bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trace Metal Acquisition by Marine Heterotrophic Bacterioplankton with Contrasting Trophic Strategies
Authors: Hogle Shane L. , Thrash J. Cameron , Dupont Chris L. , Barbeau Katherine A. 
Published: January 2016

ABSTRACT

Heterotrophic bacteria in the SAR11 and
Roseobacter
lineages shape the marine carbon, nitrogen, phosphorous, and sulfur cycles, yet they do so having adopted divergent ecological strategies. Currently, it is unknown whether these globally significant groups partition into specific niches with respect to micronutrients (e.g., trace metals) and how that may affect marine trace metal cycling. Here, we used comparative genomics to identify diverse iron, cobalt, nickel, copper, and zinc uptake capabilities in SAR11 and
Roseobacter
genomes and uncover surprising unevenness within and between lineages. The strongest predictors for the extent of the metal uptake gene content are the total number of transporters per genome, genome size, total metal transporters, and GC content, but numerous exceptions exist in both groups. Taken together, our results suggest that SAR11 have strongly minimized their trace metal uptake versatility, with high-affinity zinc uptake being a unique exception. The larger
Roseobacter
genomes have greater trace metal uptake versatility on average, but they also appear to have greater plasticity, resulting in phylogenetically similar genomes having largely different capabilities. Ultimately, phylogeny is predictive of the diversity and extent of 20 to 33% of all metal uptake systems, suggesting that specialization in metal utilization mostly occurred independently from overall lineage diversification in both SAR11 and
Roseobacter
. We interpret these results as reflecting relatively recent trace metal niche partitioning in both lineages, suggesting that concentrations and chemical forms of metals in the marine environment are important factors shaping the gene content of marine heterotrophic
Alphaproteobacteria
of the SAR11 and
Roseobacter
lineages.
Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization
Authors: Mewis Keith , Lenfant Nicolas , Lombard Vincent , Henrissat Bernard 
Published: January 2016

ABSTRACT

The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-
l
-arabinofuranosidase, β-
d
-xylosidase, α-
l
-arabinanase, and β-
d
-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides.
Ancient Evolution and Recent Evolution Converge for the Biodegradation of Cyanuric Acid and Related Triazines
Authors: Seffernick Jennifer L. , Wackett Lawrence P. 
Published: January 2016

ABSTRACT

Cyanuric acid was likely present on prebiotic Earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the United States. In light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. The initial reaction that opens the
s
-triazine ring is catalyzed by the unusual enzyme cyanuric acid hydrolase. This enzyme is in a rare protein family that consists of only cyanuric acid hydrolase (CAH) and barbiturase, with barbiturase participating in pyrimidine catabolism by some actinobacterial species. The X-ray structures of two cyanuric acid hydrolase proteins show that this family has a unique protein fold. Phylogenetic, bioinformatic, enzymological, and genetic studies are consistent with the idea that CAH has an ancient protein fold that was rare in microbial populations but is currently becoming more widespread in microbial populations in the wake of anthropogenic synthesis of cyanuric acid and other
s
-triazine compounds that are metabolized via a cyanuric acid intermediate. The need for the removal of cyanuric acid from swimming pools and spas, where it is used as a disinfectant stabilizer, can potentially be met using an enzyme filtration system. A stable thermophilic cyanuric acid hydrolase from
Moorella thermoacetica
is being tested for this purpose.
Nicotine Dehydrogenase Complexed with 6-Hydroxypseudooxynicotine Oxidase Involved in the Hybrid Nicotine-Degrading Pathway in Agrobacterium tumefaciens S33
Authors: Li Huili , Xie Kebo , Yu Wenjun , Hu Liejie , Huang Haiyan , Xie Huijun , Wang Shuning 
Published: January 2016

