Miracle-dz/UniFAR-FTUs huggingface dataset:
Poleward heat transport in the ocean

The large-scale transport of heat and carbon by the ocean circulation play an important role in the Earth's climate. Progress in developing realistic models of this process is reviewed. Sufficient numerical experiments have been carried out to indicate the role of subgrid scale mixing of temperature and salinity in the transport behavior of the models. The vertical component of subgrid diffusion in the models is essential for determining the amplitude of the thermohaline circulation of the ocean. In the case of simple geometries, poleward heat transport in models is approximately proportional to vertical mixing to the two-thirds power. The horizontal component of the diffusion appears to play almost no role in the poleward transport of heat as long as the value is less than 10 3 m 2 /s. At low values of horizontal diffusion and viscosity, mesoscale eddies are generated spontaneously in the models through baroclinic and barotropic instability. In analogy with the atmosphere one would expect these mesoscale disturbances to play an important role in poleward heat transport. The results of numerical experiments show that this may not be the case. The mesoscale eddies in the models generate mean flows which tend to cancel the eddy fluxes in much the same way that eddy-mean flow compensation occurs for atmospheric disturbances in the lower stratosphere. DOI: 10.1034/j.1600-0889.1991. t01-1-00009.x
Power reduction and the radial limit of stall delay in revolving wings of different aspect ratio

Airplanes and helicopters use high aspect ratio wings to reduce the power required to fly, but must operate at low angle of attack to prevent flow separation and stall. Animals capable of slow sustained flight, such as hummingbirds, have low aspect ratio wings and flap their wings at high angle of attack without stalling. Instead, they generate an attached vortex along the leading edge of the wing that elevates lift. Previous studies have demonstrated that this vortex and high lift can be reproduced by revolving the animal wing at the same angle of attack. How do flapping and revolving animal wings delay stall and reduce power? It has been hypothesized that stall delay derives from having a short radial distance between the shoulder joint and wing tip, measured in chord lengths. This non-dimensional measure of wing length represents the relative magnitude of inertial forces versus rotational accelerations operating in the boundary layer of revolving and flapping wings. Here we show for a suite of aspect ratios, which represent both animal and aircraft wings, that the attachment of the leading edge vortex on a revolving wing is determined by wing aspect ratio, defined with respect to the centre of revolution. At high angle of attack, the vortex remains attached when the local radius is shorter than four chord lengths and separates outboard on higher aspect ratio wings. This radial stall limit explains why revolving high aspect ratio wings (of helicopters) require less power compared with low aspect ratio wings (of hummingbirds) at low angle of attack and vice versa at high angle of attack.
Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments.

Reassembly of enzymes from peptide fragments has been used as a strategy for understanding the evolution, folding, and role of individual subdomains in catalysis and regulation of activity. We demonstrate an oligomerization-assisted enzyme reassembly strategy whereby fragments are covalently linked to independently folding and interacting domains whose interactions serve to promote efficient refolding and complementation of fragments, forming active enzyme. We show that active murine dihydrofolate reductase (E.C. 1.5.1.3) can be reassembled from complementary N- and C-terminal fragments when fused to homodimerizing GCN4 leucine zipper-forming sequences as well as heterodimerizing protein partners. Reassembly is detected by an in vivo selection assay in Escherichia coli and in vitro. The effects of mutations that disrupt fragment affinity or enzyme activity were assessed. The steady-state kinetic parameters for the reassembled mutant (Phe-31 --> Ser) were determined; they are not significantly different from the full-length mutant. The strategy described here provides a general approach for protein dissection and domain swapping studies, with the capacity both for rapid in vivo screening as well as in vitro characterization. Further, the strategy suggests a simple in vivo enzyme-based detection system for protein-protein interactions, which we illustrate with two examples: ras-GTPase and raf-ras-binding domain and FK506-binding protein-rapamycin complexed with the target of rapamycin TOR2.
Association of the risk of osteoarthritis with high innate production of interleukin-1beta and low innate production of interleukin-10 ex vivo, upon lipopolysaccharide stimulation.

