bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymmetry between ON and OFF α ganglion cells of mouse retina: integration of signal and noise from synaptic inputs
Authors: Freed Michael A. 
Published: September 2017

Key points
Bipolar and amacrine cells presynaptic to the ON sustained α cell of mouse retina provide currents with a higher signal‐to‐noise power ratio (SNR) than those presynaptic to the OFF sustained α cell.
Yet the ON cell loses proportionately more SNR from synaptic inputs to spike output than the OFF cell does.
The higher SNR of ON bipolar cells at the beginning of the ON pathway compensates for losses incurred by the ON ganglion cell, and improves the processing of positive contrasts.
AbstractON and OFF pathways in the retina include functional pairs of neurons that, at first glance, appear to have symmetrically similar responses to brightening and darkening, respectively. Upon careful examination, however, functional pairs exhibit asymmetries in receptive field size and response kinetics. Until now, descriptions of how light‐adapted retinal circuitry maintains a preponderance of signal over the noise have not distinguished between ON and OFF pathways. Here I present evidence of marked asymmetries between members of a functional pair of sustained α ganglion cells in the mouse retina. The ON cell exhibited a proportionately greater loss of signal‐to‐noise power ratio (SNR) from its presynaptic arrays to its postsynaptic currents. Thus the ON cell combines signal and noise from its presynaptic arrays of bipolar and amacrine cells less efficiently than the OFF cell does. Yet the inefficiency of the ON cell is compensated by its presynaptic arrays providing a higher SNR than the arrays presynaptic to the OFF cell, apparently to improve visual processing of positive contrasts. Dynamic clamp experiments were performed that introduced synaptic conductances into ON and OFF cells. When the amacrine‐modulated conductance was removed, the ON cell's spike train exhibited an increase in SNR. The OFF cell, however, showed the opposite effect of removing amacrine input, which was a decrease in SNR. Thus ON and OFF cells have different modes of synaptic integration with direct effects on the SNR of the spike output.
Complete Nucleotide Sequence of Klebsiella pneumoniae Bacteriophage vB_KpnM_KpV477
Authors: Komisarova Ekaterina V. , Kislichkina Angelina A. , Krasilnikova Valentina M. , Bogun Alexander G. , Fursova Nadezhda K. , Volozhantsev Nikolay V. 
Published: September 2017

ABSTRACT

The double-stranded DNA (dsDNA) bacteriophage vB_KpnM_KpV477, with a broad spectrum of lytic activity against
Klebsiella pneumoniae
, including strains of capsular serotypes K1, K2, and K57, was isolated from a clinical sample. The phage genome comprises 168,272 bp, with a G+C content of 39.3%, and it contains 275 putative coding sequences (CDSs) and 17 tRNAs.
First Whole-Genome Shotgun Sequence of a Promising Cellulase Secretor,
Trichoderma koningiopsis
Strain POS7
Authors: Castrillo María Lorena , Bich Gustavo Ángel , Modenutti Carlos , Turjanski Adrián , Zapata Pedro Darío , Villalba Laura Lidia 
Published: September 2017

ABSTRACT

Trichoderma koningiopsis
strain POS7 produces significantly large amounts of cellulase enzymes in solid-state fermentation. The Illumina-based sequence analysis reveals an approximate genome size of 36.6 Mbp, with a G+C content of 48.82% for
T. koningiopsis
POS7. Based on
ab initio
prediction, 12,661 coding genes were annotated.
Draft Genome Sequence of the Plant Pathogen
Streptomyces
sp. Strain 11-1-2
Authors: Bown Luke , Bignell Dawn R. D. 
Published: September 2017

ABSTRACT

Streptomyces
sp. strain 11-1-2 is a Gram-positive filamentous bacterium that was isolated from a common scab lesion on a potato tuber. The strain is highly pathogenic to plants but does not produce the virulence-associated
Streptomyces
phytotoxin thaxtomin A. Here, we report the draft genome sequence of
Streptomyces
sp. 11-1-2.
Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine
Authors: Jo Yeonhwa , Song Myung-Kyu , Choi Hoseong , Park Jae-Seong , Lee Jae-Wung , Lian Sen , Lee Bong Choon , Cho Won Kyong 
Published: September 2017

