Miracle-dz/UniFAR-FTUs huggingface dataset:
A proteome map of the zebrafish (Danio rerio) lens reveals similarities between zebrafish and mammalian crystallin expression

Purpose To characterize the crystallin content of the zebrafish lens using two-dimensional gel electrophoresis (2-DE). These data will facilitate future investigations of vertebrate lens development, function, and disease. Methods Adult zebrafish lens proteins were separated by 2-DE, and the resulting spots were identified by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). The relative proportion of each crystallin was quantified by image analysis, and phosphospecific staining was used to identify phosphorylated α-crystallins. The proportion of each crystallin in the soluble and insoluble fraction of the lens was also determined by resolving these lens fractions separately by 2-DE. Results α-, β-, and γ-crystallins comprised 7.8, 36.0, and 47.2% of the zebrafish lens, respectively. While the α-crystallin content of the zebrafish lens is less than the amounts found in the human lens, the ratio of αA:αB crystallin is very similar. The phosphorylation pattern of zebrafish αA-crystallins was also similar to that of humans. The most abundant γ-crystallins were the diverse γMs, comprising 30.5% of the lens. Intact zebrafish crystallins were generally more common in the soluble fraction with truncated versions more common in the insoluble fraction. Conclusions While the total α- and γ-crystallin content of the zebrafish lens differs from that of humans, similarities in α-crystallin ratios and modifications and a link between crystallin truncation and insolubility suggest that the zebrafish is a suitable model for the vertebrate lens. The proteome map provided here will be of value to future studies of lens development, function, and disease.
A Parallel Patient Treatment Time Prediction Algorithm and Its Applications in Hospital Queuing-Recommendation in a Big Data Environment

Effective patient queue management to minimize patient wait delays and patient overcrowding is one of the major challenges faced by hospitals. Unnecessary and annoying waits for long periods result in substantial human resource and time wastage and increase the frustration endured by patients. For each patient in the queue, the total treatment time of all the patients before him is the time that he must wait. It would be convenient and preferable if the patients could receive the most efficient treatment plan and know the predicted waiting time through a mobile application that updates in real time. Therefore, we propose a Patient Treatment Time Prediction (PTTP) algorithm to predict the waiting time for each treatment task for a patient. We use realistic patient data from various hospitals to obtain a patient treatment time model for each task. Based on this large-scale, realistic dataset, the treatment time for each patient in the current queue of each task is predicted. Based on the predicted waiting time, a Hospital Queuing-Recommendation (HQR) system is developed. HQR calculates and predicts an efficient and convenient treatment plan recommended for the patient. Because of the large-scale, realistic dataset and the requirement for real-time response, the PTTP algorithm and HQR system mandate efficiency and low-latency response. We use an Apache Spark-based cloud implementation at the National Supercomputing Center in Changsha to achieve the aforementioned goals. Extensive experimentation and simulation results demonstrate the effectiveness and applicability of our proposed model to recommend an effective treatment plan for patients to minimize their wait times in hospitals.
One does not fit all: new adjuvants are needed and vaccine formulation is critical

In recent years, adjuvant research has moved from empirical trial and error to a more rational approach engaging the multidisciplinary fields of immunology, biochemistry, pharmacy and physical chemistry. At the Modern Vaccines/Adjuvants Formulation meeting held in Cannes, France in October 2010, scientists from this broad field met to discuss recent progress in adjuvant research and development. The focus of the meeting was on formulation and as a result clinically and pharmaceutically relevant aspects of how to design and optimize vaccines and adjuvants were also addressed.
Response: Estimating the Age of the Common Ancestor of Men from the ZFY Intron

lution gain in depth and strength when we consider all the evidence together. Scenarios that are most parsimonious for the one dataset are not necessarily the most parsimonious when viewed globally. Jeffrey Rogers Paul B. Samollow Anthony G. Comuzzie Department of Genetics, Southwest Foundation for Biomedical Research, Post Office Box 760549, San Antonio, TX 78245, USA E-mail: jrogers@darwin.sf5r. org
The G215R Mutation in the Cl−/H+-Antiporter ClC-7 Found in ADO II Osteopetrosis Does Not Abolish Function but Causes a Severe Trafficking Defect

