Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel Communication Mechanisms for Sparse, Irregular Applications

Parallel systems are becoming a significant computing technology, not only for high performance computing, but also for commodity servers. The goal of this research is to identify core communication mechanisms which both exploit architectural trends and support real applications. We demonstrate that cache-coherent shared memory hardware is such a core mechanism, even for applications with little data re-use and data-driven synchronization. This thesis makes three major contributions. First, we perform an in-depth study of the interaction between communication mechanisms and sparse, irregular applications. Second, we present the Remote Queues (RQ) communication model, an abstraction which synthesizes more efficient synchronization for hardware-supported shared memory and other complex systems. Third, we characterize the relative performance of all of our mechanisms as processor speed and machine size scale. On the MIT Alewife Multiprocessor, we find that shared memory provides high performance with lower code complexity than message passing on our irregular problems. This is primarily due to four reasons. First, a 5-to-1 ratio between global and local cache misses makes memory copies in bulk communication expensive relative to communication via shared memory. Second, although message passing has synchronization semantics superior to shared memory for data-driven computation, efficient shared memory can overcome this handicap by using global read-modify-writes to change from the traditional owner-computes model to a producer-computes model. Third, the Remote Queues communication model generalizes such a change, providing the semantics and performance of polling active messages on a wide variety of systems. Fourth, bulk transfers can result in high processor idle times in irregular applications. Finally, we characterize multiprocessor design points where message passing and bulk transfer can perform better than shared memory. In particular, we find that shared memory uses more than four times the network bandwidth as message passing. Unless an application’s performance is already limited by local memory speeds, network bandwidth and latency threaten to become a serious problem. Our study indicates that machines based on modern microprocessors, such as the Cray T3E, must resort to expensive, high-dimensional networks to support shared-memory traffic. Furthermore, the round-trip nature of shared memory may not be able to tolerate the latencies of future networks.
Blood Nodal marginal zone lymphoma : gene expression and miRNA profiling identify diagnostic markers and potential therapeutic targets

Nodal marginal zone lymphoma (NMZL) is a small B-cell neoplasm whose molecular pathogenesis is still essentially unknown and whose differentiation from other small B-cell lymphomas is hampered by the lack of specific markers. We have analyzed gene expression, miRNA profile, and copy number data from 15 NMZL cases. For comparison, 16 follicular lymphomas (FLs), 9 extranodal marginal zone lymphomas, and 8 reactive lymph nodes and B-cell subtypes were included. The results were validated by quantitative RTPCR in an independent series, including 61 paraffin-embedded NMZLs. NMZL signature showed an enriched expression of gene sets identifying interleukins, integrins, CD40, PI3K, NFB, and TGF, and included genes expressed by normal marginal zone cells and memory B cells. The most highly overexpressed genes were SYK, TACI, CD74, CD82, and CDC42EP5. Genes linked to G2/M and germinal center were down-regulated. Comparison of the gene expression profiles of NMZL and FL showed enriched expression of CHIT1, TGFB1, and TACI in NMZL, and BCL6, LMO2, and CD10 in FL. NMZL displayed increased expression of miR-221, miR223, and let-7f, whereas FL strongly expressed miR-494. Our study identifies new candidate diagnostic molecules for NMZL and reveals survival pathways activated in NMZL. (Blood. 2012;119(3):e9-e21)
Leucocyte expression of genes implicated in the plasminogen activation cascade is modulated by yoghurt peptides

