Miracle-dz/UniFAR-FTUs huggingface dataset:
The next 700 data description languages

In the spirit of Landin, we present a calculus of dependent types to serve as the semantic foundation for a family of languages called data description languages. Such languages, which include pads, datascript, and packettypes, are designed to facilitate programming with ad hoc data, ie, data not in well-behaved relational or xml formats. In the calculus, each type describes the physical layout and semantic properties of a data source. In the semantics, we interpret types simultaneously as the in-memory representation of the data described and as parsers for the data source. The parsing functions are robust, automatically detecting and recording errors in the data stream without halting parsing. We show the parsers are type-correct, returning data whose type matches the simple-type interpretation of the specification. We also prove the parsers are "error-correct," accurately reporting the number of physical and semantic errors that occur in the returned data. We use the calculus to describe the features of various data description languages, and we discuss how we have used the calculus to improve PADS.
The Generalization Effect of Interparental Conflict in Sibling Relationships and Child Adaptation

The main goal of this study is to analyze the generalization effect of interparental conflict in sibling relationships and child adaptation. A Spanish sample made up of 100 children, aged between 7 and 18 years, was used. Interparental conflict was the independent variable, and child maladaptation the dependent variable, whereas sibling relationship and parenting style were the mediating variables. Extraversion was controlled as a covariate. Variables were measured through self-report questionnaires. The mediation model was supported. Results showed that more restrictive parental styles and a decrease of positive sibling exchanges were both associated with child maladaptation, which revealed this generalization process. The relation of these results with previous literature and future implications are discussed.
Surface modifications of influenza proteins upon virus inactivation by β-propiolactone*

Inactivation of intact influenza viruses using formaldehyde or β‐propiolactone (BPL) is essential for vaccine production and safety. The extent of chemical modifications of such reagents on viral proteins needs to be extensively investigated to better control the reactions and quality of vaccines. We have evaluated the effect of BPL inactivation on two candidate re‐assortant vaccines (NIBRG‐121xp and NYMC‐X181A) derived from A/California/07/2009 pandemic influenza viruses using high‐resolution FT‐ICR MS‐based proteomic approaches. We report here an ultra performance LC MS/MS method for determining full‐length protein sequences of hemagglutinin and neuraminidase through protein delipidation, various enzymatic digestions, and subsequent mass spectrometric analyses of the proteolytic peptides. We also demonstrate the ability to reliably identify hundreds of unique sites modified by propiolactone on the surface of glycoprotein antigens. The location of these modifications correlated with changes to protein folding, conformation, and stability, but demonstrated no effect on protein disulfide linkages. In some cases, these modifications resulted in suppression of protein function, an effect that correlated with the degree of change of the modified amino acids’ side chain length and polarity.
Molecular Pathways : GLI 1-Induced Drug Glucuronidation in Resistant Cancer Cells

Drug resistance remains a major impediment in the development of durable cancer therapies. Studies in acute myelogenous leukemia (AML) patients revealed a new form of multidrug resistance. Here, increased glioma-associated protein GLI1 leads to elevation of theUDP-glucuronosyl transferase (UGT) enzymes. UGTs add glucuronic acid to xenobiotics and metabolites. Traditionally, the loss of these enzymes is thought to contribute to cancer as a result of impaired clearance of environmental carcinogens. However, we demonstrate that overexpression of UGTs can contribute to oncogenesis by promoting drug resistance. Indeed, UGT levels in AML patients treated with ribavirin and/or cytarabine were elevated at relapse relative to diagnosis. This was reversed by GLI1 inhibition, suggesting a clinically relevant strategy to overcome drug resistance. Further, overexpression of UGTs can also lead to drug resistance in other cancers, such as certain Hsp90 inhibitors and vorinostat in colorectal and chronic lymphoblastic leukemia, respectively. Not all drugs are targets of glucuronidation, suggesting that UGT status could be relevant to treatment choice. Here, we describe several facets of UGT biology and how these could be exploited clinically. These studies demonstrate how drugs in cancer cells can be metabolized differentially than their normal counterparts. In summary, we describe a new formof drug resistance relevant to a variety of cancer contexts. Clin Cancer Res; 21(10); 2207–10. 2015 AACR.
Inhibiting Mitochondrial Na+/Ca2+ Exchange Prevents Sudden Death in a Guinea Pig Model of Heart Failure

