Miracle-dz/UniFAR-FTUs huggingface dataset:
Design , Analysis and Experience of a Partial state router

In this paper, we motivate the use of partial state schemes in a wide variety of network applications. Partial state can be used to arrive at a list of high bandwidth flows which can be made use of in containing nonresponsive flows, providing better QoS for web traffic, and alleviate certain Denial of Service (DoS) attacks. We show the practical feasibility of partial state based schemes by implementing a novel partial state scheme, LRU-FQ, on Linux platform. The scheme makes use of an LRU cache to classify flows into high bandwidth and low bandwidth classes. A class-based fair queuing algorithm is used to obtain a policy-driven control of the proportion of link bandwidth allocated to high bandwidth flows being serviced at the router. Empirical data is presented to bring out the stated uses of partial state schemes.
Fault Tolerance Techniques in Grid Computing Systems

In grid computing, resources are used outside the boundary of organizations and it becomes increasingly difficult to guarantee that resources being used are not malicious. Also, resources may enter and leave the grid at any time. So, fault tolerance is a crucial issue in grid computing. Fault tolerance can enhance grid throughput, utilization, response time and more economic profits. All mechanisms proposed to deal with fault-tolerant issues in grids are classified into: job replication and job checkpointing techniques. These techniques are used according to the requirements of the computational grid and the type of environment, resources and virtual organizations it is supposed to work with. Each has its own advantages and disadvantages which forms the subject matter of this paper.
BigDataScript: a scripting language for data pipelines

Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github. io/BigDataScript. Contact: pablo.e. cingolani@gmail.com
Multi-bit information storage by multisite phosphorylation

Cells store information in DNA and in stable programs of gene expression, which thereby implement forms of long-term cellular memory. Cells must also possess short-term forms of information storage, implemented post-translationally, to transduce and interpret external signals. CaMKII, for instance, is thought to implement a one-bit (bistable) short-term memory required for learning at post-synaptic densities. Here we show by mathematical analysis that multisite protein phosphorylation, which is ubiquitous in all eukaryotic signalling pathways, exhibits multistability for which the maximal number of steady states increases with the number of sites. If there are n sites, the maximal information storage capacity is at least log_2 (n+2)/2 bits when n is even and log_2 (n+1)/2 bits when n is odd. Furthermore, when substrate is in excess, enzyme saturation together with an alternating low/high pattern in the site-specific relative catalytic efficiencies, enriches for multistability. That is, within physiologically plausible ranges for parameters, multistability becomes more likely than monostability. We discuss the experimental challenges in pursuing these predictions and in determining the biological role of short-term information storage.
User-friendly and reliable grid computing based on imperfect middleware

Writing grid applications is hard. First, interfaces to existing grid middleware often are too low-level for application programmers who are domain experts rather than computer scientists. Second, grid APIs tend to evolve too quickly for applications to follow. Third, failures and configuration incompatibilities require applications to use different solutions to the same problem, depending on the actual sites in use. This paper describes the Java Grid Application Toolkit (Java-GAT) that provides a high-level, middleware-independent and site-independent interface to the grid. The JavaGAT uses nested exceptions and intelligent dispatching of method invocations to handle errors and to automatically select suitable grid middleware implementations for requested operations. The JavaGAT's adaptor writing framework simplifies the implementation of interfaces to new middleware releases by combining nested exceptions and intelligent dispatching with rich default functionality. The many applications and middleware adaptors that have been provided by third-party developers indicate the viability of our approach.
Research report Characterizing learning deficits and hippocampal neuron loss following transient global cerebral ischemia in rats

The 2-vessel-occlusion + hypotension (2VO + H) model of transient global cerebral ischemia results in neurodegeneration within the CA1 field of the hippocampus, but previous research has failed to demonstrate robust or reliable learning/memory deficits in rats subjected to this treatment. In the present study, sensitive behavioral protocols were developed in an effort to characterize the cognitive impairments following 2VO + H more precisely. Adult rats were exposed to 10 min of bilateral carotid occlusion with simultaneous hypotension. Following recovery, 2VO + H and control rats were subjected to a series of behavioral tests (locomotor activity, sensorimotor battery, water maze [cued, place, learning set], object recognition, and radial arm maze) over an extended recovery period followed by an assessment of neuronal loss in the dorsal hippocampus. The 2VO + H treatment was associated with long-lasting spatial learning deficits in the absence of other behavioral impairments and with neurodegeneration in dorsal hippocampal CA1. Water maze protocols that placed higher memory demands upon the rats (relatively ‘‘hard’’ vs. ‘‘easy’’) were more sensitive for detecting ischemia-induced deficits. We have shown that the use of appropriate behavioral tests (e.g., a relatively difficult place learning task) allowed for the observation of robust spatial learning deficits in a model previously shown to induce relatively subtle behavioral effects. Thus, the 2VO + H model induces both hippocampal neuronal loss and longterm learning deficits in rats, providing a potentially useful model for evaluating therapeutic efficacy. D 2005 Elsevier B.V. All rights reserved. Theme: Disorders of the nervous system Topic: Ischemia
Is dexmedetomidine superior to midazolam as a premedication in children? A meta‐analysis of randomized controlled trials

