Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic Communications of the EASST Volume 36 ( 2010 ) Proceedings of the Workshop on OCL and Textual Modelling ( OCL 2010 ) MySQL 4 OCL : A Stored Procedure-Based MySQL Code Generator for OCL

In this paper we introduce a MySQL code generator for a significant subset of OCL expressions which is based on the use of stored procedures for mapping OCL iterators. Our code generator is defined recursively over the structure of OCL expressions. We discuss the class of OCL expressions covered by our definition (which includes, possibly nested, iterator expressions) as well as some extensions needed to cover the full OCL language. We also discuss the efficiency of the MySQL code produced by our code generator, and compare it with previous known results on evaluating OCL expressions on medium-large scenarios. We have implemented our code generator in the MySQL4OCL tool.
Experimental Analysis of Bound Handling Techniques in Particle Swarm Optimization

Many practical optimization problems are constrained and have a bounded search space. In this paper, we propose and compare a wide variety of bound handling techniques for particle swarm optimization. By examining their performance on flat landscapes, we show that many bound handling techniques introduce significant search bias. Furthermore, we compare the performance of many bound handling techniques on a variety of test problems, demonstrating that the bound handling technique can have a major impact on the algorithm performance, and that the method recently proposed as the standard does not, in general, perform well.
Polymer-modified halide perovskite films for efficient and stable planar heterojunction solar cells

The UCLA team has successfully passivated perovskite film by controlling the film growth with functional polymers as additive. The solution processing of polycrystalline perovskite films introduces trap states that can adversely affect their optoelectronic properties. Motivated by the use of small-molecule surfactants to improve the optoelectronic performance of perovskites, we demonstrate the use of polymers with coordinating groups to improve the performance of solution-processed semiconductor films. The use of these polymer modifiers results in a marked change in the electronic properties of the films, as measured by both carrier dynamics and overall device performance. The devices grown with the polymer poly(4-vinylpyridine) (PVP) show significantly enhanced power conversion efficiency from 16.9 ± 0.7% to 18.8 ± 0.8% (champion efficiency, 20.2%) from a reverse scan and stabilized champion efficiency from 17.5 to 19.1% [under a bias of 0.94 V and AM (air mass) 1.5-G, 1-sun illumination over 30 min] compared to controls without any passivation. Treating the perovskite film with PVP enables a VOC of up to 1.16 V, which is among the best reported for a CH3NH3PbI3 perovskite solar cell and one of the lowest voltage deficits reported for any perovskite to date. In addition, perovskite solar cells treated with PVP show a long shelf lifetime of up to 90 days (retaining 85% of the initial efficiency) and increased by a factor of more than 20 compared to those without any polymer (degrading to 85% after ~4 days). Our work opens up a new class of chemical additives for improving perovskite performance and should pave the way toward improving perovskite solar cells for high efficiency and stability.
Annotating Discourse Relations in Spoken Language: A Comparison of the PDTB and CCR Frameworks

In discourse relation annotation, there is currently a variety of different frameworks being used, and most of them have been developed and employed mostly on written data. This raises a number of questions regarding interoperability of discourse relation annotation schemes, as well as regarding differences in discourse annotation for written vs. spoken domains. In this paper, we describe ouron annotating two spoken domains from the SPICE Ireland corpus (telephone conversations and broadcast interviews) according todifferent discourse annotation schemes, PDTB 3.0 and CCR. We show that annotations in the two schemes can largely be mappedone another, and discuss differences in operationalisations of discourse relation schemes which present a challenge to automatic mapping. We also observe systematic differences in the prevalence of implicit discourse relations in spoken data compared to written texts,find that there are also differences in the types of causal relations between the domains. Finally, we find that PDTB 3.0 addresses many shortcomings of PDTB 2.0 wrt. the annotation of spoken discourse, and suggest further extensions. The new corpus has roughly theof the CoNLL 2015 Shared Task test set, and we hence hope that it will be a valuable resource for the evaluation of automatic discourse relation labellers.
Identification of genes and pathways associated with osteoarthritis by bioinformatics analyses.