ABSTRACT

Here, we report the genome sequence of grapevine virus K (GVK), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVK is 7,476 nucleotides in length and encodes 5 open reading frames. GVK is a putative member of the genus
Vitivirus
in the family
Betaflexiviridae
.
Complete Genome Sequence of Acute Hepatopancreatic Necrosis Disease-Causing Vibrio campbellii LA16-V1, Isolated from Penaeus vannamei Cultured in a Latin American Country
Authors: Ahn Ye Som , Piamsomboon Patharapol , Tang Kathy F. J. , Han Jee Eun , Kim Ji Hyung 
Published: September 2017

ABSTRACT

We report here the complete genome sequence of
Vibrio campbellii
, isolated from
Penaeus vannamei
cultured in a Latin American country. The Tn
3
-like transposon and
pirAB
genes were encoded on the plasmid pLA16-2. These data support the geographical variations in the virulence plasmid found among acute hepatopancreatic necrosis disease (AHPND)-causing
Vibrio
isolates from Latin America and Asia.
Carbohydrate-last meal pattern lowers postprandial glucose and insulin excursions in type 2 diabetes
Authors: Shukla Alpana P , Andono Jeselin , Touhamy Samir H , Casper Anthony , Iliescu Radu G , Mauer Elizabeth , Shan Zhu Yuan , Ludwig David S , Aronne Louis J 
Published: September 2017

BackgroundThere are limited data regarding the timing of carbohydrate ingestion during a meal and postprandial glucose regulation.MethodsSixteen subjects with type 2 diabetes mellitus (T2DM) consumed the same meal on 3 days in random order: carbohydrate first, followed 10 min later by protein and vegetables; protein and vegetables first, followed 10 min later by carbohydrate; or all components together. Blood was sampled for glucose, insulin, glucagon-like peptide-1 (GLP-1), and glucagon measurements at baseline (just before meal ingestion) and subsequently at 30 min intervals up to 180 min.ResultsThe incremental areas under the curve for glucose (iAUC0–180) and incremental glucose peaks were 53% and 54% lower, respectively, when carbohydrate was consumed last compared with carbohydrate consumed first (3124.7±501.2 vs 6703.5±904.6 mg/dL×180min, p<0.001; 34.7±4.1 vs 75.0±6.5 mg/dL, p<0.001) and 44% and 40% lower, respectively, compared with the all components together condition (3124.7±501.2 vs 5587.1±828.7 mg/dL×180min, p=0.003; 34.7±4.1 vs 58.2±5.9 mg/dL, p<0.001). Postprandial insulin excursions were lower (iAUC0–180: 7354.1±897.3 vs 9769.7±1002.1 µU/mL×min, p=0.003) and GLP-1 excursions higher (iAUC0–180: 3487.56±327.7 vs 2519.11±494.8 pg/mL×min, p=0.019) following the carbohydrate-last meal order compared with carbohydrate first.ConclusionThe carbohydrate-last meal pattern may be an effective behavioral strategy to improve postprandial glycemia.
Patients with symptoms of delayed gastric emptying have a high prevalence of oesophageal dysmotility, irrespective of scintigraphic evidence of gastroparesis
Authors: Triadafilopoulos George , Nguyen Linda , Clarke John O 
Published: September 2017