Background ClC-7 is a ubiquitous transporter which is broadly expressed in mammalian tissues. It is implied in the pathogenesis of lysosomal storage disease and osteopetrosis. Because of its endosomal/lysosomal localization it is still poorly characterized. Methodology/Principal Findings An electrophysiological characterization of rat ClC-7 using solid-supported membrane-based electrophysiology is presented. The measured currents show the characteristics of ClC-7 and confirm its function as a Cl−/H+-antiporter. We have used rat ClC-7 in CHO cells as a model system to investigate the functionality and cellular localization of the wt transporter and its variant G213R ClC-7 which is the analogue of human G215R ClC-7 responsible for autosomal dominant osteopetrosis type II. Our study shows that rat G213R ClC-7 is functional but has a localization defect in CHO cells which prevents it from being correctly targeted to the lysosomal membrane. The electrophysiological assay is tested as a tool for drug discovery. The assay is validated with a number of drug candidates. It is shown that ClC-7 is inhibited by DIDS, NPPB and NS5818 at micromolar concentrations. Conclusions/Significance It is suggested that the scenario found in the CHO model system also applies to the human transporter and that mislocalization rather than impaired functionality of G215R ClC-7 is the primary cause of the related autosomal dominant osteopetrosis type II. Furthermore, the robust solid-supported membrane-based electrophysiological assay is proposed for rapid screening for potential ClC-7 inhibitors which are discussed for treatment of osteoporosis.
A hundred times faster: Novel, rapid sol‐gel synthesis of bio‐glass nanopowders (Si‐Na‐Ca‐P system, Ca:P = 1.67) without aging

Synthesis of sol-gel glass with incorporation of Na2O is extremely difficult, as such glasses have a great tendency to crystallize. Slow drying and aging over several days or weeks is usually required in sol-gel preparation procedures. This work reports a fast, novel route for the synthesis of bioglass powders in a considerably shortened period of 1 h. A comparative study of sol-gel derived glasses made by this novel route using rotary evaporator drying, and a conventional route using oven drying and aging, revealed that the two methods produce stabilized (devitrified) bio-glasses with virtually identical behavior and properties. Indeed, the rapidly dried powder exhibited slightly enhanced properties that should result in improved bioactivity. Fourier-transform infrared spectroscopy was used to understand the structures of the synthesized powders, and MAS-NMR was used to look at the degree of polymerization. This innovative, rapid route was successfully demonstrated to produce glass and devitrified glass nanopowders more than one hundred times quicker than the quickest reported standard drying methods.
Influenza A and respiratory syncytial virus hospital burden in young children in East London

SUMMARY Epidemiological studies have demonstrated high hospitalization rates attributable to influenza and RSV in children aged <24 months. We prospectively recruited 977 children, aged <6 years, presenting with influenza-like illnesses at a hospital during two winter seasons between 2002 and 2004. Nasopharyngeal aspirates were performed and sent for viral immunofluorescence and PCR. Influenza and respiratory syncytial virus (RSV) rates were stratified by age, in-patient/outpatient status and clinical diagnosis. The influenza A and RSV hospitalization incidence rates were 4 and 11/10 000 person-months respectively, whereas the accident and emergency (A&E) outpatient rates were both 32/10 000 person-months in those aged <6 years. The influenza A and RSV hospitalization rates were highest in children aged <24 months and <12 months (9·1 and 35·7/10 000 person-months) respectively. Infection rates were particularly high in those aged <6 months for both viruses. The age-specific influenza A and RSV A&E admission rates were highest in those aged >6 months and those aged <12 months, respectively (43 and 92·5/10 000 person-months, respectively). In conclusion, these high paediatric RSV and influenza incidence rates can be used to inform UK policy on childhood influenza immunization and subsequent RSV immunization in the future.
An exploration of the choices of patients with chronic kidney disease

