofilm appears to be associated with high numbers in clinical samples of patients presenting with chronic granulomatous inflammation. Strategies to reduce the risk of bacterial contamination need to be further studied and translated into clinical practice. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, V.
The Indian blood group system

Abstract The Indian blood group system (ISBT: IN/023) consists of two antithetical antigens: Ina(IN1), which is present in approximately 10 percent of some Arab populations and in 3 percent of Bombay Indians, and its allelic antigen Inb(IN2), an antigen of high incidence in all populations. In 2007, two new high-incidence antigens were identified as belonging to the IN blood group system, namely IN3 (INFI) and IN4 (INJA). The antigens in this system are located on CD44, a single-pass membrane glycoprotein that is encoded by the CD44gene on chromosome 11 at position p13. The biologic function of CD44 is as a leukocyte homing receptor and cellular adhesion molecule. The Inaand Inbpolymorphism represents a 252G>C substitution of CD44,encoding R46P, and lack of IN3 and IN4 results from homozygosity for mutations encoding H85Q and T163R in the CD44gene. The high-frequency antigen AnWj (901009) has not been assigned to the Indian system, but either is located on an isoform of CD44 or is closely associated with it. Immunohematology2011;27:89–93.
A Subset of Drosophila Integrator Proteins Is Essential for Efficient U7 snRNA and Spliceosomal snRNA 3′-End Formation

ABSTRACT Proper gene expression relies on a class of ubiquitously expressed, uridine-rich small nuclear RNAs (snRNAs) transcribed by RNA polymerase II (RNAPII). Vertebrate snRNAs are transcribed from a unique promoter, which is required for proper 3′-end formation, and cleavage of the nascent transcript involves the activity of a poorly understood set of proteins called the Integrator complex. To examine 3′-end formation in Drosophila melanogaster, we developed a cell-based reporter that monitors aberrant 3′-end formation of snRNA through the gain in expression of green fluorescent protein (GFP). We used this reporter in Drosophila S2 cells to determine requirements for U7 snRNA 3′-end formation and found that processing was strongly dependent upon nucleotides located within the 3′ stem-loop as well as sequences likely to comprise the Drosophila equivalent of the vertebrate 3′ box. Substitution of the actin promoter for the snRNA promoter abolished proper 3′-end formation, demonstrating the conserved requirement for an snRNA promoter in Drosophila. We tested the requirement for all Drosophila Integrator subunits and found that Integrators 1, 4, 9, and 11 were essential for 3′-end formation and that Integrators 3 and 10 may be dispensable for processing. Depletion of cleavage and polyadenylation factors or of histone pre-mRNA processing factors did not affect U7 snRNA processing efficiency, demonstrating that the Integrator complex does not share components with the mRNA 3′-end processing machinery. Finally, flies harboring mutations in either Integrator 4 or 7 fail to complete development and accumulate significant levels of misprocessed snRNA in the larval stages.
Patient preferences for treatment of major depressive disorder and the impact on health outcomes: a systematic review.

OBJECTIVE To summarize the peer-reviewed literature on patient preferences for depression treatments and the impact of these preferences on the outcomes of treatment. DATA SOURCES Studies were identified via a systematic search conducted simultaneously in PsycINFO and MEDLINE using EBSCOhost and EMBASE. Publications were retrieved in March 2010. STUDY SELECTION Search terms included depression OR MDD OR major depressive disorder, patient preference, treatment preference, intervention preference, and pharmacotherapy preference. There were no restrictions on years of publication. The search was restricted to research articles written in English. DATA EXTRACTION Fifteen articles contained unique information on patient preferences for depression treatments and their impact on depression-related outcomes. RESULTS The patient preference literature includes a limited number of studies examining the impact of patient preferences on outcomes such as depression severity, treatment initiation, persistence and adherence, treatment engagement, the development of the therapeutic alliance, and health-related quality of life. The majority of the preference research has focused on comparisons of psychotherapy versus pharmacotherapy, with some limited information regarding comparisons of psychotherapies. Results from the research to date suggest that the impact of patient treatment preferences is mixed. The results also indicate that patient preferences have minimal impact on depression severity outcomes within the context of controlled clinical trials but may be more strongly associated with other outcomes such as entry into treatment and development of the therapeutic alliance. However, it is important to note that the literature is limited in that the impact of patient preference has been examined only through secondary analyses, and there have been few studies designed explicitly to examine the impact of patient preferences, particularly outside the context of controlled clinical trials. CONCLUSIONS Consideration of patient preferences for depression treatments may lead to increased treatment initiation and improved therapeutic alliance. However, despite treatment guidelines and suggestions in the literature, the value of and appropriate procedures for considering patient preferences in real-world treatment decisions deserves more careful study. Further research is needed, and future studies should be conducted in more naturalistic treatment settings that examine patient preferences for other specific approaches to depression treatments including preferences related to comparisons of individual pharmacotherapies and second-step treatments.
PATHOGEN RESISTANCE AND GENETIC VARIATION AT MHC LOCI

