bluuebunny/crossref_metadata_2025 huggingface dataset:
Sombrero Uplift Above the Altiplano-Puna Magma Body: Evidence of a Ballooning Mid-Crustal Diapir
Authors: Fialko Yuri , Pearse Jill
Published: October 2012

Rise and Subside

Earth's surface tends to deform as magmatic fluids rise toward the surface from below, usually manifesting itself in uplift of continental crust.
Fialko and Pearse
(p.
250
; see the Perspective by

Brooks

), however, show that subsidence, or widespread sinking, accompanies uplift when magma rises. Satellite measurements reveal that the massive Altipano-Puna magma body in the central Andes balloons upward, causing subsidence around the region of uplift, resembling a sombrero. Melting of surrounding rocks as the magma rises likely withdraws material and causes the subsidence.
Revolution Stalled
Authors: Hyman Steven E.
Published: October 2012

Drug discovery is at a near standstill for psychiatric disorders such as schizophrenia, bipolar disorder, and depression.
Human Neural Stem Cells Induce Functional Myelination in Mice with Severe Dysmyelination
Authors: Uchida Nobuko , Chen Kevin , Dohse Monika , Hansen Kelly D. , Dean Justin , Buser Joshua R. , Riddle Art , Beardsley Douglas J. , Wan Ying , Gong Xi , Nguyen Thuan , Cummings Brian J. , Anderson Aileen J. , Tamaki Stanley J. , Tsukamoto Ann , Weissman Irving L. , Matsumoto Steven G. , Sherman Larry S. , Kroenke Christopher D. , Back Stephen A.
Published: October 2012

Transplanted banked human neural stem cells produce functional myelin detected by MRI in juvenile mice with severe dysmyelination.
Next-Generation Treatments for Mental Disorders
Authors: Insel Thomas R.
Published: October 2012

Despite a retreat by industry from developing new psychiatric medications, recent research reveals new opportunities for progress.
There’s Node Place Like Home
Authors: Collier Joel H.
Published: October 2012

Delivering liver, thymus, or pancreatic cells to the lymph nodes can restore distant, diseased organ function.
Antioxidizing Asthma
Authors: Reznik Marina
Published: October 2012

Dietary intake of magnesium has a protective effect on childhood asthma.
New Immunoenzymatic Strategy for Rapid and Selective Growth of Salmonella
Authors: Ponsard Isabelle , Soumillion Patrice
Published: October 2012

We demonstrated that an exogenous conjugate consisting of a β-lactamase and a monoclonal antibody against a surface antigen of
Salmonella
is capable of conferring selective penicillin resistance on bacteria. This immunoenzymatic approach allows the rapid growth and detection of specific bacteria and may find other applications when temporary and nongenetic antibiotic resistance is required.
Pneumococci Can Persistently Colonize Adult Patients with Chronic Respiratory Disease
Authors: Domenech A. , Ardanuy C. , Balsalobre L. , Marti S. , Calatayud L. , De la Campa A. G. , Brueggemann A. B. , Liñares J.
Published: October 2012

Streptococcus pneumoniae
plays an important role in causing acute exacerbations in patients with chronic respiratory disease. However, few data are available regarding pneumococcal persistence in adult patients with chronic respiratory diseases. Fifty pneumococci recovered from sputum samples (1995 to 2010) from 13 adult patients with ≥3 episodes of acute exacerbation or pneumonia, with the same serotype and pulsed-field gel electrophoresis (PFGE) pattern, were studied. Multilocus sequence typing (MLST) loci, penicillin-binding protein (PBP) genes (
pbp
2
x
,
pbp1a
,
pbp2b
), and the quinolone-resistant determining regions (QRDRs) of
parC
,
parE
, and
gyrA
were PCR amplified and sequenced. The average time between the first and last episode was 582 days (standard deviation [SD], ±362). All but two patients received multiple courses of β-lactam treatment, and all persistent strains were resistant to penicillin; however, the PBP sequences were stable over time apart from one variable nucleotide in
pbp
2
x
, observed among pneumococci isolated from three patients. In contrast, 7/11 patients treated with fluoroquinolones had fluoroquinolone-resistant pneumococci. In three patients, the initially fluoroquinolone-susceptible strain developed resistance after fluoroquinolone therapy, and in the remaining four patients, the persistent strain was fluoroquinolone resistant from the first episode. QRDR changes involved in fluoroquinolone resistance were frequently observed in persistent strains after fluoroquinolone treatment; however, the PBP sequences and MLST genotypes of these strains were stable over time.
Allele-Specific PCR for Determination of IL28B Genotype
Authors: Cook Linda , Diem Kurt , Kim Woo , Scott John D. , Jerome Keith R.
Published: October 2012

The IL28B genotype is a critical determinant of interferon response in patients infected with hepatitis C virus genotype 1. We describe an allele-specific PCR assay for the IL28B genotype. The assay is simple and robust, uses commonly available real-time PCR instrumentation, and is well suited for clinical laboratories offering IL28B genotyping.
Bacterial Coinfections in Travelers with Malaria: Rationale for Antibiotic Therapy
Authors: Sandlund Johanna , Naucler Pontus , Dashti Saduddin , Shokri Akhar , Eriksson Sara , Hjertqvist Marika , Karlsson Lillemor , Capraru Teodor , Färnert Anna
Published: October 2012

