Miracle-dz/UniFAR-FTUs huggingface dataset:
PHYLOGENOMICS AND SECONDARY PLASTIDS: A LOOK BACK AND A LOOK AHEAD 1

Despite their importance to evolution, ecology, and cell biology, eukaryotes that acquired plastids through secondary endosymbiosis remain poorly studied from a genomic standpoint. Chromalveolata, a eukaryotic supergroup proposed to have descended from a heterotrophic eukaryote that acquired a red algal plastid by secondary endosymbiosis, includes four major lineages (alveolates, cryptophytes, haptophytes, and heterokonts). The chromalveolates exhibit remarkable diversity of cellular organization, and the available data suggest that they exhibit equal diversity in their genome organization. One of the most obvious differences in cellular organization is the retention of a highly reduced red algal nucleus in cryptophytes (also known as cryptomonads), but there are other major differences among chromalveolate lineages, including the loss of photosynthesis in multiple lineages. Although the hypothesis of chromalveolate monophyly is appealing, there is limited support for the hypothesis from nuclear genes, and questions have even been raised about the monophyly of chromalveolate plastids. Evidence for the chromalveolate hypothesis from large‐scale nuclear data sets is reviewed, and alternative hypotheses are described. The potential for integrating information from chromalveolate genomics into functional genomics is described, emphasizing both the methodological challenges and the opportunities for future phylogenomic analyses of these groups.
New toxins homologous to ParE belonging to three‐component toxin–antitoxin systems in Escherichia coli O157:H7

Type II toxin–antitoxin (TA) systems are considered as protein pairs in which a specific toxin is associated with a specific antitoxin. We have identified a novel antitoxin family (paaA) that is associated with parE toxins. The paaA–parE gene pairs form an operon with a third component (paaR) encoding a transcriptional regulator. Two paralogous paaR–paaA–parE systems are found in E. coli O157:H7. Deletions of the paaA–parE pairs in O157:H7 allowed us to show that these systems are expressed in their natural host and that PaaA antitoxins specifically counteract toxicity of their associated ParE toxin. For the paaR2–paaA2–parE2 system, PaaR2 and Paa2–ParE2 complex are able to regulate the operon expression and both are necessary to ensure complete repression. The paaR2–paaA2–parE2 system mediates ClpXP‐dependent post‐segregational killing. The PaaR2 regulator appears to be essential for this function, most likely by maintaining an appropriate antitoxin : toxin ratio in steady‐state conditions. Ectopic overexpression of ParE2 is bactericidal and is not resuscitated by PaaA2 expression. ParE2 colocalizes with the nucleoid, while it is diffusely distributed in the cytoplasm when PaaA2 is coexpressed. This indicates that ParE2 interacts with DNA‐gyrase cycling on DNA and that coexpression of PaaA2 antitoxin sequesters ParE2 away from its target by protein–protein complex formation.
A Novel Mutation in Murine Hepatitis Virus nsp5, the Viral 3C-Like Proteinase, Causes Temperature-Sensitive Defects in Viral Growth and Protein Processing

ABSTRACT Sequencing and reversion analysis of murine hepatitis virus (MHV) temperature-sensitive (ts) viruses has identified putative ts mutations in the replicase nonstructural proteins (nsp's) of these coronaviruses. In this study, reverse transcriptase PCR sequencing of the RNA genome of an isolate of the MHV ts virus Alb ts6, referred to as Alb/ts/nsp5/V148A, identified a putative ts mutation in nsp5 (T10651C, Val148Ala), the viral 3C-like proteinase (3CLpro). The introduction of the T10651C mutation into the infectious MHV clone resulted in the recovery of a mutant virus, the nsp5/V148A virus, that demonstrated reduced growth and nsp5 proteinase activity identical to that of Alb/ts/nsp5/V148A at the nonpermissive temperature. Sequence analysis of 40°C revertants of Alb/ts/nsp5/V148A identified primary reversion to Ala148Val in nsp5, as well as two independent second-site mutations resulting in Ser133Asn and His134Tyr substitutions in nsp5. The introduction of the Ser133Asn or His134Tyr substitution into the cloned nsp5/V148A mutant virus background resulted in the recovery of viruses with increased growth fitness and the partial restoration of nsp5 activity at the nonpermissive temperature. Modeling of the nsp5 structure of Alb/ts/nsp5/V148A predicted that the Val148Ala mutation alters residue 148 interactions with residues of the substrate binding S1 subsite of the nsp5 active-site cavity. This study identifies novel residues in nsp5 that may be important for regulating substrate specificity and nsp5 proteinase activity.
Face Recognition with Discrete Cosine Transform

