bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diet and distribution of Pentacoelum kazukolinda (Kawakatsu & Mitchell, 1984), a maricolan planarian with a freshwater ecology
Authors: Sluys Ronald , Vila‐Farré Miquel , Álvarez‐Presas Marta , Riutort Marta , Kawakatsu Masaharu , Tulp Arnold S. 
Published: October 2014

Among the marine triclads or Maricola, the genus Pentacoelum represents one of the few exceptions in that species occur in brackish water or in freshwater. We examined specimens of a maricolan triclad that externally looked remarkably similar to the continental Spanish representatives of freshwater Pentacoelum hispaniense, albeit that these new samples came from habitats in Germany, the Netherlands, Mallorca and Japan. Comprehensive comparative morphological studies revealed that the animals from these populations are identical to a species described earlier from Hawaii, viz. Oahuhawaiiana kazukolinda Kawakatsu & Mitchell, 1984. It is argued that the species now should be called Pentacoelum kazukolinda (Kawakatsu & Mitchell, 1984) comb. nov. Remarkably, Dutch and German specimens of P. kazukolinda almost completely lack any signs of the presence of the lateral gonopore system, being the defining feature of their taxonomic family, the Bdellouridae. The reason for this reduction or even complete absence of this structure remains obscure. Nonetheless, morphological similarities and 18S rDNA sequences strongly suggest that all animals belong to the same species. Analyses of the mitochondrial gene sequences Cox1 and 16SrDNA of the gut content of P. kazukolinda revealed that the flatworm has a preference for different species of gastropods, while in one population annelids were detected. Our study suggests that gastropods may form the food refuge of P. kazukolinda. Circumstantial evidence suggests that the worldwide distribution of P. kazukolinda may result from human‐mediated transport of the aroid Colocasia esculenta and/or the introduced snail Potamopyrgus antipodarum. The use of P. antipodarum as a food resource may have facilitated the spread and establishment of new populations of P. kazukolinda.
The image quality of ion computed tomography at clinical imaging dose levels
Authors: Hansen David C. , Bassler Niels , Sørensen Thomas Sangild , Seco Joao 
Published: October 2014

Purpose:Accurately predicting the range of radiotherapy ions in vivo is important for the precise delivery of dose in particle therapy. Range uncertainty is currently the single largest contribution to the dose margins used in planning and leads to a higher dose to normal tissue. The use of ion CT has been proposed as a method to improve the range uncertainty and thereby reduce dose to normal tissue of the patient. A wide variety of ions have been proposed and studied for this purpose, but no studies evaluate the image quality obtained with different ions in a consistent manner. However, imaging doses ion CT is a concern which may limit the obtainable image quality. In addition, the imaging doses reported have not been directly comparable with x‐ray CT doses due to the different biological impacts of ion radiation. The purpose of this work is to develop a robust methodology for comparing the image quality of ion CT with respect to particle therapy, taking into account different reconstruction methods and ion species.Methods:A comparison of different ions and energies was made. Ion CT projections were simulated for five different scenarios: Protons at 230 and 330 MeV, helium ions at 230 MeV/u, and carbon ions at 430 MeV/u. Maps of the water equivalent stopping power were reconstructed using a weighted least squares method. The dose was evaluated via a quality factor weighted CT dose index called the CT dose equivalent index (CTDEI). Spatial resolution was measured by the modulation transfer function. This was done by a noise‐robust fit to the edge spread function. Second, the image quality as a function of the number of scanning angles was evaluated for protons at 230 MeV. In the resolution study, the CTDEI was fixed to 10 mSv, similar to a typical x‐ray CT scan. Finally, scans at a range of CTDEI's were done, to evaluate dose influence on reconstruction error.Results:All ions yielded accurate stopping power estimates, none of which were statistically different from the ground truth image. Resolution (as defined by the modulation transfer function = 10% point) was the best for the helium ions (18.21 line pairs/cm) and worst for the lower energy protons (9.37 line pairs/cm). The weighted quality factor for the different ions ranged from 1.23 for helium to 2.35 for carbon ions. For the angle study, a sharp increase in absolute error was observed below 45 distinct angles, giving the impression of a threshold, rather than smooth, limit to the number of angles.Conclusions:The method presented for comparing various ion CT modalities is feasible for practical use. While all studied ions would improve upon x‐ray CT for particle range estimation, helium appears to give the best results and deserves further study for imaging.
Identification of Inhibitors of a Bacterial Sigma Factor Using a New High-Throughput Screening Assay
Authors: El-Mowafi S. A. , Sineva E. , Alumasa J. N. , Nicoloff H. , Tomsho J. W. , Ades S. E. , Keiler K. C. 
Published: October 2014