Abstract Balancing selection in the form of heterozygote advantage, frequency-dependent selection, or selection that varies in time and/or space, has been proposed to explain the high variation at major histocompatibility complex (MHC) genes. Here the effect of variation of the presence and absence of pathogens over time on genetic variation at multiallelic loci is examined. In the basic model, resistance to each pathogen is conferred by a given allele, and this allele is assumed to be dominant. Given that s is the selective disadvantage for homozygotes (and heterozygotes) without the resistance allele and the proportion of generations, which a pathogen is present, is e, fitnesses for homozygotes become (1 − s)(n−1)e and the fitnesses for heterozygotes become (1 − s)(n−2)e, where n is the number of alleles. In this situation, the conditions for a stable, multiallelic polymorphism are met even though there is no intrinsic heterozygote advantage. The distribution of allele frequencies and consequently heterozygosity are a function of the autocorrelation of the presence of the pathogen in subsequent generations. When there is a positive autocorrelation over generations, the observed heterozygosity is reduced. In addition, the effects of lower levels of selection and dominance and the influence of genetic drift were examined. These effects were compared to the observed heterozygosity for two MHC genes in several South American Indian samples. Overall, resistance conferred by specific alleles to temporally variable pathogens may contribute to the observed polymorphism at MHC genes and other similar host defense loci.
LOR-Based Reconstruction for Super-Resolved 3D PET Image on GPU

Positron emission tomography (PET) images usually suffer from low spatial resolution mainly because of the finite dimension of crystals. To improve the spatial resolution based on wobble scanning, we previously proposed a sinogram-based super-resolution (SR) algorithm using a space-variant blur matrix. However, the algorithm may cause unwanted resolution loss owing to an inevitable interpolation process for preparing evenly spaced projections. In this article, we propose a novel one-step line of response (LOR)-based SR framework for 3D PET images. In the framework, we efficiently determine a large number of space-variant point spread functions (PSFs) in the image space by using the scanner symmetries and the proposed PSF interpolation scheme based on nonrigid registration. Furthermore, to minimize the resolution degradation in the evenly spaced parallel-beam rebinning and to reduce the computational time in the graphics processing unit (GPU) implementation, we introduce parallel-friendly LOR reconstruction based on cone-beam reordering. We then obtain a high resolution image via a one-step super-resolved 3D PET image reconstruction with the determined PSFs. The proposed framework provides noticeable improvement on the spatial resolution of PET images with a considerable reduction of computational time.
A modified lateral approach to the canine cervical spine: procedural description and clinical application in 16 dogs with lateralized compressive myelopathy or radiculopathy.

