Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Variation, Inheritance, and Parent-of-Origin Effects of Cytosine Methylation in Maize (Zea mays)

Pure epigenetic variation, or epigenetic variation that is independent of genetic context, may provide a mechanism for phenotypic variation in the absence of DNA mutations. To estimate the extent of pure epigenetic variation within and across generations and to identify the DNA regions targeted, a group of eight plants derived from a highly inbred line of maize (Zea mays) was analyzed by the methylation-sensitive amplified polymorphism (MSAP) technique. We found that cytosine methylation (mC) differences among individuals accounted for up to 7.4% of CCGG sites investigated by MSAP. Of the differentially methylated fragments (DMFs) identified in the S0 generation, ∼12% were meiotically inherited for at least six generations. We show that meiotically heritable mC variation was consistently generated for an average of 0.5% CCGG sites per generation and that it largely occurred somatically. We provide evidence that mC variation can be established and inherited in a parent-of-origin manner, given that the paternal lineage is more prone to both forward and reverse mC changes. The molecular characterization of selected DMFs revealed that the variation was largely determined by CG methylation changes that map within gene regions. The expression analysis of genes overlapping with DMFs did not reveal an obvious correlation between mC variation and transcription, reinforcing the idea that the primary function of gene-body methylation is not to control gene expression. Because this study focuses on epigenetic variation in field-grown plants, the data presented herein pertain to spontaneous epigenetic changes of the maize genome in a natural context.
High clinical and molecular response rates with fludarabine, cyclophosphamide and mitoxantrone in previously untreated patients with advanced stage follicular lymphoma

Combination chemotherapy with fludarabine, cyclophosphamide and mitoxantrone results in high complete and molecular response rates with prolonged response duration in previously untreated patients with advanced stage follicular lymphoma. Background Purine analogs have demonstrated significant activity in patients with follicular lymphoma. The aim of this study was to analyze the efficacy and toxicity of a fludarabine combination as first-line treatment in patients with advanced-stage disease. Design and Methods This is a phase II trial including 120 patients (≤65 years) treated with 6 cycles of fludarabine, cyclophosphamide and mitoxantrone (FCM). Molecular response was assessed by q-PCR in peripheral blood. Results Of 119 patients with an assessable response, complete response was achieved in 99 (83%) partial response in 13 (11%) and 7 (6%) did not respond. After treatment, 37 out of 46 (81%) patients achieved molecular response. After a median follow-up of 3.9 years, 32 patients have relapsed. The 5-year progression-free survival was 58% (95% confidence interval: 47–69). Variables associated with a shorter progression-free survival were a poor performance status (ECOG≥2), ≥2 extranodal sites and high β2-microglobulin. Sixteen episodes of grade 3–4 infections were observed. Two patients died during therapy (of progressive multifocal leukoencephalopathy and bronchoaspiration respectively). No late toxicity has been observed. Twelve patients died during follow-up (9 after relapse, 2 during chemotherapy, 1 in complete remission after surgery for meningioma). The overall survival at 5 years was 89%. ECOG ≥2 and high β2-microglobulin were associated with a shorter survival. Conclusions FCM results in high complete and molecular response rates, with prolonged response duration in younger patients with advanced-stage follicular lymphoma. The combination of FCM with rituximab as front-line treatment warrants further investigation.
Aberrant Default Mode Functional Connectivity in Early Onset Schizophrenia

Background The default mode network (DMN) has been linked to a number of mental disorders including schizophrenia. However, the abnormal connectivity of DMN in early onset schizophrenia (EOS) has been rarely reported. Methods Independent component analysis (ICA) was used to investigate functional connectivity (FC) of the DMN in 32 first-episode adolescents with EOS and 32 age and gender-matched healthy controls. Results Compared to healthy controls, patients with EOS showed increased FC between the medial frontal gyrus and other areas of the DMN. Partial correlation analyses showed that the FC of medial frontal gyrus significantly correlated with PANSS-positive symptoms (partial correlation coefficient = 0.538, Bonferoni corrected P = 0.018). Limitations Although the sample size of participants was comparable with most fMRI studies to date, it was still relatively small. Pediatric brains were registered to the MNI adult brain template. However, possible age-specific differences in spatial normalization that arise from registering pediatric brains to the MNI adult brain template may have little effect on fMRI results. Conclusion This study provides evidence for functional abnormalities of DMN in first-episode EOS. These abnormalities could be a source of abnormal introspectively-oriented mental actives.
Partial sums generation architecture for successive cancellation decoding of polar codes

Polar codes are a new family of error correction codes for which efficient hardware architectures have to be defined for the encoder and the decoder. Polar codes are decoded using the successive cancellation decoding algorithm that includes partial sums computations. We take advantage of the recursive structure of polar codes to introduce an efficient partial sums computation unit that can also implements the encoder. The proposed architecture is synthesized for several code-lengths in 65nm ASIC technology. The area of the resulting design is reduced up to 26% and the maximum working frequency is improved by 25%.
F0 peak alignment in Moroccan Arabic polar questions