Background Chronic kidney disease (CKD) is a progressive loss of renal function over a period of time. It is common, often unrecognized, and frequently coexists with other conditions, including diabetes and cardiovascular disease. There has been little research undertaken into treatment options and decision-making processes of CKD patients in general. Objectives To determine the treatment options that CKD patients are offered and their views and experiences with regard to these choices. Design A survey design was adopted. Participants Participants included patients who had CKD at the time of the study and who were on renal dialysis. Results A wide range of findings emerged from the study. Key findings showed that the majority of patients felt that written information was the main source of information, but that almost one-quarter of patients felt that they did not receive enough information about dialysis to allow them to make an informed choice. Almost one-fifth of participants did not consider that they had been strongly encouraged by health professionals to be independent with regard to their choice of dialysis. Conclusion While the majority of patients feel fully informed and involved in the decision-making processes around treatment and management of their CKD, not all patients receive sufficient information to make an informed choice about their treatment and that treatment options are not always presented to patients and their families to enable them to make a fully informed choice.
HaDeS: Architectural synthesis for heterogeneous dark silicon chip multi-processors

In this paper, we propose an efficient iterative optimization based approach for architectural synthesis of dark silicon heterogeneous chip multi-processors (CMPs). The goal is to determine the optimal number of cores of each type to provision the CMP with, such that the area and power budgets are met and the application performance is maximized. We consider general-purpose multi-threaded applications with a varying degree of parallelism (DOP) that can be set at run-time, and propose an accurate analytical model to predict the execution time of such applications on heterogeneous CMPs. Our experimental results illustrate that the synthesized heterogeneous dark silicon CMPs provide between 19% to 60% performance improvements over conventional homogeneous designs for variable and fixed DOP scenarios, respectively.
Autonomic Vertical Elasticity of Docker Containers with ELASTICDOCKER

Elasticity is the key feature of cloud computing to scale computing resources according to application workloads timely. In the literature as well as in industrial products, much attention was given to the elasticity of virtual machines, but much less to the elasticity of containers. However, containers are the new trend for packaging and deploying microservices-based applications. Moreover, most of approaches focus on horizontal elasticity, fewer works address vertical elasticity. In this paper, we propose ELASTICDOCKER, the first system powering vertical elasticity of Docker containers autonomously. Based on the well-known IBM's autonomic computing MAPE-K principles, ELASTICDOCKER scales up and down both CPU and memory assigned to each container according to the application workload. As vertical elasticity is limited to the host machine capacity, ELASTICDOCKER does container live migration when there is no enough resources on the hosting machine. Our experiments show that ELASTICDOCKER helps to reduce expenses for container customers, make better resource utilization for container providers, and improve Quality of Experience for application end-users. In addition, based on the observed migration performance metrics, the experiments reveal a high efficient live migration technique. As compared to horizontal elasticity, ELASTICDOCKER outperforms Kubernetes elasticity by 37.63%.
Reducing the Number of Comatose Servers: Automatic Tuning as an Opportunistic Cloud-Service

This paper deals with the reduction of the number of comatose servers. The characteristic of such a server is to consume electricity while not delivering useful information services. According to recent studies, up to 30% of the servers (including those in datacenters) are comatose. The existence of these servers lowers the interest in clouds for green computing. Our paper assumes a cloud provider whose services are operated on a minimal number of dedicated servers in a datacenter, we also assume that this provider delivers software as a service (SaaS). In order to reduce the number of dedicated servers that could be comatose, we propose to automatically generate and run auto-tuning tasks that, in servers idle time, will learn to calibrate the execution of the software delivered by the provider. Our proposition follows the goal of delivering auto-tuning as an opportunistic cloud-service. For this purpose we introduce an opportunistic auto-tuning service (QTuning) that exploits servers idle time. The service is based on a theoretical model that includes two computational problems: an exploration and exploitation problem. In the former problem, the goal is to evaluate the performance of a software in different configurations. In the latter, assuming a set of performance results for a given software, the goal is to compute the best configurations to run the software with. Our second contribution is to propose and evaluate solutions for the exploitation problem.
MRI assessment of iron deposition in multiple sclerosis