ABSTRACT

Nicotine, a major toxic alkaloid in tobacco wastes, is degraded by bacteria, mainly via pyridine and pyrrolidine pathways. Previously, we discovered a new hybrid of the pyridine and pyrrolidine pathways in
Agrobacterium tumefaciens
S33 and characterized its key enzyme 6-hydroxy-3-succinoylpyridine (HSP) hydroxylase. Here, we purified the nicotine dehydrogenase initializing the nicotine degradation from the strain and found that it forms a complex with a novel 6-hydroxypseudooxynicotine oxidase. The purified complex is composed of three different subunits encoded by
ndhAB
and
pno
, where
ndhA
and
ndhB
overlap by 4 bp and are ∼26 kb away from
pno
. As predicted from the gene sequences and from chemical analyses, NdhA (82.4 kDa) and NdhB (17.1 kDa) harbor a molybdopterin cofactor and two [2Fe-2S] clusters, respectively, whereas Pno (73.3 kDa) harbors an flavin mononucleotide and a [4Fe-4S] cluster. Mutants with disrupted
ndhA
or
ndhB
genes did not grow on nicotine but grew well on 6-hydroxynicotine and HSP, whereas the
pno
mutant did not grow on nicotine or 6-hydroxynicotine but grew well on HSP, indicating that NdhA and NdhB are responsible for initialization of nicotine oxidation. We successfully expressed
pno
in
Escherichia coli
and found that the recombinant Pno presented 2,6-dichlorophenolindophenol reduction activity when it was coupled with 6-hydroxynicotine oxidation. The determination of reaction products catalyzed by the purified enzymes or mutants indicated that NdhAB catalyzed nicotine oxidation to 6-hydroxynicotine, whereas Pno oxidized 6-hydroxypseudooxynicotine to 6-hydroxy-3-succinoylsemialdehyde pyridine. These results provide new insights into this novel hybrid pathway of nicotine degradation in
A. tumefaciens
S33.
Evidence of Chinese herbal medicine Duhuo Jisheng decoction for knee osteoarthritis: a systematic review of randomised clinical trials
Authors: Zhang Wenming , Wang Shangquan , Zhang Ranxing , Zhang Yuanyuan , Li Xinjian , Lin Yanping , Wei Xu 
Published: January 2016

ObjectivesDuhuo Jisheng decoction (DJD) is considered beneficial for controlling knee osteoarthritis (KOA)-related symptoms in some Asian countries. This review compiles the evidence from randomised clinical trials and quantifies the effects of DJD on KOA.Designs7 online databases were investigated up to 12 October 2015. Randomised clinical trials investigating treatment of KOA for which DJD was used either as a monotherapy or in combination with conventional therapy compared to no intervention, placebo or conventional therapy, were included. The outcomes included the evaluation of functional activities, pain and adverse effect. The risk of bias was evaluated using the Cochrane Collaboration tool. The estimated mean difference (MD) and SMD was within a 95% CI with respect to interstudy heterogeneity.Results12 studies with 982 participants were identified. The quality presented a high risk of bias. Meta-analysis found that DJD combined with glucosamine (MD 4.20 (1.72 to 6.69); p<0.001) or DJD plus meloxicam and glucosamine (MD 3.48 (1.59 to 5.37); p<0.001) had a more significant effect in improving Western Ontario and McMaster Universities Arthritis Index (total WOMAC scores). Also, meta-analysis presented more remarkable pain improvement when DJD plus sodium hyaluronate injection (MD 0.89 (0.26 to 1.53); p=0.006) was used. These studies demonstrated that active treatment of DJD in combination should be practiced for at least 4 weeks. Information on the safety of DJD or comprehensive therapies was insufficient in few studies.ConclusionsDJD combined with Western medicine or sodium hyaluronate injection appears to have benefits for KOA. However, the effectiveness and safety of DJD is uncertain because of the limited number of trials and low methodological quality. Therefore, practitioners should be cautious when applying DJD in daily practice. Future clinical trials should be well designed; more research is needed.
Outcomes of domestic violence screening at an acute London trust: are there missed opportunities for intervention?
Authors: Warren-Gash Charlotte , Bartley Angela , Bayly Jude , Dutey-Magni Peter , Edwards Sarah , Madge Sara , Miller Charlotte , Nicholas Rachel , Radhakrishnan Sheila , Sathia Leena , Swarbrick Helen , Blaikie Dee , Rodger Alison 
Published: January 2016