Malaria predisposes children in areas where malaria is endemic to concurrent bacteremia, often with severe outcomes. The importance of bacterial coinfections in patients diagnosed with malaria in nonendemic settings has, however, not been reported. A retrospective analysis of microbiology data was performed in 755 travelers diagnosed with malaria in Sweden. Bacterial cultures from blood and other locations were correlated to clinical outcome and antibiotic treatment. Blood cultures were drawn from 417 (55%) patients (88% of whom were >15 years old), and bacterial isolates of clinical relevance (
Salmonella enterica
serovar Enteritidis and
Escherichia coli
) were detected in 2 patients (0.3%). Cultures from other locations (mainly urine, nasopharyngeal, and fecal samples) were obtained from 44% of the patients with 4.9% positivity. Of the 38 patients given antibiotics, 47% had neither severe malaria nor positive cultures and/or radiology signs indicative of treatment. C-reactive protein levels were associated with bacterial infections but had only a fair predictive value. Bacterial coinfections are uncommon among travelers with malaria. These data suggest a weaker association between malaria and bacteremia than previously described in endemic settings and might indicate different patient populations with different pathophysiological mechanisms and microbial environments. The study supports a restrictive antibiotic policy in returning travelers with malaria.
Genotypic Characterization of Streptococcus infantarius subsp.
coli
Isolates from Sea Otters with Infective Endocarditis and/or Septicemia and from Environmental Mussel Samples
Authors: Counihan-Edgar Katrina L. , Gill Verena A. , Doroff Angela M. , Burek Kathleen A. , Miller Woutrina A. , Shewmaker Patricia L. , Jang Spencer , Goertz Caroline E. C. , Tuomi Pamela A. , Miller Melissa A. , Jessup David A. , Byrne Barbara A.
Published: October 2012

Pulsed-field gel electrophoresis (PFGE) was used to type 128
Streptococcus infantarius
subsp.
coli
isolates from sea otters and mussels. Six SmaI PFGE groups were detected, with one predominant group representing 57% of the isolates collected over a wide geographic region. Several sea otter and mussel isolates were highly related, suggesting that an environmental infection source is possible.
Short-Term Stability of Pathogen-Specific Nucleic Acid Targets in Clinical Samples
Authors: Hasan Mohammad R. , Tan Rusung , Al-Rawahi Ghada N. , Thomas Eva , Tilley Peter
Published: October 2012

The stability of pathogen-specific DNA or RNA amplification targets in clinical samples following short-term storage at room temperature, 4°C, and −80°C was assessed by real-time PCR. In purified nucleic acid extracts, both DNA and RNA targets were stable for up to 30 days, irrespective of storage temperature. In unextracted samples, temperature-dependent loss of targets (
P
< 0.05) was observed in serum and cerebrospinal fluid specimens, while no changes were observed for EDTA blood samples.
Cellular Protein HAX1 Interacts with the Influenza A Virus PA Polymerase Subunit and Impedes Its Nuclear Translocation
Authors: Hsu Wei-Bin , Shih Jia-Ling , Shih Jie-Ru , Du Jia-Ling , Teng Shu-Chun , Huang Li-Min , Wang Won-Bo
Published: October 2012

Transcription and replication of the influenza A virus RNA genome occur in the nucleus through the viral RNA-dependent RNA polymerase consisting of PB1, PB2, and PA. Cellular factors that associate with the viral polymerase complex play important roles in these processes. To look for cellular factors that could associate with influenza A virus PA protein, we have carried out a yeast two-hybrid screen using a HeLa cell cDNA library. We identified six cellular proteins that may interact with PA. We focused our study on one of the new PA-interacting proteins, HAX1, a protein with antiapoptotic function. By using glutathioneS-transferase pulldown and coimmunoprecipitation assays, we demonstrate that HAX1 specifically interacts with PAin vitroandin vivoand that HAX1 interacts with the nuclear localization signal domain of PA. Nuclear accumulation of PA was increased in HAX1-knockdown cells, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can impede nuclear transport of PA. As a consequence, knockdown of HAX1 resulted in a significant increase in virus yield and polymerase activity in a minigenome assay, and this phenotype could be reversed by reexpression of HAX1, indicating that HAX1 can inhibit influenza A virus propagation. Together, these results not only provide insight into the mechanism underlying nuclear transport of PA but also identify an intrinsic host factor that restricts influenza A virus infection.
Inhibition of Alpha Interferon (IFN-α)-Induced MicroRNA-122 Negatively Affects the Anti-Hepatitis B Virus Efficiency of IFN-α
Authors: Hao Junli , Jin Wensong , Li Xinghui , Wang Saifeng , Zhang Xiaojun , Fan Hongxia , Li Changfei , Chen Lizhao , Gao Bin , Liu Guangze , Meng Songdong
Published: October 2012