OBJECTIVE To describe a modified lateral surgical approach to the cervical spine in dogs and evaluate clinical outcomes of dogs with neurologic disorders treated with this technique. STUDY DESIGN Retrospective study. SAMPLE POPULATION Sixteen dogs with lesions involving the cervical spine. METHODS Medical records (1998-2002) of dogs that had a modified lateral approach to the cervical spine were reviewed. To reduce procedural morbidity, the surgical approach was modified from original descriptions of the technique by minimizing disruption of epaxial and extrinsic thoracic limb musculature and limiting the size of the operative field to the affected vertebral segment. Signalment, neurologic status on admission; onset, progression, and duration of clinical signs; diagnostic testing, etiologic diagnosis, surgical site(s), intra- and postoperative complications, hospitalization, time to optimum recovery, neurologic status at discharge, final neurologic status, and outcome were recorded. Neurologic status (0-5) was scored preoperatively, 1 day postoperatively, at discharge, and at recheck examination (8 dogs). Telephone interviews were used to obtain additional follow-up information. RESULTS None of the dogs had postoperative deterioration in neurologic status. Outcomes were good or excellent in dogs with intervertebral disc disease, 3/4 dogs with caudal cervical spondylomyelopathy, 1/2 dogs with spinal neoplasia, and in 1 dog with the vascular anomaly; long-term outcomes were unknown in 2 dogs. Intraoperative complications occurred in 3 dogs and included controllable venous plexus hemorrhage (2) and incorrect lesion localization (1). One dog was euthanatized because of postoperative complications. Hospitalization, time to optimal recovery, and overall outcome were not different from previously reported results using other surgical approaches to treat analogous neurologic conditions. CONCLUSIONS A modified lateral approach to the cervical spine is viable for surgical treatment of cervical myelopathic or radiculopathic lesions when exposure to foraminal and lateralized lesions of the vertebral canal involving the C2-C7 vertebral articulations is desirable. CLINICAL RELEVANCE A modified lateral approach to the cervical spine can be successfully used in dogs of all sizes to treat caudal cervical spondylomyelopathy, other anomalous conditions of the cervical spine, intervertebral disc disease, and spinal neoplasms. Although long-term follow-up was not available for all patients, outcomes were generally favorable.
Production of a monoclonal antibody directed against an interferon-induced 56,000-dalton protein and its use in the study of this protein

Interferon (IFN) treatment of cells induces the synthesis of several new proteins. A hybridoma cell line producing monoclonal antibody to the IFN-induced 56,000-dalton protein has been developed. The IFN-induced 56,000-dalton protein is synthesized by a variety of different cells and in response to IFN-alpha, IFN-beta, and IFN-gamma. The induction of this protein is dependent on de novo RNA synthesis, since its induction is inhibited if actinomycin D and the IFNs are added to the cells simultaneously. Labeling of IFN-treated cells at 4-h intervals at various times after the addition of the IFNs reveals that the synthesis of the 56,000-dalton protein in IFN-alpha-treated cells peaks within 12 h after the addition of the IFN and is no longer enhanced 20 h after exposure to the IFN. In contrast, IFN-gamma-treated cells continue to show an enhanced synthesis of this IFN-induced protein even after 20 h of exposure to the IFN. Thus, the synthesis of the IFN-induced 56,000-dalton protein is regulated differently by the different IFNs. When cells are treated with IFN-alpha or IFN-gamma in the presence of cycloheximide, and actinomycin D is added prior to the removal of the cycloheximide, the cells produce the IFN-induced 56,000-dalton protein and develop an antiviral state in response to both IFN-alpha and IFN-gamma. These results demonstrate that the synthesis of the 56,000-dalton protein is not dependent on the synthesis of an intermediary protein and that the establishment of an antiviral state occurs in the absence of multiple transcriptional events.
Estrogenic and toxic effects of methoxychlor on zebrafish (Danio rerio)

Although zebrafish (Danio rerio) have been suggested as a good candidate for screening potential endocrine disruptors, little information is available on the effects of weak estrogens on this species. We investigated the sensitivity of different life stages of zebrafish toward toxic and estrogenic properties of methoxychlor (MXC). Short‐term tests with adults resulted in a sex‐specific 96‐h lethal concentration for 50% (LC50) of the test animals of 36 μg/L for males and 129 μg/L for females. To determine the estrogenic capacity of MXC, adult zebrafish were exposed to 0, 0.5, 5, and 50 μg MXC/L for 14 d. Induction of vitellogenin ([VTG] measured with protein electrophoresis and Western blot) in males was detected at 5 and 50 μg MXC/L. Females, however, did not exhibit higher blood VTG concentrations at the tested MXC concentrations. In a second series of experiments, juvenile zebrafish were exposed to 0, 0.05, 0.5, and 5 μg MXC/L for 33 d. Survival, length, weight, and condition of larvae were examined as indicators of toxic stress and the VTG content in whole body homogenates of juveniles was measured to determine xenoestrogenic effects. No effects of the tested concentrations of MXC were observed. Finally, the effect of MXC on zebrafish eggs, exposed to 0, 1, 10, and 32 μg MXC/L, was examined. Hatching and survival of hatched zebrafish were affected at 10 and 32 μg MXC/L. This study demonstrated that adult male zebrafish are sensitive toward the estrogenic effects of MXC. However, the use of VTG induction to detect effects of (xeno)estrogens in early life stages has to be further investigated, as low concentrations of VTG were detectable in exposed as well as unexposed juvenile fish.
Premature translation termination mediates triosephosphate isomerase mRNA degradation

