bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using machine learning to improve automatic vectorization
Authors: Stock Kevin , Pouchet Louis-Noël , Sadayappan P. 
Published: January 2012

Automatic vectorization is critical to enhancing performance of compute-intensive programs on modern processors. However, there is much room for improvement over the auto-vectorization capabilities of current production compilers through careful vector-code synthesis that utilizes a variety of loop transformations (e.g., unroll-and-jam, interchange, etc.).As the set of transformations considered is increased, the selection of the most effective combination of transformations becomes a significant challenge: Currently used cost models in vectorizing compilers are often unable to identify the best choices. In this paper, we address this problem using machine learning models to predict the performance of SIMD codes. In contrast to existing approaches that have used high-level features of the program, we develop machine learning models based on features extracted from the generated assembly code. The models are trained offline on a number of benchmarks and used at compile-time to discriminate between numerous possible vectorized variants generated from the input code.We demonstrate the effectiveness of the machine learning model by using it to guide automatic vectorization on a variety of tensor contraction kernels, with improvements ranging from 2× to 8× over Intel ICC's auto-vectorized code. We also evaluate the effectiveness of the model on a number of stencil computations and show good improvement over auto-vectorized code.
VSim
Authors: Ryckbosch Frederick , Polfliet Stijn , Eeckhout Lieven 
Published: January 2012

Simulating contemporary computer systems is a challenging endeavor, especially when it comes to simulating high-end setups involving multiple servers. The simulation environment needs to run complete software stacks, including operating systems, middleware, and application software, and it needs to simulate network and disk activity next to CPU performance. In addition, it needs the ability to scale out to a large number of server nodes while attaining good accuracy and reasonable simulation speeds.
This paper presents VSim, a novel simulation methodology for multi-server systems. VSim leverages virtualization technology for simulating a target system on a host system. VSim controls CPU, network and disk performance on the host, and it gives the illusion to the software stack to run on a target system through time dilation. VSim can simulate multiple targets per host, and it employs a distributed simulation scheme across multiple hosts for simulations at scale. Our experimental results demonstrate VSim's accuracy: typical errors are below 6% for CPU, disk, and network performance. Real-life workloads involving the Lucene search engine and the Olio Web 2.0 benchmark illustrate VSim's utility and accuracy (average error of 3.2%). Our current setup can simulate up to five target servers per host, and we provide a Hadoop workload case study in which we simulate 25 servers. These simulation results are obtained at a simulation slowdown of one order of magnitude compared to native hardware execution.
A transactional memory with automatic performance tuning
Authors: Wang Qingping , Kulkarni Sameer , Cavazos John , Spear Michael 
Published: January 2012

A significant obstacle to the acceptance of transactional memory (TM) in real-world parallel programs is the abundance of substantially different TM algorithms. Each TM algorithm appears well-suited to certain workload characteristics, but the best choice of algorithm is sensitive to program inputs, available cores, and program phases. Furthermore, operating system and hardware characteristics can affect which algorithm is best, with tradeoffs changing across iterations of a single ISA.
This paper introduces methods for constructing policies to dynamically select the most appropriate TM algorithm based on static and dynamic information. We leverage intraprocedural static analysis to create a static profile of the application. We also introduce a low-overhead framework for dynamic profiling of a running transactional application. Armed with these complementary descriptions of a program's behavior, we present novel expert adaptivity policies as well as machine learning policies that are trained off-line using simple microbenchmarks. In our evaluation, we find that both the expert and learned policies provide better performance than any single TM algorithm across the entire STAMP benchmark suite. In addition, policies that combine expert and learned policies offer the best combination of performance, maintainability, and flexibility.
Efficient page caching algorithm with prediction and migration for a hybrid main memory
Authors: Seok Hyunchul , Park Youngwoo , Park Ki-Woong , Park Kyu Ho 
Published: January 2012

Emerging next generation memories, NVRAMs, such as Phase-change RAM (PRAM), Ferroelectric RAM (FRAM), and Magnetic RAM (MRAM) are rapidly becoming promising candidates for large scale main memory because of their high density and low power consumption. Many researchers have attempted to construct a main memory with NVRAMs, in order to make up for the limits of NVRAMs. However, we find that the preexisting page caching algorithms, such as LRU, LIRS, and CLOCK-Pro, are often sub-optimal for NVRAMs due to its DRAM-oriented design including uniform access latency and unlimited endurance. Consequently, the algorithms cannot be directly adapted to the hybrid main memory architecture with PRAM.
To mitigate this design limitation, we propose a new page caching algorithm for the hybrid main memory. It is designed to overcome the long latency and low endurance of PRAM. On the basis of the LRU replacement algorithm, we propose a prediction of page access pattern and migration schemes to maintain write-bound access pages to DRAM. The experiment results have convinced us that our page caching algorithm minimizes the number of the write access of PRAM while maintaining the cache hit ratio. The results show that we can reduce the total write access count by a maximum of 52.9% and the consumed energy by 19.9%. Therefore, we can enhance the average page cache performance and reduce the endurance problem in the hybrid main memory.
High EGFR Gene Copy Number and Skin Rash as Predictive Markers for EGFR Tyrosine Kinase Inhibitors in Patients with Advanced Squamous Cell Lung Carcinoma
Authors: Lee Youngjoo , Shim Hyo Sup , Park Moo Suk , Kim Joo-Hang , Ha Sang-Jun , Kim Se Hoon , Cho Byoung Chul 
Published: January 2012