Alpha interferon (IFN-α)-based therapy can effectively treat chronic hepatitis B virus (HBV) infection, which causes life-threatening complications. Responses to IFN-α therapy vary greatly in chronic hepatitis B (CHB) patients, but underlying mechanisms are almost unknown. In this study, we found that IFN-α treatment induced a marked decrease of microRNA-122 (miR-122) expression in hepatocytes. We next showed that IFN-α-induced miR-122 downregulation was only partly due to transcriptional suppression. One IFN-stimulated gene (ISG), NT5C3, which was identified as a miR-122 target, efficiently inhibited miR-122 by binding and sequestering miR-122 with its mRNA 3′-untranslated region (3′-UTR), indicating that this ISG is involved in IFN-α-mediated miR-122 suppression. Notably, the inhibitory effect of IFN-α on miR-122 was completely abolished by blocking IFN-α-induced upregulation of NT5C3 mRNA expression by RNA interference (RNAi). Meanwhile, we observed that miR-122 dramatically inhibited HBV expression and replication. Finally, we showed that IFN-α-mediated HBV-inhibitory effects could be enhanced significantly by blocking IFN-α-induced downregulation of miR-122. We therefore concluded that IFN-α-induced inhibition of miR-122 may negatively affect the anti-HBV function of IFN-α. These data provide valuable insights for a better understanding of the antiviral mechanism of IFN-α and raise further potential interest in enhancing its anti-HBV efficacy.
Distinct Evolutionary Pressures Underlie Diversity in Simian Immunodeficiency Virus and Human Immunodeficiency Virus Lineages
Authors: Fischer Will , Apetrei Cristian , Santiago Mario L. , Li Yingying , Gautam Rajeev , Pandrea Ivona , Shaw George M. , Hahn Beatrice H. , Letvin Norman L. , Nabel Gary J. , Korber Bette T.
Published: October 2012

Simian immunodeficiency virus (SIV) infection of rhesus macaques causes immune depletion and disease closely resembling human AIDS and is well recognized as the most relevant animal model for the human disease. Experimental investigations of viral pathogenesis and vaccine protection primarily involve a limited set of related viruses originating in sooty mangabeys (SIVsmm). The diversity of human immunodeficiency virus type 1 (HIV-1) has evolved in humans in about a century; in contrast, SIV isolates used in the macaque model evolved in sooty mangabeys over millennia. To investigate the possible consequences of such different evolutionary histories for selection pressures and observed diversity in SIVsmm and HIV-1, we isolated, sequenced, and analyzed 20 independent isolates of SIVsmm, including representatives of 7 distinct clades of viruses isolated from natural infection. We found SIVsmm diversity to be lower overall than HIV-1 M group diversity. Reduced positive selection (i.e., less diversifying evolution) was evident in extended regions of SIVsmm proteins, most notably in Gag p27 and Env gp120. In addition, the relative diversities of proteins in the two lineages were distinct: SIVsmm Env and Gag were much less diverse than their HIV-1 counterparts. This may be explained by lower SIV-directed immune activity in mangabeys relative to HIV-1-directed immunity in humans. These findings add an additional layer of complexity to the interpretation and, potentially, to the predictive utility of the SIV/macaque model, and they highlight the unique features of human and simian lentiviral evolution that inform studies of pathogenesis and strategies for AIDS vaccine design.
Diversity and Distribution of Hantaviruses in South America
Authors: Firth Cadhla , Tokarz Rafal , Simith Darlene B. , Nunes Marcio R. T. , Bhat Meera , Rosa Elizabeth S. T. , Medeiros Daniele B. A. , Palacios Gustavo , Vasconcelos Pedro F. C. , Lipkin W. Ian
Published: October 2012

Hantaviruses are important contributors to disease burden in the New World, yet many aspects of their distribution and dynamics remain uncharacterized. To examine the patterns and processes that influence the diversity and geographic distribution of hantaviruses in South America, we performed genetic and phylogeographic analyses of all available South American hantavirus sequences. We sequenced multiple novel and previously described viruses (Anajatuba, Laguna Negra-like, two genotypes of Castelo dos Sonhos, and two genotypes of Rio Mamore) from BrazilianOligoryzomysrodents and hantavirus pulmonary syndrome cases and identified a previously uncharacterized species ofOligoryzomysassociated with a new genotype of Rio Mamore virus. Our analysis indicates that the majority of South American hantaviruses fall into three phylogenetic clades, corresponding to Andes and Andes-like viruses, Laguna Negra and Laguna Negra-like viruses, and Rio Mamore and Rio Mamore-like viruses. In addition, the dynamics and distribution of these viruses appear to be shaped by both the geographic proximity and phylogenetic relatedness of their rodent hosts. The current system of nomenclature used in the hantavirus community is a significant impediment to understanding the ecology and evolutionary history of hantaviruses; here, we suggest strict adherence to a modified taxonomic system, with species and strain designations resembling the numerical system of the enterovirus genus.
The Oncogenic MicroRNA OncomiR-21 Overexpressed during Marek's Disease Lymphomagenesis Is Transactivated by the Viral Oncoprotein Meq
Authors: Stik Grégoire , Dambrine Ginette , Pfeffer Sébastien , Rasschaert Denis
Published: October 2012