OBJECTIVE This study aimed to explore the molecular mechanism of osteoarthritis (OA) development and discover underlying genes associated with OA. DATA AND METHODS Gene expression profile GSE48556 including 106 peripheral blood mononuclear cells (PBMCs) of osteoarthritis patients and 33 PBMCs of healthy controls was downloaded from the Gene Expression Omnibus database. The limma package was used to identify the differentially expressed genes (DEGs) by paired t-test. The functional enrichment analyses of DEGs was performed, followed by the construction of protein-protein interaction (PPI) network. RESULTS Total 432 DEGs including 178 up-regulated DEGs and 254 down-regulated DEGs were identified. Pathways of cytokine-cytokine receptor interaction and T cell receptor signaling pathway were significantly up-regulated in OA. Biological processes of negative regulation of transcription from RNA polymerase II promoter and negative regulation of transcription, DNA-dependent were significantly down-regulated in OA. The platelet-derived growth factor receptor, beta polypeptide (PDGFRB), interferon, gamma (IFNG), early growth response 1 (EGR1), Fas ligand (TNF superfamily, member 6) (FASLG), H3 histone, family 3B (H3.3B) (H3F3B) and so on had higher connectivity degree in the PPI networks. CONCLUSIONS DEGs of OA were mainly enriched in the pathways associated with cytokine-cytokine receptor interaction and T cell receptor signaling pathway. The DEGs such as PDGFRB, IFNG, EGR1, FASLG and H3F3B may be the potential targets for OA diagnosis and treatment.
Both Caspase-Dependent and Caspase-Independent Pathways May Be Involved in Hippocampal CA1 Neuronal Death Because of Loss of Cytochrome c from Mitochondria in a Rat Forebrain Ischemia Model

In a rat forebrain ischemia model, the authors examined whether loss of cytochrome c from mitochondria correlates with ischemic hippocampal CA1 neuronal death and how cytochrome c release may shape neuronal death. Forebrain ischemia was induced by bilateral common carotid artery occlusion with simultaneous hypotension for 10 minutes. After reperfusion, an early rapid depletion of mitochondrial cytochrome c and a late phase of diffuse redistribution of cytochrome c occurred in the hippocampal CA1 region, but not in the dentate gyrus and CA3 regions. Intracerebroventricular administration of Z-DEVD-FMK, a relatively selective caspase-3 inhibitor, provided limited but significant protection against ischemic neuronal damage on day 7 after reperfusion. Treatment with 3 minutes of ischemia (ischemic preconditioning) 48 hours before the 10-minute ischemia attenuated both the early and late phases of cytochrome c redistribution. In another subset of animals treated with cycloheximide, a general protein synthesis inhibitor, the late phase of cytochrome c redistribution was inhibited, whereas most hippocampal CA1 neurons never regained mitochondrial cytochrome c. Examination of neuronal survival revealed that ischemic preconditioning prevents, whereas cycloheximide only delays, ischemic hippocampal CA1 neuronal death. DNA fragmentation detected by terminal deoxytransferase-mediated dUTP-nick end labeling (TUNEL) in situ was largely attenuated by ischemic preconditioning and moderately reduced by cycloheximide. These results indicate that the loss of cytochrome c from mitochondria correlates with hippocampal CA1 neuronal death after transient cerebral ischemia in relation to both caspase-dependent and -independent pathways. The amount of mitochondrial cytochrome c regained may determine whether ischemic hippocampal CA1 neurons survive or succumb to late-phase death.
Automatic Detection of Malware-Generated Domains with Recurrent Neural Models

Modern malware families often rely on domain-generation algorithms (DGAs) to determine rendezvous points to their command-and-control server. Traditional defence strategies (such as blacklisting domains or IP addresses) are inadequate against such techniques due to the large and continuously changing list of domains produced by these algorithms. This paper demonstrates that a machine learning approach based on recurrent neural networks is able to detect domain names generated by DGAs with high precision. The neural models are estimated on a large training set of domains generated by various malwares. Experimental results show that this data-driven approach can detect malware-generated domain names with a F_1 score of 0.971. To put it differently, the model can automatically detect 93 % of malware-generated domain names for a false positive rate of 1:100.
Barriers to listing for HIV‐infected patients being evaluated for kidney transplantation