The urokinase-plasminogen activator (u-PA), its receptor (u-PAR) and the inhibitors of u-PA (PAI-1 and PAI-2) provide a multi-molecular system in leucocytes that exerts pleiotropic functions influencing the development of inflammatory and immune responses. The objective of the present study was to examine the ability of water soluble extracts (WSE) obtained from traditional Greek yoghurt made from bovine or ovine milk to modulate the expression of u-PA, u-PAR, PAI-1 and PAI-2 in ovine monocytes and neutrophils. WSE were obtained from 8 commercial traditional type Greek yoghurts made from ovine or bovine milk. WSE upregulated the expression of all 4 u-PA related genes in monocytes but the upregulation was much higher in the PAI-1 (10-fold) than in u-PA and u-PAR (3–4 fold) thus, shifting the system towards inhibition. In line with this observation, WSE reduced total and membrane-bound u-PA activity in monocytes. In neutrophils, WSE caused small (50–60%) but significant (P < 0·05) reductions in expression of u-PAR and PAI-2 but had no effect on expression of u-PA, PAI-1 and on total cell-associated and membrane-bound u-PA activity. WSE from yoghurts made from bovine or ovine milk were essentially equally effective in affecting the u-PA system except for the u-PAR gene in ovine neutrophils that was affected (reduced) by the ovine and not the bovine WSE. In conclusion, peptides present in WSE modulated the expression of u-PA related genes but the effect was much more prominent in monocytes than in neutrophils.
Multi-Scale Attention with Dense Encoder for Handwritten Mathematical Expression Recognition

Handwritten mathematical expression recognition is a challenging problem due to the complicated two-dimensional structures, ambiguous handwriting input and variant scales of handwritten math symbols. To settle this problem, recently we propose the attention based encoder-decoder model that recognizes mathematical expression images from two-dimensional layouts to one-dimensional LaTeX strings. In this study, we improve the encoder by employing densely connected convolutional networks as they can strengthen feature extraction and facilitate gradient propagation especially on a small training set. We also present a novel multi-scale attention model which is employed to deal with the recognition of math symbols in different scales and restore the fine-grained details dropped by pooling operations. Validated on the CROHME competition task, the proposed method significantly outperforms the state-of-the-art methods with an expression recognition accuracy of 52.8% on CROHME 2014 and 50.1% on CROHME 2016, by only using the official training dataset.
The neurobiology of bipolar disorder

The neurobiology of bipolar disorder is reviewed. Bipolar disorder is associated with alterations in central nervous system (CNS) function from the level of large‐scale brain circuits to intracellular signal transduction mechanisms. Because of the broad spectrum over which these abnormalities appear, the causative effects are most likely present in the lowest common denominator of all of these systems. Current evidence points to subtle alterations in signal transduction that reverberate downstream both intra‐ and extracellularly to produce the symptoms of bipolar disorder. © 2003 Wiley‐Liss, Inc.
Randomized study of the duration of treatment with interferon alfa-2B in patients with hairy cell leukemia.

Several previous studies have demonstrated that both partially purified and recombinant alpha-interferons (alpha-IFNs) have high response rates in advanced hairy cell leukemia. However, the optimal dose and duration of therapy have not yet been defined. In this study, 90 patients were randomized after 12 months of IFN alfa-2b therapy with a standard dose of 2 X 10(6) U/m2 sc three times weekly to either no further therapy or an additional 6 months of therapy (18 mo total). There was no significant difference in the peripheral blood cell counts between the two groups (when analyzed) dating from the end of IFN therapy rather than from the time of randomization. Eighteen evaluable patients relapsed and were re-treated with IFN: 11 in the no-further-therapy group and 7 in the treated group. No patient was resistant to re-treatment with IFN. There was a significantly greater incidence of fatigue in the treated group (44% vs. 21%; P = .02) during the first 6 postrandomization months. We conclude that the duration of IFN therapy does not influence the clinical course after therapy is discontinued, but responses are maintained while patients receive therapy. However, because of a high incidence of fatigue with prolonged therapy and the ability to reinduce a second response, we recommend that IFN therapy be discontinued after 12 months in asymptomatic patients.
Effect of Carotenoid Supplemented Formula on Carotenoid Bioaccumulation in Tissues of Infant Rhesus Macaques: A Pilot Study Focused on Lutein