Gallid herpesvirus 2 (GaHV-2) is an oncogenic herpesvirus that causes T lymphoma in chicken. GaHV-2 encodes a basic leucine zipper (bZIP) protein of the AP-1 family, Meq. Upon formation of homo- or heterodimers with c-Jun, Meq may modulate the expression of viral and cellular genes involved in lymphomagenesis. GaHV-2 also encodes viral microRNAs (miRNAs) involved in latency and apoptosis escape. However, little is known about cellular miRNA deregulation during the development of GaHV-2-associated lymphoma. We determined the cellular miRNA expression profiles of chickens infected with a very virulent strain (RB-1B) or a vaccine strain (CVI988) or noninfected. Among the most deregulated cellular miRNAs, we focused our efforts on gga-miR-21, which is upregulated during GaHV-2 infection. We mapped the gga-miR-21 promoter to the 10th intron of the
TMEM49
gene and found it to be driven by AP-1- and Ets-responsive elements. We show here that the viral oncoprotein Meq binds to this promoter, thereby transactivating gga-miR-21 expression. We confirmed that this miRNA targets chicken programmed death cell 4 (PDCD4) and promotes tumor cell growth and apoptosis escape. Finally, gga-miR-21 was overexpressed only during infection with a very virulent strain (RB-1B) and not during infection with a nononcogenic strain (CVI988), providing further evidence for its role in GaHV-2 lymphomagenesis. Our data therefore suggest an additional role for Meq in GaHV-2-mediated lymphomagenesis through the induction of miR-21 expression.
Dyskalaemia following diffuse axonal injury: case report and review of the literature
Authors: Cronin David , Kaliaperumal Chandrasekaran , Kumar Ramanathan , Kaar George
Published: October 2012

Traumatic brain injury, and its management, commonly causes derangements in potassium balance. There are a number of recognised causative factors including head trauma, hypothermia and iatrogenic factors such as pharmacological agents and permissive cooling. We describe a case of a 19-year-old man with a severe traumatic brain injury. In a 36-h period, his intracranial pressure increased despite maximal medical therapy and he developed refractory hypokalaemia. Immediately following a decompressive craniectomy, the patient was noted to be profoundly hyperkalaemic; this led to the development of ventricular tachycardia and cardiac arrest, from which the patient did not recover. The effects of brain injury on potassium balance are not well appreciated; the effect of decompressive craniectomy on potassium (K+) balance has not been described previously. We would like to emphasise the potential effect of diffuse axonal injury, a severe form of brain injury and decompressive craniectomy on potassium balance.
An unusual cause for recurrent chest infections
Authors: Lobo Ronstan , Mulloy Eithne M T
Published: October 2012

We present a case of an elderly non-smoking gentleman who, since 2005, had been admitted multiple times for recurrent episodes of shortness of breath, wheeze, cough and sputum. The patient was treated as exacerbations of chronic obstructive pulmonary disease (COPD) and/or lower respiratory tract infections. Bronchoscopy was done which revealed multiple hard nodules in the trachea and bronchi with posterior tracheal wall sparing. Biopsies confirmed this as tracheopathia osteochondroplastica (TO). He had increasing frequency of admission due to methicillin-resistantStaphylococcus aureusand pseudomonas infections, which failed to clear despite intravenous, prolonged oral and nebulised antibiotics. The patient developed increasing respiratory distress and respiratory failure. The patient died peacefully in 2012. This case report highlights the typical pathological and radiological findings of TO and the pitfalls of misdiagnosing patients with recurrent chest infections as COPD.
Calcific myonecrosis: a case report and review of the literature
Authors: Jalil Rozh , Roach Joy , Smith Andrew , Mukundan Chandrika
Published: October 2012

Calcific myonecrosis is a rare post-traumatic sequel of the lower limb, presenting in a delayed manner several years after the initial injury. We report a case of a 43-year-old gentleman who presented emergently with an enlarging painful mass in the lateral side of his left leg, that although present for several years had recently worsened with respect to the pain and erythema. Following laboratory and radiological investigations this was diagnosed to be calcific myonecrosis, which was then treated conservatively, and patient discharged when symptomatically improved.
Alternative scenarios to the
Authors: Taylor Nolan J. , Loiacono Eleanor T. , Watson Richard T.
Published: October 2012

A test of alternative formats to Web banner ads.
Women and men in the IT profession
Authors: McKinney Vicki R. , Wilson Darryl D. , Brooks Nita , O'Leary-Kelly Anne , Hardgrave Bill
Published: October 2012

Fewer women entering IT drives the underrepresentation problem.
Managing large collections of data mining models
Authors: Liu Bing , Tuzhilin Alexander
Published: October 2012

Data analysts and naive users alike in information-intensive organizations need automated ways to build, analyze, and maintain very large collections of data mining models.
Moving the needle, computer architecture research in academe and industry
Authors: Dally William J.
Published: October 2012

The goal of computer architecture research is to move the needle, that is to affect the future of computing in a positive way. Publications, prototypes, and studies are all just different means to this common end. This talk will address how to move the needle in academic and industrial settings discussing what works and what doesn't. Our work is constrained by applications, technology, and commercial reality. The architecture funnel starts with many concepts that proceed through stages of evaluation and refinement. A relatively few successful concepts make it out the far side to deployment. Most concepts fail, and good researchers cut their losses early. The funnel has many years of latency and good researchers aim for results that are relevant beyond this latency. Academics are best at the early stages of the concept funnel -- where their long-term perspective and freedom from constraints are advantages. Industry excels at the later stages of the pipeline where resources and experience are well suited to refining ideas for deployment. Too often good concepts fall into a chasm between the two. Good partnerships are needed to bridge this chasm. This talk will give illustrate this exploration of architecture research with numerous examples of successes and failures. It will give recommended best practices for academic and industrial research. I will close with a glimpse of the future of architecture.
Re-architecting DRAM memory systems with monolithically integrated silicon photonics
Authors: Beamer Scott , Sun Chen , Kwon Yong-Jin , Joshi Ajay , Batten Christopher , Stojanović Vladimir , Asanović Krste
Published: October 2012