Rationale: In cardiomyocytes from failing hearts, insufficient mitochondrial Ca2+ accumulation secondary to cytoplasmic Na+ overload decreases NAD(P)H/NAD(P)+ redox potential and increases oxidative stress when workload increases. These effects are abolished by enhancing mitochondrial Ca2+ with acute treatment with CGP-37157 (CGP), an inhibitor of the mitochondrial Na+/Ca2+ exchanger. Objective: Our aim was to determine whether chronic CGP treatment mitigates contractile dysfunction and arrhythmias in an animal model of heart failure (HF) and sudden cardiac death (SCD). Methods and Results: Here, we describe a novel guinea pig HF/SCD model using aortic constriction combined with daily &bgr;-adrenergic receptor stimulation (ACi) and show that chronic CGP treatment (ACi plus CGP) attenuates cardiac hypertrophic remodeling, pulmonary edema, and interstitial fibrosis and prevents cardiac dysfunction and SCD. In the ACi group 4 weeks after pressure overload, fractional shortening and the rate of left ventricular pressure development decreased by 36% and 32%, respectively, compared with sham-operated controls; in contrast, cardiac function was completely preserved in the ACi plus CGP group. CGP treatment also significantly reduced the incidence of premature ventricular beats and prevented fatal episodes of ventricular fibrillation, but did not prevent QT prolongation. Without CGP treatment, mortality was 61% in the ACi group <4 weeks of aortic constriction, whereas the death rate in the ACi plus CGP group was not different from sham-operated animals. Conclusions: The findings demonstrate the critical role played by altered mitochondrial Ca2+ dynamics in the development of HF and HF-associated SCD; moreover, they reveal a novel strategy for treating SCD and cardiac decompensation in HF.
Autistic Traits and Aggressive Behavior in Chinese College Students: A Serial Mediation Model and the Gender Difference

Background The existence of aggressive behavior in autism spectrum disorders (ASD) raises questions about whether cognitive and emotional factors in social information processing play a role between autistic traits (ATs) and aggressive behavior in the general population, especially in the context of Chinese culture. Moreover, given a possible gender difference in these variables, the study aimed to examine the effect of ATs on aggressive behavior, and the potential mediating role of hostile attribution bias and alexithymia on this association, as well as gender difference. Methods 850 Chinese college students participated in the assessment, including their ATs, hostile attribution bias, alexithymia, and aggressive behavior. Pearson correlation, mediation effects analyses, and multiple-group comparison were conducted. Results The results indicated that ATs indirectly predicted increased aggressive behavior through attribution bias and alexithymia. Gender difference in mediating effects was revealed: ATs indirectly predicted increased aggressive behavior through the serial mediating effect only in males. Conclusion Hostile attribution bias and alexithymia completely mediated the association between ATs and aggressive behavior, which contained the separate mediating effects of (a) hostile attribution bias and (b) alexithymia and the serial mediating effect of (c) hostile attribution bias and alexithymia. Gender differences in mediating effects were found only in the serial mediating effect, which was significant in males but not in females. The findings revealed the internal mechanism of ATs affecting aggressive behavior and gender difference, which have implications for the intervention of aggressive behavior of individuals with autism and those with high levels of ATs.
Glycolytic enzymes associated with the cell surface of Streptococcus pneumoniae are antigenic in humans and elicit protective immune responses in the mouse