Human immunodeficiency virus (HIV)‐infected patients have excellent outcomes following kidney transplantation (KT) but still might face barriers in the evaluation and listing process. The aim of this study was to characterize the patient population, referral patterns, and outcomes of HIV‐infected patients who present for KT evaluation. We performed a single‐center retrospective cohort study of HIV‐infected patients who were evaluated for KT. The primary outcome was time to determination of eligibility for KT. Between 2011 and 2015, 105 HIV‐infected patients were evaluated for KT. Of the 105 patients, 73 were listed for transplantation by the end of the study period. For those who were deemed ineligible, the most common reasons cited were active substance abuse (n = 7, 22%) and failure to complete the full transplant evaluation (n = 7, 22%). Our cohort demonstrated a higher proportion of HIV‐infected patients eligible for KT than in previous studies, likely secondary to advances in HIV management. Among those who were denied access to transplantation, we identified that many were unable to complete the evaluation process, and that active substance abuse was common. Future prospective studies should examine reasons and potential interventions for the lack of follow‐through and drug use we observed in this population.
From K-Means to Higher-Way Co-Clustering: Multilinear Decomposition With Sparse Latent Factors

Co-clustering is a generalization of unsupervised clustering that has recently drawn renewed attention, driven by emerging data mining applications in diverse areas. Whereas clustering groups entire columns of a data matrix, co-clustering groups columns over select rows only, i.e., it simultaneously groups rows and columns. The concept generalizes to data “boxes” and higher-way tensors, for simultaneous grouping along multiple modes. Various co-clustering formulations have been proposed, but no workhorse analogous to K-means has emerged. This paper starts from K-means and shows how co-clustering can be formulated as a constrained multilinear decomposition with sparse latent factors. For three- and higher-way data, uniqueness of the multilinear decomposition implies that, unlike matrix co-clustering, it is possible to unravel a large number of possibly overlapping co-clusters. A basic multi-way co-clustering algorithm is proposed that exploits multilinearity using Lasso-type coordinate updates. Various line search schemes are then introduced to speed up convergence, and suitable modifications are proposed to deal with missing values. The imposition of latent sparsity pays a collateral dividend: it turns out that sequentially extracting one co-cluster at a time is almost optimal, hence the approach scales well for large datasets. The resulting algorithms are benchmarked against the state-of-art in pertinent simulations, and applied to measured data, including the ENRON e-mail corpus.
Mixed Mode Partition in one Dimensional Fractures

Taking a double cantilever beam (DCB) as a representative of one dimensional fracture, a unique pair of pure fracture modes I and II are successfully found in the absence of axial forces, which are orthogonal to each other with respect to the coefficient matrix of the energy release rate. Although the pair are pure modes there still exist interactions between them. The interactions result in energy flow between the two modes and are successfully determined. With the presence of axial forces, there are two independent pure modes I and two independent pure modes II, which are orthogonal to each other as well. They are found and used to partition the total energy release rate.
Primary Phagocytosis of Neurons by Inflamed Microglia: Potential Roles in Neurodegeneration

Microglial phagocytosis of dead or dying neurons can be beneficial by preventing the release of damaging and/or pro-inflammatory intracellular components. However, there is now evidence that under certain conditions, such as inflammation, microglia can also phagocytose viable neurons, thus executing their death. Such phagocytic cell death may result from exposure of phosphatidylserine (PS) or other eat-me signals on otherwise viable neurons as a result of physiological activation or sub-toxic insult, and neuronal phagocytosis by activated microglia. In this review, we discuss the mechanisms of phagocytic cell death and its potential roles in Alzheimer’s Disease, Parkinson’s Disease, and Frontotemporal Dementia.
Structure-Guided Expansion of the Substrate Range of Methylmalonyl Coenzyme A Synthetase (MatB) of Rhodopseudomonas palustris