OBJECTIVE In a sibpair study of osteoarthritis (OA) patients, we investigated whether, upon stimulation with lipopolysaccharide (LPS), variations in the innate ex vivo production of interleukin-1beta (IL-1beta), IL-1 receptor antagonist (IL-1Ra), IL-10, and tumor necrosis factor alpha (TNFalpha) in whole-blood assays contribute to the risk of OA. METHODS Data from 305 patients with OA at multiple sites (hand, knee, hip, and spine), whose median age was 60 years (range 43-79 years), were compared with those from 137 controls. OA was defined in accordance with the American College of Rheumatology criteria. Whole-blood samples were stimulated with LPS (10 ng/ml). In the supernatants, cytokines were measured by enzyme-linked immunosorbent assay. Odds ratios (ORs) were used as measures of the relative risk of OA in relation to quartiles of IL-1beta, IL-1Ra, TNFalpha, and IL-10 production. The ORs were adjusted for sex and age, and 95% confidence intervals (95% CIs) were computed using robust standard errors to take into account the intrafamily effect. RESULTS Subjects in the highest quartile of IL-1beta and IL-1Ra had an increased risk of OA (OR 3.3, 95% CI 1.4-7.9 and OR 8.0, 95% CI 3.7-17.4, respectively), while subjects in the lowest quartile of IL-10 had a 3-fold increased risk of OA (OR 3.1, 95% CI 1.5-6.5). High innate ex vivo production of TNFalpha was not associated with an increased risk of OA. CONCLUSION Subjects with a high innate ex vivo production of IL-1beta and IL-1Ra and low innate ex vivo production of IL-10 have an increased risk of OA. These results suggest that a proportion of the genetic susceptibility to OA may be encoded for by variations in innate cytokine activity.
Decreased Neutrophil Apoptosis in Quiescent ANCA-Associated Systemic Vasculitis

Background ANCA-Associated Systemic Vasculitis (AASV) is characterized by leukocytoclasis, accumulation of unscavenged apoptotic and necrotic neutrophils in perivascular tissues. Dysregulation of neutrophil cell death may contribute directly to the pathogenesis of AASV. Methods Neutrophils from Healthy Blood Donors (HBD), patients with AASV most in complete remission, Polycythemia Vera (PV), Systemic Lupus Erythematosus (SLE), Rheumatoid Arthritis (RA) and renal transplant recipients (TP) were incubated in vitro, and the rate of spontaneous apoptosis was measured by FACS. Plasma levels of cytokines and sFAS were measured with cytometric bead array and ELISA. Expression of pro/anti-apoptotic factors, transcription factors C/EBP-α, C/EBP-β and PU.1 and inhibitors of survival/JAK2-pathway were measured by real-time-PCR. Results AASV, PV and RA neutrophils had a significantly lower rate of apoptosis compared to HBD neutrophils (AASV 50±14% vs. HBD 64±11%, p<0.0001). In RA but not in AASV and PV, low apoptosis rate correlated with increased plasma levels of GM-CSF and high mRNA levels of anti-apoptotic factors Bcl-2A1 and Mcl-1. AASV patients had normal levels of G-CSF, GM-CSF and IL-3. Both C/EBP-α, C/EBP-β were significantly higher in neutrophils from AASV patients than HBD. Levels of sFAS were significantly higher in AASV compared to HBD. Conclusion Neutrophil apoptosis rates in vitro are decreased in AASV, RA and PV but mechanisms seem to differ. Increased mRNA levels of granulopoiesis-associated transcription factors and increased levels of sFAS in plasma were observed in AASV. Additional studies are required to define the mechanisms behind the decreased apoptosis rates, and possible connections with accumulation of dying neutrophils in regions of vascular lesions in AASV patients.
Complex Behavior at Scale: An Experimental Study of Low-Power Wireless Sensor Networks

A new class of networked systems is emerging that involve very large numbers of small, low-power, wireless devices. We present findings from a large scale empirical study involving over 150 such nodes operated at various transmission power settings. The instrumentation in our experiments permits us to separate effects at the various layers of the protocol stack. At the link layer, we present statistics on packet reception, effective communication range and link asymmetry; at the MAC layer, we measure contention, collision and latency; and at the application layer, we analyze the structure of trees constructed using flooding. The study reveals that even a simple protocol, flooding, can exhibit surprising complexity at scale. The data and analysis lay a foundation for a much wider set of algorithmic studies in this space.
Models of scientific progress and the role of theory in taxonomy development: a case study of the DSM.

