bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Bacillus subtilis tyrZ Gene Encodes a Highly Selective Tyrosyl-tRNA Synthetase and Is Regulated by a MarR Regulator and T Box Riboswitch
Authors: Williams-Wagner Rebecca N. , Grundy Frank J. , Raina Medha , Ibba Michael , Henkin Tina M. 
Published: March 2015

ABSTRACTMisincorporation ofd-tyrosine (d-Tyr) into cellular proteins due to mischarging of tRNATyrwithd-Tyr by tyrosyl-tRNA synthetase inhibits growth and biofilm formation ofBacillus subtilis. Furthermore, manyB. subtilisstrains lack a functional gene encodingd-aminoacyl-tRNA deacylase, which prevents misincorporation ofd-Tyr in most organisms.B. subtilishas two genes that encode tyrosyl-tRNA synthetase:tyrSis expressed under normal growth conditions, andtyrZis known to be expressed only whentyrSis inactivated by mutation. We hypothesized thattyrZencodes an alternate tyrosyl-tRNA synthetase, expression of which allows the cell to grow whend-Tyr is present. We show that TyrZ is more selective forl-Tyr overd-Tyr than is TyrS; however, TyrZ is less efficient overall. We also show that expression oftyrZis required for growth and biofilm formation in the presence ofd-Tyr. BothtyrSandtyrZare preceded by a T box riboswitch, buttyrZis found in an operon withywaE, which is predicted to encode a MarR family transcriptional regulator. Expression oftyrZis repressed by YwaE and also is regulated at the level of transcription attenuation by the T box riboswitch. We conclude that expression oftyrZmay allow growth when excessd-Tyr is present.IMPORTANCEAccurate protein synthesis requires correct aminoacylation of each tRNA with the cognate amino acid and discrimination against related compounds.Bacillus subtilisproducesd-Tyr, an analog ofl-Tyr that is toxic when incorporated into protein, during stationary phase. Most organisms utilize ad-aminoacyl-tRNA deacylase to prevent misincorporation ofd-Tyr. This work demonstrates that the increased selectivity of the TyrZ form of tyrosyl-tRNA synthetase may provide a mechanism by whichB. subtilisprevents misincorporation ofd-Tyr in the absence of a functionald-aminoacyl-tRNA deacylase gene.
Mechanism for Inhibition of Vibrio cholerae ToxT Activity by the Unsaturated Fatty Acid Components of Bile
Authors: Plecha Sarah C. , Withey Jeffrey H. 
Published: March 2015

ABSTRACT

The Gram-negative curved bacillus
Vibrio cholerae
causes the severe diarrheal illness cholera. During host infection, a complex regulatory cascade results in production of ToxT, a DNA-binding protein that activates the transcription of major virulence genes that encode cholera toxin (CT) and toxin-coregulated pilus (TCP). Previous studies have shown that bile and its unsaturated fatty acid (UFA) components reduce virulence gene expression and therefore are likely important signals upon entering the host. However, the mechanism for the bile-mediated reduction of TCP and CT expression has not been clearly defined. There are two likely hypotheses to explain this reduction: (i) UFAs decrease DNA binding by ToxT, or (ii) UFAs decrease dimerization of ToxT. The work presented here elucidates that bile or UFAs directly affect DNA binding by ToxT. UFAs, specifically linoleic acid, can enter
V. cholerae
when added exogenously and are present in the cytoplasm, where they can then interact with ToxT. Electrophoretic mobility shift assays (EMSAs) with ToxT and various virulence promoters in the presence or absence of UFAs showed a direct reduction in ToxT binding to DNA, even in promoters with only one ToxT binding site. Virstatin, a synthetic ToxT inhibitor, was previously shown to reduce ToxT dimerization. Here we show that virstatin affects DNA binding only at ToxT promoters with two binding sites, unlike linoleic acid, which affects ToxT binding promoters having either one or two ToxT binding sites. This suggests a mechanism in which UFAs, unlike virstatin, do not affect dimerization but affect monomeric ToxT binding to DNA.

IMPORTANCE
Vibrio cholerae
must produce the major virulence factors cholera toxin (CT) and toxin-coregulated pilus (TCP) to cause cholera. CT and TCP production depends on ToxT, the major virulence transcription activator. ToxT activity is negatively regulated by unsaturated fatty acids (UFAs) present in the lumen of the upper small intestine. This study investigated the mechanism for inhibition of ToxT activity by UFAs and found that UFAs directly reduce specific ToxT binding to DNA at virulence promoters and subsequently reduce virulence gene expression. UFAs inhibit ToxT monomers from binding DNA. This differs from the inhibitory mechanism of a synthetic ToxT inhibitor, virstatin, which inhibits ToxT dimerization. Understanding the mechanisms for inhibition of virulence could lead to better cholera therapeutics.
Sociality in Escherichia coli: Enterochelin Is a Private Good at Low Cell Density and Can Be Shared at High Cell Density
Authors: Scholz Rebecca L. , Greenberg E. Peter 
Published: March 2015