ABSTRACT

Gram-negative bacteria are formidable pathogens because their cell envelope presents an adaptable barrier to environmental and host-mediated challenges. The stress response pathway controlled by the alternative sigma factor σ
E
is critical for maintenance of the cell envelope. Because σ
E
is required for the virulence or viability of several Gram-negative pathogens, it might be a useful target for antibiotic development. To determine if small molecules can inhibit the σ
E
pathway, and to permit high-throughput screening for antibiotic lead compounds, a σ
E
activity assay that is compatible with high-throughput screening was developed and validated. The screen employs a biological assay with positive readout. An
Escherichia coli
strain was engineered to express yellow fluorescent protein (YFP) under negative regulation by the σ
E
pathway, such that inhibitors of the pathway increase the production of YFP. To validate the screen, the reporter strain was used to identify σ
E
pathway inhibitors from a library of cyclic peptides. Biochemical characterization of one of the inhibitory cyclic peptides showed that it binds σ
E
, inhibits RNA polymerase holoenzyme formation, and inhibits σ
E
-dependent transcription
in vitro
. These results demonstrate that alternative sigma factors can be inhibited by small molecules and enable high-throughput screening for inhibitors of the σ
E
pathway.
Complete Genome Sequence of Cell Culture-Attenuated Guinea Pig Cytomegalovirus Cloned as an Infectious Bacterial Artificial Chromosome
Authors: Yang Dongmei , Alam Zohaib , Cui Xiaohong , Chen Michael , Sherrod Carly J. , McVoy Michael A. , Schleiss Mark R. , Dittmer Dirk P. 
Published: October 2014

ABSTRACT
The complete genome sequence of attenuated guinea pig cytomegalovirus cloned as bacterial artificial chromosome N13R10 was determined. Comparison to pathogenic salivary gland-derived virus revealed 13 differences, 1 of which disrupted overlapping open reading frames encoding GP129 and GP130. Attenuation of N13R10 may arise from an inability to express GP129 and/or GP130.
Complete Genome Sequences of Fish Pathogenic Weissella ceti Strains WS74 and WS105
Authors: Figueiredo H. C. P. , Leal C. A. G. , Dorella F. A. , Carvalho A. F. , Soares S. C. , Pereira F. L. , Azevedo V. A. C. 
Published: October 2014

ABSTRACT

We describe here the genome sequencing and annotation of
Weissella ceti
strains WS74 and WS105, isolated from diseased rainbow trout in Brazil. The two genomes were sequenced with an Ion Torrent personal genome machine (PGM) using a fragment library. The genomes of strains WS74 and WS105 consist of circular chromosomes 1,389,513 bp and 1,390,396 bp long, respectively, both presenting a G+C content of 40.75%.
Complete Genome Sequence of a Dimethyl Sulfide-Utilizing Bacterium, Acinetobacter guillouiae Strain 20B (NBRC 110550)
Authors: Yee LiiMien , Hosoyama Akira , Ohji Shoko , Tsuchikane Keiko , Shimodaira Jun , Yamazoe Atsushi , Fujita Nobuyuki , Suzuki-Minakuchi Chiho , Nojiri Hideaki 
Published: October 2014

ABSTRACT

Acinetobacter guillouiae
strain 20B can utilize dimethyl sulfide (DMS) as the sole sulfur source and degrade chloroethylenes. We report here the complete 4,648,418-bp genome sequence for this strain, which contains 4,367 predicted coding sequences (CDSs), including a well-characterized DMS degradative operon.
Draft Genome Sequence of the Ionic Liquid-Tolerant Bacterium Bacillus amyloliquefaciens CMW1
Authors: Kurata Atsushi , Hirose Yuu , Misawa Naomi , Hurunaka Kohei , Kishimoto Noriaki 
Published: October 2014