This paper contributes phonetic evidence to ongoing debate regarding the position of Moroccan Arabic in prosodic typology, with the aim of determining how phrase-edge tonal events should be represented in the intonational phonology of the language. A salient phrase-final rise-fall tonal event, found in MA polar questions, is used as a case study. We examined the alignment of the f0 peak of this tonal movement, relative to potential landmarks in prosodic structure, in a set of 112 polar questions extracted from a corpus of read and spontaneous speech collected in Casablanca. A comparison of f0 peak alignment in tokens containing an unstressable final CV syllable vs. a stressable final CVC syllable suggests that the rise-fall tonal event observed in MA polar questions is best understood as a pitch accent marking prominence at the phrasal level.
Anisotropic Perfectly Matched Layers for Elastic Waves in Cartesian and Curvilinear Coordinates

We develop new numerical anisotropic perfectly matched layer (PML) boundaries for elastic waves in Cartesian, cylindrical and spherical coordinate systems. The elasticity tensor of this absorbing boundary is chosen to be anisotropic and complex so that waves from the computational domain are attenuated in the boundary layer without reflection. The new PMLs are easy to formulate for both isotropic and anisotropic solid media. They utilize fewer unknowns in a general three-dimensional problem than the existing elastic wave PMLs using the field splitting scheme. Moreover, it can be implemented directly to the finite element method (FEM), as well as the finite difference time domain (FDTD) method. The high efficiency of these PMLs is illustrated by some numerical samples in FEM.
Measuring software aging effects through OS kernel instrumentation

Software aging is a phenomenon defined as the continuing degradation of software systems during runtime, being particularly noticeable in long-running applications. Measuring aging effects is a very important step towards identifying the most significant causes of software aging, so rejuvenation mechanisms can be applied effectively. The literature has already discussed aging monitoring from a userspace perspective. In this paper we present an innovative study where we explore OS kernel instrumentation techniques to measure software aging effects. Kernel instrumentations are available in practically all modern operating systems and we show how this powerful mechanism can be used to monitor either application-specific or system-wide aging indicators. In addition to the theoretical study, we present numerical results obtained from controlled experiments.
Evaluation of In Vitro Antioxidant Properties of Methanol and Aqueous Extracts of Parkinsonia aculeata L. Leaves

In the present study, methanol and aqueous extracts of Parkinsonia aculeata L. leaves were prepared and analyzed for phytochemical analysis and antioxidant potential in different in vitro assays. Antioxidant activity was studied using DPPH, CUPRAC, reducing power assay, deoxyribose degradation (site and nonsite specific), ferric reducing antioxidant potential (FRAP), ferric thiocyanate (FTC), thiobarbituric acid (TBA), and molybdate ion reduction, respectively. The total phenolic contents of the methanol and aqueous leaf extract were 39 mg GAE/g and 38 mg GAE/g, whereas flavonoid contents of these extracts were found to be 0.013 mg RE/g and 0.006 mg RE/g, respectively. From the two extracts, the methanol extract shows maximum inhibition (%) of 57.82%, 71.23%, 48.26%, 69.85%, and 52.78% in DPPH, nonsite- and site-specific, FTC, and TBA assays and absorbance of 0.669 and 0.241 in reducing power and CUPRAC assays at the highest concentration tested. UPLC analysis was done to determine the presence of various types of polyphenols present in plant extracts.
Astrocyte Elevated Gene-1 is a Novel Prognostic Marker for Breast Cancer Progression and Overall Patient Survival

Purpose: The present study was aimed at clarifying the expression of astrocyte elevated gene-1 (AEG-1), one of the target genes of oncogenic Ha-ras, in breast cancer and its correlation with clinicopathologic features, including the survival of patients with breast cancer. Experimental Design: The expression of AEG-1 in normal breast epithelial cells, breast cancer cell lines, and in four cases of paired primary breast tumor and normal breast tissue was examined using reverse transcription-PCR and Western blot. Real-time reverse transcription-PCR was applied to determine the mRNA level of AEG-1 in the four paired tissues, each from the same subject. Furthermore, AEG-1 protein expression was analyzed in 225 clinicopathologically characterized breast cancer cases using immunohistochemistry. Statistical analyses were applied to test for the prognostic and diagnostic associations. Results: Western blot and reverse transcription-PCR showed that the expression level of AEG-1 was markedly higher in breast cancer cell lines than that in the normal breast epithelial cells at both mRNA and protein levels. AEG-1 expression levels were significantly up-regulated by up to 35-fold in primary breast tumors in comparison to the paired normal breast tissue from the same patient. Immunohistochemical analysis revealed high expression of AEG-1 in 100 of 225 (44.4%) paraffin-embedded archival breast cancer biopsies. Statistical analysis showed a significant correlation of AEG-1 expression with the clinical staging of the patients with breast cancer (P = 0.001), as well as with the tumor classification (P = 0.004), node classification (P = 0.026), and metastasis classification (P = 0.001). Patients with higher AEG-1 expression had shorter overall survival time, whereas patients with lower AEG-1 expression had better survival. Multivariate analysis suggested that AEG-1 expression might be an independent prognostic indicator for the survival of patients with breast cancer. Conclusions: Our results suggest that AEG-1 protein is a valuable marker of breast cancer progression. High AEG-1 expression is associated with poor overall survival in patients with breast cancer.
Add-on treatment of benzoate for schizophrenia: a randomized, double-blind, placebo-controlled trial of D-amino acid oxidase inhibitor.