In the current published literature, there are controversial results regarding the effectiveness of dexmedetomidine compared with midazolam as premedication in children. The aim of this meta‐analysis was to compare the use of dexmedetomidine as a premedication in pediatric patients with that of midazolam.
Improve in Neurogenesis with Socialization can Reduce Behaviors that are Related to Poor Prognosis in Withdrawal Period in Male Rats

Introduction: Morphine withdrawal period is associated with a wide variety of problems. Neurogenesis seems necessary for brain functions. Socialization is a lifelong process that helps getting behavioural norms from society. The aim of this study is to investigate if better neurogenesis in socialization can alleviate problems encountered during withdrawal period. Method and material: Rats were randomly divided to: control rats, isolated rats, withdrawal isolated rats and withdrawal socialized rats. Animals received morphine 7 days and 14 days Brdu was injected. At the end of experiment, memory, neurogenesis, emotional reactivity and sucrose, NaCl consumption was assessed. Results: Rats in withdrawal socialized group had better reference memory and working memory, and they decrease relapse. Furthermore, neurogenesis was higher in withdrawal socialized rats as compared to isolated rats. Enough neurogenesis is necessary for proper brain function. Sucrose preference test and force swim test were well performed in withdrawal socialized rats. These indicate lower incidence of co morbid psychiatric disorder in withdrawal period. Salt consumption as indicator of more relapse to drug abuse was seen to be higher in withdrawal isolated group of animals. Conclusion: Socialization during withdrawal period can help to better tolerate withdrawal period and its adverse effects. So socialization reduces relapse and establishes behavioural norms for successful healthy life.
Isolation and characterization of corneal endothelial cells from wild type and thrombospondin-1 deficient mice.

PURPOSE To isolate and characterize primary corneal endothelial cells (CEC) from wild type and transgenic mice to facilitate the study of their properties in vitro. METHODS CEC were isolated from wild type or transgenic-immortomice corneas. The Descemet's membrane was gently peeled from the periphery of the cornea towards the central region and placed into wells of a 96 well tissue culture plate coated with fibronectin in growth medium. Cells that grew out were trypsinized and expanded on fibronectin-coated wells and used for further characterization. CEC were evaluated for expression and localization of specific markers and adhesion molecules by FACS analysis and indirect immunofluorescence staining. The migration properties of CEC were evaluated using a scratch wound and transwell assay, while their ability to undergo capillary morphogenesis was assessed on Matrigel. RESULTS Isolation of CEC from transgenic mice has been somewhat challenging and not previously reported. Here we describe a method for isolation of CEC from wild type and thrombospondin-1 deficient (TSP1-/-) immortomice. Our results indicate that nearly 100% of selected cells express B4-lectin and VE-cadherin, but not PECAM-1. These cells were successfully passaged and maintained in culture for several months without a significant loss in expression of these markers. The wild type CEC, like vascular EC, organized and formed a capillary-like cell network on Matrigel. The ability of the CEC from TSP1-/- mice to form such a network was somewhat compromised. This may be attributed, at least in part, to altered adhesive and migratory properties of these cells. CONCLUSIONS The CEC can be readily obtained from wild type and transgenic mice, which facilitate the comparison and identification of the physiologic role of specific genes in CEC function.
[Diagnostic ability of stratus optical coherence tomography (OCT) in pre-perimetric glaucoma diagnosis].

OBJECTIVE To compare retinal nerve fiber layer (RNFL) measurements performed with Stratus OCT 3000 in normal, ocular hypertensive, pre-perimetric and glaucomatous eyes. METHODS 98 normal subjects, 156 ocular hypertensives with short-wavelength automated perimetry (SWAP), 21 ocular hypertensives with altered SWAP (pre-perimetric glaucoma) and 66 glaucomatous eyes were included in the study. Diagnostic groups were classified based on intraocular pressure, optic nerve head appearance, achromatic automatic perimetry and SWAP. RNFL parameters were obtained using a Stratus OCT 3000 (Humphrey Zeiss instruments). RNFL measurements were compared among the groups. RESULTS RNFL average thickness, superior, inferior and nasal quadrant thickness, and each 12 clock-hour positions except for H9, H10 and H11 showed significant differences between glaucomatous and pre-perimetric glaucoma eyes. RNFL average thickness, inferior quadrant and H10 clock-hour position showed significant differences between normal and ocular hypertensive subjects. Pre-perimetric glaucomas and ocular hypertensives showed differences in H11 clock-hour position exclusively. CONCLUSION RNFL measurements performed using Stratus OCT showed differences between the study groups. OCT may be as useful as SWAP in early glaucoma diagnosis.
Who Should Pay for Two-Way Interconnection?

