Miracle-dz/UniFAR-FTUs huggingface dataset:
Complexity/performance tradeoffs with non-blocking loads

Non-blocking loads are a very effective technique for tolerating the cache-miss latency on data cache references. The authors describe several methods for implementing non-blocking loads. A range of resulting hardware complexity/performance tradeoffs are investigated using an object-code translation and instrumentation system. The authors investigate the SPEC92 benchmarks and have found that for the integer benchmarks, a simple hit-under-miss implementation achieves almost all of the available performance improvement for relatively little cost. However, for most of the numeric benchmarks, more expensive implementations are worthwhile. The results also point out the importance of using a compiler capable of scheduling load instructions for cache misses rather than cache hits in non-blocking systems. <<ETX>>
Characterization of P40, a Cytadhesin of Mycoplasma agalactiae

ABSTRACT An immunodominant protein, P40, of Mycoplasma agalactiae was analyzed genetically and functionally. The gene encoding P40 was cloned from type strain PG2, sequenced, submitted to point mutagenesis in order to convert mycoplasma-specific TGATrp codon to the universal TGGTrp codon, and subsequently expressed in Escherichia coli. Nucleotide sequence-derived amino acid sequence comparisons revealed a similarity of P40 to the adhesin P50 of Mycoplasma hominis and to protein P89 of Spiroplasma citri, which is expected to be involved in adhesion. The amino acid sequence of P40 revealed a recognition site for a signal peptidase and strong antigenic and hydrophilic motifs in the C-terminal domain. Triton X-114 phase partitioning confirmed that P40 is a membrane protein. Fab fragments of antibodies directed against recombinant purified P40 significantly inhibited adherence of M. agalactiae strains PG2 to lamb joint synovial cells LSM 192. Sera taken sequentially from sheep infected with PG2 revealed that P40 induced a strong and persistent immune response that gave strong signals on immunoblots containing recombinant P40 even 3 months after infection. The gene encoding P40 was present in a single copy in all of the 26 field strains of M. agalactiae analyzed and was not detected in closely related mycoplasma species. P40 was expressed as a protein with an apparent molecular mass of 37 kDa on sodium dodecyl sulfate-acrylamide gels by all M. agalactiae strains except for serotype C strains, which showed nonsense mutations in their p40 genes.
Prealbumin and inflammatory markers in dialysis patients

Inflammation is one of the main causes of high mortality and morbidity rates in patients with chronic renal failure treated with dialysis. In these cases, the use of anthropometric or biochemical markers alone, is not enough, but it is important to use the combination of them. The aim of this study is to evaluate serum prealbumin as an inflammatory and nutritional marker and determine whether there is an association between prealbumin and other anthropometric and biochemical markers. A total of 30, clinically stable dialysis patients (15 HD and 15 PD) participated in the study. The investigated anthropometric and biochemical measurements of the study are body weight (BW), Body Mass Index (BMI), serum prealbumin, albumin, transferrin, C - reactive protein (CRP), creatinine, ferritin, Interleukin-6 (IL-6), cholesterol, Iron (Fe) and Prognostic Inflammatory and Nutritional index (PINI). There are no significant differences in age, duration of dialysis, dry weight and BMI between patients on HD or PD. Albumin is significantly lower in the PD group, whereas, transferrin and total cholesterol are significantly greater in the HD group. A higher percentage of the HD patients have inflammation with CRP>5g/l and IL-6>8.8ng/ml compared with the PD patients. According to the present study, prealbumin levels are lower in the PD group compared with the HD group but it is not significantly correlated with any of the investigated parameters, apart from ferritin, in the HD group. Moreover, further analysis showed that patients are malnourished independently whether they have inflammation or not.
Anti-membrane-bound transferrin-like protein antibodies induce cell-shape change and chondrocyte differentiation in the presence or absence of concanavalin A

Membrane-bound transferrin-like protein (MTf), a glycosylphosphatidylinositol-anchored protein, is expressed at high levels in many tumors and in several fetal and adult tissues including cartilage and the intestine, as well as in the amyloid plaques of Alzheimer's disease, although its role remains unknown. MTf is one of the major concanavalin A-binding proteins of the cell surface. In this study, we examined the effects of anti-MTf antibodies and concanavalin A on cell shape and gene expression, using cultures of chondrocytes and MTf-overexpressing ATDC5 and C3H10T1/2 cells. In cultures expressing MTf at high levels, concanavalin A induced cell-shape changes from fibroblastic to spherical cells, whereas no cell-shape changes were observed with wild-type ATDC5 or C3H10T1/2 cells expressing MTf at very low levels. The cell-shape changes were associated with enhanced proteoglycan synthesis and expression of cartilage-characteristic genes, including aggrecan and type II collagen. Some anti-MTf antibodies mimicked this action of concanavalin A, whereas other antibodies blocked the lectin action. The findings suggest that the crosslinking of MTf changes the cell shape and induces chondrogenic differentiation. MTf represents the first identification of a plant lectin receptor involved in cell-shape changes and the differentiation of animal cells.
A comprehensive survey on replication based protocols of delay tolerant networks

In challenged networks, such as opportunistic networks or Delay Tolerant Networks (DTNs), due to frequent network partition an end-to-end connection between source and destination may not always be possible due to nodes move unpredictably with high speeds. For such type of networks, traditional routing protocols fails to transmit and also no guarantee on delivery of data to specified destination because these protocols deliver data definitely whenever there exists continuous end-to-end connectivity between source and destination over time. To provide efficient routing for such networks replication based routing schemes were proposed to achieve higher delivery probability. Unlike Internet protocols, Delay Tolerant Networks routing protocols follow store-carry-forward mechanism to reduce packets dropping probability, tolerate delays and improve delivery performance in terms of delivery ratio and delivery latency. This paper defines the most efficient replication based routing protocols such as epidemic, PROPHET, spray and wait and Encounter based routing. This paper also explains how message TTL, buffer sizes and area of grid impact performance of replication based routing protocol in terms of delivery ratio and Average latency and overhead ratio.
Actions of caffeine on fast‐ and slow‐twitch muscles of the rat.

1. The effects of caffeine (0.2‐20 mmol l‐1) have been examined on calcium transients (measured with aequorin) and isometric force in intact bundles of fibres from soleus (slow‐twitch) and extensor digitorum longus (EDL; fast‐twitch) muscles of the rat. 2. At 25 degrees C, threshold caffeine concentration for an observable increase in resting [Ca2+]i was 0.2 and 1.0 mmol l‐1 for soleus and EDL muscles respectively. Increases in resting force were first detectable at about 0.5 mmol l‐1 caffeine for soleus muscles and 5.0 mmol l‐1 caffeine for EDL muscles and occurred in the range 0.2‐0.4 mumol l‐1 [Ca2+]i for soleus and 0.7‐0.9 mumol l‐1 for EDL. 3. Caffeine potentiated the twitch responses of soleus and EDL in a dose‐related manner. The soleus was more sensitive in this respect, with 50% potentiation occurring at 1 mmol l‐1 caffeine compared with 3.5 mmol l‐1 for the EDL. Concentrations of caffeine below 2 mmol l‐1 potentiated Ca2+ transients associated with twitches in both soleus and EDL muscles with no apparent change in the decay rate constant. 4. High concentrations of caffeine (greater than 2 mmol l‐1) further potentiated peak Ca2+ in the EDL but depressed it in the soleus. The rate of decay of the Ca2+ transient in high caffeine was significantly prolonged in the soleus but remained unaffected in the EDL. 5. The phosphodiesterase inhibitor, 3‐isobutyl‐1‐methylxanthine (IBMX) had little effect on force or [Ca2+]i at concentrations known to significantly increase intracellular cyclic AMP levels. 6. The Ca2+ transient during fused tetani was characterized by an initial peak, a decline to a plateau level and sometimes a gradual rise towards the end of the stimulus train. Peak [Ca2+]i during normal tetani ranged between 1.1 and 2.4 mumol l‐1 in the soleus and 1.9 and 4.0 mumol l‐1 in the EDL. 7. Caffeine potentiated both force and [Ca2+]i during tetanus. Since the increase of the Ca2+ transient was significantly greater than potentiation of force, it is likely that saturation of myofilaments occurs. The primary effect of caffeine on the Ca2+ transient was an elevation of the plateau phase. 8. Caffeine concentrations below 5 mmol l‐1 potentiate twitch and tetanic force in both fast‐ and slow‐twitch mammalian skeletal muscles primarily by increasing both the basal and stimulus‐evoked release of Ca2+ from the sarcoplasmic reticulum.
Selection for virulence and organ‐specific metastasis of herpesvirus‐transformed lymphoma cells