The proliferation of categories in recent editions of the Diagnostic and Statistical Manual of Mental Disorders (e.g., 4th ed.; DSM; American Psychiatric Association, 1994) is discussed as an indication that the underlying classification scheme is inadequate and unlikely to produce the scientific progress originally envisioned. In any nosological system, it eventually becomes necessary to reduce the number of categories by an organizing theory that describes the fundamental principles underlying the taxonomy. The DSM has put itself in an awkward position by claiming to be atheoretical. Although taking such a tack had historical advantages to promote the acceptability of the 3rd edition of the DSM, it now limits the progression of science. It is argued that the DSM should not be used as the basis for guiding scientific research programs because it emphasizes primarily behavioral topography rather than providing an explicit theory that would allow for an evaluation of scientific progress. Theoretically driven taxonomies should be allowed to compete on the basis of how successful they are at achieving their specified goals that might include illuminating etiology, course, and response to treatment. Such systems are not likely to attend primarily to behavioral topography alone and would probably organize behavior differently than the current categorical syndromes seen in the 4th edition of the DSM.
The T cell repertoire in tumors overlaps with pulmonary inflammatory lesions in patients treated with checkpoint inhibitors

ABSTRACT Cancer immunotherapy with antibodies targeting immune checkpoints such as the PD-1/PD-L1 pathway have emerged as breakthrough treatment for multiple solid tumors with high response rates and durable remissions. Despite the benefit for patients and encouraging safety profile, severe inflammatory reactions are observed in some patients. Such immune-related adverse events (irAEs) frequently lead to temporary or permanent cessation of the treatment and require systemic immunosuppression yet underlying mechanisms of irAEs are not known in detail. Here, we describe the T cell-mediated immune reaction in irAE lesions of four patients that developed pneumonitis during therapy with a PD-1 blocking antibody. Immunohistochemical analysis was performed to map the environment of the inflammatory lesions. Tumor infiltrating T cell clones were identified by sequencing the T cell receptor, and comparison with clones from peripheral blood or secondary lymphoid organs. A significant overlap of clones infiltrating irAE lesions and tumors was found. The most prevalent clones were also expanded in peripheral blood, but only a minor fraction of clonal overlap was found. Our findings suggest that irAE lesions in patients under PD-1 blockade are infiltrated by T cells with similar specificity as tumor-infiltrating T cells. These results raise the possibility that the immune response is elicited in these patients against antigens shared by the tumor and distant organs affected by irAEs.
One Semiring to Rule Them All

In this paper we look at the well known phenomenon of conjunction fallacies (Tversky & Kahneman, 1983) from a linguistic perspective. We are particularly interested in understanding the impact of this phenomenon on our understanding of compositionality, a core assumption of contemporary linguistic theories about language meaning. We will argue that contra Hertwig, Benz, and Krauss (2008), conjunction fallacies do not arise because of the ambiguity of coordinating conjunctions such as and, but rather because there are two different strategies available for computing the composite likelihood of a collection of events. Crucially, in our analysis the two strategies are two variants of the same underlying general structure that simultaneously allows subjects 1. to reason in purely logical terms; 2. to follow the rules of probability and 3. to commit fallacies depending on the conditions under which they evaluate linguistic expressions relating uncertain events. We will explain the choice between the two strategies in terms of cognitive/computational economy and the consequences of overestimating the likelihood of an event.
Demographic senescence in herbaceous plants