ObjectivesDomestic violence screening is advocated in some healthcare settings. Evidence that it increases referral to support agencies or improves health outcomes is limited. This study aimed to (1) investigate the proportion of hospital patients reporting domestic violence, (2) describe characteristics and previous hospital attendances of affected patients and (3) assess referrals to an in-house domestic violence advisor from Camden Safety Net.DesignA series of observational studies.SettingThree outpatient clinics at the Royal Free London NHS Foundation Trust.Participants10 158 patients screened for domestic violence in community gynaecology, genitourinary medicine (GUM) and HIV medicine clinics between 1 October 2013 and 30 June 2014. Also 2253 Camden Safety Net referrals over the same period.Main outcome measures(1) Percentage reporting domestic violence by age group gender, ethnicity and clinic. (2) Rates of hospital attendances in the past 3 years for those screening positive and negative. (3) Characteristics, uptake and risk assessment results for hospital in-house domestic violence referrals compared with Camden Safety Net referrals from other sources.ResultsOf the 10 158 patients screened, 57.4% were female with a median age of 30 years. Overall, 7.1% reported ever-experiencing domestic violence, ranging from 5.7% in GUM to 29.4% in HIV services. People screening positive for domestic violence had higher rates of previous emergency department attendances (rate ratio (RR) 1.63, 95% CI 1.09 to 2.48), emergency inpatient admissions (RR 2.27, 95% CI 1.37 to 3.84) and day-case admissions (RR 2.03, 95% CI 1.23 to 3.43) than those screening negative. The 77 hospital referrals to the hospital-based domestic violence advisor during the study period were more likely to be taken up and to be classified as high risk than referrals from elsewhere.ConclusionsSelective screening for domestic violence in high-risk hospital clinic populations has the potential to identify affected patients and promote good uptake of referrals for in-house domestic violence support.
Management of the anticoagulated trauma patient in the emergency department: a survey of current practice in England and Wales
Authors: Battle Ceri E , Lecky Fiona E , Stacey Tom , Edwards Antoinette , Evans Phillip A 
Published: January 2016

ObjectiveThe aim of this study was to investigate current management of the anticoagulated trauma patient in the emergency departments (EDs) in England and Wales.MethodsA survey exploring management strategies for anticoagulated trauma patients presenting to the ED was developed with two patient scenarios concerning assessment of coagulation status, reversal of international normalised ratio (INR), management of hypotension and management strategies for each patient. Numerical data are presented as percentages of total respondents to that particular question.Results106 respondents from 166 hospitals replied to the survey, with 24% of respondents working in a major trauma unit with a specialist neurosurgical unit. Variation was reported in the assessment and management strategies of the elderly anticoagulated poly-trauma patient described in scenario one. Variation was also evident in the responses between the neurosurgical and non-neurosurgical units for the head-injured, anticoagulated trauma patient in scenario two.ConclusionThe results of this study highlight the similarities and variation in the management strategies used in the EDs in England and Wales for the elderly, anticoagulated trauma patient. The variations in practice reported may be due to the differences evident in the available guidelines for these patients.
Helmet regulation in Vietnam: impact on health, equity and medical impoverishment
Authors: Olson Zachary , Staples John A , Mock Charles , Nguyen Nam Phuong , Bachani Abdulgafoor M , Nugent Rachel , Verguet Stéphane 
Published: January 2016