ABSTRACT Malonyl coenzyme A (malonyl-CoA) and methylmalonyl-CoA are two of the most commonly used extender units for polyketide biosynthesis and are utilized to synthesize a vast array of pharmaceutically relevant products with antibacterial, antiparasitic, anticholesterol, anticancer, antifungal, and immunosuppressive properties. Heterologous hosts used for polyketide production such as Escherichia coli often do not produce significant amounts of methylmalonyl-CoA, however, requiring the introduction of other pathways for the generation of this important building block. Recently, the bacterial malonyl-CoA synthetase class of enzymes has been utilized to generate malonyl-CoA and methylmalonyl-CoA directly from malonate and methylmalonate. We demonstrate that in the purple photosynthetic bacterium Rhodopseudomonas palustris, MatB (RpMatB) acts as a methylmalonyl-CoA synthetase and is required for growth on methylmalonate. We report the apo (1.7-Å resolution) and ATP-bound (2.0-Å resolution) structure and kinetic analysis of RpMatB, which shows similar activities for both malonate and methylmalonate, making it an ideal enzyme for heterologous polyketide biosynthesis. Additionally, rational, structure-based mutagenesis of the active site of RpMatB led to substantially higher activity with ethylmalonate and butylmalonate, demonstrating that this enzyme is a prime target for expanded substrate specificity.
Salmonella enterica Serovar TyphimuriumsurA Mutants Are Attenuated and Effective Live Oral Vaccines

ABSTRACT A previously described attenuated TnphoA mutant (BRD441) of Salmonella enterica serovar Typhimurium C5 (I. Miller, D. Maskell, C. Hormaeche, K. Johnson, D. Pickard, and G. Dougan, Infect. Immun. 57:2758–2763, 1989) was characterized, and the transposon was shown to be inserted in surA, a gene which encodes a peptidylprolyl-cis,trans-isomerase. A defined surA deletion mutation was introduced into S. enterica serovar Typhimurium C5 and the mutant strain, namedS. enterica serovar Typhimurium BRD1115, was extensively characterized both in vitro and in vivo. S. entericaserovar Typhimurium BRD1115 was found to be defective in the ability to adhere to and invade eukaryotic cells. Furthermore, S. enterica serovar Typhimurium BRD1115 was attenuated by at least 3 log units when administered orally or intravenously to BALB/c mice. Complementation of the mutation with a plasmid carrying the intactsurA gene almost completely restored the virulence of BRD1115. In addition, S. enterica serovar Typhimurium BRD1115 demonstrated potential as a vaccine candidate, since mice immunized with BRD1115 were protected against subsequent challenge withS. enterica serovar Typhimurium C5. S. entericaserovar Typhimurium BRD1115 also showed potential as a vehicle for the effective delivery of heterologous antigens, such as the nontoxic, protective fragment C domain of tetanus toxin, to the murine immune system.
Urinary Composition During Decongestive Treatment in Heart Failure With Reduced Ejection Fraction

Background—The urinary composition, including sodium (Na+) and chloride (Cl−) concentrations, might provide useful information in addition to urine output during decongestive treatment in heart failure. Methods and Results—Consecutive patients with heart failure (n=61), ejection fraction ⩽45%, worsening symptoms, and scheduled treatment with intravenous loop diuretics were included. Patients received protocol-driven therapy until complete decongestion, assessed clinically and by echocardiography. Three consecutive 24-hour urinary collections were performed. With 2 mg (1–4 mg), 1 mg (0–2 mg), and 1 mg (0–1 mg) bumetanide administered in bolus during consecutive 24-hour intervals, in addition to combinational diuretic therapy in ≈70% and both oral spironolactone and vasodilators in ≈90%, euvolemia was reached, often within 24 hours. Urine output was higher during the first when compared with the second or third 24-hour interval (2700 versus 1550 or 1375 mL, respectively; P<0.001), but this was no longer significant after correction for diuretic dose (P=0.263), indicating preserved diuretic efficiency during the study. In contrast, urinary Na+ and Cl− excretion both decreased significantly, even after correction for diuretic dose (P=0.040 and 0.004, respectively), leading to decreasing urinary concentrations with progressive decongestion. After reaching euvolemia, lower urinary Na+/Cr and Cl−/Cr ratios were both associated with urine output ⩽1500 mL (area under the curve, 0.830 and 0.826, respectively; P<0.001 for both), in contrast to plasma N-terminal pro–B-type natriuretic peptide levels that were not (area under the curve, 0.515; P=0.735) Conclusions—The urinary composition during progressive decongestion in heart failure with reduced ejection fraction is characterized by a drop in urinary Na+ and Cl− concentrations. The urinary Na+/Cr or Cl−/Cr ratio might provide insightful information to titrate diuretic therapy.
Body Weight Dissatisfaction Among Israeli Jewish and Arab Women With Normal or Overweight-Obese Body Mass Index, Israeli INHIS-1, 2003-2004