Abstract
Purpose: This study aimed to search for predictors of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) efficacy in previously treated patients with advanced squamous cell lung carcinoma in which EGFR mutations are very rare.
Experimental Design: EGFR gene copy numbers were assessed by FISH and evaluated as predictors of EGFR-TKI efficacy in 71 patients with advanced squamous cell lung cancer who received gefitinib or erlotinib as a second-line or higher therapy. The tumors were classified into EGFR/FISH-positive (high polysomy/gene amplification) and EGFR/FISH-negative (other) groups.
Results: EGFR/FISH was positive in 19 (26.7%) patients. Only EGFR/FISH positive status was correlated with the EGFR-TKIs response (EGFR/FISH+ vs. EGFR/FISH−, 26.3% vs. 2.0%; P = 0.005). In a multivariate analysis, the risk of progression was lower in EGFR/FISH-positive patients (HR of EGFR/FISH+ vs. EGFR/FISH−, 0.57; P = 0.057) or patients experiencing grade 2 or more rash (HR for rash grade 2 or more vs. less than 2, 0.54; P = 0.042), compared with EGFR/FISH-negative patients or those experiencing grade of less than 2 rash, respectively. When the combined criteria of EGFR/FISH and skin rash severity were analyzed, EGFR/FISH-negative patients with grade less than 2 rash had poorer clinical outcomes than patients with positive EGFR/FISH or grade 2 or more rash, apparent as a lower response rate (0.0% vs. 21.4%; P = 0.003) and a shorter median progression-free survival (1.13 months vs. 3.90 months; P = 0.0002).
Conclusions: EGFR/FISH and skin rash severity may be used to identify which patients are likely to gain a benefit from EGFR-TKIs in this population. Clin Cancer Res; 18(6); 1760–8. ©2012 AACR.
Surviving or thriving? Do teachers have lower perceived control and well-being than other professions?
Authors: Grenville-Cleave Bridget , Boniwell Ilona 
Published: January 2012

Teaching is not what it used to be. The complexity and intensity of the pressures on teachers and the pace of education reform are unprecedented. The aim of this research was to explore perceived control and well-being in teachers and other professionals. A mixed methods design was selected. Phase 1 consisted of an online quantitative survey (298 participants, 222 females, 76 males). Perceived control was measured using the Brief Levenson LOC and Generalised Self-Efficacy Scales, well-being was measured using the Life Orientation Test-Revised, Satisfaction with Life, Subjective Happiness and Ego Resilience Scales. Phase 2 consisted of semi-structured interviews (n = 6); thematic analysis was carried out. It was hypothesised that teachers have lower perceived control and well-being than other professionals, and that older teachers have higher internal control than younger teachers. Independent t-tests using teachers (n = 150) and non-teachers (n = 148) revealed that teachers’ mean scores were significantly different to those of non-teachers. Teachers’ perceived control and well-being were significantly lower than those of non-teachers (p > 0.001). The hypothesis that teachers have significantly lower perceived control and well-being than other professionals was supported. Four themes related to control were located in the qualitative analysis: autonomy, authenticity, connection to others and resilience. The study found that there were similarities between professions in terms of need for control over one’s work. Teachers value connections more highly; non-teachers value objectivity and independence more highly. It is suggested that non-teachers are better prepared to deal with change than teachers. The results are discussed in the context of ongoing reform in the education system, focusing on what actions can be taken to enhance teachers’ well-being.
Competition Law and Competition Issues Affecting the Energy Sector in India
Authors: Panda Aurobinda , Patel Atul 
Published: January 2012

India faces endemic electrical energy and peaking shortages. The power sector is plagued with mounting commercial losses due to various inefficiencies, colossal commercial and technical losses and increasing subsidy burden on the states. These shortages have had a very detrimental effect on the overall economic growth of the country. In order to revitalise the sector and improve the techno-economic performance, the Government of India initiated the reform process in 1991. This article analyses the pre-reform era and identifies the key concerns which led to the initiation of the reforms. It also analyses the likely impact of the major policy and regulatory initiatives that have been undertaken since 1991 including the provisions of the new enactments which have come into force eventually in the form of the Electricity Act, 2003. This article details out the key features of the Act and its likely impact on the Indian electricity industry in the emerging scenario. The article also discusses major issues like role of the regulator in the new regime, issue of open access, power trading, introduction of power markets and role of the Appellate Tribunal for Electricity in harmonising the orders of the various regulators. JEL Classification: K21, Q43
Damodar Valley Corporation, the Missed Opportunity
Authors: Choudhury Sujit 
Published: January 2012