IMPORTANCE In addition to dopaminergic hyperactivity, hypofunction of the N-methyl-d-aspartate receptor (NMDAR) has an important role in the pathophysiology of schizophrenia. Enhancing NMDAR-mediated neurotransmission is considered a novel treatment approach. To date, several trials on adjuvant NMDA-enhancing agents have revealed beneficial, but limited, efficacy for positive and negative symptoms and cognition. Another method to enhance NMDA function is to raise the levels of d-amino acids by blocking their metabolism. Sodium benzoate is a d-amino acid oxidase inhibitor. OBJECTIVE To examine the clinical and cognitive efficacy and safety of add-on treatment of sodium benzoate for schizophrenia. DESIGN, SETTING, AND PARTICIPANTS A randomized, double-blind, placebo-controlled trial in 2 major medical centers in Taiwan composed of 52 patients with chronic schizophrenia who had been stabilized with antipsychotic medications for 3 months or longer. INTERVENTIONS Six weeks of add-on treatment of 1 g/d of sodium benzoate or placebo. MAIN OUTCOMES AND MEASURES The primary outcome measure was the Positive and Negative Syndrome Scale (PANSS) total score. Clinical efficacy and adverse effects were assessed biweekly. Cognitive functions were measured before and after the add-on treatment. RESULTS Benzoate produced a 21% improvement in PANSS total score and large effect sizes (range, 1.16-1.69) in the PANSS total and subscales, Scales for the Assessment of Negative Symptoms-20 items, Global Assessment of Function, Quality of Life Scale and Clinical Global Impression and improvement in the neurocognition subtests as recommended by the National Institute of Mental Health's Measurement and Treatment Research to Improve Cognition in Schizophrenia initiative, including the domains of processing speed and visual learning. Benzoate was well tolerated without significant adverse effects. CONCLUSIONS AND RELEVANCE Benzoate adjunctive therapy significantly improved a variety of symptom domains and neurocognition in patients with chronic schizophrenia. The preliminary results show promise for d-amino acid oxidase inhibition as a novel approach for new drug development for schizophrenia.
An algorithm for distributed groupware applications

Computer supported cooperative work (CSCW) is a rapidly growing field. Real-time groupware systems are addressed that allow a group of users to edit a shared document. The architecture and concurrency control algorithm used in this system are described. The algorithm is based on the semantics of the application and can be used by the developers of other groupware systems. The authors begin by introducing the notion of a purely replicated architecture and then present GroupDesign, a shared drawing tool implemented with this architecture. They then present the main parts of the algorithm that implement the distribution. The algorithm gives the best response time for the interface and reduces the number of undo and redo operations when conflicts occur. <<ETX>>
Barcelona Economics Working Paper Series Monetary Policy and Unemployment Monetary Policy and Unemployment

Much recent research has focused on the development and analysis of extensions of the New Keynesian framework that model labor market frictions and unemployment explicitly. The present paper describes some of the essential ingredients and properties of those models, and their implications for monetary policy. of the insights contained in the present paper are based on earlier joint work with Olivier Blanchard, who sparked my interest in the subject. I also thank the editors, Jan Eeckhout, Chris Pissarides, Carlos Thomas, and participants at the CREI Faculty Lunch and the Conference on "Key Development in Monetary Economics," for helpful comments at di¤erent stages of this project. Tomaz Cajner and Lien Laureys provided excellent research assistance. I acknowledge …nancial support from the European Research Council, the Ministerio de Ciencia e Inno-vación and the Government of Catalonia.
Genetic and Environmental Influences on Retinopathy of Prematurity