Streptococcus pneumoniae is a leading cause of otitis media, sinusitis, pneumonia, bacteraemia and meningitis worldwide. The drawbacks associated with the limited number of various capsular polysaccharides that can be included in the polysaccharide‐based vaccines focuses much attention on pneumococcal proteins as vaccine candidates. We extracted an enriched cell wall fraction from S. pneumoniae WU2. Approximately 150 soluble proteins could be identified by 2D gel electrophoresis. The proteins were screened by 2D‐Western blotting using sera that were obtained longitudinally from children attending day‐care centres at 18, 30 and 42 months of age and sera from healthy adult volunteers. The proteins were further identified using matrix‐assisted laser desorption ionization‐time of flight mass spectrometry. Seventeen proteins were antigenic in children and adults, of which 13 showed an increasing antibody response with age in all eight children analysed. Two immunogenic proteins, fructose–bisphosphate aldolase (FBA) and glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH), and a control protein with known low immunogenicity, heat shock protein 70 (DnaK), were expressed in Escherichia coli, purified and used to immunize mice. Mouse antibodies elicited to the recombinant (r) FBA and rGAPDH were cross‐reactive with several genetically unrelated strains of different serotypes and conferred protection to respiratory challenge with virulent pneumococci. In addition, the FBA used in this study (NP_345117) does not have a human ortholog and warrants further investigation as a candidate for a pneumococcal vaccine. In conclusion, the immunoproteomics based approach utilized in the present study appears to be a suitable tool for identification of novel S. pneumoniae vaccine candidates.
Accounting for eXentricities: Analysis of the X Chromosome in GWAS Reveals X-Linked Genes Implicated in Autoimmune Diseases

Many complex human diseases are highly sexually dimorphic, suggesting a potential contribution of the X chromosome to disease risk. However, the X chromosome has been neglected or incorrectly analyzed in most genome-wide association studies (GWAS). We present tailored analytical methods and software that facilitate X-wide association studies (XWAS), which we further applied to reanalyze data from 16 GWAS of different autoimmune and related diseases (AID). We associated several X-linked genes with disease risk, among which (1) ARHGEF6 is associated with Crohn’s disease and replicated in a study of ulcerative colitis, another inflammatory bowel disease (IBD). Indeed, ARHGEF6 interacts with a gastric bacterium that has been implicated in IBD. (2) CENPI is associated with three different AID, which is compelling in light of known associations with AID of autosomal genes encoding centromere proteins, as well as established autosomal evidence of pleiotropy between autoimmune diseases. (3) We replicated a previous association of FOXP3, a transcription factor that regulates T-cell development and function, with vitiligo; and (4) we discovered that C1GALT1C1 exhibits sex-specific effect on disease risk in both IBDs. These and other X-linked genes that we associated with AID tend to be highly expressed in tissues related to immune response, participate in major immune pathways, and display differential gene expression between males and females. Combined, the results demonstrate the importance of the X chromosome in autoimmunity, reveal the potential of extensive XWAS, even based on existing data, and provide the tools and incentive to properly include the X chromosome in future studies.
Antigenic analysis of echoviruses 1 and 8.

The antigenic relationship between prototype and isolate strains of echovirus types 1 and 8 was confirmed by double-diffusion gel-precipitation studies. All strains shared a common antigen. In addition, some strains possessed a second antigen that related them more closely to one or the other of the prototype strains. The prototype and isolate strains failed to show the classical prime relationship described for echovirus type 6. The antigenic variation is similar to that described for echovirus types 4 and 9. For this reason the diagnostic laboratory should consider the use of antisera to both prototype and variant strains.
Prediction of cumulative infiltration of sandy soil using random forest approach

This paper aims to examine the performance of soft computing models (bagged and unbagged with Random Forest (RF) and M5P tree regression models) in the estimation of cumulative infiltration. Performances of these soft computing techniques were compared with previous studies of cumulative infiltration of soil. Laboratory experiments were carried out on soil samples with predetermined moisture contents and different compositions of rice husk ash and fly ash and accordingly, 413 observations were obtained. The evaluation of results suggests that the RF model performs better than other considered models and it could effectively be used in the modeling of the cumulative infiltration. The bagged approach was found to perform well with the M5P tree model than the RF model. Sensitivity analysis concludes that cumulative time, suction head and moisture content were the most important parameters. In addition, parametric studies were also carried out.
A Survey on Circuit Modeling of Spin-Transfer-Torque Magnetic Tunnel Junctions

