Miracle-dz/UniFAR-FTUs huggingface dataset:
A Naïve Time Analysis and its Theory of Cost Equivalence

Techniques for reasoning about extensional properties of functional programs are well understood, but methods for analysing the underlying intensional or operational properties have been much neglected. This paper begins with the development of a simple but useful calculus for time analysis of non-strict functional programs with lazy lists. One limitation of this basic calculus is that the ordinary equational reasoning on functional programs is not valid. In order to buy back some of these equational properties we develop a non-standard operational equivalence relation called cost equivalence, by considering the number of computation steps as an ‘observable’ component of the evaluation process. We define this relation by analogy with Park’s definition of bisimulation in CCS. This formulation allows us to show that cost equivalence is a contextual congruence (and thus is substitutive with respect to the basic calculus) and provides useful proof techniques for establishing cost-equivalence laws. It is shown that basic evaluation time can be derived by demonstrating a certain form of cost equivalence, and we give an axiomatization of cost equivalence which is complete with respect to this application. This shows that cost equivalence subsumes the basic calculus. Finally we show how a new operational interpretation of evaluation demands can be used to provide a smooth interface between this time analysis and more compositional approaches, retaining the advantages of both.
Lowly methylated region analysis identifies EBF1 as a potential epigenetic modifier in breast cancer

ABSTRACT Breast cancer (BC) encompasses heterogeneous pathologies with different subtypes exhibiting distinct molecular changes, including those related to DNA methylation. However, the role of these changes in mediating BC heterogeneity is poorly understood. Lowly methylated regions (LMRs), non-CpG island loci that usually contain transcription factor (TF) binding sites, have been suggested to act as regulatory elements that define cellular identity. In this study, we aimed to identify the key subtype-specific TFs that may lead to LMR generation and shape the BC methylome and transcription program. We initially used whole-genome bisulfite sequencing (WGBS) data available at The Cancer Genome Atlas (TCGA) portal to identify subtype-specific LMRs. Differentially methylated regions (DMRs) within the BC PAM50 subtype-specific LMRs were selected by comparing tumors and normal tissues in a larger TCGA cohort assessed by HumanMethylation450 BeadChip (450K) arrays and TF enrichment analyses were performed. To assess the impact of LMRs on gene expression, TCGA RNA sequencing data were downloaded and Pearson correlations between methylation levels of loci presenting subtype-specific TF motifs and expression of the nearest genes were calculated. WGBS methylome data revealed a large number of LMRs for each of the BC subtypes. Analysis of these LMRs in the 450K datasets available for a larger sample set identified 7,765, 5,657, and 19 differentially methylated positions (DMPs) between normal adjacent tissues and tumor tissues from basal, luminal, and HER2-enriched subtypes, respectively. Unsupervised clustering showed that the discriminatory power of the top DMPs was remarkably strong for basal BC. Interestingly, in this particular subtype, we found 4,409 differentially hypomethylated positions grouped into 1,185 DMRs with a strong enrichment for the early B-cell factor 1 (EBF1) motifs. The methylation levels of the DMRs containing EBF1 motifs showed a strong negative correlation with the expression of 719 nearby genes, including BTS2 and CD74, two oncogenes known to be specific for basal BC subtype and for poor outcome. This study identifies LMRs specific to the three main BC subtypes and reveals EBF1 as a potentially important regulator of BC subtype-specific methylation and gene expression program.
The stability of house dust mite allergens in glycerinated extracts.