For herbaceous plants, in contrast to many higher animals but similarly to other modular and sedentary life forms, it is not so much a question of how senescence progresses as it is a question of whether senescence occurs at all for most species. Overall, both the empirical evidence and theoretical predictions provide contrasting evidence. Monocarpic species and other semelparous life forms are an extreme example of senescence. For polycarpic, iteroparous plants, however, there is only limited evidence that senescence occurs at all. Our review of studies with herbaceous plants also shows that there are only a few studies with detailed age-based demographic data, and here too the evidence for senescence is limited. Moreover, the detrimental effects of ageing are hard to detect in the observational studies upon which most of our current knowledge is built. Our theoretical expectations suggest that it is likely that the evolutionary pressure that shapes senescence in other organisms also acts on plants, but there are also several aspects of plant biology that conflict with some of the assumptions in classical models of the evolution of senescence.
Cancer Association Study of Aminoacyl-tRNA Synthetase Signaling Network in Glioblastoma

Aminoacyl-tRNA synthetases (ARSs) and ARS-interacting multifunctional proteins (AIMPs) exhibit remarkable functional versatility beyond their catalytic activities in protein synthesis. Their non-canonical functions have been pathologically linked to cancers. Here we described our integrative genome-wide analysis of ARSs to show cancer-associated activities in glioblastoma multiforme (GBM), the most aggressive malignant primary brain tumor. We first selected 23 ARS/AIMPs (together referred to as ARSN), 124 cancer-associated druggable target genes (DTGs) and 404 protein-protein interactors (PPIs) of ARSs using NCI’s cancer gene index. 254 GBM affymetrix microarray data in The Cancer Genome Atlas (TCGA) were used to identify the probe sets whose expression were most strongly correlated with survival (Kaplan-Meier plots versus survival times, log-rank t-test <0.05). The analysis identified 122 probe sets as survival signatures, including 5 of ARSN (VARS, QARS, CARS, NARS, FARS), and 115 of DTGs and PPIs (PARD3, RXRB, ATP5C1, HSP90AA1, CD44, THRA, TRAF2, KRT10, MED12, etc). Of note, 61 survival-related probes were differentially expressed in three different prognosis subgroups in GBM patients and showed correlation with established prognosis markers such as age and phenotypic molecular signatures. CARS and FARS also showed significantly higher association with different molecular networks in GBM patients. Taken together, our findings demonstrate evidence for an ARSN biology-dominant contribution in the biology of GBM.
Fast light-map computation with virtual polygon lights

We propose a new method for the fast computation of light maps using a many-light global-illumination solution. A complete scene can be light mapped on the order of seconds to minutes, allowing fast and consistent previews for editing or even generation at loading time. In our method, virtual point lights are clustered into a set of virtual polygon lights, which represent a compact description of the illumination in the scene. The actual light-map generation is performed directly on the GPU. Our approach degrades gracefully, avoiding objectionable artifacts even for very short computation times.
Essential role of p53 phosphorylation by p38 MAPK in apoptosis induction by the HIV-1 envelope

The proapoptotic activity of the transcription factor p53 critically depends on the phosphorylation of serine 46 (p53S46P). Here, we show that syncytia containing p53S46P could be detected in lymph node biopsies from human immunodeficiency virus (HIV)-1 carriers, in the brain of patients with HIV-1–associated dementia and in cocultures of HeLa expressing the HIV-1 envelope glycoprotein complex (Env) with HeLa cells expressing CD4. In this latter model, cell death was the result of a sequential process involving cell fusion, nuclear fusion (karyogamy), phosphorylation of serine 15 (p53S15P), later on serine 46 (p53S46P), and transcription of p53 target genes. Cytoplasmic p38 mitogen-activated protein kinase (MAPK) was found to undergo an activating phosphorylation (p38T180/Y182P [p38 with phosphorylated threonine 180 and tyrosine 182]) before karyogamy and to translocate into karyogamic nuclei. p38T180/Y182P colocalized and coimmunoprecipitated with p53S46P. Recombinant p38 phosphorylated recombinant p53 on serine 46 in vitro. Inhibition of p38 MAPK by pharmacological inhibitors, dominant-negative p38, or small interfering RNA, suppressed p53S46P (but not p53S15P), the expression of p53-inducible genes, the conformational activation of proapoptotic Bax and Bak, the release of cytochrome c from mitochondria, and consequent apoptosis. p38T180/Y182P was also detected in HIV-1–induced syncytia, in vivo, in patients' lymph nodes and brains. Dominant-negative MKK3 or MKK6 inhibited syncytial activation of p38, p53S46P, and apoptosis. Altogether, these findings indicate that p38 MAPK-mediated p53 phosphorylation constitutes a critical step of Env-induced apoptosis.
Life Satisfaction among the Very Old: A Survey on a Cognitively Intact Sample Aged 90 Years or Above