ABSTRACT

Here, we report the draft genome sequence of an ionic liquid-tolerant bacterium,
Bacillus amyloliquefaciens
CMW1, which is newly isolated from a Japanese fermented soybean paste. The genome sequence will allow for a characterization of the molecular mechanism of its ionic liquid tolerance.
RelA Inhibits Bacillus subtilis Motility and Chaining
Authors: Ababneh Qutaiba O. , Herman Jennifer K. 
Published: October 2014

ABSTRACT

The nucleotide second messengers pppGpp and ppGpp [(p)ppGpp] are responsible for the global downregulation of transcription, translation, DNA replication, and growth rate that occurs during the stringent response. More recent studies suggest that (p)ppGpp is also an important effector in many nonstringent processes, including virulence, persister cell formation, and biofilm production. In
Bacillus subtilis
, (p)ppGpp production is primarily determined by the net activity of RelA, a bifunctional (p)ppGpp synthetase/hydrolase, and two monofunctional (p)ppGpp synthetases, YwaC and YjbM. We observe that in
B. subtilis
, a
relA
mutant grows exclusively as unchained, motile cells, phenotypes regulated by the alternative sigma factor SigD. Our data indicate that the
relA
mutant is trapped in a SigD “on” state during exponential growth, implicating RelA and (p)ppGpp levels in the regulation of cell chaining and motility in
B. subtilis
. Our results also suggest that minor variations in basal (p)ppGpp levels can significantly skew developmental decision-making outcomes.
Structure-Based Functional Characterization of Repressor of Toxin (Rot), a Central Regulator of Staphylococcus aureus Virulence
Authors: Killikelly April , Benson Meredith A. , Ohneck Elizabeth A. , Sampson Jared M. , Jakoncic Jean , Spurrier Brett , Torres Victor J. , Kong Xiang-Peng 
Published: October 2014

ABSTRACT

Staphylococcus aureus
is responsible for a large number of diverse infections worldwide. In order to support its pathogenic lifestyle,
S. aureus
has to regulate the expression of virulence factors in a coordinated fashion. One of the central regulators of the
S. aureus
virulence regulatory networks is the transcription factor repressor of toxin (Rot). Rot plays a key role in regulating
S. aureus
virulence through activation or repression of promoters that control expression of a large number of critical virulence factors. However, the mechanism by which Rot mediates gene regulation has remained elusive. Here, we have determined the crystal structure of Rot and used this information to probe the contribution made by specific residues to Rot function. Rot was found to form a dimer, with each monomer harboring a winged helix-turn-helix (WHTH) DNA-binding motif. Despite an overall acidic pI, the asymmetric electrostatic charge profile suggests that Rot can orient the WHTH domain to bind DNA. Structure-based site-directed mutagenesis studies demonstrated that R
91
, at the tip of the wing, plays an important role in DNA binding, likely through interaction with the minor groove. We also found that Y
66
, predicted to bind within the major groove, contributes to Rot interaction with target promoters. Evaluation of Rot binding to different activated and repressed promoters revealed that certain mutations on Rot exhibit promoter-specific effects, suggesting for the first time that Rot differentially interacts with target promoters. This work provides insight into a precise mechanism by which Rot controls virulence factor regulation in
S. aureus
.
Value Driven Outcomes (VDO): a pragmatic, modular, and extensible software framework for understanding and improving health care costs and outcomes
Authors: Kawamoto Kensaku , Martin Cary J , Williams Kip , Tu Ming-Chieh , Park Charlton G , Hunter Cheri , Staes Catherine J , Bray Bruce E , Deshmukh Vikrant G , Holbrook Reid A , Morris Scott J , Fedderson Matthew B , Sletta Amy , Turnbull James , Mulvihill Sean J , Crabtree Gordon L , Entwistle David E , McKenna Quinn L , Strong Michael B , Pendleton Robert C , Lee Vivian S 
Published: October 2014