We analyze how termination charges aect retail prices when taking into account that receivers derive some utility from a call and when rms may charge consumers for receiving calls. We assume that consumers form expectations about network sizes in a passive, but ex-post rational way. We show that the receiver-pays regime enlarges the set of equilibria compared to the caller-pays regime. For a given termination charge and inelastic subscription demand, the receiver-pays regime allows rms to obtain higher prots at the expense of consumers. Socially optimal termination charges are below cost and lower under the caller-pays regime than under the receiver-pays regime. We also analyze elastic subscription demand. Total surplus, consumer surplus, and market penetration are all maximized by the same positive but below cost termination charge. Firms’ prots typically increase when the termination charged is removed away from
Active Learning with Human-Like Noisy Oracle

When active learning is applied to real-world applications, human experts usually act as oracles to provide labels. However, human make mistakes, thus noise might be introduced during the learning process. Most previous studies simplify the problem by assuming uniformly-distributed noise over the sample space. Such assumption, however, might fail to precisely reflect the human experts' behaviour in real-world situations. In this paper, we therefore study active learning with such human-like oracles, by making a more realistic assumption that the noise is example-dependent (i.e., non-uniformly distributed over the sample space). More specifically, when the human-like oracle is highly confident in labelling examples, it is naturally less likely to provide incorrect answers, whereas when such confidence is low, the noise would be more likely to be introduced. Based on the analysis of such human-like oracle, we propose a generic yet simple active learning algorithm to simultaneously explore the unlabelled data and exploit the labelled data. Empirical study on both synthetic and real-world data sets verifies the superiority of the proposed algorithm, compared with the traditional uncertainty sampling.
Definitive Altered Fractionation Radiotherapy and Concomitant Weekly Cisplatin for Locally Advanced Head and Neck Cancer

Background:The purpose of this study was to determine the efficacy and toxicities of single-agent weekly cisplatin for patients with squamous cell carcinoma of the head and neck treated definitively with radiation therapy (RT). Methods:Thirty-five patients with American Joint Committee of Cancer stage II (3%), stage III (14%), or stage IV (83%) squamous cell carcinoma of the oropharynx, larynx, or hypopharynx treated from June 2000 to November 2003 at the University of Florida were retrospectively reviewed. Subjects received radiation therapy (RT; median, 74.4 Gy) and cisplatin, 30 mg/m2/wk. Altered fractionation was used in 34 of 35 (97%) patients. The endpoints were best response, percentage of grade III or IV toxicities, local-regional control, disease-free survival, cause-specific survival, and overall survival. Results:The median number of cycles of cisplatin administered was 6. Grade III or IV toxicities were: anemia, 11%; thrombocytopenia, 6%; leukopenia, 26%; and mucositis, 23%. No patients had renal failure and 1 patient (3%) died because of therapy-related complications. Responses to therapy included 71% complete response, 17% partial response, and 6% stable disease. Median follow-up for all patients was 1.8 years (range, 0.1–7.8 years); median follow-up for living patients was 4.4 years (range, 2.6–7.8 years). The 3-year outcomes were: local-regional control, 85%; disease-free survival, 56%; cause-specific survival, 59%; and overall survival, 40%. Conclusion:Concomitant weekly CDDP with definitive RT is feasible, tolerable, highly active, and comparable with more complex, costly, and toxic regimens. Intercurrent disease was a significant contributor to mortality in our population. Our regimen is an attractive alternative to sequential chemoradiotherapy programs.
A double‐blind comparative study of remoxipride and haloperidol in acute schizophrenia.

