Miracle-dz/UniFAR-FTUs huggingface dataset:
A bloat-aware design for big data applications

Over the past decade, the increasing demands on data-driven business intelligence have led to the proliferation of large-scale, data-intensive applications that often have huge amounts of data (often at terabyte or petabyte scale) to process. An object-oriented programming language such as Java is often the developer's choice for implementing such applications, primarily due to its quick development cycle and rich community resource. While the use of such languages makes programming easier, significant performance problems can often be seen --- the combination of the inefficiencies inherent in a managed run-time system and the impact of the huge amount of data to be processed in the limited memory space often leads to memory bloat and performance degradation at a surprisingly early stage. This paper proposes a bloat-aware design paradigm towards the development of efficient and scalable Big Data applications in object-oriented GC enabled languages. To motivate this work, we first perform a study on the impact of several typical memory bloat patterns. These patterns are summarized from the user complaints on the mailing lists of two widely-used open-source Big Data applications. Next, we discuss our design paradigm to eliminate bloat. Using examples and real-world experience, we demonstrate that programming under this paradigm does not incur significant programming burden. We have implemented a few common data processing tasks both using this design and using the conventional object-oriented design. Our experimental results show that this new design paradigm is extremely effective in improving performance --- even for the moderate-size data sets processed, we have observed 2.5x+ performance gains, and the improvement grows substantially with the size of the data set.
EFEMP1 as a Novel DNA Methylation Marker for Prostate Cancer: Array-Based DNA Methylation and Expression Profiling

Purpose: Abnormal DNA methylation is associated with many human cancers. The aim of the present study was to identify novel methylation markers in prostate cancer (PCa) by microarray analysis and to test whether these markers could discriminate normal and PCa cells. Experimental Design: Microarray-based DNA methylation and gene expression profiling was carried out using a panel of PCa cell lines and a control normal prostate cell line. The methylation status of candidate genes in prostate cell lines was confirmed by real-time reverse transcriptase-PCR, bisulfite sequencing analysis, and treatment with a demethylation agent. DNA methylation and gene expression analysis in 203 human prostate specimens, including 106 PCa and 97 benign prostate hyperplasia (BPH), were carried out. Further validation using microarray gene expression data from the Gene Expression Omnibus (GEO) was carried out. Results: Epidermal growth factor–containing fibulin-like extracellular matrix protein 1 (EFEMP1) was identified as a lead candidate methylation marker for PCa. The gene expression level of EFEMP1 was significantly higher in tissue samples from patients with BPH than in those with PCa (P < 0.001). The sensitivity and specificity of EFEMP1 methylation status in discriminating between PCa and BPH reached 95.3% (101 of 106) and 86.6% (84 of 97), respectively. From the GEO data set, we confirmed that the expression level of EFEMP1 was significantly different between PCa and BPH. Conclusion: Genome-wide characterization of DNA methylation profiles enabled the identification of EFEMP1 aberrant methylation patterns in PCa. EFEMP1 might be a useful indicator for the detection of PCa. Clin Cancer Res; 17(13); 4523–30. ©2011 AACR.
The effect of perioperative esmolol infusion on the postoperative nausea, vomiting and pain after laparoscopic appendectomy

Background Perioperative opioid administration results in postoperative nausea and vomiting (PONV) and acute opioid tolerance that manifests in increased postoperative pain. Esmolol is an ultra short acting cardioselective β1-adrenergic receptor antagonist, and it has been successfully used for perioperative sympatholysis and it reduces the opioid requirement during total intravenous anesthesia. We tested the hypothesis that perioperative esmolol administration results in decreased PONV and postoperative pain. Methods Sixty patients undergoing laparoscopic appendectomy were randomly assigned to two groups (Group E and Group C). The Group E patients were administered 5-10 µg/kg/min esmolol with remifentanil that was titrated to the autonomic response. The Group C patients received normal saline that was of the same volume as the esmolol in Group E, and the remifentanil was also titrated to the vital sign. Before intubation and extubation, the Group E patients were administered 1.0 mg/kg esmolol, and the Group C patients were administered normal saline of the same volume. The incidence and severity of PONV, the pain score, the rescue antiemetics and the rescue analgesics were assessed 30 min, 6 h and 24 h after surgery. The mean arterial pressure and heart rate under anesthesia were also recorded. Results PONV and postoperative pain were significantly increased in Group C. These patients needed more antiemetics and analgesics in the first 24 postoperative hours. The mean arterial pressure and heart rate were significantly higher in Group C at the time of intubation and extubation. Conclusions Perioperative esmolol administration contributes to the significant decrease in PONV and postoperative pain, and so this facilitates earlier discharge.
ABCB4 mutations underlie hormonal cholestasis but not pediatric idiopathic gallstones.