Objective. The goals were to isolate and study the genetic susceptibility to retinopathy of prematurity (ROP), as well as the gene-environment interaction established in this disease. Methods. A retrospective study (2000–2014) was performed about the heritability of retinopathy of prematurity in 257 infants who were born at a gestational age of ≤32 weeks. The ROP was studied and treated by a single pediatric ophthalmologist. A binary logistic regression analysis was completed between the presence or absence of ROP and the predictor variables. Results. Data obtained from 38 monozygotic twins, 66 dizygotic twins, and 153 of simple birth were analyzed. The clinical features of the cohorts of monozygotic and dizygotic twins were not significantly different. Genetic factors represented 72.8% of the variability in the stage of ROP, environmental factors 23.08%, and random factors 4.12%. The environmental variables representing the highest risk of ROP were the number of days of tracheal intubation (p < 0.001), postnatal weight gain (p = 0.001), and development of sepsis (p = 0.0014). Conclusion. The heritability of ROP was found to be 0.73. The environmental factors regulate and modify the expression of the genetic code.
Effects of dietary leucine supplementation on the hepatic mitochondrial biogenesis and energy metabolism in normal birth weight and intrauterine growth-retarded weanling piglets

BACKGROUND/OBJECTIVES The study was conducted to evaluate the effects of dietary leucine supplementation on mitochondrial biogenesis and energy metabolism in the liver of normal birth weight (NBW) and intrauterine growth-retarded (IUGR) weanling piglets. MATERIALS/METHODS A total of sixteen pairs of NBW and IUGR piglets from sixteen sows were selected according to their birth weight. At postnatal day 14, all piglets were weaned and fed either a control diet or a leucine-supplemented diet for 21 d. Thereafter, a 2 × 2 factorial experimental design was used. Each treatment consisted of eight replications with one piglet per replication. RESULTS Compared with NBW piglets, IUGR piglets had a decreased (P < 0.05) hepatic adenosine triphosphate (ATP) content. Also, IUGR piglets exhibited reductions (P < 0.05) in the activities of hepatic mitochondrial pyruvate dehydrogenase (PDH), citrate synthase (CS), α-ketoglutarate dehydrogenase (α-KGDH), malate dehydrogenase (MDH), and complexes I and V, along with decreases (P < 0.05) in the concentration of mitochondrial DNA (mtDNA) and the protein expression of hepatic peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α). Dietary leucine supplementation increased (P < 0.05) the content of ATP, and the activities of CS, α-KGDH, MDH, and complex V in the liver of piglets. Furthermore, compared to those fed a control diet, piglets given a leucine-supplemented diet exhibited increases (P < 0.05) in the mtDNA content and in the mRNA expressions of sirtuin 1, PGC-1α, nuclear respiratory factor 1, mitochondrial transcription factor A, and ATP synthase, H+ transporting, mitochondrial F1 complex, β polypeptide in liver. CONCLUSIONS Dietary leucine supplementation may exert beneficial effects on mitochondrial biogenesis and energy metabolism in NBW and IUGR weanling piglets.
Results of the Scandinavian Sarcoma Group XIV protocol for classical osteosarcoma

Background and purpose The Scandinavian Sarcoma Group (SSG) XIV protocol is based on experience from previous SSG trials and other osteosarcoma intergroup trials, and has been considered the best standard of care for patients with extremity localized, non-metastatic osteosarcoma. We analyzed the outcome in 63 consecutive patients. Patients and methods From 2001 through 2005, 63 patients recruited from centers in Sweden, Norway, and Finland were included. They received preoperative chemotherapy consisting of 2 cycles of paired methotrexate (12 g/m2), cisplatin (90 mg/m2), and doxorubicin (75 mg/m2). 3 cycles were administered postoperatively, and poor histological responders were given 3 additional cycles of ifosfamide (10–12 g/m2) as a salvage strategy. Results With a median follow-up of 77 months for survivors, the estimated metastasis-free and sarcoma-related survival at 5 years was 70% and 76%, respectively. 53 patients were treated with limb salvage surgery or rotationplasty and 2 patients experienced a local recurrence. 3 toxic deaths were recorded, all related to acute toxicity from chemotherapy. The 5-year metastasis-free survival of poor histological responders receiving add-on treatment with ifosfamide was 47%, as compared to 89% for good histological responders. Interpretation Outcome from the SSG XIV protocol compares favorably with the results of previous SSG trials and other published osteosarcoma trials. However, salvage therapy given to poor responders did not improve outcome to a similar degree as for good responders. In a multi-institutional setting, more than four-fifths of the patients were operated with limb salvage surgery or rotationplasty, with few local recurrences.
Embedded implicatures?!?

Over the last decade, various proposals have been made for supplanting the classical Gricean theory of scalar implicature with conventionalist (i.e. lexicalist or syntax-based) treatments. In contradistinction to the classical view, conventionalist theories predict that scalar inferences occur systematically and freely in embedded positions. We present experimental evidence that disproves this prediction, arguing along the way that there are rather good reasons to suspect that introspection isn’t always a reliable tool for gathering data on pragmatic inferences.
Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone.