Miracle-dz/UniFAR-FTUs huggingface dataset:
Synchronization of cardiovascular oscillators in the presence of noise.

It has long been known that the heart of a healthy human subject in repose does not beat regularly. The rhythmic variation in the heart rate occurring at the frequency of respiration, known as respiratory sinus arrhythmia, has been the most studied cardio-respiratory interaction since Hales described changes in blood pressure related to the respiratory pattern in a horse [1]. Since then there has been much significant work on the cardio-respiratory interaction (e.g. [2, 3, 4]). However, studies of the interactions between the other processes involved in the dynamics of the cardiovascular system (CVS) are still in their infancy. It has recently come to be appreciated that, on the time scale of one average circulation period, the cardiovascular system behaves in many ways as a set of 5 coupled, autonomous, nonlinear oscillators of widely differing frequencies [5]. Synchronization and modulation of this cardiovascular oscillatory activity are important under both physiological and pathophysiological conditions. For example, there seems to be a relationship between the cardiorespiratory synchronization index (defined in [6]) and the standard deviation of the variability of heart rate [7], and an inverse relationship between the average cardiac frequency and the extent of its variation [8]. Control of the CVS appears to be maintained by a fine balance between variations of the oscillator eigenfrequencies. This further results in mutual amplitude and frequency modulation and, sometimes, mutual synchronization between the phases of the oscillators. In this paper, we present and discuss the results of numerical simulations of the proposed model, focusing on the type of couplings and the effect of noise on the dynamics of the oscillators’ interactions. In Section 2 we summarise very briefly the experimental observations that have been made to date, and which a satisfactory model may be expected to encompass; a fuller account is given in [9, 10, 11]. Section 3 discusses how the model is constructed, and Section 4 reports the results obtained from it under different assumptions about the coupling constants and the presence or absence of random fluctuations (noise) representing external influences and parts of the CVS that are not included explicitly in the model. Section 5 summarises the results and draws conclusions.
Studies on Relevance, Ranking and Results Display

This study considers the extent to which users with the same query agree as to what is relevant, and how what is considered relevant may translate into a retrieval algorithm and results display. To combine user perceptions of relevance with algorithm rank and to present results, we created a prototype digital library of scholarly literature. We confine studies to one population of scientists (paleontologists), one domain of scholarly scientific articles (paleo-related), and a prototype system (PaleoLit) that we built for the purpose. Based on the principle that users do not pre-suppose answers to a given query but that they will recognize what they want when they see it, our system uses a rules-based algorithm to cluster results into fuzzy categories with three relevance levels. Our system matches at least 1/3 of our participants' relevancy ratings 87% of the time. Our subsequent usability study found that participants trusted our uncertainty labels but did not value our color-coded horizontal results layout above a standard retrieval list. We posit that users make such judgments in limited time, and that time optimization per task might help explain some of our findings. Index Terms—knowledge retrieval; uncertainty, "fuzzy," and probabilistic reasoning; knowledge representation formalisms and methods ——————————  ——————————
Determination of the Processes Driving the Acquisition of Immunity to Malaria Using a Mathematical Transmission Model

Acquisition of partially protective immunity is a dominant feature of the epidemiology of malaria among exposed individuals. The processes that determine the acquisition of immunity to clinical disease and to asymptomatic carriage of malaria parasites are poorly understood, in part because of a lack of validated immunological markers of protection. Using mathematical models, we seek to better understand the processes that determine observed epidemiological patterns. We have developed an age-structured mathematical model of malaria transmission in which acquired immunity can act in three ways (“immunity functions”): reducing the probability of clinical disease, speeding the clearance of parasites, and increasing tolerance to subpatent infections. Each immunity function was allowed to vary in efficacy depending on both age and malaria transmission intensity. The results were compared to age patterns of parasite prevalence and clinical disease in endemic settings in northeastern Tanzania and The Gambia. Two types of immune function were required to reproduce the epidemiological age-prevalence curves seen in the empirical data; a form of clinical immunity that reduces susceptibility to clinical disease and develops with age and exposure (with half-life of the order of five years or more) and a form of anti-parasite immunity which results in more rapid clearance of parasitaemia, is acquired later in life and is longer lasting (half-life of >20 y). The development of anti-parasite immunity better reproduced observed epidemiological patterns if it was dominated by age-dependent physiological processes rather than by the magnitude of exposure (provided some exposure occurs). Tolerance to subpatent infections was not required to explain the empirical data. The model comprising immunity to clinical disease which develops early in life and is exposure-dependent, and anti-parasite immunity which develops later in life and is not dependent on the magnitude of exposure, appears to best reproduce the pattern of parasite prevalence and clinical disease by age in different malaria transmission settings. Understanding the effector mechanisms underlying these two immune functions will assist in the design of transmission-reducing interventions against malaria.
Long-term antibiotic treatment for Crohn's disease: systematic review and meta-analysis of placebo-controlled trials.