The performance of future manycore processors will only scale with the number of integrated cores if there is a corresponding increase in memory bandwidth. Projected scaling of electrical DRAM architectures appears unlikely to suffice, being constrained by processor and DRAM pin-bandwidth density and by total DRAM chip power, including off-chip signaling, cross-chip interconnect, and bank access energy. In this work, we redesign the DRAM main memory system using a proposed monolithically integrated silicon photonics technology and show that our photonically interconnected DRAM (PIDRAM) provides a promising solution to all of these issues. Photonics can provide high aggregate pin-bandwidth density through dense wavelength-division multiplexing. Photonic signaling provides energy-efficient communication, which we exploit to not only reduce chip-to-chip interconnect power but to also reduce cross-chip interconnect power by extending the photonic links deep into the actual PIDRAM chips. To complement these large improvements in interconnect bandwidth and power, we decrease the number of bits activated per bank to improve the energy efficiency of the PIDRAM banks themselves. Our most promising design point yields approximately a 10x power reduction for a single-chip PIDRAM channel with similar throughput and area as a projected future electrical-only DRAM. Finally, we propose optical power guiding as a new technique that allows a single PIDRAM chip design to be used efficiently in several multi-chip configurations that provide either increased aggregate capacity or bandwidth.
Rethinking DRAM design and organization for energy-constrained multi-cores
Authors: Udipi Aniruddha N. , Muralimanohar Naveen , Chatterjee Niladrish , Balasubramonian Rajeev , Davis Al , Jouppi Norman P.
Published: October 2012

DRAM vendors have traditionally optimized the cost-per-bit metric, often making design decisions that incur energy penalties. A prime example is the overfetch feature in DRAM, where a single request activates thousands of bit-lines in many DRAM chips, only to return a single cache line to the CPU. The focus on cost-per-bit is questionable in modern-day servers where operating costs can easily exceed the purchase cost. Modern technology trends are also placing very different demands on the memory system: (i)queuing delays are a significant component of memory access time, (ii) there is a high energy premium for the level of reliability expected for business-critical computing, and (iii) the memory access stream emerging from multi-core systems exhibits limited locality. All of these trends necessitate an overhaul of DRAM architecture, even if it means a slight compromise in the cost-per-bit metric.

This paper examines three primary innovations. The first is a modification to DRAM chip microarchitecture that re tains the traditional DDRx SDRAMinterface. Selective Bit-line Activation (SBA) waits for both RAS (row address) and CAS (column address) signals to arrive before activating exactly those bitlines that provide the requested cache line. SBA reduces energy consumption while incurring slight area and performance penalties. The second innovation, Single Subarray Access (SSA), fundamentally re-organizes the layout of DRAM arrays and the mapping of data to these arrays so that an entire cache line is fetched from a single subarray. It requires a different interface to the memory controller, reduces dynamic and background energy (by about 6X), incurs a slight area penalty (4%), and can even lead to performance improvements (54% on average) by reducing queuing delays. The third innovation further penalizes the cost-per-bit metric by adding a checksum feature to each cache line. This checksum error-detection feature can then be used to build stronger RAID-like fault tolerance, including chipkill-level reliability. Such a technique is especially crucial for the SSA architecture where the entire cache line is localized to a single chip. This DRAM chip microarchitectural change leads to a dramatic reduction in the energy and storage overheads for reliability. The proposed architectures will also apply to other emerging memory technologies (such as resistive memories) and will be less disruptive to standards, interfaces, and the design flow if they can be incorporated into first-generation designs.
ColorSafe
Authors: Lucia Brandon , Ceze Luis , Strauss Karin
Published: October 2012

In this paper, we propose ColorSafe, an architecture that detects and dynamically avoids single- and multi-variable atomicity violation bugs. The key idea is to group related data into colors and then monitor access interleavings in the "color space". This enables detection of atomicity violations involving any data of the same color. We leverage support for meta-data to maintain color information, and signatures to efficiently keep recent color access histories. ColorSafe dynamically avoids atomicity violations by inserting ephemeral transactions that prevent erroneous interleavings. ColorSafe has two modes of operation: (1)
debugging mode
makes detection more precise, producing fewer false positives and collecting more information; and, (2)
deployment mode
provides robust, efficient dynamic bug avoidance with less precise detection. This makes ColorSafe useful throughout the lifetime of programs, not just during development. Our results show that, in deployment mode, ColorSafe is able to successfully avoid the majority of multi-variable atomicity violations in bug kernels, as well as in large applications (Apache and MySQL). In debugging mode, ColorSafe detects bugs with few false positives.
A dynamically configurable coprocessor for convolutional neural networks
Authors: Chakradhar Srimat , Sankaradas Murugan , Jakkula Venkata , Cadambi Srihari
Published: October 2012