BACKGROUND Mite allergen vaccines are important diagnostic and immunotherapeutic reagents. Previous studies on mite allergen stability under different storage conditions have yielded contradictory results. OBJECTIVE We sought to compare, over a 12-month period, the stability of mite allergens reconstituted in 50% glycerol and stored at different temperatures and to examine the role of protease inhibitors in enhancing allergen stability. METHODS Lyophilized allergen extracts were reconstituted in 50% glycerol, with and without protease inhibitors, and stored at -70 degrees C, -20 degrees C, 4 degrees C, or 37 degrees C for 12 months. At 6 and 12 months, the extracts were compared with freshly dissolved extracts by competition ELISA with pooled allergic sera, 2-site ELISA with mite-specific mAbs, and immunoblot analyses. RESULTS The overall potencies of the stored extracts measured by competition ELISA were stable at -20 degrees C and 4 degrees C. As determined by means of the immunoblot and 2-site ELISA, Der f 1 levels decreased at 4 degrees C. Levels of Der f 2, Der p 1, and Der p 2 decreased in at least one of the allergen-specific assays. Storage at 37 degrees C led to overall loss of potency and allergen content, whereas storage at -70 degrees C was associated with a moderate loss of potency that increased with multiple freeze-thaw cycles. Protease inhibitors had no effect on allergen stability. CONCLUSION Although overall potency of the extracts, as measured by competition ELISA, was preserved at -20 degrees C and 4 degrees C, allergen-specific assays indicated loss of allergens. These findings suggest that the competition ELISA is insensitive to decreases in the concentrations of individual allergens.
Cellular and Phenotypic Characterization of Canine Osteosarcoma Cell Lines

Canine and human osteosarcoma (OSA) have many similarities, with the majority of reported cases occurring in the appendicular skeleton, gender predominance noted, high rate of metastasis at the time of presentation, and a lack of known etiology for this devastating disease. Due to poor understanding of the molecular mechanisms underlying OSA, we have characterized seven different OSA canine cell lines: Abrams, D17, Grey, Hughes, Ingles, Jarques, and Marisco and compared them to U2, a human OSA cell line, for the following parameters: morphology, growth, contact inhibition, migrational tendencies, alkaline phosphatase staining, heterologous tumor growth, double-strand DNA breaks, and oxidative damage. All results demonstrated the positive characteristics of the Abrams cell line for use in future studies of OSA. Of particular interest, the robust growth of a subcutaneous tumor and rapid pulmonary metastasis of the Abrams cell line in an immunocompromised mouse shows incredible potential for the future use of Abrams as a canine OSA model. Further investigations utilizing a canine cell model of OSA, such as Abrams, will be invaluable to understanding the molecular events underlying OSA, pharmaceutical inhibition of metastasis, and eventual prevention of this devastating disease.
A novel miniaturized filter on micromachined multilayered substrates

Stepped impedance lowpass filters require large low to high impedance ratios to obtain high performance. Such high ratios results in filter having large step discontinuities and thereby introduce losses. Miniaturized filters on micromachined multilayered substrates are capable of addressing the above issues and realize optimal performance filters. In this paper a micromachined multilayered filter is designed on a multilayered substrate with silicon (/spl epsiv//sub r/=11.7) and silicon dioxide (/spl epsiv//sub r/=3.9) and simulated in ADS 2002C (Varadan et al., 2003) and HFSS 9.2. 1 (Blondy et al., 1998). The filters show an insertion loss of less than ldB and a return loss of less than -30dB at the desired cutoff frequency.
Endogenous bradykinin activates ischaemically sensitive cardiac visceral afferents through kinin B2 receptors in cats