AIM To investigate the contribution of ABCB4 mutations to pediatric idiopathic gallstone disease and the potential of hormonal contraceptives to prompt clinical manifestations of multidrug resistance protein 3 deficiency. METHODS Mutational analysis of ABCB4, screening for copy number variations by multiplex ligation-dependent probe amplification, genotyping for low expression allele c.1331T>C of ABCB11 and genotyping for variation c.55G>C in ABCG8 previously associated with cholesterol gallstones in adults was performed in 35 pediatric subjects with idiopathic gallstones who fulfilled the clinical criteria for low phospholipid-associated cholelithiasis syndrome (LPAC, OMIM #600803) and in 5 young females with suspected LPAC and their families (5 probands, 15 additional family members). The probands came to medical attention for contraceptive-associated intrahepatic cholestasis. RESULTS A possibly pathogenic variant of ABCB4 was found only in one of the 35 pediatric subjects with idiopathic cholesterol gallstones whereas 15 members of the studied 5 LPAC kindreds were confirmed and another one was highly suspected to carry predictably pathogenic mutations in ABCB4. Among these 16, however, none developed gallstones in childhood. In 5 index patients, all young females carrying at least one pathogenic mutation in one allele of ABCB4, manifestation of LPAC as intrahepatic cholestasis with elevated serum activity of gamma-glutamyltransferase was induced by hormonal contraceptives. Variants ABCB11 c.1331T>C and ABCG8 c.55G>C were not significantly overrepresented in the 35 examined patients with suspect LPAC. CONCLUSION Clinical criteria for LPAC syndrome caused by mutations in ABCB4 cannot be applied to pediatric patients with idiopathic gallstones. Sexual immaturity even prevents manifestation of LPAC.
A Non-VH1-69 Heterosubtypic Neutralizing Human Monoclonal Antibody Protects Mice against H1N1 and H5N1 Viruses

Influenza viruses are among the most important human pathogens and are responsible for annual epidemics and sporadic, potentially devastating pandemics. The humoral immune response plays an important role in the defense against these viruses, providing protection mainly by producing antibodies directed against the hemagglutinin (HA) glycoprotein. However, their high genetic variability allows the virus to evade the host immune response and the potential protection offered by seasonal vaccines. The emergence of resistance to antiviral drugs in recent years further limits the options available for the control of influenza. The development of alternative strategies for influenza prophylaxis and therapy is therefore urgently needed. In this study, we describe a human monoclonal antibody (PN-SIA49) that recognizes a highly conserved epitope located on the stem region of the HA and able to neutralize a broad spectrum of influenza viruses belonging to different subtypes (H1, H2 and H5). Furthermore, we describe its protective activity in mice after lethal challenge with H1N1 and H5N1 viruses suggesting a potential application in the treatment of influenza virus infections.
A Search for Radio Emission from Type Ia Supernovae