The Marek's Disease virus‐transformed, non‐producer, lymphoma cell line, MDCC‐RP1, was selected by sequential transplantation to produce a highly malignant variant, MDCC‐AL1. This is evidenced by an 18‐fold decrease in LD50‐. The new cell line has an increased ability to form metastatic lesions in a distribution which mimics the natural disease. Further selections for organ‐specific metastasis were undertaken with the isolation of two cell lines, MDCC‐AL2, selected for liver metastasis, and MDCC‐AL3, selected for ovary metastasis. In vivo studies show that the selection was unsuccessful in the case of the ovary but successful in the case of the liver. Two assays were developed, utilizing the chick embryo and intravenous injection of lymphoma variants. One measures liver‐specific metastasis by the enumeration of tumour foci on the embryonic liver. The second, chorioallantoic membrane (CAM) focus formation, correlates with the virulence of the injected lymphoma cells. The liver‐selected tumour variant cells form more liver foci than any other tumour variant cells. The genetic background of the embryo does not affect formation of liver foci. Resistance to CAM focus formation correlates with major histocompatibility complex associated resistance to MD.
Tiotropium for Treatment of Stable COPD: A Meta-analysis of Clinically Relevant Outcomes

OBJECTIVE: To systematically review recent evidence on the effectiveness of tiotropium versus placebo, ipratropium, and long-acting β2 agonists on outcomes relevant to patients with stable COPD, including health-related quality of life, dyspnea, exacerbations and hospitalizations. METHODS: Our inclusion criteria for trials were: ≥ 12 weeks; compared tiotropium to placebo, ipratropium, or long-acting β agonists; patients ≥ 40 y old and with stable COPD. Sixteen trials (16,301 patients) met the inclusion criteria. RESULTS: Tiotropium improved health-related quality of life (measured with St George's Respiratory Questionnaire) compared to placebo (odds ratio [OR] 1.61, 95% CI 1.38–1.88, P < .001) and ipratropium (OR 2.03, 95% CI 1.34–3.07, P = .001). Tiotropium also improved dyspnea (measured with the Transitional Dyspnea Index) compared to placebo (OR 1.96, 95% CI 1.58–2.44, P < .001) and ipratropium (OR 2.10, 95% CI 1.28–3.44, P = .003). Tiotropium decreased the likelihood of an exacerbation (OR 0.83, 95% CI 0.72–0.94, P = .004) and related hospitalizations (OR 0.89, 95% CI 0.80–0.98, P = .02) but not serious adverse events (OR 1.06, 95% CI 0.97–1.17, P = .19), compared to placebo. The cumulative incidence of dry mouth was 7.4% with tiotropium, compared to 3.9% with ipratropium, 1.6% with salmeterol, and 2.0% with placebo. CONCLUSIONS: In stable COPD, tiotropium showed superior efficacy in improving quality of life and dyspnea, compared to placebo and ipratropium. However, tiotropium's differences with salmeterol were less clear.
HouseScan : Building-scale interior 3 D reconstruction with KinectFusion Master ’ s esis – Imperial College London

Recent advances in reconstruction systems like KinectFusion allow us to quickly take 3D models of scenes in high quality using low-cost commodity RGB-D cameras. Unfortunately, creating models of whole buildings is difficult because simple geometry prevents camera tracking from traversing doors, and dri accumulated from small tracking errors degrades the quality of the model. While existing systems use loop closure to correct dri, they do not exploit architectural knowledge when loop closure is not applicable. In this thesis I present a semi-automatic system for performing multi-room, multi-storey interior 3D reconstruction that uses the simple geometry prevalent in buildings to its advantage. Individual rooms are scanned using a KinectFusion implementation and cuboids are fit to them. ey are combined to a high-resolution, coloured mesh model using a globally consistent room pose optimisation algorithm, in which a constraint graph over the possible positions of each room is reformulated as an inconsistent system of linear equations and then solved with minimal error. e presented system can be applied by non-technical users and aims to bring building-scale reconstruction to a wider audience. To demonstrate the effectiveness of the system, a house with 23 rooms on 3 levels is scanned and the accuracy of the generatedmodel is evaluated using ground truth obtainedwith a laser rangefinder. e results show that the reconstruction error of the final model is low, that room pose optimisation does not introduce significant error on top of the error in the individual rooms, and that the achieved accuracy is close to that of conventional 1D consumer measuring tools.
MIP-2 Recruits NKT Cells to the Spleen During Tolerance Induction1