Convolutional neural networks (CNN) applications range from recognition and reasoning (such as handwriting recognition, facial expression recognition and video surveillance) to intelligent text applications such as semantic text analysis and natural language processing applications. Two key observations drive the design of a new architecture for CNN. First, CNN workloads exhibit a
widely varying mix of three types of parallelism
: parallelism within a convolution operation, intra-output parallelism where multiple input sources (features) are combined to create a single output, and inter-output parallelism where multiple, independent outputs (features) are computed simultaneously. Workloads differ significantly across different CNN applications, and across different layers of a CNN. Second, the number of processing elements in an architecture continues to scale (as per Moore's law) much faster than off-chip memory bandwidth (or pin-count) of chips. Based on these two observations, we show that for a given number of processing elements and off-chip memory bandwidth, a new CNN hardware architecture that dynamically configures the hardware on-the-fly to match the specific mix of parallelism in a given workload gives the best throughput performance. Our CNN compiler automatically translates high abstraction network specification into a parallel microprogram (a sequence of low-level VLIW instructions) that is mapped, scheduled and executed by the coprocessor. Compared to a 2.3 GHz quad-core, dual socket Intel Xeon, 1.35 GHz C870 GPU, and a 200 MHz FPGA implementation, our 120 MHz dynamically configurable architecture is 4x to 8x faster. This is the
first CNN architecture to achieve real-time video stream processing
(25 to 30 frames per second) on a wide range of object detection and recognition tasks.
RETCON
Authors: Blundell Colin , Raghavan Arun , Martin Milo M.K.
Published: October 2012

Over the past decade there has been a surge of academic and industrial interest in optimistic concurrency,
i.e.
the speculative parallel execution of code regions that have the semantics of isolation. This work analyzes scalability bottlenecks of workloads that use optimistic concurrency. We find that one common bottleneck is updates to auxiliary program data in otherwise non-conflicting operations,
e.g.
reference count updates and hashtable occupancy field increments.

To eliminate the performance impact of conflicts on such auxiliary data, this work proposes RETCON, a hardware mechanism that tracks the relationship between input and output values symbolically and uses this symbolic information to transparently repair the output state of a transaction at commit. RETCON is inspired by instruction replay-based mechanisms but exploits simplifying properties of the nature of computations on auxiliary data to perform repair
without
replay. Our experiments show that RETCON provides significant speedups for workloads that exhibit conflicts on auxiliary data, including transforming a transactionalized version of the Python interpreter from a workload that exhibits no scaling to one that exhibits near-linear scaling on 32 cores.
Evolution of thread-level parallelism in desktop applications
Authors: Blake Geoffrey , Dreslinski Ronald G. , Mudge Trevor , Flautner Krisztián
Published: October 2012

As the effective limits of frequency and instruction level parallelism have been reached, the strategy of microprocessor vendors has changed to increase the number of processing cores on a single chip each generation. The implicit expectation is that software developers will write their applications with concurrency in mind to take advantage of this sudden change in direction. In this study we analyze whether software developers for laptop/desktop machines have followed the recent hardware trends by creating software for chip multi-processing. We conduct a study of a wide range of applications on Microsoft Windows 7 and Apple's OS X Snow Leopard, measuring
Thread Level Parallelism
on a high performance workstation and a low power desktop. In addition, we explore graphics processing units (GPUs) and their impact on chip multi-processing. We compare our findings to a study done 10 years ago which concluded that a second core was sufficient to improve system responsiveness. Our results on today's machines show that, 10 years later, surprisingly 2-3 cores are more than adequate for most applications and that the GPU often remains under-utilized. However, in some application specific domains an 8 core SMT system with a 240 core GPU can be effectively utilized. Overall these studies suggest that many-core architectures are not a natural fit for current desktop/laptop applications.
Improving the future by examining the past
Authors: Thacker Charles P.
Published: October 2012

During the last fifty years, the technology underlying computer systems has improved dramatically. As technology has evolved, designers have made a series of choices in the way it was applied in computers. In some cases, decisions that were made in the twentieth century make less sense in the twenty-first. Conversely, paths not taken might now be more attractive given the state of technology today, particularly in light of the limits the field is facing, such as the increasing gap between processor speed and storage access times and the difficulty of cooling today's computers.

In this talk, I'll discuss some of these choices and suggest some possible changes that might make computing better in the twenty-first century.
BlackjackBench
Authors: Danalis Anthony , Luszczek Piotr , Marin Gabriel , Vetter Jeffrey S. , Dongarra Jack
Published: October 2012

DARPA's AACE project aimed to develop Architecture Aware Compiler Environments that automatically characterizes the hardware and optimizes the application codes accordingly. We present the BlackjackBench -- a suite of portable benchmarks that automate system characterization, plus statistical analysis techniques for interpreting the results. The BlackjackBench discovers the effective sizes and speeds of the hardware environment rather than the often unattainable peak values. We aim at hardware characteristics that can be observed by running standard C codes. We characterize the memory hierarchy, including cache sharing and NUMA characteristics of the system, properties of the processing cores affecting instruction execution speed, and the length of the OS scheduler time slot. We show how they all could potentially interfere with each other and how established classification and statistical analysis techniques reduce experimental noise and aid automatic interpretation of results.
LINE-1 Retrotransposition in the Nervous System
Authors: Thomas Charles A. , Paquola Apuã C.M. , Muotri Alysson R.
Published: October 2012