BackgroundPatients with symptoms suggestive of gastroparesis exhibit several symptoms, such as epigastric pain, postprandial fullness, bloating and regurgitation. It is uncertain if such symptoms reflect underlying oesophageal motor disorder.AimsTo examine whether patients with epigastric pain and postprandial distress syndrome suggestive of functional dyspepsia and/or gastroparesis also have concomitant oesophageal motility abnormalities and, if so, whether there are any associations between these disturbances.MethodsIn this retrospective cohort study, consecutive patients with functional gastrointestinal symptoms suggestive of gastric neuromuscular dysfunction (gastroparesis or functional dyspepsia) underwent clinical assessment, gastric scintigraphy, oesophageal high-resolution manometry and ambulatory pH monitoring using standard protocols.ResultsWe studied 61 patients with various functional upper gastrointestinal symptoms who underwent gastric scintigraphy, oesophageal high-resolution manometry and ambulatory pH monitoring. Forty-four patients exhibited gastroparesis by gastric scintigraphy. Oesophageal motility disorders were found in 68% and 42% of patients with or without scintigraphic evidence of gastroparesis respectively, suggesting of overlapping gastric and oesophageal neuromuscular disorder. Forty-three per cent of patients with gastroparesis had abnormal oesophageal acid exposure with mean % pH <4.0 of 7.5 in contrast to 38% of those symptomatic controls with normal gastric emptying, with mean %pH <4.0 of 5.4 (NS). Symptoms of epigastric pain, heartburn/regurgitation, bloating, nausea, vomiting, dysphagia, belching and weight loss could not distinguish patients with or without gastroparesis, although weight loss was significantly more prevalent and severe (p<0.002) in patients with gastroparesis. There was no relationship between oesophageal symptoms and motor or pH abnormalities in either groups.ConclusionsIrrespective of gastric emptying delay by scintigraphy, patients with symptoms suggestive of gastric neuromuscular dysfunction have a high prevalence of oesophageal motor disorder and pathological oesophageal acid exposure that may contribute to their symptoms and may require therapy. High-resolution oesophageal manometry and pH monitoring are non-invasive and potentially useful in the assessment and management of these patients.
Assessing oral medication adherence among patients with type 2 diabetes mellitus treated with polytherapy in a developed Asian community: a cross-sectional study
Authors: Lee Cia Sin , Tan Jane Hwee Mian , Sankari Usha , Koh Yi Ling Eileen , Tan Ngiap Chuan 
Published: September 2017

ObjectivesThe disease burden of type 2 diabetes mellitus (T2DM) is rising due to suboptimal glycaemic control leading to vascular complications. Medication adherence (MA) directly influences glycaemic control and clinical consequences. This study aimed to assess the MA of patients with T2DM and identify associated factors.DesignAnalysis of data from a cross-sectional survey and electronic medical records.SettingPrimary care outpatient clinic in Singapore.ParticipantsAdult patients with T2DM.Main outcome measuresMA to each prescribed oral hypoglycaemic agent (OHA) was measured using the five-question Medication Adherence Report Scale (MARS-5). Low MA is defined as a MARS-R score of <25. Demographic data, clinical characteristics and investigation results were collected to identify factors that are associated with low MA.ResultsThe study population comprised 382 patients with a slight female predominance (53.4%) and a mean±SD age of 62.0±10.4 years. 57.1% of the patients had low MA to at least one OHA. Univariate analysis showed that patients who were younger, of Chinese ethnicity, married or widowed, self-administering their medications or taking fewer (four or less) daily medications tended to have low MA to OHA. Logistic regression revealed that younger age (OR 0.97; 95% CI 0.95 to0.99), Chinese ethnicity (OR 2.80; 95% CI 1.53 to5.15) and poorer glycaemic control (HbA1c level) (OR 1.27; 95% CI 1.06 to1.51) were associated with low MA to OHA.ConclusionsYounger patients with T2DM and of Chinese ethnicity were susceptible to low MA to OHA, which was associated with poorer glycaemic control. Polytherapy was not associated with low MA.
Early-onset drug-induced parkinsonism after exposure to offenders implies nigrostriatal dopaminergic dysfunction
Authors: Chung Seok Jong , Yoo Han Soo , Moon Hyojeong , Oh Jungsu S , Kim Jae Seung , Park Yong Hee , Hong Jin Yong , Ye Byoung Seok , Sohn Young H , Lee Phil Hyu 
Published: September 2017