BACKGROUND We investigated the effectiveness of long-term antibiotic treatment in patients with Crohn's disease. METHODS We performed a systematic review and meta-analysis of randomized clinical trials. Data sources were Medline (from 1966 through June 2009), EMBASE (from 1980 through June 2009), Cochrane Central Register of Controlled Trials (issue 3, 2009), and references from relevant publications. Trials that compared antibiotic therapy during at least 3 months with placebo were included. Outcomes were remission in patients with active disease and relapse in patients with inactive disease. Results from intention-to-treat analyses were combined in a random-effects meta-analysis, stratified by class of drug. Odds ratios (ORs) >1 indicate superiority of antibacterial treatment over placebo. Numbers needed to treat for 1 year to keep 1 additional patient in remission were calculated. RESULTS Sixteen trials that examined 13 treatment regimens in 865 patients were included in the meta-analysis. The median duration of treatment was 6 months (range, 3-24 months). Three trials of nitroimidazoles showed benefit, with a combined OR of 3.54 (95% confidence interval [CI], 1.94-6.47). Similarly, the combined OR from 4 trials of clofazimine was 2.86 (95% CI, 1.67-4.88). For patients with active disease, the number needed to treat was 3.4 (95% CI, 2.3-7.0) for nitroimidazoles and 4.2 (95% CI, 2.7-9.3) for clofazimine. The corresponding numbers needed to treat for inactive disease were 6.1 (95% CI, 5.0-9.7) and 6.9 (95% CI, 5.4-12.0). No benefit was evident for classic drugs against tuberculosis (3 trials; OR, 0.58; 95% CI, 0.29-1.18). Results for clarithromycin were heterogeneous (I(2)=77%; P=. 005) and not combined in the meta-analysis. CONCLUSIONS Long-term treatment with nitroimidazoles or clofazimine appears to be effective in patients with Crohn's disease.
Ultrastructural evidence for a paucity of projections from the lumbosacral cord to the pontine micturition center or M‐region in the cat: A new concept for the organization of the micturition reflex with the periaqueductal gray as central relay

Information concerning the rate of bladder filling is determined by receptors in the bladder wall and conveyed via afferent fibers in the pelvic nerve to sensory neurons in the lumbosacral cord. It was assumed that this information is relayed from the lumbosacral cord to a medial cell group in the dorsolateral pontine tegmentum, called the M‐region, the pontine micturition center, or Barrington's nucleus. The M‐region, in turn, projects via long descending pathways to the sacral parasympathetic motoneurons. In the present electron microscopic study, it was investigated in cats whether monosynaptic projections from lumbosacral neurons to the M‐region indeed exist. Wheat‐germ agglutinin‐horseradish peroxidase injections were made into the lumbosacral cord. Many retrogradely labeled dendrites and somata were found in the M‐region, but no labeled terminals were found on retrogradely labeled dendrites or somata. Only a small number of anterogradely labeled terminals, which were filled with mainly round vesicles, contacted unlabeled dendrites in the M‐region. In contrast, many more anterogradely labeled terminals, which were filled with mainly round and, to a limited extent, dense core vesicles and with asymmetrical synapses, were found on dendrites in the lateral part of the periaqueductal gray (PAG). Previously (Blok and Holstege [1994] Neurosci. Lett. 166:93–96), it was demonstrated that the lateral part of the PAG contains neurons projecting to the M‐region.
General herbivore outbreak following an El Niño-related drought in a lowland Panamanian forest