BackgroundVietnam's 2007 comprehensive motorcycle helmet policy increased helmet use from about 30% of riders to about 93%. We aimed to simulate the effect that this legislation might have on: (a) road traffic deaths and non-fatal injuries, (b) individuals’ direct acute care injury treatment costs, (c) individuals’ income losses from missed work and (d) individuals’ protection against medical impoverishment.Methods and findingsWe used published secondary data from the literature to perform a retrospective extended cost-effectiveness analysis simulation study of the policy. Our model indicates that in the year following its introduction a helmet policy employing standard helmets likely prevented approximately 2200 deaths and 29 000 head injuries, saved individuals US$18 million in acute care costs and averted US$31 million in income losses. From a societal perspective, such a comprehensive helmet policy would have saved $11 000 per averted death or $830 per averted non-fatal injury. In terms of financial risk protection, traffic injury is so expensive to treat that any injury averted would necessarily entail a case of catastrophic health expenditure averted.ConclusionsThe high costs associated with traffic injury suggest that helmet legislation can decrease the burden of out-of-pocket payments and reduced injuries decrease the need for access to and coverage for treatment, allowing the government and individuals to spend resources elsewhere. These findings suggest that comprehensive motorcycle helmet policies should be adopted by low-income and middle-income countries where motorcycles are pervasive yet helmet use is less common.
Gauge concepts in theoretical applied physics
Authors: Tan Seng Ghee , Jalil Mansoor B. A. 
Published: January 2016

Gauge concept evolves in the course of nearly one century from Faraday’s rather obscure electrotonic state of matter to the physically significant Yang–Mills that underpin today’s standard model. As gauge theories improve, links are established with modern observations, e.g. in the Aharonov–Bohm effect, the Pancharatnam–Berry’s phase, superconductivity, and quantum Hall effects. In this century, emergent gauge theory is formulated in numerous fields of applied physics like topological insulators, spintronics, and graphene. We will show in this paper the application of gauge theory in two particularly useful spin-based phenomena, namely the spin orbit spin torque and the spin Hall effect. These are important fields of study in the engineering community due to great commercial interest in the technology of magnetic memory (MRAM), and magnetic field sensors. Both spin orbit torque and spin Hall perform magnetic switching at low power and high speed. Furthermore, spin Hall is also a promising source of pure spin current, as well as a reliable form of detection mechanism for the magnetic state of a material.
Page overlays
Authors: Seshadri Vivek , Pekhimenko Gennady , Ruwase Olatunji , Mutlu Onur , Gibbons Phillip B. , Kozuch Michael A. , Mowry Todd C. , Chilimbi Trishul 
Published: January 2016

Many recent works propose mechanisms demonstrating the potential advantages of managing memory at a fine (e.g., cache line) granularity---e.g., fine-grained deduplication and fine-grained memory protection. Unfortunately, existing virtual memory systems track memory at a larger granularity (e.g., 4 KB pages), inhibiting efficient implementation of such techniques. Simply reducing the page size results in an unacceptable increase in page table overhead and TLB pressure.
We propose a new virtual memory framework that enables efficient implementation of a variety of fine-grained memory management techniques. In our framework, each virtual page can be mapped to a structure called a page overlay, in addition to a regular physical page. An overlay contains a subset of cache lines from the virtual page. Cache lines that are present in the overlay are accessed from there and all other cache lines are accessed from the regular physical page. Our page-overlay framework enables cache-line-granularity memory management without significantly altering the existing virtual memory framework or introducing high overheads.
We show that our framework can enable simple and efficient implementations of seven memory management techniques, each of which has a wide variety of applications. We quantitatively evaluate the potential benefits of two of these techniques: overlay-on-write and sparse-data-structure computation. Our evaluations show that overlay-on-write, when applied to fork, can improve performance by 15% and reduce memory capacity requirements by 53% on average compared to traditional copy-on-write. For sparse data computation, our framework can outperform a state-of-the-art software-based sparse representation on a number of real-world sparse matrices. Our framework is general, powerful, and effective in enabling fine-grained memory management at low cost.
Profiling a warehouse-scale computer
Authors: Kanev Svilen , Darago Juan Pablo , Hazelwood Kim , Ranganathan Parthasarathy , Moseley Tipp , Wei Gu-Yeon , Brooks David 
Published: January 2016