The purpose of the study was to measure life satisfaction and the factors believed to influence it. The study involved 105 very old people, ninety years and above, who were not cognitively impaired, living in the inner part of Stockholm, Sweden. In order to assess life satisfaction, the Life Satisfaction Index-B (LSI-B) and Life Satisfaction Index-Z (LSI-Z) were used. Information about life events, activities, personality and social contacts were collected in order to determine their relative influence on life satisfaction. Factors associated with life satisfaction were also investigated in a content analysis to find out what the elderly themselves believe gives them life satisfaction. Results showed that health and an emotionally stable personality were, independently of other factors, the most important factors for life satisfaction among the very old.
Influence of different system abstractions on the performance analysis of distributed real-time systems

System level performance analysis plays a fundamental role in the design process of real-time embedded systems. Several different approaches have been presented so far to address the problem of accurate performance analysis of distributed embedded systems in early design stages. The existing formal analysis methods are based on essentially different concepts of abstraction. However, the influence of these different models on the accuracy of the system analysis is widely unknown, as a direct comparison of performance analysis methods has not been considered so far. We define a set of benchmarks aimed at the evaluation of performance analysis techniques for distributed systems. We apply different analysis methods to the benchmarks and compare the results obtained in terms of accuracy and analysis times, highlighting the specific effects of the various abstractions. We also point out several pitfalls for the analysis accuracy of single approaches and investigate the reasons for pessimistic performance predictions.
Complexity of Linear Boolean Operators Stasys Jukna

How to compute a linear Boolean operator by a small circuit using only unbounded fanin addition gates? Because this question is about one of the simplest and most basic circuit models, it has been considered by many authors since the early 1950s. This has led to a variety of upper and lower bound arguments—ranging from algebraic (determinant and matrix rigidity), to combinatorial (Ramsey properties, coverings, and decompositions) to graph-theoretic (the superconcentrator method). We provide a thorough survey of the research in this direction, and prove some new results to fill out the picture. The focus is on the cases in which the addition operation is either the boolean OR or XOR, but the model in which arbitrary boolean functions are allowed as gates is considered as well. S. Jukna and I. Sergeev. Complexity of Linear Boolean Operators. Foundations and Trends R © in Theoretical Computer Science, vol. 9, no. 1, pp. 1–123, 2013. DOI: 10.1561/0400000063. Full text available at: http://dx.doi. org/10.1561/0400000063
Adaptive graph walk-based similarity measures for parsed text

Abstract We consider a dependency-parsed text corpus as an instance of a labeled directed graph, where nodes represent words and weighted directed edges represent the syntactic relations between them. We show that graph walks, combined with existing techniques of supervised learning that model local and global information about the graph walk process, can be used to derive a task-specific word similarity measure in this graph. We also propose and evaluate a new learning method in this framework, a path-constrained graph walk variant, in which the walk process is guided by high-level knowledge about meaningful edge sequences (paths) in the graph. Empirical evaluation on the tasks of named entity coordinate term extraction and general word synonym extraction show that this framework is preferable to, or competitive with, vector-based models when learning is applied, and using small to moderate size text corpora.
500 Mb/s soft output Viterbi decoder

Two 8-state, 7-bit soft output Viterbi decoders matched to an EPR4 channel and a rate-8/9 convolutional code are implemented in 0. 18µm CMOS technology. Architectural transformation of the add-compare-select structures and modification of the register exchange allow a high throughput with small area overhead. The 4mm2chip has been verified to decode at 500Mb/s with 1.8V supply. These decoders are used with Turbo codes, which have been demonstrated to achieve information rates very close to the Shannon limit.