A severe outbreak of Lepidoptera followed the 1997–98 El Niño Southern Oscillation event, during which the climate in central Panama was unusually dry. The outbreak involved the larvae of at least 12 species of Lepidoptera and occurred at a seasonally dry, deciduous forest site, where extensive background data were available regarding climate, tree species and non-outbreak herbivory levels. Most Lepidoptera were associated with only one or two larval host plant species belonging to the same family, and the majority were monophagous during this study. During the outbreak, caterpillar densities for the major outbreak species averaged 1.6 larvae per young leaf and 0.18 larvae per leaf for leaves of all ages. For canopy trees and lianas, the mean level of leaf damage was 13.8%, ranging from 1–100%. Seven out of 20 tree species sustained most of the damage, with 21–37% of the leaf area consumed. Relative to non-outbreak years, damage levels increased by more than 250% during the outbreak. Single-species outbreaks were observed in other areas with a similar drought, but wetter forests in central Panama did not experience outbreaks during this period. Historically, fewer outbreaks have been reported from tropical forests than from temperate forests, however, similar El Niño-related outbreaks have occurred recently in several other locations throughout the tropics.
The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro

Mycobacterium tuberculosis contains five resuscitation‐promoting factor (Rpf)‐like proteins, RpfA‐E, that are implicated in resuscitation of this organism from dormancy via a mechanism involving hydrolysis of the peptidoglycan by Rpfs and partnering proteins. In this study, the rpfA‐E genes were shown to be collectively dispensable for growth of M. tuberculosis in broth culture. The defect in resuscitation of multiple mutants from a ‘non‐culturable’ state induced by starvation under anoxia was reversed by genetic complementation or addition of culture filtrate from wild‐type organisms confirming that the phenotype was associated with rpf‐like gene loss and that the ‘non‐culturable’ cells of the mutant strains were viable. Other phenotypes uncovered by sequential deletion mutagenesis revealed a functional differentiation within this protein family. The quintuple mutant and its parent that retained only rpfD displayed delayed colony formation and hypersensitivity to detergent, effects not observed for mutants retaining only rpfE or rpfB. Furthermore, mutants retaining rpfD or rpfE were highly attenuated for growth in mice with the latter persisting better than the former in late‐stage infection. In conjunction, these results are indicative of a hierarchy in terms of function and/or potency with the Rpf family, with RpfB and RpfE ranking above RpfD.
Solventogenesis in Clostridium acetobutylicum fermentations related to carboxylic acid and proton concentrations

The mechanism primarily implicated in the solventogenesis process in batch fermentations of Clostridium acetobutylicum is examined in considerable detail. A variety of fermentations with or without pH control in the pH range of 3.7–6 have been carried out in order to examine which of a host of suspect parameters correlate with the initiation of solventogenesis. The parameters that did not correlate are the external (pH0) and intracellular (pHi) pH, and ΔpH, and the external or intracellular butyrate and acetate concentrations. Undissociated butyric acid (UBA) correlated well with the initiation of solventogenesis. A linear relationship between UBA and butanol concentrations was found at the onset of solventogenesis in all fermentations examined. The intercept of this linear relationship was 6–13mM UBA for the pH0 range of 3.7–5 and approximately zero for pH0 at or above 6. The required minimal UBA was interpreted as a dependency of the solventogenesis process on both H+ and butyrate concentrations. Undissociated acetic acid was found not to correlate with the initiation of solventogenesis. Addition of acetoacetate (AA) and propionate enhanced the effect of UBA on the solventogenesis process. The action of a nonmetabolizable (FCCP) and a metabolizable (AA) uncoupler on the ΔpH, pH0, pHi, and solventogenesis were also studied in order to gain further understanding of the solventogenesis mechanism.
On the stability of distance-based formation control