We present and discuss the radio observations of 27 Type Ia supernovae (SNe Ia), observed over two decades with the Very Large Array. No SN Ia has been detected so far in the radio, implying a very low density for any possible circumstellar material established by the progenitor, or progenitor system, before explosion. We derive 2 σ upper limits to a steady mass-loss rate for individual SN systems as low as ~3 × 10-8 M☉ yr-1, which argues strongly against white dwarf accretion via a stellar wind from a massive binary companion in the symbiotic star, an example of the "single-degenerate" scenario. However, a white dwarf accreting from a relatively low mass companion via a sufficiently high efficiency (>60%-80%) Roche lobe overflow is still consistent with our limits. The "double-degenerate" merger scenario also cannot be excluded.
Minimally Invasive Versus Open Laminectomy/Discectomy, Transforaminal Lumbar, and Posterior Lumbar Interbody Fusions: A Systematic Review

Minimally invasive spine surgeries (MISS) are becoming increasingly favored as alternatives to open spine procedures because of the reduced blood loss, postoperative pain, and recovery time. Studies have shown mixed results regarding the efficacy and safety of minimally invasive procedures compared to the traditional, open counterparts. The objectives of this systematic analysis are to compare clinical outcomes between the three MISS and open procedures: (1) laminectomy/discectomy, (2) transforaminal lumbar interbody fusion (TLIF), and (3) posterior lumbar interbody fusion (PLIF). The Cochrane and PubMed databases were queried according to the preferred reporting items for systematic review and meta-analyses (PRISMA) statement. The primary outcome measures included the visual analog scale (VAS), the Oswestry disability index (ODI), and blood loss. A total of 32 studies were included in the analysis. Of the three procedures investigated, only MISS TLIF showed significantly improved VAS for leg pain (p = 0.02), ODI (p = 0.05), and reduced blood loss (p = 0.005). MISS-laminectomy/discectomy, TLIF, and PLIF appear to be similar in terms of postoperative pain and perioperative blood loss. MISS TLIF is perhaps more effective in specific outcome measures and results in less intraoperative blood loss than open TLIF.
Natural Killer Cell Immunotherapy: From Bench to Bedside

The potential of natural killer (NK) cells to target numerous malignancies in vitro has been well documented; however, only limited success has been seen in the clinic. Although NK cells prove non-toxic and safe regardless of the cell numbers injected, there is often little persistence and expansion observed in a patient, which is vital for mounting an effective cellular response. NK cells can be isolated directly from peripheral blood, umbilical cord blood, or bone marrow, expanded in vitro using cytokines or differentiated in vitro from hematopoietic stem cells. Drugs that support NK cell function such as lenalidomide and bortezomib have also been studied in the clinic, however, the optimum combination, which can vary among different malignancies, is yet to be identified. NK cell proliferation, persistence, and function can further be improved by various activation techniques such as priming and cytokine addition though whether stimulation pre- or post-injection is more favorable is another obstacle to be tackled. Here, we review the various methods of obtaining and activating NK cells for use in the clinic while considering the ideal product and drug complement for the most successful cellular therapy.
Efficient lossless compression of colour image data with diverse characteristics

Lossless compression of data is the attempt to model the data in such a manner that the resulting file contains the pure information without any redundancy. This paper presents a universal compression system which is able to compress colour images efficiently with a broad range of characteristics from natural images to synthetic images with sparse histograms. The proposed compression scheme uses a novel adaptive parameter selection and a pre-coding stage, which utilizes not only local correlation of the signal values, but also exploits long-distance dependencies. The new approach was tested against several state-of-the-art compressors for a set of seventeen images demonstrating that the average compression efficiency of the proposed scheme is superior.
TEACHING THE VIOLENT PAST IN SECONDARY SCHOOLS IN NEWLY INDEPENDENT SOUTH SUDAN

This article analyses the teaching and learning of South Sudan history from 1955â€“2005 in secondary schools in South Sudan with a specific focus on national unity. The article draws on two periods of focused ethnography, from September to December 2014 and July to September 2015, including classroom observation and interviews with teachers, student teachers and students in two geographical locations. Additionally, 69 written essays from secondary school students of History have been analysed in order to get an insight into their knowledge of the recent violent past. The use of classroom video observation makes a significant contribution to the field as most studies focus on documents and textbooks. The analysis focuses on national unity and uses theories of collective memory and attribution to examine the narratives of the past. The article argues that the national narrative of South Sudan is still closely tied to enemy images of the former enemy of Sudan in the north, while internal ethnic tensions are suppressed and excluded from the official national narrative taught in the classroom.
Risk of solid tumors and myeloid hematological malignancies among first-degree relatives of patients with monoclonal gammopathy of undetermined significance