Abstract
Objective To develop expeditiously a pragmatic, modular, and extensible software framework for understanding and improving healthcare value (costs relative to outcomes).
Materials and methods In 2012, a multidisciplinary team was assembled by the leadership of the University of Utah Health Sciences Center and charged with rapidly developing a pragmatic and actionable analytics framework for understanding and enhancing healthcare value. Based on an analysis of relevant prior work, a value analytics framework known as Value Driven Outcomes (VDO) was developed using an agile methodology. Evaluation consisted of measurement against project objectives, including implementation timeliness, system performance, completeness, accuracy, extensibility, adoption, satisfaction, and the ability to support value improvement.
Results A modular, extensible framework was developed to allocate clinical care costs to individual patient encounters. For example, labor costs in a hospital unit are allocated to patients based on the hours they spent in the unit; actual medication acquisition costs are allocated to patients based on utilization; and radiology costs are allocated based on the minutes required for study performance. Relevant process and outcome measures are also available. A visualization layer facilitates the identification of value improvement opportunities, such as high-volume, high-cost case types with high variability in costs across providers. Initial implementation was completed within 6 months, and all project objectives were fulfilled. The framework has been improved iteratively and is now a foundational tool for delivering high-value care.
Conclusions The framework described can be expeditiously implemented to provide a pragmatic, modular, and extensible approach to understanding and improving healthcare value.
Harnessing ISA diversity
Authors: Venkat Ashish , Tullsen Dean M. 
Published: October 2014

Heterogeneous multicore architectures have the potential for high performance and energy efficiency. These architectures may be composed of small power-efficient cores, large high-performance cores, and/or specialized cores that accelerate the performance of a particular class of computation. Architects have explored multiple dimensions of heterogeneity, both in terms of micro-architecture and specialization. While early work constrained the cores to share a single ISA, this work shows that allowing heterogeneous ISAs further extends the effectiveness of such architectures
This work exploits the diversity offered by three modern ISAs: Thumb, x86-64, and Alpha. This architecture has the potential to outperform the best single-ISA heterogeneous architecture by as much as 21%, with 23% energy savings and a reduction of 32% in Energy Delay Product.
The dirty-block index
Authors: Seshadri Vivek , Bhowmick Abhishek , Mutlu Onur , Gibbons Phillip B. , Kozuch Michael A. , Mowry Todd C. 
Published: October 2014

On-chip caches maintain multiple pieces of metadata about each cached block---e.g., dirty bit, coherence information, ECC. Traditionally, such metadata for each block is stored in the corresponding tag entry in the tag store. While this approach is simple to implement and scalable, it necessitates a full tag store lookup for any metadata query---resulting in high latency and energy consumption. We find that this approach is inefficient and inhibits several cache optimizations.
In this work, we propose a new way of organizing the dirty bit information that enables simpler and more efficient implementations of several optimizations. In our proposed approach, we remove the dirty bits from the tag store and organize it differently in a separate structure, which we call the Dirty-Block Index (DBI). The organization of DBI is simple: it consists of multiple entries, each corresponding to some row in DRAM. A bit vector in each entry tracks whether or not each block in the corresponding DRAM row is dirty
We demonstrate the benfits of DBI by using it to simultaneously and efficiently implement three optimizations proposed by prior work: 1) Aggressive DRAM-aware writeback, 2) Bypassing cache lookups, and 3) Heterogeneous ECC for clean/dirty blocks. DBI, with all three optimizations enabled, improves performance by 31% compared to the baseline (by 6% compared to the best previous mechanism) while reducing overall cache area cost by 8% compared to prior approaches.
Going vertical in memory management
Authors: Liu Lei , Li Yong , Cui Zehan , Bao Yungang , Chen Mingyu , Wu Chengyong 
Published: October 2014