ObjectivesThe onset of parkinsonism in patients with drug-induced parkinsonism (DIP) exhibits extensive individual variability following exposure to offending drugs. We investigated whether the individual variations in the onset time of parkinsonism reflected the underlying subtle dopaminergic dysfunction in DIP.MethodsWe enrolled 71 patients with DIP who had visually normal striatal dopamine transporter (DAT) availability in 18F-FP-CIT positron emission tomography scans. According to their exposure durations to the offending drugs prior to onset of the parkinsonism, the patients were divided into the early-onset group (duration ≤6 months; n=35) and delayed-onset group (duration >6 months; n=36). We performed the quantitative analysis of the DAT availability in each striatal subregion between the groups.ResultsNo patients with DIP had DAT availability that was more than 2 SD below the normal mean of DAT availability. Compared with the delayed-onset group, the early-onset DIP group had decreased DAT availability in the striatal subregions including the posterior putamen (p=0.018), anterior putamen (p=0.011), caudate (p=0.035) and ventral striatum (p=0.027). After adjusting for age, sex and cross-cultural smell identification test scores, a multivariate analysis revealed that the DAT availability in the striatal subregions of the patients with DIP was significantly and positively associated with the natural logarithm of the duration of drug exposure.ConclusionsThese results suggest that a short exposure to the offending drugs before the development of parkinsonism would be associated with subtle nigrostriatal dopaminergic dysfunction in patients with DIP.
Bringing the web up to speed with WebAssembly
Authors: Haas Andreas , Rossberg Andreas , Schuff Derek L. , Titzer Ben L. , Holman Michael , Gohman Dan , Wagner Luke , Zakai Alon , Bastien JF 
Published: September 2017

The maturation of the Web platform has given rise to sophisticated and demanding Web applications such as interactive 3D visualization, audio and video software, and games. With that, efficiency and security of code on the Web has become more important than ever. Yet JavaScript as the only built-in language of the Web is not well-equipped to meet these requirements, especially as a compilation target.
Engineers from the four major browser vendors have risen to the challenge and collaboratively designed a portable low-level bytecode called WebAssembly. It offers compact representation, efficient validation and compilation, and safe low to no-overhead execution. Rather than committing to a specific programming model, WebAssembly is an abstraction over modern hardware, making it language-, hardware-, and platform-independent, with use cases beyond just the Web. WebAssembly has been designed with a formal semantics from the start. We describe the motivation, design and formal semantics of WebAssembly and provide some preliminary experience with implementations.
Systematic black-box analysis of collaborative web applications
Authors: Billes Marina , Møller Anders , Pradel Michael 
Published: September 2017

Web applications, such as collaborative editors that allow multiple clients to concurrently interact on a shared resource, are difficult to implement correctly. Existing techniques for analyzing concurrent software do not scale to such complex systems or do not consider multiple interacting clients. This paper presents Simian, the first fully automated technique for systematically analyzing multi-client web applications.
Naively exploring all possible interactions between a set of clients of such applications is practically infeasible. Simian obtains scalability for real-world applications by using a two-phase black-box approach. The application code remains unknown to the analysis and is first explored systematically using a single client to infer potential conflicts between client events triggered in a specific context. The second phase synthesizes multi-client interactions targeted at triggering misbehavior that may result from the potential conflicts, and reports an inconsistency if the clients do not converge to a consistent state.
We evaluate the analysis on three widely used systems, Google Docs, Firepad, and ownCloud Documents, where it reports a variety of inconsistencies, such as incorrect formatting and misplaced text fragments. Moreover, we find that the two-phase approach runs 10x faster compared to exhaustive exploration, making systematic analysis practically applicable.
Just-In-Time GPU Compilation for Interpreted Languages with Partial Evaluation
Authors: Fumero Juan , Steuwer Michel , Stadler Lukas , Dubach Christophe 
Published: September 2017

Computer systems are increasingly featuring powerful parallel devices with the advent of many-core CPUs and GPUs. This offers the opportunity to solve computationally-intensive problems at a fraction of the time traditional CPUs need. However, exploiting heterogeneous hardware requires the use of low-level programming language approaches such as OpenCL, which is incredibly challenging, even for advanced programmers.
On the application side, interpreted dynamic languages are increasingly becoming popular in many domains due to their simplicity, expressiveness and flexibility. However, this creates a wide gap between the high-level abstractions offered to programmers and the low-level hardware-specific interface. Currently, programmers must rely on high performance libraries or they are forced to write parts of their application in a low-level language like OpenCL. Ideally, nonexpert programmers should be able to exploit heterogeneous hardware directly from their interpreted dynamic languages.
In this paper, we present a technique to transparently and automatically offload computations from interpreted dynamic languages to heterogeneous devices. Using just-in-time compilation, we automatically generate OpenCL code at runtime which is specialized to the actual observed data types using profiling information. We demonstrate our technique using R, which is a popular interpreted dynamic language predominately used in big data analytic. Our experimental results show the execution on a GPU yields speedups of over 150x compared to the sequential FastR implementation and the obtained performance is competitive with manually written GPU code. We also show that when taking into account start-up time, large speedups are achievable, even when the applications run for as little as a few seconds.
Decoupled Affine Computation for SIMT GPUs
Authors: Wang Kai , Lin Calvin 
Published: September 2017