Lutein is the predominant carotenoid in the developing primate brain and retina, and may have important functional roles. However, its bioaccumulation pattern during early development is not understood. In this pilot study, we investigated whether carotenoid supplementation of infant formula enhanced lutein tissue deposition in infant rhesus macaques. Monkeys were initially breastfed; from 1 to 3 months of age they were fed either a formula supplemented with lutein, zeaxanthin, β-carotene and lycopene, or a control formula with low levels of these carotenoids, for 4 months (n = 2/group). All samples were analyzed by high pressure liquid chromatography (HPLC). Final serum lutein in the supplemented group was 5 times higher than in the unsupplemented group. All brain regions examined showed a selective increase in lutein deposition in the supplemented infants. Lutein differentially accumulated across brain regions, with highest amounts in occipital cortex in both groups. β-carotene accumulated, but zeaxanthin and lycopene were undetectable in any brain region. Supplemented infants had higher lutein concentrations in peripheral retina but not in macular retina. Among adipose sites, abdominal subcutaneous adipose tissue exhibited the highest lutein level and was 3-fold higher in the supplemented infants. The supplemented formula enhanced carotenoid deposition in several other tissues. In rhesus infants, increased intake of carotenoids from formula enhanced their deposition in serum and numerous tissues and selectively increased lutein in multiple brain regions.
Explanation-based learning: a survey of programs and perspectives

Explanation-based learning (EBL) is a technique by which an intelligent system can learn by observing examples. EBL systems are characterized by the ability to create justified generalizations from single training instances. They are also distinguished by their reliance on background knowledge of the domain under study. Although EBL is usually viewed as a method for performing generalization, it can be viewed in other ways as well. In particular, EBL can be seen as a method that performs four different learning tasks: generalization, chunking, operationalization, and analogy. This paper provides a general introduction to the field of explanation-based learning. Considerable emphasis is placed on showing how EBL combines the four learning tasks mentioned above. The paper begins with a presentation of an intuitive example of the EBL technique. Subsequently EBL is placed in its historical context and the relation between EBL and other areas of machine learning is described. The major part of this paper is a survey of selected EBL programs, which have been chosen to show how EBL manifests each of the four learning tasks. Attempts to formalize the EBL technique are also briefly discussed. The paper concludes with a discussion of the limitations of EBL and the major open questions in the field.
Robust transmit beampattern design for uniform linear arrays using correlated LFM waveforms

This paper presents a robust design of the transmit beampattern for uniform linear antenna arrays. Existing designs are usually completed at the stage of achieving an optimal transmit covariance matrix from identifying a weighting matrix with the assumption of ideally orthogonal waveforms. However, we propose a compensation technique to achieve the optimal covariance matrix without the requirement of orthogonality. The corresponding solutions identify a set of weighting matrices that are robust against the imperfection of the waveforms. As a result, a set of easy-to-generate partially correlated linear frequency modulated (LFM) waveforms can be used to achieve identical transmit beampatterns which could be synthesized by ideally orthogonal multiple-input multiple-output (MIMO) radar waveforms. The proposed robust design is evaluated via numerical examples.
Perinatal outcome following third trimester exposure to paroxetine.