Damodar River basin is one of the most important river basins in India. The rich natural resource base of the basin in terms of coal, minerals, forests and fertile agricultural lands have supported livelihood of millions of people over centuries. The Damodar basin morphology character causes frequent flooding in the lower catchment during monsoon. Over the centuries this natural disaster severely affects the life and property of the lower catchment. Presence of coal and minerals initiated mining and industrialisation in the basin since last 150 years. Damodar Valley Corporation was formed in 1948 to manage water resources and sustainable development of the basin. But DVC at present became a large power corporate with little role for basin management. The fast unplanned economic development with rapid urbanisation is damaging the Damodar River ecosystem. This in turn affects the life and livelihood of large number of people in the basin. A new basin management strategy needs to be adopted in the present situation to save the river and the people of the basin area from the imminent environmental disasters. JEL Classification: Q56
Attempting the Production of Public Goods through Microfinance
Authors: Mader Philip 
Published: January 2012

This article critically evaluates attempts to create public goods via microfinance loans in reference to the specific example of water and sanitation. The microfinancing of water and sanitation is a private business model which requires households to privately recognise, internalise and capitalise the bene-fits from improved water and sanitation. But household water and sanitation, being closely linked to underlying common pool resources, and being merit goods, have strong public goods characteristics and therefore depend on collective solutions. Two cases, from Vietnam and India, are presented and evaluated. Despite their dissimilar settings and designs, evidence is found that both projects encountered similar and comparable problems at the collective level which individual microfinance loans could not address. The problems encountered warn against an emergent micro-privatisation of water and sanitation through microfinance. JEL Classification: O16, O18, Q25, Z18
Transcriptional signature of accessory cells in the lateral line, using the Tnk1bp1:EGFP transgenic zebrafish line
Authors: Behra Martine , Gallardo Viviana E , Bradsher John , Torrado Aranza , Elkahloun Abdel , Idol Jennifer , Sheehy Jessica , Zonies Seth , Xu Lisha , Shaw Kenna M , Satou Chie , Higashijima Shin-ichi , Weinstein Brant M , Burgess Shawn M 
Published: January 2012

Abstract
Background
Because of the structural and molecular similarities between the two systems, the lateral line, a fish and amphibian specific sensory organ, has been widely used in zebrafish as a model to study the development/biology of neuroepithelia of the inner ear. Both organs have hair cells, which are the mechanoreceptor cells, and supporting cells providing other functions to the epithelium. In most vertebrates (excluding mammals), supporting cells comprise a pool of progenitors that replace damaged or dead hair cells. However, the lack of regenerative capacity in mammals is the single leading cause for acquired hearing disorders in humans.

Results
In an effort to understand the regenerative process of hair cells in fish, we characterized and cloned an egfp transgenic stable fish line that trapped tnks1bp1, a highly conserved gene that has been implicated in the maintenance of telomeres' length. We then used this Tg(tnks1bp1:EGFP) line in a FACsorting strategy combined with microarrays to identify new molecular markers for supporting cells.

Conclusions
We present a Tg(tnks1bp1:EGFP) stable transgenic line, which we used to establish a transcriptional profile of supporting cells in the zebrafish lateral line. Therefore we are providing a new set of markers specific for supporting cells as well as candidates for functional analysis of this important cell type. This will prove to be a valuable tool for the study of regeneration in the lateral line of zebrafish in particular and for regeneration of neuroepithelia in general.
The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis
Authors: De Paola Domenico , Cattonaro Federica , Pignone Domenico , Sonnante Gabriella 
Published: January 2012