Monoclonal gammopathy of undetermined significance (MGUS) is one of the most common pre-malignant disorders in western countries with a prevalence of 3.2% in the Caucasian general population 50 years of age or older. [1][1] It is characterized by the presence of a monoclonal immunoglobulin (M-protein
An Encapsulated Yersinia pseudotuberculosis Is a Highly Efficient Vaccine against Pneumonic Plague

Background Plague is still a public health problem in the world and is re-emerging, but no efficient vaccine is available. We previously reported that oral inoculation of a live attenuated Yersinia pseudotuberculosis, the recent ancestor of Yersinia pestis, provided protection against bubonic plague. However, the strain poorly protected against pneumonic plague, the most deadly and contagious form of the disease, and was not genetically defined. Methodology and Principal Findings The sequenced Y. pseudotuberculosis IP32953 has been irreversibly attenuated by deletion of genes encoding three essential virulence factors. An encapsulated Y. pseudotuberculosis was generated by cloning the Y. pestis F1-encoding caf operon and expressing it in the attenuated strain. The new V674pF1 strain produced the F1 capsule in vitro and in vivo. Oral inoculation of V674pF1 allowed the colonization of the gut without lesions to Peyer's patches and the spleen. Vaccination induced both humoral and cellular components of immunity, at the systemic (IgG and Th1 cells) and the mucosal levels (IgA and Th17 cells). A single oral dose conferred 100% protection against a lethal pneumonic plague challenge (33×LD50 of the fully virulent Y. pestis CO92 strain) and 94% against a high challenge dose (3,300×LD50). Both F1 and other Yersinia antigens were recognized and V674pF1 efficiently protected against a F1-negative Y. pestis. Conclusions and Significance The encapsulated Y. pseudotuberculosis V674pF1 is an efficient live oral vaccine against pneumonic plague, and could be developed for mass vaccination in tropical endemic areas to control pneumonic plague transmission and mortality.
Prevalence of foot and limb lesions in 528 weaned pigs from 15 units in south-west England

Correspondence to Dr Green TRAUMATIC injuries of the limbs and feet affect the majority of farmed animals to a varying degree and occur in pigs of all age groups. Much of the literature describing foot damage and limb lesions of pigs focuses on finished or adult pigs (Penny and Osborne 1963, Penny and others 1965, Mouttotou and others 1997) or preweaning piglets (Penny and others 1971, Smith and Mitchell 1976, Mouttotou and others 1999a). However, foot and limb problems in weaned pigs are not uncommon. In a postal survey carried by MAFF (1981), 20 per cent and 35 per cent of the herds which used solid and perforated floors, respectively, in the weaner accommodation reported pigs with foot lesions. Risk factors associated with foot and limb lesions in all age groups of pigs include floor type, nutrition and genetics. These lesions are undesirable for several reasons: they presumably cause discomfort to the animals; they provide an entry for infection; and, they can result in lameness (Penny and others 1971). A cross-sectional study of the nature, distribution and prevalence of foot and limb lesions in weaned pigs from 15 convenience-selected farms in south-west England (Wiltshire, Avon, Hampshire and Gloucestershire counties) was carried out in 1995. It was estimated that a total of 400 animals should be examined from the study farms to detect an expected prevalence of 50 per cent with a minimum acceptable error of ±5 per cent and 80 per cent power (Epi Info 6.03) and calculated that examining 4 per cent of the weaned pigs on each farm, would provide data on approximately 400 pigs. The selection of pigs on the farm was done randomly (using a list of random numbers), following a routine procedure: all the pigs on the farm were counted (from the left to right side of the pen) and the selected ones were marked, restrained and then examined for foot and limb lesions. Foot lesions were classified using the definitions described in a previous paper (Mouttotou and others 1997) and limb lesions using the definitions described for limb lesions in preweaning piglets (Mouttotou and Green 1999) and finishing pigs (Mouttotou and others 1999a). Data on lesions were recorded as present or absent and were stored on a database (Foxpro 2-6, Microsoft, 1994). Frequency tables were used to describe the data in Epi Info (Dean and others 1990). A pig was defined as affected with foot lesions if it had at least one digit with a lesion. The following proportions were calculated:
Knowledge sharing: game and reasoned action perspectives