Face recognition has been a hot issue of concern to people, existing algorithms mainly for how to improve face recognition accuracy, and reduce the use of the feature vector dimension. A face recognition method based on the discrete cosine transform and SVM-based feature classification is presented. Face Recognition on the DCT coefficients as feature vectors in the problem of effective choice. In the training process of SVM, the training sample is divided into two parts, one part of the training samples using the test results of feature selection, and use the resulting accuracy rate as the feature selection criteria, the proposed algorithm on ORL face image standard library of verified experiments, and achieved good results prove the effective and reliable.
A Meta-Meta-Analysis: Empirical Review of Statistical Power, Type I Error Rates, Effect Sizes, and Model Selection of Meta-Analyses Published in Psychology

This article uses meta-analyses published in Psychological Bulletin from 1995 to 2005 to describe meta-analyses in psychology, including examination of statistical power, Type I errors resulting from multiple comparisons, and model choice. Retrospective power estimates indicated that univariate categorical and continuous moderators, individual moderators in multivariate analyses, and tests of residual variability within individual levels of categorical moderators had the lowest and most concerning levels of power. Using methods of calculating power prospectively for significance tests in meta-analysis, we illustrate how power varies as a function of the number of effect sizes, the average sample size per effect size, effect size magnitude, and level of heterogeneity of effect sizes. In most meta-analyses many significance tests were conducted, resulting in a sizable estimated probability of a Type I error, particularly for tests of means within levels of a moderator, univariate categorical moderators, and residual variability within individual levels of a moderator. Across all surveyed studies, the median effect size and the median difference between two levels of study level moderators were smaller than Cohen's (1988) conventions for a medium effect size for a correlation or difference between two correlations. The median Birge's (1932) ratio was larger than the convention of medium heterogeneity proposed by Hedges and Pigott (2001) and indicates that the typical meta-analysis shows variability in underlying effects well beyond that expected by sampling error alone. Fixed-effects models were used with greater frequency than random-effects models; however, random-effects models were used with increased frequency over time. Results related to model selection of this study are carefully compared with those from Schmidt, Oh, and Hayes (2009), who independently designed and produced a study similar to the one reported here. Recommendations for conducting future meta-analyses in light of the findings are provided.
SACAT: Streaming-Aware Conflict-Avoiding Thrashing-Resistant GPGPU Cache Management Scheme

Modern graphical processing units (GPUs) are equipped with general-purpose L1 and L2 caches to reduce the memory bandwidth demand and improve the performance of some irregular general-purpose GPU (GPGPU) applications. However, due to the massive multithreading, GPGPU caches suffer from severe resource contention and low data-sharing which may lead to performance degradation instead. This paper proposes a low-cost streaming-aware conflict-avoiding thrashing-resistant (SACAT) GPGPU cache management scheme that efficiently utilizes the GPGPU cache resources and addresses all the problems associated with GPGPU caches. The proposed scheme employs three orthogonal techniques. First, it dynamically detects and bypasses streaming applications at fine granularity. Second, a dynamic warp throttling via cores sampling (DWT-CS) is proposed to alleviate cache thrashing. DWT-CS runs an exhaustive search over cores to find the best number of warps that achieves the highest performance. Third, it employs pseudo random interleaving cache (PRIC), which is an improved cache indexing function based on polynomial modulus mapping, to mitigate associativity stalls and eliminate conflict misses. Experimental results demonstrate that the proposed scheme achieves a 1.87<inline-formula><tex-math notation="LaTeX">$\times$</tex-math><alternatives> <inline-graphic xlink:href="abdallah-ieq1-2627560.gif"/></alternatives></inline-formula> and a 1.5<inline-formula> <tex-math notation="LaTeX">$\times$</tex-math><alternatives><inline-graphic xlink:href="abdallah-ieq2-2627560.gif"/> </alternatives></inline-formula> performance improvement over the cache-conscious wavefront scheduler (CCWS) and the memory request prioritization buffer (MRPB), respectively.
Effects of a tobacco control intervention for teachers in India: results of the Bihar school teachers study.