Peripheral tolerance occurs after intraocular administration of Ag and is dependent on an increase in splenic NKT cells. New data here show that macrophage inflammatory protein-2 (MIP-2) is selectively up-regulated in tolerance-conferring APCs and serves to recruit NKT cells to the splenic marginal zone, where they form clusters with APCs and T cells. In the absence of the high-affinity receptor for MIP-2 (as in CXCR2-deficient mice) or in the presence of a blocking Ab to MIP-2, peripheral tolerance is prevented, and Ag-specific T regulatory cells are not generated. Understanding the regulation of lymphocyte traffic during tolerance induction may lead to novel therapies for autoimmunity, graft acceptance, and tumor rejection.
Developing a move-set for protein model refinement

MOTIVATION A wide variety of methods for the construction of an atomic model for a given amino acid sequence are known, the more accurate being those that use experimentally determined structures as templates. However, far fewer methods are aimed at refining these models. The approach presented here carefully blends models created by several different means, in an attempt to combine the good quality regions from each into a final, more refined, model. RESULTS We describe here a number of refinement operators (collectively, 'move-set') that enable a relatively large region of conformational space to be searched. This is used within a genetic algorithm that reshuffles and repacks structural components. The utility of the move-set is demonstrated by introducing a cost function, containing both physical and other components guiding the input structures towards the target structure. We show that our move-set has the potential to improve the conformation of models and that this improvement can be beyond even the best template for some comparative modelling targets. AVAILABILITY The populus software package and the source code are available at http://bmm.cancerresearchuk. org/~offman01/populus.html.
Human body impedance modelling for ESD simulations

Motivated by understanding the ESD-induced currents from body-worn, wire and hose connected medical equipment is exposed to, a computer simulation is presented to estimate the impedance of a human body relative to ground. This 3D model is the basis for transient field calculation. A Method of Moments (MoM) frequency domain solution is transformed into time domain via IFFT for further circuit level time domain simulations. The human body is modeled as a homogeneous dielectric with frequency-dependent complex permittivity. Dependence of the impedance on the position of discharge and posture of the human body is investigated. The simulation results are compared with measurements and demonstrate capturing of general tendencies of measured curves.
A Transparently-Scalable Metadata Service for the Ursa Minor Storage System

The metadata service of the Ursa Minor distributed storage system scales metadata throughput as metadata servers are added. While doing so, it correctly handles metadata operations that involve items served by different metadata servers, consistently and atomically updating the items. Unlike previous systems, it does so by reusing existing metadata migration functionality to avoid complex distributed transaction protocols. It also assigns item IDs to minimize the occurrence of multiserver operations. Ursa Minor's approach allows one to implement a desired feature with less complexity than alternative methods and with minimal performance penalty (under 1% in non-pathological cases).
Resizable, Scalable, Concurrent Hash Tables via Relativistic Programming

We present algorithms for shrinking and expanding a hash table while allowing concurrent, wait-free, linearly scalable lookups. These resize algorithms allow Read-Copy Update (RCU) hash tables to maintain constant-time performance as the number of entries grows, and reclaim memory as the number of entries decreases, without delaying or disrupting readers. We call the resulting data structure a relativistic hash table. Benchmarks of relativistic hash tables in the Linux kernel show that lookup scalability during resize improves 125x over reader-writer locking, and 56% over Linux's current state of the art. Relativistic hash lookups experience no performance degradation during a resize. Applying this algorithm to memcached removes a scalability limit for get requests, allowing memcached to scale linearly and service up to 46% more requests per second. Relativistic hash tables demonstrate the promise of a new concurrent programming methodology known as relativistic programming. Relativistic programming makes novel use of existing RCU synchronization primitives, namely the wait-for-readers operation that waits for unfinished readers to complete. This operation, conventionally used to handle reclamation, here allows ordering of updates without read-side synchronization or memory barriers.
Esmolol reduces perioperative ischemia in cardiac surgery: a meta-analysis of randomized controlled studies.