BACKGROUND Paroxetine hydrochloride is commonly used for maternal depression, panic disorder, and obsessive-compulsive disorder. The drug readily crosses the human placenta. Although it does not appear to increase teratogenic risk, there have been case reports of neonatal withdrawal. Symptoms were described soon after birth and lasted up to 1 month. OBJECTIVE To investigate whether there is a clinically important discontinuation syndrome in neonates exposed to paroxetine in utero. METHODS Prospective, controlled cohort study. PATIENTS Fifty-five pregnant women counseled prospectively by the Motherisk program in Toronto, Ontario, regarding third-trimester exposure to paroxetine and their infants were included in the study group. Pregnant women who discontinued paroxetine before the third trimester or those receiving other drugs known to cause withdrawal-type symptoms, such as opioids or benzodiazepines, were excluded. A comparison group of 27 women using paroxetine during the first or second trimester and 27 women using nonteratogenic drugs were matched for maternal age, gravity, parity, social drug use, and nonteratogenic drug use. RESULTS Of the 55 neonates exposed to paroxetine in late gestation, 12 had complications necessitating intensive treatment and prolonged hospitalization. The most prevalent clinical picture was respiratory distress (n = 9), followed by hypoglycemia (n = 2), and jaundice (n = 1). The symptoms disappeared within 1 to 2 weeks. In the comparison group, only 3 infants experienced complications (P =.03). In logistic regression, only third-trimester exposure to paroxetine was associated with neonatal distress (odds ratio, 9.53; 95% confidence interval, 1.14-79.3). CONCLUSION When used near term, paroxetine is associated with a high rate of neonatal complications, possibly caused by its common discontinuation syndrome.
Live Imaging of Shoot Meristems on an Inverted Confocal Microscope Using an Objective Lens Inverter Attachment

Live imaging of above ground meristems can lead to new insights in plant development not possible from static imaging of fixed tissue. The use of an upright confocal microscope offers several technical and biological advantages for live imaging floral or shoot meristems. However, many departments and core facilities possess only inverted confocal microscopes and lack the funding for an additional upright confocal microscope. Here we show that imaging of living apical meristems can be performed on existing inverted confocal microscopes with the use of an affordable and detachable InverterScope accessory.
Parasites and Their Heterophagic Appetite for Disease

Heterophagy (literally meaning “other eat”) is the process of a cell consuming material from its environment. Heterophagy involves vesicular uptake and thus is distinct from cellular acquisition of small metabolites by solute transport, which typically occurs via membrane channels or transporters in a way that is akin to sipping or siphoning from the environment. Endocytosis, macropinocytosis, trogocytosis, and phagocytosis are forms of heterophagy that contribute distinctly to ingestion of substances ranging from soluble macromolecules to insoluble substances, including other cells. Ingestion is typically coupled with digestion by hydrolytic enzymes in the endolysosomal system of the cell. Although less commonly used than its counterpart autophagy (“self eat”), the term heterophagy describes a distinct process that is rarely discussed in a cohesive manner and yet is often crucial for cell survival. Because heterophagy encompasses vesicular transport, this process is largely confined to eukaryotes. Consistent with the scope of PLOS Pathogens, this article will focus principally on eukaryotic pathogens, especially protozoan parasites.
Link budget analysis in the network designed mobile WiMAX technology in the territory of the urban area of the city of Gjakova

Wireless communication has now entered the second century of its use and has valuable merits of improving the quality of life of all mankind. Technologies for wireless and mobile communications are replaced every 2-3 years. The current version of the Protocol provides Internet access up to 40 Mbps and this version is expected to increase the bandwidth. The telecommunications sector leaves much to be desired in improving service quality. This paper presents the possibilities of implementation of WiMAX technology in the territory of Gjakova. Also, here are discussed some aspects of mobile network on calculating the budget link of the mobile network with WiMAX technology. Calculating the link budget, the radius of cell to a base station in urban areas is about 0.6 km. In the planning area and the frequency band of 3.5GHz, with channel width of 5 MHz TDD and spectrum 30MHz. The link margin used in this case is 133.5 dB.
Cost-Effectiveness of Percutaneous Coronary Intervention in Optimally Treated Stable Coronary Patients