OBJECTIVES We assessed a school-based intervention designed to promote tobacco control among teachers in the Indian state of Bihar. METHODS We used a cluster-randomized design to test the intervention, which comprised educational efforts, tobacco control policies, and cessation support and was tailored to the local social context. In 2009 to 2011, we randomly selected 72 schools from participating school districts and randomly assigned them in blocks (rural or urban) to intervention or delayed-intervention control conditions. RESULTS Immediately after the intervention, the 30-day quit rate was 50% in the intervention and 15% in the control group (P = .001). At the 9-month postintervention survey, the adjusted 6-month quit rate was 19% in the intervention and 7% in the control group (P = .06). Among teachers employed for the entire academic year of the intervention, the adjusted 6-month abstinence rates were 20% and 5%, respectively, for the intervention and control groups (P = .04). CONCLUSIONS These findings demonstrate the potent impact of an intervention that took advantage of social resources among teachers, who can serve as role models for tobacco control in their communities.
Retained Nitrate, Hydrated Sulfates, and Carbonaceous Mass in Federal Reference Method Fine Particulate Matter for Six Eastern U.S. Cities

Abstract Material balance of fine particulate matter (PM2.5) measured with the Federal Reference Method (FRM) is developed for one rural and five urban locations in the eastern half of the United States using routine Speciation Trends Network (STN) and FRM chemical measurements and thermodynamic models. The Aerosol Inorganics Model is used to estimate retained particle bound water, and an ammonium nitrate evaporation model is used to estimate nitrate concentrations retained on the Teflon-membrane filter of the FRM. To address large uncertainties in carbonaceous mass calculated from STN carbon measurements, retained carbonaceous mass is derived by material balance between PM2.5 FRM mass and estimates of its non-carbon constituents. The resulting sulfate, adjusted nitrate, derived water, inferred carbonaceous material balance approach (SANDWICH) is compared with reconstructed fine mass (RCFM) using the Interagency Monitoring of Protected Visual Environments monitoring program equation. For this study, the SANDWICH method resulted in ∼21–27% higher sulfate mass and ∼24–85% lower nitrate mass. The combined mass associated with sulfates and nitrates, however, are well within ±10% of the proportion derived using the more traditional RCFM method. The discrepancies between SANDWICH and measurement-derived carbonaceous mass vary from −21% to +56% on an annual basis and are attributed in part to urban–rural source influences and uncertainties in estimating FRM-retained carbonaceous mass.
Immunogenetic predisposing factors for mesial temporal lobe epilepsy with hippocampal sclerosis

ABSTRACT Purpose: Neuroinflammation appears as an important epileptogenic mechanism. Experimental and clinical studies have demonstrated an upregulation of pro-inflammatory cytokines such as IL-1β and TNF-α, in mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS). Expression of these cytokines can be modulated by polymorphisms such as rs16944 and rs1800629, respectively, both of which have been associated with febrile seizures (FS) and MTLE-HS development. The human leukocyte antigen (HLA) system has also been implicated in diverse epileptic entities, suggesting a variable role of this system in epilepsy. Our aim was to analyse the association between immunogenetic factors and MTLE-HS development. For that rs16944 (-511 T>C, IL-1β), rs1800629 (-308 G>A, TNF-α) polymorphisms and HLA-DRB1 locus were genotyped in a Portuguese Population. Methods: We studied 196 MTLE-HS patients (108 females, 88 males, 44.7 ± 12.0 years, age of onset = 13.6 ± 10.3 years, 104 with FS antecedents) and 282 healthy controls in a case–control study. Results: The frequency of rs16944 TT genotype was higher in MTLE-HS patients compared to controls (14.9% in MTLE-HS vs. 7.7% in controls, p = 0.021, OR [95% CI] = 2.20 [1.13–4.30]). This association was independent of FS antecedents. No association was observed between rs1800629 genotypes or HLA-DRB1 alleles and MTLE-HS susceptibility. Also, no correlation was observed between the studied polymorphisms and disease age of onset. Conclusion: The rs16944 TT genotype is associated with MTLE-HS development what may be explained by the higher IL-1β levels produced by this genotype. High IL-1β levels may have neurotoxic effects or imbalance neurotransmission leading to seizures.
Randomized clinical study on the analgesic effect of local infiltration versus spinal block for hemorrhoidectomy