Long interspersed element-1 (LINE-1 or L1) is a repetitive DNA retrotransposon capable of duplication by a copy-and-paste genetic mechanism. Scattered throughout mammalian genomes, L1 is typically quiescent in most somatic cell types. In developing neurons, however, L1 can express and retrotranspose at high frequency. The L1 element can insert into various genomic locations including intragenic regions. These insertions can alter the dynamic of the neuronal transcriptome by changing the expression pattern of several nearby genes. The consequences of L1 genomic alterations in somatic cells are still under investigation, but the high level of mutagenesis within neurons suggests that each neuron is genetically unique. Furthermore, some neurological diseases, such as Rett syndrome and ataxia telangiectasia, misregulate L1 retrotransposition, which could contribute to some pathological aspects. In this review, we survey the literature related to neurodevelopmental retrotransposition and discuss possible relevance to neuronal function, evolution, and neurological disease.
Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies
Authors: O'Connell Jeremy D. , Zhao Alice , Ellington Andrew D. , Marcotte Edward M.
Published: October 2012

Both focused and large-scale cell biological and biochemical studies have revealed that hundreds of metabolic enzymes across diverse organisms form large intracellular bodies. These proteinaceous bodies range in form from fibers and intracellular foci—such as those formed by enzymes of nitrogen and carbon utilization and of nucleotide biosynthesis—to high-density packings inside bacterial microcompartments and eukaryotic microbodies. Although many enzymes clearly form functional mega-assemblies, it is not yet clear for many recently discovered cases whether they represent functional entities, storage bodies, or aggregates. In this article, we survey intracellular protein bodies formed by metabolic enzymes, asking when and why such bodies form and what their formation implies for the functionality—and dysfunctionality—of the enzymes that comprise them. The panoply of intracellular protein bodies also raises interesting questions regarding their evolution and maintenance within cells. We speculate on models for how such structures form in the first place and why they may be inevitable.
Multiple components of eIF4F are required for protein synthesis-dependent hippocampal long-term potentiation
Authors: Hoeffer Charles A. , Santini Emanuela , Ma Tao , Arnold Elizabeth C. , Whelan Ashley M. , Wong Helen , Pierre Philippe , Pelletier Jerry , Klann Eric
Published: October 2012

Persistent forms of synaptic plasticity are widely thought to require the synthesis of new proteins. This feature of long-lasting forms of plasticity largely has been demonstrated using inhibitors of general protein synthesis, such as either anisomycin or emetine. However, these drugs, which inhibit elongation, cannot address detailed questions about the regulation of translation initiation, where the majority of translational control occurs. Moreover, general protein synthesis inhibitors cannot distinguish between cap-dependent and cap-independent modes of translation initiation. In the present study, we took advantage of two novel compounds, 4EGI-1 and hippuristanol, each of which targets a different component of the eukaryotic initiation factor (eIF)4F initiation complex, and investigated their effects on long-term potentiation (LTP) at CA3-CA1 synapses in the hippocampus. We found that 4EGI-1 and hippuristanol both attenuated long-lasting late-phase LTP induced by two different stimulation paradigms. We also found that 4EGI-1 and hippuristanol each were capable of blocking the expression of newly synthesized proteins immediately after the induction of late-phase LTP. These new pharmacological tools allow for a more precise dissection of the role played by translational control pathways in synaptic plasticity and demonstrate the importance of multiple aspects of eIF4F in processes underlying hippocampal LTP, laying the foundation for future studies investigating the role of eIF4F in hippocampus-dependent memory processes.
Rapid feedback corrections during a bimanual postural task
Authors: Omrani Mohsen , Diedrichsen Jörn , Scott Stephen H.
Published: October 2012

An important observation in motor physiology is that even the fastest feedback responses can be modified in a task-dependent manner. However, whether or not such responses in one limb can be modulated based on online sensory feedback from other limbs is still unknown. We tested this using a bimanual postural control task, in which the two hands either controlled two separate cursors (double-cursor task) or a single cursor displayed at the spatial average between the hands (single-cursor task). In the first experiment, the two hands were symmetrically perturbed outwards. In the double-cursor task, the participants therefore had to return their hands to the targets, whereas in the single-cursor task no correction was necessary. Within 50 ms, the electromyographic activity showed significantly smaller responses in the single- compared with the double-cursor task. In the second experiment, the perturbation direction of the left hand (inward/outward) was randomized, such that participants could not preplan their response before perturbation onset. Results show that the behavior of the right arm in the one-cursor task depended on online feedback coming from the left arm: the muscular response was modulated within 75 ms based on directionally specific information of the left arm. These results suggest that sensory feedback from one limb can quickly modify the perturbation response of another limb in a task-dependent manner.
A New Hyperbolic Shear Deformation Theory for Bending Analysis of Functionally Graded Plates
Authors: Daouadji Tahar Hassaine , Hadj Henni Abdelaziz , Tounsi Abdelouahed , El Abbes Adda Bedia
Published: October 2012

Theoretical formulation, Navier’s solutions of rectangular plates based on a new higher order shear deformation model are presented for the static response of functionally graded plates. This theory enforces traction-free boundary conditions at plate surfaces. Shear correction factors are not required because a correct representation of transverse shearing strain is given. Unlike any other theory, the number of unknown functions involved is only four, as against five in case of other shear deformation theories. The mechanical properties of the plate are assumed to vary continuously in the thickness direction by a simple power-law distribution in terms of the volume fractions of the constituents. Numerical illustrations concern flexural behavior of FG plates with metal-ceramic composition. Parametric studies are performed for varying ceramic volume fraction, volume fractions profiles, aspect ratios, and length to thickness ratios. Results are verified with available results in the literature. It can be concluded that the proposed theory is accurate and simple in solving the static bending behavior of functionally graded plates.
Whistle from Afar: A Case of Endotracheal Metastasis in Papillary Thyroid Cancer
Authors: Chattopadhyay Bitoti , Bhattacharya Biswamit , Chatterjee Atri , Biswas Pijush Kanti , Debnath Nirod Baran
Published: October 2012