We characterized an anemia-inducing mutation in the human gene for triosephosphate isomerase (TPI) that resulted in the production of prematurely terminated protein and mRNA with a reduced cytoplasmic half-life. The mutation converted a CGA arginine codon to a TGA nonsense codon and generated a protein of 188 amino acids, instead of the usual 248 amino acids. To determine how mRNA primary structure and translation influence mRNA stability, in vitro-mutagenized TPI alleles were introduced into cultured L cells and analyzed for their effect on TPI RNA metabolism. Results indicated that mRNA stability is decreased by all nonsense and frameshift mutations. To determine the relative contribution of the changes in mRNA structure and translation to the altered half-life, the effects of individual mutations were compared with the effects of second-site reversions that restored translation termination to normal. All mutations that resulted in premature translation termination reduced the mRNA half-life solely or mainly by altering the length of the mRNA that was translated. The only mutation that altered translation termination and that reduced the mRNA half-life mainly by affecting the mRNA structure was an insertion that shifted termination to a position downstream of the normal stop codon.
Clinical comparison of contour and applanation tonometry and their relationship to pachymetry.

OBJECTIVES To compare intraocular pressure readings of recently introduced dynamic contour tonometry (DCT) with pneumatonometry (PTG) and Goldmann applanation tonometry (GAT) and to correlate central corneal thickness (CCT) with these readings. DESIGN Prospective, cross-sectional observation and instrument validation study. We included 258 independent eyes with normal anterior segment examinations results, irrespective of glaucoma diagnosis or glaucoma suspect. After pachymetry, DCT, PTG, and GAT were performed in a randomized order. Intraocular pressures as measured by DCT, PTG, and GAT were compared with each other and with CCT. RESULTS Eyes with thinner CCTs tended to yield lower intraocular pressure measurements by GAT. A significant correlation (Pearson product moment correlation, P<.001) between CCT and GAT was found with a regression of 0.25 mm Hg per 10 microm (R2 = 0.060). Variation of CCT had no significant effect on intraocular pressure measurements by PTG (P = .10; R2 = 0.01) and DCT (P = .80; R2<0.01). A piecewise regression model showed that GAT readings are not linearly correlated with CCT. Comparison of the slopes below and above 535 microm showed the highest significance (P<.001). CONCLUSIONS Goldmann applanation tonometry readings are potentially influenced by CCT, whereas PTG and DCT seem to be less dependent on CCT. Correlation between CCT and GAT is not linear. A simple correction formula suggesting a linear relationship might not be correct.
The UTIAS multi-robot cooperative localization and mapping dataset

This paper presents a two-dimensional multi-robot cooperative localization and mapping dataset collection for research and educational purposes. The dataset consists of nine sub-datasets, which can be used for studying problems such as robot-only cooperative localization, cooperative localization with a known map, and cooperative simultaneous localization and mapping (SLAM) . The data collection process is discussed in detail, including the equipment we used, how measurements were made and logged, and how we obtained groundtruth data for all robots and landmarks. The format of each file in each sub-dataset is also provided. The dataset is available for download at http://asrl.utias. utoronto.ca/datasets/mrclam/.
Influence of Pancreas Transplantation on Cardiorespiratory Reflexes, Nerve Conduction, and Mortality in Diabetes Mellitus

Cardiorespiratory reflexes (CRR) were studied by measuring heart-rate variation during 6 breaths/min respiration and a Valsalva maneuver in 232 insulin-dependent diabetic subjects. Abnormalities were found in 175 patients. During a 7-yr follow-up, 41 (23.4%) patients with abnormal and 2 (3.5%) with normal CRR tests died. The mortality rates of diabetic patients with abnormal autonomie function tests were 17% at 2.5 yr, 33% at 5 yr, and 40% at 7 yr, significantly higher (P < 0.002) than in patients with normal tests (rates of 4.6, 4.6, and 13.8% at the respective intervals). Nerve conduction studies (NCS) were indicative of somatic neuropathy in 148 of 205 patients. Mortality rates were higher in patients with abnormal NCS than in those with normal results (P < 0.025). Among patients with abnormal autonomie function, patients with a functioning pancreas transplantation (PTx) had better survival rates than patients with a failed PTx (P < 0.005) and, on long-term follow-up, better rates than patients without PTx. Similar results were found comparing the same group of patients who had abnormal NCS.