Introduction In Israel, 58.9% of Jewish and Arab Israeli women aged 25 to 64 years are overweight or obese (body mass index ≥25 kg/m2). The objective of this analysis is to describe body weight dissatisfaction differences between Jewish and Arab Israeli women with normal or overweight-obese body mass index. Methods This analysis included 1,393 Jewish and Arab women who participated in the Israeli National Health Interview Survey, 2003-2004. The survey covered a random sample of the Israeli general population aged 21 years or older. All variables were based on self-report. Body weight dissatisfaction was a multiple-choice question in the survey that offered the following responses: very satisfied, satisfied, reasonably satisfied, not satisfied, or very unsatisfied. Univariate and multivariate analyses were conducted. Results Overall, 39.1% of Jewish women reported body weight dissatisfaction, compared with 29.1% of Arab women. Older overweight-obese Arab women had a lower prevalence of body weight dissatisfaction than Jewish women of the same age group, which indicates cultural differences in body weight dissatisfaction among older overweight-obese women. However, cultural differences do not appear to influence body weight dissatisfaction among younger Jewish and Arab women of normal weight. Conclusion This study suggests that Jewish and Arab women differ in their perceptions of body weight. Interventions tailored to each group are needed to promote healthy dietary and physical activity behaviors.
A 14 Bit 1 GS/s RF Sampling Pipelined ADC With Background Calibration

We discuss a 14 bit 1 GS/s RF sampling pipelined ADC that utilizes correlation-based background calibration to correct the inter-stage gain, settling and memory errors. To improve the sampling linearity and RF sampling performance, the ADC employs input distortion cancellation and a digital background calibration technique to compensate for the non-linear charge injection (kick-back) from the sampling capacitors on the input driver. In addition, an effective dithering technique is embedded in the calibration signal to break the dependence of the calibration's convergence on the input signal amplitude. The ADC is fabricated on a 65 nm CMOS process and has an integrated input buffer. With a 140 MHz and 2 Vpp input signal, the SNR is 69 dB, the SFDR is 86 dB, and the power is 1.2 W.
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus

V1 interneurons are inhibitory neurons that play an essential role in vertebrate locomotion. The molecular mechanisms underlying their genesis remain, however, largely undefined. Here, we show that the transcription factor Prdm12 is selectively expressed in p1 progenitors of the hindbrain and spinal cord in the frog embryo, and that a similar restricted expression profile is observed in the nerve cord of other vertebrates as well as of the cephalochordate amphioxus. Using frog, chick and mice, we analyzed the regulation of Prdm12 and found that its expression in the caudal neural tube is dependent on retinoic acid and Pax6, and that it is restricted to p1 progenitors, due to the repressive action of Dbx1 and Nkx6-1/2 expressed in the adjacent p0 and p2 domains. Functional studies in the frog, including genome-wide identification of its targets by RNA-seq and ChIP-Seq, reveal that vertebrate Prdm12 proteins act as a general determinant of V1 cell fate, at least in part, by directly repressing Dbx1 and Nkx6 genes. This probably occurs by recruiting the methyltransferase G9a, an activity that is not displayed by the amphioxus Prdm12 protein. Together, these findings indicate that Prdm12 promotes V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes, and suggest that this function might have only been acquired after the split of the vertebrate and cephalochordate lineages. Summary: In vertebrates, V1 interneuron specification requires Prdm12, whose expression depends on Pax6 and retinoic acid and is restricted to the p1 domain by Dbx1 and Nkx6.1/2, themselves repressed by Prdm12.