This paper examines stability properties of distance-based formations. These are formations encoded by inter-agent relative distances. A negative gradient control law is proposed and is shown to be provably correct when the formation graph is a tree. Moreover, it is shown that the tree structure is a necessary and sufficient condition for distance-based formation stabilization with negative gradient control laws. For graphs that contain cycles, a characterization of the resulting equilibria is given based on the properties of the cycle space of the graph. The results are also applied to flocking motion for double integrator agents.
Human interleukin 4 receptor confers biological responsiveness and defines a novel receptor superfamily

IL-4, a pleiotropic cytokine produced by T lymphocytes, plays an important role in immune responsiveness by regulating proliferation and differentiation of a variety of lymphoid and myeloid cells via binding to high affinity receptors. In this report we describe the isolation and functional expression of a human IL-4-R cDNA. When transfected into COS-7 cells, the cDNA encodes a 140-kD cell-surface protein. After transfection into a murine T cell line, the cDNA encodes a protein that binds human IL-4 with high affinity and can confer responsiveness to human IL-4. The predicted extracellular domain of the IL-4-R exhibits significant amino acid sequence homology with the beta subunit of the IL-2-R (p75), and the receptors for IL-6, erythropoietin, and prolactin. These receptors comprise a novel superfamily with extracellular domains characterized by four conserved cysteine residues and a double tryptophan-serine (WSXWS) motif located proximal to the transmembrane region.
HamleDT: To Parse or Not to Parse?

We propose HamleDT ― HArmonized Multi-LanguagE Dependency Treebank. HamleDT is a compilation of existing dependency treebanks (or dependency conversions of other treebanks), transformed so that they all conform to the same annotation style. While the license terms prevent us from directly redistributing the corpora, most of them are easily acquirable for research purposes. What we provide instead is the software that normalizes tree structures in the data obtained by the user from their original providers.
Service-Level Differentiation in Call Centers with Fully Flexible Servers

We study large-scale service systems with multiple customer classes and many statistically identical servers. The following question is addressed: How many servers are required (staffing) and how does one match them with customers (control) to minimize staffing cost, subject to class-level quality-of-service constraints? We tackle this question by characterizing scheduling and staffing schemes that are asymptotically optimal in the limit, as system load grows to infinity. The asymptotic regimes considered are consistent with the efficiency-driven (ED), quality-driven (QD), and quality-and-efficiency-driven (QED) regimes, first introduced in the context of a single-class service system. Our main findings are as follows: (a) Decoupling of staffing and control, namely, (i) staffing disregards the multiclass nature of the system and is analogous to the staffing of a single-class system with the same aggregate demand and a single global quality-of-service constraint, and (ii) class-level service differentiation is obtained by using a simple idle-server-based threshold-priority (ITP) control (with state-independent thresholds); and (b) robustness of the staffing and control rules: our proposed single-class staffing (SCS) rule and ITP control are approximately optimal under various problem formulations and model assumptions. Particularly, although our solution is shown to be asymptotically optimal for large systems, we numerically demonstrate that it performs well also for relatively small systems.
Soft budget constraints, transaction and financial systems

This paper surveys a number of contributions that deal with the "soft budget constraint problem," that is, the refinancing of loss-making enterprises. This problem is particularly prevalent in transition economies but is also pervasive in market economies. Following DEWATRIPONT AND MASKIN [1995], the paper looks at soft budget constraints as dynamic commitment problems in the presence of sunk costs. Various ways to harden budget constraints are analyzed: privatization, demonopolization, decentralization of government, decentralization of credit, and banking reform. Finally, the paper looks at the role of budget constraints on risk taking and innovation.
Trigeneous Platforms for Energy Efficient Computing of HPC Applications