OBJECTIVE beta-Blockers were associated with a reduction of mortality and morbidity in noncardiac surgery until recently when the POISE trial showed that beta-blockers could be harmful in the perioperative period because of hypotension and bradycardia. Esmolol is an ultra-short-acting beta-blocker mostly used in emergency and high-risk patients. The authors performed a meta-analysis to evaluate the clinical effects of esmolol in cardiac surgery. DESIGN Meta-analysis. SETTING Hospitals. PARTICIPANTS A total of 778 patients from 20 randomized trials. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULT Three investigators independently searched BioMedCentral and PubMed. Inclusion criteria were random allocation to treatment and comparison of esmolol versus other drugs, placebo, or standard of care in cardiac surgery. Exclusion criteria were duplicate publications, nonhuman experimental studies, and no data on clinical outcomes. The use of esmolol was associated with a significant reduction of myocardial ischemia episodes (15/122 [12.2%] in the esmolol group v 36/140 [25.7%] in the control arm, odds ratio [OR] =0.42 [0.23-0.79], p = 0.007) and development of arrhythmias after cardiopulmonary bypass (15/65 [23.07%] v 23/64 [35.9%], OR = 0.42 [0.18-1.01], p = 0.05). The authors did not find a reduction in the use of inotropic drugs in esmolol-treated patients (29/153 [18.9%] v 48/146 [32.8%], OR = 0.43 [0.16-1.10], p = 0.08). Esmolol-treated patients had more episodes of bradycardia (19/129 [14.72%] v 3/133 [2.25%], OR = 5.49 [2.21-13.62], p = 0.0002) and hypotension (28/113 [24.77%] v 14/119 [11.76%], OR = 2.73 [0.83-9.04], p = 0.10). CONCLUSIONS Esmolol reduces the incidence of myocardial ischemia and arrhythmias in cardiac surgery. An increase in bradycardia was noted as well.
Test Case Prioritization for Web Service Regression Testing

Regression testing is necessary to assure the quality of service-oriented business applications in their evolutions. However, because of the constraint of testing resource, entire test suite may not run as a result. Therefore, test case prioritization technique is required to increase the efficiency of Web service application regression testing. In this paper, we propose a dependence analysis based test case prioritization technique. First, we analyze the dependence relationship using control and data flow information in an orchestration language: WS-BPEL. Then we construct a weighted graph and do impact analysis to identify modification-affected elements. After that, we prioritize test cases according to covering more modification-affected elements with the highest weight. Finally we conduct a case study to illustrate the applicability of our method.
Advances in toxicogenomics.

Toxicogenomics is an emerging scientific discipline that combines the tools of traditional toxicology with those of genomics, bioinformatics, and high throughput experimentation (1). The underlying premise of toxicogenomics is that a global assessment of the biology of chemical exposure will lead to a more thorough understanding of how toxicants act. It is the promise of toxicogenomics that such information will lead to better judgments regarding human health risks and improved pipelines for the next generation of therapeutics. Toxicogenomics had its origins in the technologies related to transcriptional profiling. To date, dozens of manuscripts have appeared in the peer-reviewed literature that employ global transcriptional profiling methods to link toxic sequelae with changes in specific batteries of mRNAs. These data sets have the potential to provide insights into toxic mechanism and to identify sensitive biomarkers of exposure. These early experiments also * To whom correspondence should be addressed. Tel: 608-262-2024. Fax: 608-262-2824. E-mail: Bradfield@oncology.wisc. edu. MARCH 2005 VOLUME 18, NUMBER 3
NNS:A Novel Neighborhood Negative Selection algorithm

As the security issue becomes more complex, more and more anomaly detection schemes involve high-dimension data. Negative selection algorithms have been widely used in anomaly detection, fault detection, and fraud detection. However, these algorithms perform poorly when dealing with high- dimension data. To address this issue, we propose a novel Neighborhood Negative Selection (NNS) algorithm in this paper. In NNS, we use a neighborhood set to represent a self-sample (or a detector), instead of a single data point. As a result, the delay for training detectors is greatly reduced. We further introduce a special matching mechanism to limit the negative effect of the dimensionality of a shape space and improve the detecting performance in high dimensions. The experimental results show that NNS can provide a more accurate and stable detection performance. Meanwhile, both theoretical analysis and experimental results show that NNS further improves the training efficiency.