1 Activity of ischaemically sensitive cardiac visceral afferents during myocardial ischaemia induces both angina and cardiovascular reflexes. Increased production of bradykinin (BK) and cyclo‐oxygenase products (i.e. prostaglandins (PGs)) occurs during myocardial ischaemia. However, the role of these agents in activation of ischaemically sensitive cardiac afferents has not been established. The present study tested the hypothesis that BK produced during ischaemia activates cardiac afferents through kinin B2 receptors. 2 Single‐unit activity of cardiac afferents innervating the left ventricle was recorded from the left thoracic sympathetic chain (T1‐T4) of anaesthetized cats. Ischaemically sensitive cardiac afferents were identified according to their response to 5 min of myocardial ischaemia. The mechanism of BK in activation of ischaemically sensitive cardiac afferents was determined by injection of BK (1 μg kg−1 i.a.), des‐Arg9‐BK (1 μg kg−1 i.a., a specific kinin B1 receptor agonist), kinin B2 receptor antagonists: HOE140 (30 μg kg−1 i.v.) and NPC‐17731 (40 μg kg−1 i.v.), cyclo‐oxygenase inhibition with indomethacin (5 mg kg−1 i.v.) and NPC‐17731 (40 μg kg−1 i.v.) after pretreatment with indomethacin (5 mg kg−1 i.v.). 3 We observed that BK increased the discharge rate of all eleven ischaemically sensitive cardiac afferents from 0.39 ± 0.12 to 1.47 ± 0.37 impulses s−1 (P < 0.05). Conversely, des‐Arg9‐BK did not significantly increase the activity of eleven ischaemically sensitive fibres (0.58 ± 0.02 vs. 0.50 ± 0.18 impulses s−1). HOE140 significantly attenuated the response of twelve afferents to ischaemia (0.61 ± 0.22 to 1.85 ± 0.5 vs. 0.53 ± 0.16 to 1.09 ± 0.4 impulses s−1). NPC‐17731, another kinin B2 receptor antagonist, had similar inhibitory effects on six other ischaemically sensitive cardiac afferents (0.35 ± 0.14 to 1.19 ± 0.29 vs. 0.22 ± 0.08 to 0.23 ± 0.07 impulses s−1). Indomethacin significantly reduced the responses of seven afferents to ischaemia (0.35 ± 0.13 to 1.89 ± 0.48 vs. 0.40 ± 0.10 to 0.76 ± 0.24 impulses s−1). Indomethacin also significantly reduced the responses of six ischaemically sensitive cardiac afferents to BK (2.65 ± 1.23 to 1.2 ± 0.51 impulses s−1). In six cats pretreated with indomethacin, NPC‐17731 attenuated the impulse activity of six ischaemically sensitive cardiac afferents (0.39 ± 0.12 to 1.0 ± 0.3 vs. 0.26 ± 0.14 to 0.48 ± 0.20 impulses s−1). 4 This study demonstrates that BK produced during ischaemia contributes to stimulation of ischaemically sensitive cardiac visceral afferents through activation of kinin B2 receptors. Furthermore, BK stimulates ischaemically sensitive cardiac visceral afferents through a mechanism that is, at least in part, independent of cyclo‐oxygenase activation.
DSICE: A Dynamic Stochastic Integrated Model of Climate and Economy

This paper introduces a dynamic stochastic integrated model of climate and economy (DSICE), and a numerical dynamic programming algorithm for its solution. More specifically, we solve an example with annual time periods, a six hundred year horizon, and shocks to the economic and climate system. Our dynamic programming methods solve such models on a laptop in about an hour, and do so with good accuracy. This decisively refutes the pessimism one often hears about the possibility of solving such models.
Succinct Non-Interactive Zero-Knowledge Proofs with Preprocessing for LOGSNP

Let Lambda : {0, 1}n times {0,1}m rarr {0,1} be a Boolean formula of size d, or more generally, an arithmetic circuit of degree d, known to both Alice and Bob, and let y isin {0,1} m be an input known only to Alice. Assume that Alice and Bob interacted in the past in a preamble phase (that is, applied a preamble protocol that depends only on the parameters, and not on Lambday). We show that Alice can (non-interactively) commit to y, by a message of size poly(m, log d), and later on prove to Bob any N statements of the form Lambda (x1, y) = z1,. , Lambda(xN ,y) = zN by a (computationally sound) non-interactive zero-knowledge proof of size poly(d, log N). (Note the logarithmic dependence on N). We give many applications and motivations for this result. In particular, assuming that Alice and Bob applied in the past the (poly-logarithmic size) preamble protocol: 1. given a CNF formula Psi(w1,., wm) of size N, Alice can prove the satisfiability of Psi by a (computationally sound) non-interactive zero-knowledge proof of size poly(m). That is, the size of the proof depends only on the size of the witness and not on the size of the formula. 2. Given a language L in the class LOGSNP and an input x isin {0, 1}n, Alice can prove the membership x isin L by a (computationally sound) non-interactive zero-knowledge proof of size polylog n. 3. Alice can commit to a Boolean formula y of size m, by a message of size poly(m), and later on prove to Bob any N statements of the form y(x1) = z1,. , y(xN) = zN by a (computationally sound) non-interactive zero-knowledge proof of size poly(m, log N). Our cryptographic assumptions include the existence of a poly-logarithmic symmetric-private-information-retrieval (SPIR) scheme, as defined in (C. Cachin et. al, 1999), and the existence of commitment schemes, secure against circuits of size exponential in the security parameter
Activity of the Funai Fault and Radiocarbon Age Offsets of Shell and Plant Pairs from the Latest Pleistocene to Holocene Sediments Beneath the Oita Plain, Western Japan