In this paper, we present two novel real-time heterogeneous platforms with three kinds of devices (CPU, GPU, FPGA), i.e. trigeneous platforms, for efficiently accelerating computation intensive applications in both the high-performance computing and the embedded system domains. In the high-performance computing domain, the entire platform is implemented on a workstation which consists of an Intel Xeon E5 processor, a Nvidia Tesla GPU and a Xilinx Virtex 7 FPGA. The second platform is built for achieving high-performance in the real-time embedded system domain. For this platform, we use a Xilinx Zynq and Nvidia Jetson TK1 board. In these platforms, the communication is performed using PCIe Gen3 and PCIe Gen2 cards respectively. We conducted experiments using 5 real-time and high throughput computation-data-intensive applications, namely cone beam computed tomography, face recognition, HEVC UHD decoding, number plate recognition and motion tracking. All the applications are mapped to the devices of the proposed trigeneous platforms, based on the energy efficiency of the different tasks on each device but also minimizing data transfers and maximizing parallelism. With this trigeneous platform, we are able to achieve an average speed-up of 21x compared to a CPU-GPU platform, 24x compared to a CPU-FPGA platform and 70x compared to Quad-core CPU alone execution. The proposed trigeneous platforms save 43%, 56% and 64% of the energy when compared to CPU-GPU, CPU-FPGA and quad-core CPU platforms respectively. Furthermore, we also implemented these applications by using a single programming language (OpenCL) on the trigeneous platforms and achieved 6x of speed-up on average over the quad-core setup.
High Frequencies of Naive Melan-a/Mart-1–Specific Cd8+ T Cells in a Large Proportion of Human Histocompatibility Leukocyte Antigen (Hla)-A2 Individuals

Using fluorescent HLA-A*0201 tetramers containing the immunodominant Melan-A/MART-1 (Melan-A) tumor-associated antigen (Ag), we previously observed that metastatic lymph nodes of melanoma patients contain high numbers of Ag-experienced Melan-A–specific cytolytic T lymphocytes (CTLs). In this paper, we enumerated and characterized ex vivo Melan-A–specific cells in peripheral blood samples from both melanoma patients and healthy individuals. High frequencies (≥1 in 2,500 CD8+ T cells) of Melan-A–specific cells were found in 10 out of 13 patients, and, surprisingly, in 6 out of 10 healthy individuals. Virtually all Melan-A–specific cells from 6 out of 6 healthy individuals and from 7 out of 10 patients displayed a naive CD45RAhi/RO− phenotype, whereas variable proportions of Ag-experienced CD45RAlo/RO+ Melan-A–specific cells were observed in the remaining 3 patients. In contrast, ex vivo influenza matrix–specific CTLs from all individuals exhibited a CD45RAlo/RO+ memory phenotype as expected. Ag specificity of tetramer-sorted A2/Melan-A+ cells from healthy individuals was confirmed after mitogen-driven expansion. Likewise, functional limiting dilution analysis and interferon γ ELISPOT assays independently confirmed that most of the Melan-A–specific cells were not Ag experienced. Thus, it appears that high frequencies of naive Melan-A–specific CD8+ T cells can be found in a large proportion of HLA-A*0201+ individuals. Furthermore, as demonstrated for one patient followed over time, dramatic phenotype changes of circulating Melan-A–specific cells can occur in vivo.
Duplication of noncoding sequences in polyomavirus specifically augments the development of thymic tumors in mice

A 40-base-pair duplication of noncoding sequences in polyomavirus specifically augmented the development of thymic epitheliomas following inoculation of virus into newborn mice. Virus strains carrying only one copy of this sequence induced a full spectrum of tumors except for overt thymic tumors. This 40-base-pair repeat, on the early side of the replication origin, constituted a tissue-specific regulatory determinant for tumor induction.
Comparative Study of Physical And Elastic Properties of Jute And Glass Fiber Reinforced LDPE Composites

Jute fiber reinforced low density polyethylene (LDPE) composites and glass fiber reinforced LDPE composites were prepared at variable proportions using compression molding technique at 120 °C. Few physical and mechanical properties such as bulk density, water absorption%, tensile strength, elongation at break (Eb%), Young's modulus, flexural stress and strain and tangent modulus of both composites were studied and compared. Throughout the study, it was revealed that glass composites had better mechanical stability as compared to LDPE jute composites.