Iron deposition in the human brain tissue occurs in the process of normal aging and in many neurodegenerative diseases. Elevated iron levels in certain brain regions are also an increasingly recognized finding in multiple sclerosis (MS). The exact mechanism(s) for this phenomenon and its implication in terms of pathophysiology and clinical significance are still largely unknown and debated. Reliable methods to exactly quantify brain iron are a first step to clarify these issues. Therefore, the aim of this review is to present currently available magnetic resonance imaging (MRI) techniques for the assessment of brain iron. These include relaxation time mapping, phase imaging, susceptibility‐weighted imaging, susceptibility mapping, magnetic field correlation imaging, and direct saturation imaging. After discussing their advantages and disadvantages, existing MRI clinical correlations with brain iron concentration in MS are summarized and future research directions are shown. J. Magn. Reson. Imaging 2011;. © 2011 Wiley‐Liss, Inc.
Adaptive buffer sizing for TCP flows in 802.11e WLANs

We consider the provision of access point buffers in WLANs. We first demonstrate that the default use of static buffers in WLANs leads to either undesirable channel under-utilisation or unnecessary high delays, which motivates the use of dynamic buffer sizing. Although adaptive algorithms have been proposed for wired Internet, a number of fundamental new issues arise in WLANs which necessitates new algorithms to be designed. These new issues include the fact that channel bandwidth is time-varying, the mean service rate is dependent on the level of channel contention, and packet inter-service times vary stochastically due to the random nature of CSMA/CA operation. We propose an adaptive sizing algorithms which is demonstrated to be able to maintain high throughput efficiency whilst achieving low delay.
Signaling and Regulation miRNAs Associated with Mitogen-Activated Protein Kinase in Human Pancreatic Cancer

Aberrant expression of miRNAs is associated with phenotypes of various cancers, including pancreatic cancer. However, the mechanism of the aberrant expression is largely unknown. Activation of the mitogen-activated protein kinase (MAPK) signaling pathway plays a crucial role in gene expression related to themalignant phenotype of pancreatic cancer. Hence, we studied the role of MAPK in the aberrant expression of miRNAs in pancreatic cancer cells. The alterations in expression of 183 miRNAs induced by activation or inactivation of MAPK were assayed in cultured pancreatic cancer cells and HEK293 cells by means of the quantitative real-time PCR method. We found that four miRNAs, namely, miR-7-3, miR-34a, miR-181d, and miR-193b, were preferentially associated with MAPK activity. Among these miRNAs, miR-7-3 was upregulated by active MAPK, whereas the others were downregulated. Promoter assays indicated that the promoter activities of the host genes of miR-7-3 and miR-34a were both downregulated by alteration in MAPK activity. Exogenous overexpression of the MAPK-associated miRNAs had the effect of inhibition of the proliferation of cultured pancreatic cancer cells; miR-193b was found to exhibit the most remarkable inhibition. A search for target genes of miR-193b led to identification ofCCND1,NT5E,PLAU, STARD7, STMN1, andYWHAZ as the targets. Translational suppression of these genes by miR-193b was confirmed by reporter assay. These results indicate that activation of MAPK may play a significant role in aberrant expression of miRNAs and their associated phenotypes in pancreatic cancer. Mol Cancer Res; 1–11. 2011 AACR.
WCET Analysis of Parallel Benchmarks using On-Demand Coherent Cache