Endotracheal metastasis is a rare situation, usually associated with malignancies of breast and gastrointestinal tract, specially colon. Papillary carcinoma of thyroid commonly disseminates through lymphatic channels and tracheal involvement through vascular route is rarely reported. Here, we report a case of tracheal metastasis from papillary carcinoma of thyroid. The patient responded to external beam radiation therapy with cobalt 60 beams in a dose of 44 Gy followed by a 16 Gy boost. The patient is under followup and is presently asymptomatic. This paper adds to the repertoire of evidence in treatment of endotracheal metastasis.
Metallisation and Interconnection of e-Beam Evaporated Polycrystalline Silicon Thin-Film Solar Cells on Glass
Authors: Kim Taekyun , Gress Peter J. , Varlamov Sergey
Published: October 2012

One inherent advantage of thin-film technology is the possibility of using monolithic integration for series interconnection of individual cells within large-area modules. Polycrystalline silicon thin-film solar cells do not rely on transparent conducting oxide layers as the high sheet conductivity of the emitter and BSF layers enables the lateral flow of current from the film to the metal contacts. This paper presents a new method for the fabrication of e-beam evaporated polycrystalline thin-film photovoltaic minimodules on glass. The method involves electrically isolating minicells, by laser scribing, and then forming an isolation layer on each laser scribe. The main advantage of this metallisation is to have a single aluminium evaporation step for the formation of finger and busbar features, as well as for series interconnection.
Proximal Dissection and Rupture of a Popliteal Cyst: A Case Report
Authors: Abdelrahman M. H. , Tubeishat S. , Hammoudeh M.
Published: October 2012

Popliteal cysts are swellings in the popliteal fossa due to enlargement of the gastrocnemius semimembranous bursa. These cysts might burst, and they usually rupture posteriorly and inferiorly with severe pain in the calf. We describe a patient with popliteal cyst that dissected proximally and ruptured in the soft tissue of the thigh.
Determination of Polycyclic Aromatic Hydrocarbons in Water Using Nanoporous Material Prepared from Waste Avian Egg Shell
Authors: Nuhu Abdulmumin A. , Basheer Chanbasha , Shaikh Amjad Ashfaque , Al-Arfaj Abdul Rahman
Published: October 2012

For the first time a biocompatible calcium carbonate vateritic polymorph was recrystallized from eggshell waste and its application for the extraction of polycyclic aromatic hydrocarbons in water samples was demonstrated. This nanoporous calcium carbonate was used as sorbent in dispersive micro‐solid‐phase extraction method. In this approach 50 mg of the calcium carbonate material having about 25 nm pores was placed in a 5 mL of water sample and ultrasonicated for 30 min. The cloudy sample was centrifuged at 13500 rpm for 2 min. The aqueous layer was then discarded and the CaCO3 material was dabbed dry with a lint‐free tissue. The analytes were then desorbed with 100 μL of dichloromethane by ultrasonication for 5 min. Finally, the extract was analyzed by gas chromatography flame ionization detector. Experimental parameters affecting the extraction recoveries were optimized. Using optimum extraction conditions, calibration curves were linear with correlation coefficients of 0.9853 to 0.9973 over the concentration range of 0.05 to 30 ng/mL. This method showed a detection limit as low as 0.004 ng/mL (at signal‐to‐noise ratio of 3). Performance of the dispersive micro‐solid‐phase extraction was compared with a previously optimized solid‐phase extraction technique. The developed method displayed good extraction recoveries (85 ± 8–110 ± 4%) with high enhancement factors (388–1433‐fold) and good repeatability (% RSD < 13) and involved the use of minimal solvents. Analysis of seawater from Dammam Port revealed the presence of the analytes at concentrations between 0.15 ± 0.01 and 13.43 ± 1.54 ng/mL.
Ischemic Colitis in an Endurance Runner
Authors: Grames Chase , Berry-Cabán Cristóbal S.
Published: October 2012

A 20-year-old female running the Marine Corps Marathon developed diarrhea at mile 12. After finishing the race she noted that she was covered in bloody stool. A local emergency department suspected ischemic colitis. After discharge, her primary care physician instructed her to discontinue the use of all nonsteroidal anti-inflammatory drugs. Her symptoms resolved and she returned to running without any complications. This paper describes the pathophysiology, diagnostic approach, and management options.
Target Q-Coverage Problem with Bounded Service Delay in Directional Sensor Networks
Authors: Li Deying , Liu Hui , Lu Xianling , Chen Wenping , Du Hongwei
Published: October 2012

Maximizing network lifetime is an important objective for the target-coverage problem. With practicable manufacture and cost reduction, directional sensor has been widely used in wireless sensor networks to save energy. In this paper, we address the target Q-coverage (TQC) problem to prolong the network lifetime with bounded service delay constraint in directional sensor networks. We propose a protocol to find a collection of coverage sets that satisfy the coverage quality requirement and the bounded service delay constraint, where the target in each coverage set may not be served continuously but can be served with tolerant service delay. By steering some sensors' directional antennas, our protocol could deal with the changes of network topology or monitoring tasks. Simulation results show that the performance of our protocol is close to the upper bound of the optimal solution.