This paper introduces a method of decoupling affine computations---a class of expressions that produces extremely regular values across SIMT threads---from the main execution stream, so that the affine computations can be performed with greater efficiency and with greater independence from the main execution stream. This decoupling has two benefits: (1) For compute-bound programs, it significantly reduces the dynamic warp instruction count; (2) for memory-bound workloads, it significantly reduces memory latency, since it acts as a non-speculative prefetcher for the data specified by the many memory address calculations that are affine computations.
We evaluate our solution, known as Decoupled Affine Computation (DAC), using GPGPU-sim and a set of 29 GPGPU programs. We find that on average, DAC improves performance by 40% and reduces energy consumption by 20%. For the 11 compute-bound benchmarks, DAC improves performance by 34%, compared with 11% for the previous state-of-the-art. For the 18 memory-bound programs, DAC improves performance by an average of 44%, compared with 16% for state-of-the-art GPU prefetcher.
MTraceCheck
Authors: Lee Doowon , Bertacco Valeria 
Published: September 2017

This work presents a minimally-intrusive, high-performance, post-silicon validation framework for validating memory consistency in multi-core systems. Our framework generates constrained-random tests that are instrumented with observability-enhancing code for memory consistency verification. For each test, we generate a set of compact signatures reflecting the memory-ordering patterns observed over many executions of the test, with each of the signatures corresponding to a unique memory-ordering pattern. We then leverage an efficient and novel analysis to quickly determine if the observed execution patterns represented by each unique signature abide by the memory consistency model. Our analysis derives its efficiency by exploiting the structural similarities among the patterns observed.
We evaluated our framework, MTraceCheck, on two platforms: an x86-based desktop and an ARM-based SoC platform, both running multi-threaded test programs in a bare-metal environment. We show that MTraceCheck reduces the perturbation introduced by the memory-ordering monitoring activity by 93% on average, compared to a baseline register flushing approach that saves the register's state after each load operation. We also reduce the computation requirements of our consistency checking analysis by 81% on average, compared to a conventional topological sorting solution. We finally demonstrate the effectiveness of MTraceCheck on buggy designs, by evaluating multiple case studies where it successfully exposes subtle bugs in a full-system simulation environment.
Hiding the Long Latency of Persist Barriers Using Speculative Execution
Authors: Shin Seunghee , Tuck James , Solihin Yan 
Published: September 2017

Byte-addressable non-volatile memory technology is emerging as an alternative for DRAM for main memory. This new Non-Volatile Main Memory (NVMM) allows programmers to store important data in data structures in memory instead of serializing it to the file system, thereby providing a substantial performance boost. However, modern systems reorder memory operations and utilize volatile caches for better performance, making it difficult to ensure a consistent state in NVMM. Intel recently announced a new set of persistence instructions, clflushopt, clwb, and pcommit. These new instructions make it possible to implement fail-safe code on NVMM, but few workloads have been written or characterized using these new instructions.
In this work, we describe how these instructions work and how they can be used to implement write-ahead logging based transactions. We implement several common data structures and kernels and evaluate the performance overhead incurred over traditional non-persistent implementations. In particular, we find that persistence instructions occur in clusters along with expensive fence operations, they have long latency, and they add a significant execution time overhead, on average by 20.3% over code with logging but without fence instructions to order persists.
To deal with this overhead and alleviate the performance bottleneck, we propose to speculate past long latency persistency operations using checkpoint-based processing. Our speculative persistence architecture reduces the execution time overheads to only 3.6%.