Purpose – The purpose of this paper is to investigate knowledge sharing (KS) to characterize its behavior in companies based on the concepts of theory of reasoned action and game theory (GT). Design/methodology/approach – The paper proposes two models: Model A: KS process is constructed by capturing personal psychological feelings; and Model B: KS process is not only constructed by personal psychological feelings but also takes into consideration other people's decisions. By comparing the two knowledge‐sharing models' predictability performance, the authors are able to characterize the process of KS.Findings – The results show that different companies require different models. On average, Model B with game concept has lower predictive accuracy than the Model A without game concept.Research limitations/implications – The paper provides practical implications for manager to frame effective KS policies and also suggests future studies to improve measurement.Originality/value – The values of this paper are: pr.
Measuring Fidelity and Adaptation

There is a need to standardize methods for assessing fidelity and adaptation. Such standardization would allow program implementation to be examined in a manner that will be useful for understanding the moderating role of fidelity in dissemination research. This article describes a method for collecting data about fidelity of implementation for school-based prevention programs, including measures of adherence, quality of delivery, dosage, participant engagement, and adaptation. We report about the reliability of these methods when applied by four observers who coded video recordings of teachers delivering All Stars, a middle school drug prevention program. Interrater agreement for scaled items was assessed for an instrument designed to evaluate program fidelity. Results indicated sound interrater reliability for items assessing adherence, dosage, quality of teaching, teacher understanding of concepts, and program adaptations. The interrater reliability for items assessing potential program effectiveness, classroom management, achievement of activity objectives, and adaptation valences was improved by dichotomizing the response options for these items. The item that assessed student engagement demonstrated only modest interrater reliability and was not improved through dichotomization. Several coder pairs were discordant on items that overall demonstrated good interrater reliability. Proposed modifications to the coding manual and protocol are discussed.
Dynamics of one-pass germinal center models: Implications for affinity maturation

During an immune response, the affinity of antibodies that react with the antigen that triggered the response increases with time, a phenomenon known as affinity maturation. The molecular basis of affinity maturation has been partially elucidated. It involves the somatic mutation of immunoglobulin V-region genes within antigen-stimulated germinal center B cells and the subsequent selection of high affinity variants. This mutation and selection process is extremely efficient and produces large numbers of high affinity variants. Studies of the architecture of germinal centers suggested that B cells divide in the dark zone of the germinal center, then migrate to the light zone, where they undergo selection based on their interaction with antigen-loaded follicular dendritic cells, after which they exit the germinal center through the mantle zone. Kepler and Perelson questioned this architecturally driven view of the germinal center reaction. They, as well as others, argued that the large number of point mutations observed in germinal center B cell V-region genes, frequently 5 to 10 and sometimes higher, would most likely render cells incapable of binding the antigen, if no selection step was interposed between rounds of mutations. To clarify this issue, we address the question of whether a mechanism in which mutants are generated and then selected in one pass, with no post-selection amplification, can account for the observed efficiency of affinity maturation. We analyse a set of one-pass models of the germinal center reaction, with decaying antigen, and mutation occurring at transcription or at replication. We show that under all the scenarios, the proportion of high affinity cells in the output of a germinal center varies logarithmically with their selection probability. For biologically realistic parameters, the efficiency of this process is in clear disagreement with the experimental data. Furthermore, we discuss a set of, possibly counterintuitive, more general features of one-pass selection models that follow from our analysis. We believe that these results may also provide useful intuitions in other cases where a population is subjected to selection mediated by a selective force that decays over time.