With the increasing prevalence of warehouse-scale (WSC) and cloud computing, understanding the interactions of server applications with the underlying microarchitecture becomes ever more important in order to extract maximum performance out of server hardware. To aid such understanding, this paper presents a detailed microarchitectural analysis of live datacenter jobs, measured on more than 20,000 Google machines over a three year period, and comprising thousands of different applications.
We first find that WSC workloads are extremely diverse, breeding the need for architectures that can tolerate application variability without performance loss. However, some patterns emerge, offering opportunities for co-optimization of hardware and software. For example, we identify common building blocks in the lower levels of the software stack. This "datacenter tax" can comprise nearly 30% of cycles across jobs running in the fleet, which makes its constituents prime candidates for hardware specialization in future server systems-on-chips. We also uncover opportunities for classic microarchitectural optimizations for server processors, especially in the cache hierarchy. Typical workloads place significant stress on instruction caches and prefer memory latency over bandwidth. They also stall cores often, but compute heavily in bursts. These observations motivate several interesting directions for future warehouse-scale computers.
Multiple clone row DRAM
Authors: Choi Jungwhan , Shin Wongyu , Jang Jaemin , Suh Jinwoong , Kwon Yongkee , Moon Youngsuk , Kim Lee-Sup 
Published: January 2016

Several previous works have changed DRAM bank structure to reduce memory access latency and have shown performance improvement. However, changes in the area-optimized DRAM bank can incur large area-overhead. To solve this problem, we propose Multiple Clone Row DRAM (MCR-DRAM), which uses existing DRAM bank structure without any modification.
Our key idea is Multiple Clone Row (MCR), in which multiple rows are simultaneously turned on or off to consist of a logically single row. MCR provides two advantages which enable our low-latency mechanisms (Early-Access, Early-Precharge and Fast-Refresh). First, MCR increases the speed of the sensing process by increasing the number of sensed-cells. Thus, it enables a READ/WRITE command to an MCR to be issued earlier than possible for a normal row (Early-Access). Second, DRAM cells in an MCR exhibit more frequent refreshes without additional REFRESH commands, thereby reducing the amount of charge leakage during the refresh interval for the identical cell. The reduced amount of charge leakage enables a PRECHARGE command to be served before the activated-cells are fully restored (Early-Precharge) and a REFRESH operation to be completed before the refreshed-cells are fully restored (Fast-Refresh).
Even though MCR-DRAM sacrifices memory capacity for low-latency, it can be dynamically reconfigured from low-latency to full-capacity DRAM. MCR-DRAM improves both performance and energy efficiency for both single-core and multi-core systems.
PrORAM
Authors: Yu Xiangyao , Haider Syed Kamran , Ren Ling , Fletcher Christopher , Kwon Albert , van Dijk Marten , Devadas Srinivas 
Published: January 2016

Oblivious RAM (ORAM) is an established technique to hide the access pattern to an untrusted storage system. With ORAM, a curious adversary cannot tell what address the user is accessing when observing the bits moving between the user and the storage system. All existing ORAM schemes achieve obliviousness by adding redundancy to the storage system, i.e., each access is turned into multiple random accesses. Such redundancy incurs a large performance overhead.
Although traditional data prefetching techniques successfully hide memory latency in DRAM based systems, it turns out that they do not work well for ORAM because ORAM does not have enough memory bandwidth available for issuing prefetch requests. In this paper, we exploit ORAM locality by taking advantage of the ORAM internal structures. While it might seem apparent that obliviousness and locality are two contradictory concepts, we challenge this intuition by exploiting data locality in ORAM without sacrificing security. In particular, we propose a dynamic ORAM prefetching technique called PrORAM (Dynamic Prefetcher for ORAM) and comprehensively explore its design space. PrORAM detects data locality in programs at runtime, and exploits the locality without leaking any information on the access pattern.
Our simulation results show that with PrORAM, the performance of ORAM can be significantly improved. PrORAM achieves an average performance gain of 20% over the baseline ORAM for memory intensive benchmarks among Splash2 and 5.5% for SPEC06 workloads. The performance gain for YCSB and TPCC in DBMS benchmarks is 23.6% and 5% respectively. On average, PrORAM offers twice the performance gain than that offered by a static super block scheme.