AbstractBackgroundPlant microRNAs (miRNAs) are involved in post-transcriptional regulatory mechanisms of several processes, including the response to biotic and abiotic stress, often contributing to the adaptive response of the plant to adverse conditions. In addition to conserved miRNAs, found in a wide range of plant species a number of novel species-specific miRNAs, displaying lower levels of expression can be found. Due to low abundance, non conserved miRNAs are difficult to identify and isolate using conventional approaches. Conversely, deep-sequencing of small RNA (sRNA) libraries can detect even poorly expressed miRNAs.No miRNAs from globe artichoke have been described to date. We analyzed the miRNAome from artichoke by deep sequencing four sRNA libraries obtained from NaCl stressed and control leaves and roots.ResultsConserved and novel miRNAs were discovered using accepted criteria. The expression level of selected miRNAs was monitored by quantitative real-time PCR. Targets were predicted and validated for their cleavage site. A total of 122 artichoke miRNAs were identified, 98 (25 families) of which were conserved with other plant species, and 24 were novel. Some miRNAs were differentially expressed according to tissue or condition, magnitude of variation after salt stress being more pronounced in roots. Target function was predicted by comparison toArabidopsisproteins; the 43 targets (23 for novel miRNAs) identified included transcription factors and other genes, most of which involved in the response to various stresses. An unusual cleaved transcript was detected for miR393 target, transport inhibitor response 1.ConclusionsThe miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom.
The transcriptional activator ZNF143 is essential for normal development in zebrafish
Authors: Halbig Kari M , Lekven Arne C , Kunkel Gary R 
Published: January 2012

Abstract

Background
ZNF143 is a sequence-specific DNA-binding protein that stimulates transcription of both small RNA genes by RNA polymerase II or III, or protein-coding genes by RNA polymerase II, using separable activating domains. We describe phenotypic effects following knockdown of this protein in developing Danio rerio (zebrafish) embryos by injection of morpholino antisense oligonucleotides that target znf143 mRNA.

Results
The loss of function phenotype is pleiotropic and includes a broad array of abnormalities including defects in heart, blood, ear and midbrain hindbrain boundary. Defects are rescued by coinjection of synthetic mRNA encoding full-length ZNF143 protein, but not by protein lacking the amino-terminal activation domains. Accordingly, expression of several marker genes is affected following knockdown, including GATA-binding protein 1 (gata1), cardiac myosin light chain 2 (cmlc2) and paired box gene 2a (pax2a). The zebrafish pax2a gene proximal promoter contains two binding sites for ZNF143, and reporter gene transcription driven by this promoter in transfected cells is activated by this protein.

Conclusions
Normal development of zebrafish embryos requires ZNF143. Furthermore, the pax2a gene is probably one example of many protein-coding gene targets of ZNF143 during zebrafish development.
Plasma membrane protein OsMCA1 is involved in regulation of hypo-osmotic shock-induced Ca2+influx and modulates generation of reactive oxygen species in cultured rice cells
Authors: Kurusu Takamitsu , Nishikawa Daisuke , Yamazaki Yukari , Gotoh Mariko , Nakano Masataka , Hamada Haruyasu , Yamanaka Takuya , Iida Kazuko , Nakagawa Yuko , Saji Hikaru , Shinozaki Kazuo , Iida Hidetoshi , Kuchitsu Kazuyuki 
Published: January 2012

Abstract

Background
Mechanosensing and its downstream responses are speculated to involve sensory complexes containing Ca2+-permeable mechanosensitive channels. On recognizing osmotic signals, plant cells initiate activation of a widespread signal transduction network that induces second messengers and triggers inducible defense responses. Characteristic early signaling events include Ca2+ influx, protein phosphorylation and generation of reactive oxygen species (ROS). Pharmacological analyses show Ca2+ influx mediated by mechanosensitive Ca2+ channels to influence induction of osmotic signals, including ROS generation. However, molecular bases and regulatory mechanisms for early osmotic signaling events remain poorly elucidated.

Results
We here identified and investigated OsMCA1, the sole rice homolog of putative Ca2+-permeable mechanosensitive channels in Arabidopsis (MCAs). OsMCA1 was specifically localized at the plasma membrane. A promoter-reporter assay suggested that OsMCA1 mRNA is widely expressed in seed embryos, proximal and apical regions of shoots, and mesophyll cells of leaves and roots in rice. Ca2+ uptake was enhanced in OsMCA1-overexpressing suspension-cultured cells, suggesting that OsMCA1 is involved in Ca2+ influx across the plasma membrane. Hypo-osmotic shock-induced ROS generation mediated by NADPH oxidases was also enhanced in OsMCA1-overexpressing cells. We also generated and characterized OsMCA1-RNAi transgenic plants and cultured cells; OsMCA1-suppressed plants showed retarded growth and shortened rachises, while OsMCA1-suppressed cells carrying Ca2+-sensitive photoprotein aequorin showed partially impaired changes in cytosolic free Ca2+ concentration ([Ca2+]cyt) induced by hypo-osmotic shock and trinitrophenol, an activator of mechanosensitive channels.

Conclusions
We have identified a sole MCA ortholog in the rice genome and developed both overexpression and suppression lines. Analyses of cultured cells with altered levels of this putative Ca2+-permeable mechanosensitive channel indicate that OsMCA1 is involved in regulation of plasma membrane Ca2+ influx and ROS generation induced by hypo-osmotic stress in cultured rice cells. These findings shed light on our understanding of mechanical sensing pathways.