Abstract Seventy‐one patients were entered into a multicentre, double‐blind randomized study to compare the efficacy and safety of remoxipride with those of haloperidol in the acute treatment of schizophrenia or schizophreniform disorder. The patients, who were well‐matched regarding demographic characteristics, were aged 18–64 years. Four patients in the remoxipride group and 6 in the haloperidol group discontinued treatment prematurely. The mean daily doses during the last week of treatment were 363 mg remoxipride and 9 mg haloperidol. At this time 22% of patients on remoxipride and 66% of those on haloperidol were taking anticholinergics (p < 0.001). The clinical efficacy was similar in both groups as judged by Present State Examination (PSE) profile and Brief Psychiatric Rating Scale (BPRS) ratings. Several adverse symptoms occurred significantly more frequently during treatment with haloperidol than with remoxipride, particularly where extrapyramidal symptoms were concerned. No clinically relevant changes occurred in the laboratory tests in either group.
Randomized Approximation Schemes for Scheduling Unrelated Parallel Machines

The problem of Scheduling n Independent Jobs on m Unrelated Parallel Machines, when the number of machines m is xed, is considered. The standard problem of minimizing the makespan of the schedule (SUM) and the bicriteria problem of scheduling with bounded makespan and cost (SUMC) are addressed, and randomized fully linear time approximation schemes are shown for both of them. While matching the approximation guarantee and the complexity of the best known sequential results of Jansen and Porkolab ((12]), the proposed algorithms exhibit a signiicantly simpler and more general rounding scheme, especially for the bicriteria SUMC problem, and admit simple optimal work parallelizations 1 of O(log n){time complexity. The core of the algorithms, which also draw techniques from other related works ((12], 11], 1]), is an interesting new randomized rounding procedure, the Filtered Randomized Rounding (FRR). In the settings of the problems considered, FRR boosts the deviation bounds of the rounded linear packing constraints to any given constant ratio. Finally, the notion of poly{bottleneck combinatorial optimization problems is deened and used to build O(n log n log log n) time approximation schemes for two natural optimization versions of SUMC, that is minimizing the makespan when the cost of the schedule is bounded (SUMCoptT) and minimizing the cost when the makespan is bounded (SUMCoptC). These algorithms too, admit simple optimal work parallelizations. 1 Optimal work parallelization means that the parallel work (product of running time and number of processors) is equal to the sequential running time.
Advantages of Dual Channel MAC for Wireless Sensor Networks

Traditional low cost radios for wireless sensor networks operate with one frequency channel at any given time. However, recent advances in radio hardware for WSNs made available transceivers that can support two simultaneous channels. In this work, we investigate the benefits of using two parallel independent frequency channels at the MAC layer. In particular, the paper introduces a technique of dual channel multiple access with adaptive preamble (DCMA/AP). The protocol uses two separate frequencies for data and control packets to avoid the use of handshake mechanisms (e.g. RTS/CTS) in order to reduce energy consumption and packet delay. To address the hidden and exposed terminal problems, DCMA/AP enables a receiver to send a busy tone signal on the control channel to notify neighbors that an ongoing reception is in progress. As a result, packet collisions are nullified with an increase of node throughput. Furthermore, an adaptive preamble mechanism in DCMA/AP avoids secondary processes of node synchronization together with a reduction of idle listening of receiving nodes that are considered to be one of the major sources of energy consumption in wireless sensor networks. Finally, DCMA/AP introduces a mechanism of opportunistic crossover speeds up the process of packet forwarding by pre-announcing the successive candidate node intended to receive the packet
Digital compared with screen-film mammography: performance measures in concurrent cohorts within an organized breast screening program.

PURPOSE To evaluate the performance of digital direct radiography (DR) and computed radiography (CR) compared with that of screen-film mammography (SFM) in large concurrent cohorts. MATERIALS AND METHODS This study was approved by the University of Toronto Research Ethics Board and did not require informed consent. Concurrent cohorts of women aged 50-74 years screened with DR (n = 220 520), CR (n = 64 210), or SFM (n = 403 688) between 2008 and 2009 were identified and followed for 12 months. Performance was compared between cohorts, with SFM as the referent cohort. Associations were examined by using mixed-effect logistic regression. RESULTS The cancer detection rate was similar for DR (4.9 per 1000; 95% confidence interval [CI]: 4.7, 5.2) and SFM (4.8 per 1000; 95% CI: 4.7, 5.0); however, the rate was significantly lower for CR (3.4 per 1000; 95% CI: 3.0, 3.9) (odds ratio, 0.79; 95% CI: 0.68, 0.93). Recall rates were higher for DR (7.7%; 95% CI: 7.6%, 7.8%) and lower for CR (6.6%; 95% CI: 6.5%, 6.7%) than for SFM (7.4%; 95% CI: 7.3%, 7.5%). Positive predictive value was lower for CR (5.2%; 95% CI: 4.7%, 5.8%) than for SFM (6.6%; 95% CI: 6.4%, 6.8%); however, the adjusted odds were not significant. CONCLUSION Although DR is equivalent to SFM for breast screening among women aged 50-74 years, the cancer detection rate was lower for CR. Screening programs should monitor the performance of CR separately and may consider informing women of the potentially lower cancer detection rates.