The rise of multi-core architectures has reached the embedded hard real-time domain, in which predictable timing behaviour is the key factor. Although cache memory and even cache coherence mechanisms are provided in most of these systems, when it comes to the execution of timing critical applications, caches are typically disregarded and accesses to shared data are performed uncached. There is a strong demand for time predictable cache coherence solutions in the hard-real time domain to overcome the performance loss entailed by the bypassing of cache memory. In this paper, we illustrate how todays cache coherence protocols negatively affect the timing behaviour of a cache and thereby impede a reasonable static worst-case execution time (WCET) analysis. Using the OTAWA toolbox, we then perform static WCET estimations applying the On-Demand Coherent Cache (ODC). The elimination of unpredictable inter-cache communication with ODC leads to a reasonable static cache analysis and a tight WCET estimation. We present WCET results of parallelised benchmarks using the ODC on a multi-core platform and compare them with other time predictable approaches to access shared data.
Root Biomodification in Periodontics - The Changing Concepts

Periodontitis is a multifactorial chronic inflammatory disease characterized by destruction of tooth supporting tissues. Repair of the periodontium and the regeneration of periodontal tissues remains a major goal in the treatment of periodontal disease and is an area still in need of major research attention. Periodontal regeneration has come to the forefront of periodontal research and practice. Research regarding periodontal therapy has made it clear that standard treatment techniques do not result in periodontal regeneration. It has become apparent that, if the goal of periodontal regeneration is to be realized, the problem of regeneration needs to be approached from a biological perspective. One important consideration in periodontal regenerative attempts is the root surface which has become exposed to the oral cavity as a result of Periodontitis. In regenerative attempts the root surface functions as one of the wound margins and must provide an appropriate surface for cell attachment and fiber development if regeneration is to occur. Changes in the pathologically exposed root surface are well documented. Varying results from clinical and histological studies have created controversies about the clinical effectiveness of biomodification of root surfaces. This review attempts to provide an insight into the present scenario of root biomodification in clinical conditions along with an overview of related studies.
Chest pain emergency centers: Improving acute myocardial infarction care

Uncertainty and delay are common in the diagnosis of acute coronary syndromes (ACS). In the last 20 years, the need for faster, more accurate, and more cost‐effective diagnosis gave rise to the concept of specialized treatment of patients with chest pain in emergency departments (EDs). The original strategy dedicated a separate section of the ED and a nursing staff to the task of rapid intervention in patients with acute myocardial infarction (MI) and triage of low‐risk patients. Chest pain centers grew quickly in popularity but evolved with a variety of goals, staffing plans, diagnostic resources, and levels of commitment. Three existing centers—the University of Cincinnati Heart ER, Brigham and Women's Hospital, and the Medical College of Virginia—have implemented chest pain strategies with the common aims of (1) screening for the entire spectrum of coronary artery disease, (2) avoiding unnecessary admissions, and (3) using multiple diagnostic modalities. Yet, they differ in the specifics of their approaches and diagnostic methods (e.g., echocardiography vs. treadmill vs. myocardial perfusion imaging). The safety and cost effectiveness of these centers are discussed.
A note on the hardness results for the labeled perfect matching problems in bipartite graphs

In this note, we strengthen the inapproximation bound of O(logn) for the labeled perfect matching problem established in J. Monnot, The Labeled perfect matching in bipartite graphs, Information Processing Letters 96 (2005) 81-88, using a self improving operation in some hard instances. It is interesting to note that this self improving operation does not work for all instances. Moreover, based on this approach we deduce that the problem does not admit constant approximation algorithms for connected planar cubic bipartite graphs.
Parameterized Complexity of Finding Elementary Modes in Metabolic Networks

The concept of elementary (flux) modes provides a rigorous description of pathways in metabolic networks. Finding the elementary modes with minimum number of reactions (shortest elementary modes) is an interesting problem and has potential uses in various applications. However, this problem is NP-hard. This work is an initial step to analyze this problem from a parameterized computation view. With the number of reactions in elementary modes as natural parameter, we prove that finding the shortest elementary modes in metabolic networks is W[1]-hard.