ABSTRACT BACKGROUND AND OBJECTIVES: Postoperative analgesia and early recovery are important for hospital discharge. The primary objective of this study was to compare the analgesic effectiveness of perianal infiltration and subarachnoid anesthesia for hemorrhoidectomy. The secondary objective was to compare time to discharge, adverse effects and complications. DESIGN AND SETTING: Randomized, prospective and comparative study at Dr. Mário Gatti Hospital. METHODS: Forty patients aged 18-60, in American Society of Anesthesiologists physical status category 1 or 2, were included. The local group (LG) received local infiltration (0.75% ropivacaine) under general anesthesia; the spinal group (SG) received subarachnoid block (2 ml of 0.5% bupivacaine). Analgesic supplementation consisted of fentanyl for LG and lidocaine for SG. Postoperative pain intensity, sphincter relaxation, lower-limb strength, time to discharge, analgesic dose over one week and adverse effects were assessed. RESULTS: Eleven LG patients (52.4%) required supplementation, but no SG patients. Pain intensity was higher for LG up to 120 min, but there were no differences at 150 or 180 min. There were no differences in the need for paracetamol or tramadol. Times to first analgesic supplementation and hospital discharge were longer for SG. The adverse effects were nausea, dizziness and urinary retention. CONCLUSIONS: Pain intensity was higher in LG than in SG over the first 2 h, but without differences after 150 and 180 min. Time to first supplementation was shorter in LG. There were no differences in doses of paracetamol and tramadol, or in adverse effects.
Wear resistance of the biocompatible phospholipid polymer‐grafted highly cross‐linked polyethylene liner against larger femoral head

The use of larger femoral heads to prevent the dislocation of artificial hip joints has recently become more common. However, concerns about the subsequent use of thinner polyethylene liners and their effects on wear rate have arisen. Previously, we prepared and evaluated the biological and mechanical effects of a novel highly cross‐linked polyethylene (CLPE) liner with a nanometer‐scaled graft layer of poly(2‐methacryloyloxyethyl phosphorylcholine) (PMPC). Our findings showed that the PMPC‐grafted particles were biologically inert and caused no subsequent bone resorptive responses and that the PMPC‐grafting markedly decreased wear in a hip joint simulator. However, the metal or ceramic femoral heads used in this previous study had a diameter of 26 mm. Here, we investigated the wear‐resistance of the PMPC‐grafted CLPE liner with a 40‐mm femoral head during 10 × 106 cycles of loading in the hip joint simulator. The results provide preliminary evidence that the grafting markedly decreased gravimetric wear rate and the volume of wear particles, even when coupled with larger femoral heads. Thus, we believe the PMPC‐grafting will prolong artificial hip joint longevity both by preventing aseptic loosening and by improving the stability of articular surface. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:1103–1110, 2015.
Deletion of cathepsin H perturbs angiogenic switching, vascularization and growth of tumors in a mouse model of pancreatic islet cell cancer

Abstract Proteases can regulate many aspects of tumor development as their actions, which include degradation of the extracellular matrix, proteolytic processing of chemokines and activation of other enzymes, influence several key tumorigenic processes. Members of one protease class, the cysteine cathepsins, have received increasing recognition for their involvement in cancer development, and numerous clinical studies have reported correlations between elevated cathepsin levels and malignant progression. This is also the case for cathepsin H, a member of the cysteine cathepsin family, and its utility as a prognostic marker has been analyzed extensively. However, there is limited information available on its specific functions in tumor development and progression. To gain further insight into the role of this protease in cancer, we crossed cathepsin H-deficient mice with the RIP1-Tag2 model of pancreatic islet carcinogenesis. Deletion of cathepsin H significantly impaired angiogenic switching of the pre-malignant hyperplastic islets and resulted in a reduction in the subsequent number of tumors that formed. Moreover, the tumor burden in cathepsin H null RT2 mice was significantly reduced, in association with defects in the blood vasculature and increased apoptosis. Thus, we demonstrate here for the first time important tumor-promoting roles for cathepsin H in vivo using a mouse model of human cancer.
[Validation of the Alvarado score in the diagnosis of acute appendicitis].