Accurate modeling of magnetic tunnel junction (MTJ) is critical for design of memories such as spin-transfer-torque magnetoresistive random access memory (STT-MRAM) and spin logic circuits such as spin flip flops. This paper reviews several static and dynamic models for the MTJ and compares them for their capabilities and limitations. Furthermore, a Verilog-A model is developed to predict dynamic characteristics of the MTJ. These models are used in simulating a prototype circuit to illustrate their strengths and weaknesses.
Survival and Long-Run Dynamics with Heterogeneous Beliefs under Recursive Preferences

I analytically characterize the long-run behavior of an economy with two types of agents who differ in their beliefs and are endowed with homothetic recursive preferences. Agents with more incorrect beliefs dominate, or agents with different accuracy of their beliefs coexist in the long run, for broad ranges of plausible parameterizations when risk aversion is greater than the inverse of the intertemporal elasticity of substitution. The results highlight a crucial interaction between risk sharing, speculative behavior and consumption-saving choice of agents with heterogeneous beliefs, and the role of equilibrium prices in shaping long-run outcomes.
Saccharomyces cerevisiae Bzz1p Is Implicated with Type I Myosins in Actin Patch Polarization and Is Able To Recruit Actin-Polymerizing Machinery In Vitro

ABSTRACT In Saccharomyces cerevisiae, the WASP (Wiskott-Aldrich syndrome protein) homologue Las17p (also called Bee1p) is an important component of cortical actin patches. Las17p is part of a high-molecular-weight protein complex that regulates Arp2/3 complex-dependent actin polymerization at the cell cortex and that includes the type I myosins Myo3p and Myo5p and verprolin (Vrp1p). To identify other factors implicated with this complex in actin regulation, we isolated proteins that bind to Las17p by two-hybrid screening and affinity chromatography. Here, we report the characterization of Lsb7/Bzz1p (for Las seventeen binding protein 7), an Src homology 3 (SH3) domain protein that interacts directly with Las17p via a polyproline-SH3 interaction. Bzz1p coimmunoprecipitates in a complex with Las17p, Vrp1p, Myo3/5p, Bbc1p, Hsp70p, and actin. It colocalizes with cortical actin patches and with Las17p. This localization is dependent on Las17p, but not on F-actin. Bzz1p interacts physically and genetically with type I myosins. While deletion of BZZ1 shows no obvious phenotype, simultaneous deletion of the BZZ1, MYO3, and MYO5 genes is lethal. Overexpression of Bzz1p inhibits cell growth, and a bzz1Δ myo5Δ double mutant is unable to restore actin polarity after NaCl stress. Finally, Bzz1p in vitro is able to recruit a functional actin polymerization machinery through its SH3 domains. Its interactions with Las17p, Vrp1p, and the type I myosins are essential for this process. This suggests that Bzz1p could be implicated in the regulation of actin polymerization.
Phenological Observations on Classical Prehistoric Sites in the Middle and Lower Reaches of the Yellow River Based on Landsat NDVI Time Series

Buried archeological features show up as crop marks that are mostly visible using high-resolution image data. Such data are costly and restricted to small regions and time domains. However, a time series of freely available medium resolution imagery can be employed to detect crop growth changes to reveal subtle surface marks in large areas. This paper aims to study the classical Chinese settlements of Taosi and Erlitou over large areas using Landsat NDVI time series crop phenology to determine the optimum periods for detection and monitoring of crop anomalies. Burial areas (such as the palace area and the sacrificial area) were selected as the research area while the surrounding empty fields with a low density of ancient features were used as reference regions. Landsat NDVI covering two years’ growth periods of wheat and maize were computed and analyzed using Pearson’s correlation coefficient and Euclidean distance. Similarities or disparities between the burial areas and their empty areas were computed using the Hausdorff distance. Based on the phenology of crop growth, the time series NDVI images of winter wheat and summer maize were generated to analyze crop anomalies in the archeological sites. Results show that the Hausdorff distance was high during the critical stages of water for both crops and that the images of high Hausdorff distance can provide more obvious subsurface archeological information.
Admittance Control for Robotic Loading: Design and Experiments with a 1‐Tonne Loader and a 14‐Tonne Load‐Haul‐Dump Machine