Many emerging applications from various domains often exhibit heterogeneous memory characteristics. When running in combination on parallel platforms, these applications present a daunting variety of workload behaviors that challenge the effectiveness of any memory allocation strategy. Prior partitioning-based or random memory allocation schemes typically manage only one level of the memory hierarchy and often target specific workloads.
To handle diverse and dynamically changing memory and cache allocation needs, we augment existing "horizontal" cache/DRAM bank partitioning with vertical partitioning and explore the resulting multi-policy space. We study the performance of these policies for over 2000 workloads and correlate the results with application characteristics via a data mining approach. Based on this correlation we derive several practical memory allocation rules that we integrate into a unified multi-policy framework to guide resources partitioning and coalescing for dynamic and diverse multiprogrammed/ threaded workloads. We implement our approach in Linux kernel 2.6.32 as a restructured page indexing system plus a series of kernel modules. Extensive experiments show that, in practice, our framework can select proper memory allocation policy and consistently outperforms the unmodified Linux kernel, achieving up to 11% performance gains compared to prior techniques
Fine-grain task aggregation and coordination on GPUs
Authors: Orr Marc S. , Beckmann Bradford M. , Reinhardt Steven K. , Wood David A. 
Published: October 2014

In general-purpose graphics processing unit (GPGPU) computing, data is processed by concurrent threads execut-ing the same function. This model, dubbed single-instruction/multiple-thread (SIMT), requires programmers to coordinate the synchronous execution of similar opera-tions across thousands of data elements. To alleviate this programmer burden, Gaster and Howes outlined the chan-nel abstraction, which facilitates dynamically aggregating asynchronously produced fine-grain work into coarser-grain tasks. However, no practical implementation has been proposed
To this end, we propose and evaluate the first channel im-plementation. To demonstrate the utility of channels, we present a case study that maps the fine-grain, recursive task spawning in the Cilk programming language to channels by representing it as a flow graph. To support data-parallel recursion in bounded memory, we propose a hardware mechanism that allows wavefronts to yield their execution resources. Through channels and wavefront yield, we im-plement four Cilk benchmarks. We show that Cilk can scale with the GPU architecture, achieving speedups of as much as 4.3x on eight compute units
Enabling preemptive multiprogramming on GPUs
Authors: Tanasic Ivan , Gelado Isaac , Cabezas Javier , Ramirez Alex , Navarro Nacho , Valero Mateo 
Published: October 2014

GPUs are being increasingly adopted as compute accelerators in many domains, spanning environments from mobile systems to cloud computing. These systems are usually running multiple applications, from one or several users. However GPUs do not provide the support for resource sharing traditionally expected in these scenarios. Thus, such systems are unable to provide key multiprogrammed workload requirements, such as responsiveness, fairness or quality of service.
In this paper, we propose a set of hardware extensions that allow GPUs to efficiently support multiprogrammed GPU workloads. We argue for preemptive multitasking and design two preemption mechanisms that can be used to implement GPU scheduling policies. We extend the architecture to allow concurrent execution of GPU kernels from different user processes and implement a scheduling policy that dynamically distributes the GPU cores among concurrently running kernels, according to their priorities. We extend the NVIDIA GK110 (Kepler) like GPU architecture with our proposals and evaluate them on a set of multiprogrammed workloads with up to eight concurrent processes. Our proposals improve execution time of high-priority processes by 15.6x, the average application turnaround time between 1.5x to 2x, and system fairness up to 3.4x
Replay debugging
Authors: Honarmand Nima , Torrellas Josep 
Published: October 2014

Hardware-assisted Record and Deterministic Replay (RnR) of programs has been proposed as a primitive for debugging hard-to-repeat software bugs. However, simply providing support for repeatedly stumbling on the same bug does not help diagnose it. For bug diagnosis, developers typically want to modify the code, e.g., by creating and operating on new variables, or printing state. Unfortunately, this renders the RnR log inconsistent and makes Replay Debugging (i.e., debugging while using an RnR log for replay) dicey at best
This paper presents rdb, the first scheme for replay debugging that guarantees exact replay. rdb relies on two mechanisms. The first one is compiler support to split the instrumented application into two executables: one that is identical to the original program binary, and another that encapsulates all the added debug code. The second mechanism is a runtime infrastructure that replays the application and, without affecting it in any way, invokes the appropriate debug code at the appropriate locations. We describe an implementation of rdb based on LLVM and Pin, and show an example of how rdb's replay debugging helps diagnose a real bug