AIM The aim of the study was to find out the values of the Alvarado score in diagnosis of acute appendicitis and its clinical applicability in our conditions. MATERIAL AND METHODS A prospective study performed from November 15 to January 20, 2001 included 68 patients of whom 52 were operated. Patients were examined at the emergency department, and all received Alvarado score, whereas the surgeon made the decision if there were indications for surgery. In order to verify the diagnosis, we also used histopathological findings. RESULTS From 52 operated patients, 43 (82.7%) had Alvarado score 7 or more, which confirms the diagnosis of acute appendicitis, and in all these patients the diagnosis was proved both intraoperatively and histopathologically. From 9 (17.2%) operated patients that had score less than 7, diagnosis of chronic appendicitis was proved in 3; in the rest 6 acute appendicitis was established. Alvarado score has high sensitivity of 87%, and average specificity of 60%. CONCLUSION In diagnosis of acute appendicitis Alvarado score has a high diagnostic value (82.7%). Alvarado score is a noninvasive, safe diagnostic procedure, which is simple, fast, reliable and repeatable, it can be used in all conditions, without expensive and complicated supportive diagnostic methods. Alvarado score increases the diagnostic certainty of clinical examination in diagnosis of acute appendicitis.
Identification and Functional Characterization of Chicken Toll-Like Receptor 5 Reveals a Fundamental Role in the Biology of Infection with Salmonella enterica Serovar Typhimurium

ABSTRACT Toll-like receptors (TLRs) are a major component of the pattern recognition receptor repertoire that detect invading microorganisms and direct the vertebrate immune system to eliminate infection. In chickens, the differential biology of Salmonella serovars (systemic versus gut-restricted localization) correlates with the presence or absence of flagella, a known TLR5 agonist. Chicken TLR5 (chTLR5) exhibits conserved sequence and structural similarity with mammalian TLR5 and is expressed in tissues and cell populations of immunological and stromal origin. Exposure of chTLR5+ cells to flagellin induced elevated levels of chicken interleukin-1β (chIL-1β) but little upregulation of chIL-6 mRNA. Consistent with the flagellin-TLR5 hypothesis, an aflagellar Salmonella enterica serovar Typhimurium fliM mutant exhibited an enhanced ability to establish systemic infection. During the early stages of infection, the fliM mutant induced less IL-1β mRNA and polymorphonuclear cell infiltration of the gut. Collectively, the data represent the identification and functional characterization of a nonmammalian TLR5 and indicate a role in restricting the entry of flagellated Salmonella into systemic sites of the chicken.
Composite tissue allotransplantation: classification of clinical acute skin rejection.

BACKGROUND Composite tissue allotransplantation (CTA) is a recently introduced option for limb replacement and reconstruction of other nonreconstructible tissue defects. As with recipients of other allotransplants, CTA recipients can experience rejection episodes that are presumed to be mediated by immune mechanisms similar to those affecting solid organ grafts. However, a systematic examination of this process has not been performed, and there are no standardized criteria for the description of severity or type of rejection METHODS We collected biopsies from human limb allografts and abdominal walls in various stages of rejection for histological and immunohistochemical analysis to formulate a CTA rejection scheme. Biopsies were ranked by severity and reproducibility of the system was tested using a second set of biopsies. Tissue slides were examined blindly by three pathologists and the nonparametric Kendall coefficient of concordance (W) was used to assess the amount of agreement among the pathologists in their classification grades. RESULTS Rejection initially appeared as a perivascular infiltrate progressing to involve the dermis. Arteritis was observed only in the medium to large size arteries of the subcutis. Myositis was seen occasionally. Perineural involvement without frank neuritis was present in advanced rejection. The infiltrate was predominantly CD4+ in milder cases and CD8+ in advanced cases. HLA-DR was minimally expressed in keratinocytes even in severe rejection. Kendall's W was 0.9375 (p<or=0.0001). CONCLUSIONS Based on this survey, we proposed an initial classification system for acute rejection in the skin of a CTA and demonstrated that this system is easily reproduced by independent pathologists.