Abstract Beppu Bay is located on east-central Kyushu, southwest Japan, and is characterized by hydrothermal activity, tectonic deformation, and recent volcanism under the influence of convergence of the Philippine Sea plate. This area, occupying the western portion of an arc-bisecting dextral fault system, is a tectonic depression that has existed since ca. 5 Ma. Sedimentary facies, mollusk assemblages, and radiocarbon (14C) ages of 25 terrestrial plant fragments and 16 marine carbonate shells from a 70-m drill core were determined to estimate the activity of the Funai Fault, which consists of normal faults along the southern margin of the tectonic basin. Based on the analysis, six sedimentary facies, namely braided river channel, estuary, prodelta, delta front, delta plain, and artificial soil, were identified. The vertical slip rate was calculated as 2.6–2.7 mm/yr based on displacements of the braided river channel sediments of the last glacial period and the base of Kikai-Akayoya tephra in the Holocene highstand sediments of this area. Reservoir ages during 6180–10,410 cal BP were determined from marine shell and terrestrial plant pairs from the sediments of the estuary, prodelta and delta front facies, and were correlated with values from a northern coast of Kyushu and the Korean Peninsula.
Real Time Cache Performance Analyzing for Multi-core Parallel Programs

Modern processors mostly use cache to hide the memory access latency, so cache performance is very important to application program. A detailed cache performance analysis will provide programmers a clear view of their program behaviors, which can help them to identify the performance bottleneck and to optimize the source code. As the chip industry turn to integrate multiple cores into one chip, multi-core/many-core processor becomes the new approach to maintain the Moor's Law. Therefore, Parallel programs turn to be more important even in the personal computers. In parallel programs, the interaction between tasks is the source of bugs and errors and is hard to handling for most of programmers. The detailed cache behaviors will greatly helpful to the programmer to find the errors and optimize the programs. However, the existing cache performance analysis tools, due to the limitations of the hardware performance counters they depend on to get data, cannot get as much data as we expected. Those tools cannot reveal the program routines characteristics on shared cache and the source of cache misses with limited metrics on cache misses. In this paper, we propose a method to obtain and analysis real time cache performance with binary instrumentation and cache emulation. We instrument the parallel program while it is running, and get the trace data about memory access. Then we transport the trace data to an carefully configured cache emulation module to get the detailed cache behavior information. The emulation module can not only get more information than hardware performance counter but also can be configured to simulate different target hardware environment. Additionally, we use the performance data to form a group of cache performance metrics which can intuitively help programmers to optimize their codes. The accuracy of this method is demonstrated by comparing the summary result with the hardware performance counter. Finally, we design an cache performance analysis tool named CC-Analyzer for parallel programs. Comparing with the existing technologies, CC-Analyzer is able to analyze the cause of cache misses and gather much more performance statistics when the parallel program is running on different cache architectures.
Insights into the applicability of microbial fuel cells in wastewater treatment plants for a sustainable generation of electricity

ABSTRACT Microbial fuel cells (MFCs) are often discussed as a part of a sustainable generation of electricity for the coming ‘energy revolution’. In particular, the application of MFCs in wastewater treatment plants (WWTPs) are often regarded as an attractive alternative to reduce costs while generating electricity. Field surveys are necessary to show the applicability of MFCs in WWTPs considering daily fluctuations and environmental effects such as rain events affecting the MFC performance remarkably. In this study, a MFC system was tested in four municipal WWTPs using different modes of operation. A correlation between current densities and sludge loading (SL) was identified. At low SLs, the activated sludge needs a large amount of the energy derived from the substrate for the maintenance metabolism resulting in quite low current densities of the MFC. At high SLs much more of the energy can be transferred from the activated sludge to the electrode, resulting in higher currents. Furthermore, the effect of environmental conditions on the current densities was evaluated. WWTPs have daily fluctuations depending on the wastewater composition, weather phenomena and population equivalents. Our data show that these daily fluctuations can only be observed in the MFC performance at WWTPs below 50,000 population equivalents.
Unexpectedly limited durability of immunity following acellular pertussis vaccination in preadolescents in a North American outbreak.