This paper describes the design, tuning, and extensive field testing of an admittance‐based autonomous loading controller (ALC) for robotic excavation. Several iterations of the ALC were tuned and tested in fragmented rock piles—similar to those found in operating mines—by using both a robotic 1‐tonne capacity Kubota R520S diesel‐hydraulic surface loader and a 14‐tonne capacity Atlas Copco ST14 underground load‐haul‐dump (LHD) machine. On the R520S loader, the ALC increased payload by 18% with greater consistency, although with more energy expended and longer dig times when compared with digging at maximum actuator velocity. On the ST14 LHD, the ALC took 61% less time to load 39% more payload when compared to a single manual operator. The manual operator made 28 dig attempts by using three different digging strategies, and had one failed dig. The tuned ALC made 26 dig attempts at 10 and 11 MN target force levels. All 10 11 MN digs succeeded while 6 of the 16 10 MN digs failed. The results presented in this paper suggest that the admittance‐based ALC is more productive and consistent than manual operators, but that care should be taken when detecting entry into the rock pile.
Proximate determinants of telomere length in sand lizards (Lacerta agilis)

Telomeres are repeat sequences of non-coding DNA that cap the ends of chromosomes and contribute to their stability and the genomic integrity of cells. In evolutionary ecology, the main research target regarding these genomic structures has been their role in ageing and as a potential index of age. However, research on humans shows that a number of traits contribute to among-individual differences in telomere length, in particular traits enhancing cell division and genetic erosion, such as levels of free radicals and stress. In lizards, tail loss owing to predation attempts results in a stress-induced shift to a more cryptic lifestyle. In sand lizard (Lacerta agilis) males, telomere length was compromised by tail regrowth in a body size-related manner, so that small males, which already exhibit more cryptic mating tactics, were less affected than larger males. Tail regrowth just fell short of having a significant relationship with telomere length in females, and so did age in males. In females, there was a significant positive relationship between age and telomere length. We conclude that the proximate effect of compromised antipredation and its associated stress seems to have a more pronounced effect in males than in females and that age-associated telomere dynamics differ between the sexes.
Cardiac resynchronization therapy: from treatment to prevention.

This editorial refers to ‘Response to preventive cardiac resynchronization therapy in patients with ischaemic and nonischaemic cardiomyopathy in MADIT-CRT’[†][1], by A. Barsheshet et al. , on page 1622, ‘Time-dependent benefit of preventive cardiac resynchronization therapy after myocardial infarction’[‡][2], by A. Barsheshet et al. , on page 1614, and ‘Cost-effectiveness of cardiac resyncronization therapy in patients with asymptomatic to mild heart failure: insights from the European cohort of the REVERSE (Resynchronization Reverses remodeling in Systolic Left Ventricular Dysfunction)’[§][3], by C. Linde et al. , on page 1631 After the publication of the COMPANION and the CARE-HF trials,1,2 cardiac resynchronization therapy (CRT) has become accepted as an efficient therapeutic modality, over and above optimal drug treatment.3 CRT not only improves symptoms and quality of life but also reduces morbidity and mortality in patients with New York Hear Association (NYHA) class III and IV, depressed left ventricular ejection fraction (LVEF), and a wide QRS.3 More recently, the guidelines on device therapy in heart failure from the European Society of Cardiology recommended CRT also in patients with NYHA class II despite optimal drug treatment, with an LVEF <35% and very wide QRS ≥150 ms, to reduce morbidity and/or to prevent disease progression.4 This important commendation to prevent disease progression by CRT was based on the results of the REVERSE and MADIT-CRT trials.5,6 The recent publication of the RAFT trial confirmed the benefits of CRT in preventing clinical disease progression in patients with mild heart failure.7 Importantly, in contrast to REVERSE and MADIT-CRT, the RAFT study showed that CRT reduced mortality in this mild heart failure cohort.5–7 This significant effect … [1]: #fn-2 [2]: #fn-3 [3]: #fn-4