Background—The COURAGE (Clinical Outcomes Utilizing Revascularization and Aggressive druG Evaluations) trial compared the effect of percutaneous coronary intervention (PCI) plus optimal medical therapy with optimal medical therapy alone on cardiovascular events in 2287 patients with stable coronary disease. After 4.6 years, there was no difference in the primary end point of death or myocardial infarction, although PCI improved quality of life. The present study evaluated the relative cost and cost-effectiveness of PCI in the COURAGE trial. Methods and Results—Resource use was assessed by diagnosis-related group for hospitalizations and by current procedural terminology code for outpatient visits and tests and then converted to costs by use of 2004 Medicare payments. Medication costs were assessed with the Red Book average wholesale price. Life expectancy beyond the trial was estimated from Framingham survival data. Utilities were assessed by the standard gamble method. The incremental cost-effectiveness ratio was expressed as cost per life-year and cost per quality-adjusted life-year gained. The added cost of PCI was approximately $10 000, without significant gain in life-years or quality-adjusted life-years. The incremental cost-effectiveness ratio varied from just over $168 000 to just under $300 000 per life-year or quality-adjusted life-year gained with PCI. A large minority of the distributions found that medical therapy alone offered better outcome at lower cost. The costs per patient for a significant improvement in angina frequency, physical limitation, and quality of life were $154 580, $112 876, and $124 233, respectively. Conclusions—The COURAGE trial did not find the addition of PCI to optimal medical therapy to be a cost-effective initial management strategy for symptomatic, chronic coronary artery disease.
Tradeoffs between Maize Silage Yield and Nitrate Leaching in a Mediterranean Nitrate-Vulnerable Zone under Current and Projected Climate Scenarios

Future climatic changes may have profound impacts on cropping systems and affect the agronomic and environmental sustainability of current N management practices. The objectives of this work were to i) evaluate the ability of the SALUS crop model to reproduce experimental crop yield and soil nitrate dynamics results under different N fertilizer treatments in a farmer’s field, ii) use the SALUS model to estimate the impacts of different N fertilizer treatments on NO3- leaching under future climate scenarios generated by twenty nine different global circulation models, and iii) identify the management system that best minimizes NO3- leaching and maximizes yield under projected future climate conditions. A field experiment (maize-triticale rotation) was conducted in a nitrate vulnerable zone on the west coast of Sardinia, Italy to evaluate N management strategies that include urea fertilization (NMIN), conventional fertilization with dairy slurry and urea (CONV), and no fertilization (N0). An ensemble of 29 global circulation models (GCM) was used to simulate different climate scenarios for two Representative Circulation Pathways (RCP6.0 and RCP8.5) and evaluate potential nitrate leaching and biomass production in this region over the next 50 years. Data collected from two growing seasons showed that the SALUS model adequately simulated both nitrate leaching and crop yield, with a relative error that ranged between 0.4% and 13%. Nitrate losses under RCP8.5 were lower than under RCP6.0 only for NMIN. Accordingly, levels of plant N uptake, N use efficiency and biomass production were higher under RCP8.5 than RCP6.0. Simulations under both RCP scenarios indicated that the NMIN treatment demonstrated both the highest biomass production and NO3- losses. The newly proposed best management practice (BMP), developed from crop N uptake data, was identified as the optimal N fertilizer management practice since it minimized NO3- leaching and maximized biomass production over the long term.
Resilience and Controllability of Dynamic Collective Behaviors

The network paradigm is used to gain insight into the structural root causes of the resilience of consensus in dynamic collective behaviors, and to analyze the controllability of the swarm dynamics. Here we devise the dynamic signaling network which is the information transfer channel underpinning the swarm dynamics of the directed interagent connectivity based on a topological neighborhood of interactions. The study of the connectedness of the swarm signaling network reveals the profound relationship between group size and number of interacting neighbors, which is found to be in good agreement with field observations on flock of starlings [Ballerini et al. (2008) Proc. Natl. Acad. Sci. USA, 105: 1232]. Using a dynamical model, we generate dynamic collective behaviors enabling us to uncover that the swarm signaling network is a homogeneous clustered small-world network, thus facilitating emergent outcomes if connectedness is maintained. Resilience of the emergent consensus is tested by introducing exogenous environmental noise, which ultimately stresses how deeply intertwined are the swarm dynamics in the physical and network spaces. The availability of the signaling network allows us to analytically establish for the first time the number of driver agents necessary to fully control the swarm dynamics.