BACKGROUND Despite widespread childhood vaccination against Bordetella pertussis, disease remains prevalent. It has been suggested that acellular vaccine may be less effective than previously believed. During a large outbreak, we examined the incidence of pertussis and effectiveness of vaccination in a well-vaccinated, well-defined community. METHODS Our center provides care to 135 000 patients, 40% of the population of Marin County, California. A total of 171 patients tested positive for B. pertussis from 1 March to 31 October 2010 by polymerase chain reaction (PCR). Electronic medical records were reviewed for demographic characteristics and vaccination status. RESULTS We identified 171 cases of clinical pertussis, 132 of which were in pediatric patients. There was a notable increase in cases among patients aged 8-12 years. The rate of testing peaked among infants but remained relatively constant across ages until 12 years. The rate of positive tests was low for ages 0-6 years and increased among preadolescents, peaking among those aged 12 years. The vaccination rate among PCR-positive preadolescents were approximately equal to that of controls. The vaccine effectiveness was 41%, 24%, and 79% for children aged 2-7 years, 8-12 years, 13-18 years, respectively. CONCLUSIONS Our data suggests that the current schedule of acellular pertussis vaccine doses is insufficient to prevent outbreaks of pertussis. We noted a markedly increased rate of disease from ages 8-12 years, proportionate to the interval since the last scheduled vaccine. Stable rates of testing ruled out selection bias. The possibility of earlier or more numerous booster doses of acellular pertussis vaccine either as part of routine immunization or for outbreak control should be entertained.
Intravenous Infusion Tests Have Limited Utility for Selecting Long-term Drug Therapy in Patients with Chronic Pain: A Systematic Review

Since the first description in the early 1990s, the scope of intravenous infusions tests has expanded to encompass multiple drug classes and indications. Purported advantages of these tests include elucidating mechanisms of pain, providing temporary relief of symptoms, and usefulness as prognostic tools in guiding drug therapy. In an attempt to discern the value of these tests, the authors conducted a systematic review to explore the rationale and evidence behind the following intravenous infusion tests: lidocaine, ketamine, opioid, and phentolamine. The studies evaluating all intravenous infusion tests were characterized by lack of standardization, wide variations in outcome measures, and methodological flaws. The strongest evidence found was for the intravenous lidocaine test, with the phentolamine test characterized by the least convincing data. Whereas intravenous opioid infusions are the most conceptually appealing test, their greatest utility may be in predicting poor responders to sustained-release formulations.
Diphenylcarbene Protected by Four ortho-Iodine Groups: An Unusually Persistent Triplet Carbene

Diphenyldiazomethane with four iodine groups at the ortho positions and two tert-butyl groups at the para positions, i.e., bis(4-tert-butyl-2,6-diiodophenyl)diazomethane (1a-N2), was synthesized as a sterically hindered triplet carbene precursor. Irradiation of 1a-N2 in solution effectively generated the corresponding triplet diphenylcarbene 31a, which was characterized by UV-vis spectroscopy at low temperature, along with laser flash photolysis techniques at room temperature. The UV-vis spectrum of 31a was obtained by irradiating 1a-N2 in a 2-methyltetrahydrofuran matrix at 77 K. The ESR spectrum showed no triplet carbene signals, while a radical species was observed at the anticipated temperature of the decomposition of triplet carbene 31a. Transient absorption bands ascribable to 31a were observed by laser flash photolysis of 1a-N2 in a degassed benzene solution and decayed very slowly with a second-order rate constant (2k/εl) of 5.5 × 10−3·s−1. Steady-state irradiation of 1a-N2 in degassed benzene afforded 9,10-diarylphenanthrene derivative 2a in a 31% yield. Triplet carbene 31a was also trapped by either oxygen (kO2 = 6.5 × 105 M−1·s−1) or 1,4-cyclohexadiene (kCHD = 1.5 M−1·s−1) to afford the corresponding ketone 1a-O or the diarylmethane 1a-H2. The carbene was shown to be much less reactive than the triplet diphenylcarbene that is protected by two ortho-iodo and two ortho-bromo groups, 31b.