ABSTRACTMany bacteria produce secreted iron chelators called siderophores, which can be shared among cells with specific siderophore uptake systems regardless of whether the cell produces siderophores. Sharing secreted products allows freeloading, where individuals use resources without bearing the cost of production. Here we show that theEscherichia colisiderophore enterochelin is not evenly shared between producers and nonproducers. Wild-typeEscherichia coligrows well in low-iron minimal medium, and an isogenic enterochelin synthesis mutant (ΔentF) grows very poorly. The enterochelin mutant grows well in low-iron medium supplemented with enterochelin. At high cell densities the ΔentFmutant can compete equally with the wild type in low-iron medium. At low cell densities the ΔentFmutant cannot compete. Furthermore, the growth rate of the wild type is unaffected by cell density. The wild type grows well in low-iron medium even at very low starting densities. Our experiments support a model where at least some enterochelin remains associated with the cells that produce it, and the cell-associated enterochelin enables iron acquisition even at very low cell density. Enterochelin that is not retained by producing cells at low density is lost to dilution. At high cell densities, cell-free enterochelin can accumulate and be shared by all cells in the group. Partial privatization is a solution to the problem of iron acquisition in low-iron, low-cell-density habitats. Cell-free enterochelin allows for iron scavenging at a distance at higher population densities. Our findings shed light on the conditions under which freeloaders might benefit from enterochelin uptake systems.IMPORTANCESociality in microbes has become a topic of great interest. One facet of sociality is the sharing of secreted products, such as the iron-scavenging siderophores. We present evidence that theEscherichia colisiderophore enterochelin is relatively inexpensive to produce and is partially privatized such that it can be efficiently shared only at high producer cell densities. At low cell densities, cell-free enterochelin is scarce and only enterochelin producers are able to grow in low-iron medium. Because freely shared products can be exploited by freeloaders, this partial privatization may help explain how enterochelin production is stabilized inE. coliand may provide insight into when enterochelin is available for freeloaders.
Chapter 10 Palaeo-Mesoproterozoic sedimentation and tectonics of the Singhbhum Craton, eastern India, and implications for global and craton-specific geological events
Authors: Mazumder Rajat , De Shuvabrata , Ohta Tohru , Flannery David , Mallik Leena , Chaudhury Trisrota , Chatterjee Priyanka , Ranaivoson Marinah A. , Arima Makoto 
Published: March 2015

Abstract
The Singhbhum Craton in eastern India preserves a depositional record from the Palaeo-Mesoarchaean to the Mesoproterozoic. Herein, we have summarized the Palaeo-Mesoproterozoic supracrustal record of the Singhbhum Craton, discussed tectonosedimentary processes and discriminated Palaeo-Mesoproterozoic global and craton-specific events. The late Palaeo-Mesoproterozoic supracrustal record of the Singhbhum Craton is limited. It includes evidence for high continental freeboard conditions during 2.6–2.1 Ga in the form of terrestrial deposits (alluvial fan–fluvial) of the Dhanjori Formation. This was followed by a major transgression and a transition to the relatively deeper-water shelf to shallow intertidal environments recorded by the Chaibasa Formation. A long hiatus ensued before deposition of the Dhalbhum Formation and conformably overlying Dalma and Chandil formations, suggesting continued high continental freeboard during 2.2–1.6 Ga. In significant contrast to the craton-specific Dhanjori Formation volcanism, the 1.7–1.6 Ga plume-related Dalma volcanism was probably part of a global tectonothermal event.
Chapter 17 Sedimentation in the Papaghni Group of rocks in the Papaghni sub-basin of the Proterozoic Cuddapah Basin, India
Authors: Chakrabarti G. , Eriksson P. G. , Shome D. 
Published: March 2015

Abstract
The Gulcheru Quartzite (30–200 m thick) overlies Archaean basement rocks, and comprises an impersistent conglomerate at the base of more widespread quartzites, with shale and ferruginous interbeds. The overlying Vempalle Formation (≤1500 m) comprises mainly stromatolitic carbonates, lesser cherts and mudrocks. Together, these two units make up the Palaeoproterozoic Papaghni Group, which displays an arcuate outcrop belt in the SW Cuddapah Basin, bearing no obvious relationship to the tectonic grain in the basement lithologies. Facies defined in the Gulcheru Quartzite are ascribed to initial alluvial fans, which transitioned into a shallow-marine coastline and shelf, as transgression occurred under overall thermal subsidence, possibly related to post-plume thermal relaxation. The shallow siliciclastic Gulcheru shelf is inferred to have evolved to a stromatolitic ramp that accommodated deposition of the Vempalle chemical sediments. The abrupt vertical transition from clastic to carbonate deposits is ascribed to rapid sea-level rise. Late-stage shoreline progradation during uppermost Vempalle times and concomitant clastic inflows terminated the carbonate factory.
Chapter 2 Classification of basins, with special reference to Proterozoic examples
Authors: Allen P. A. , Eriksson P. G. , Alkmim F. F. , Betts P. G. , Catuneanu O. , Mazumder R. , Meng Q. , Young G. M. 
Published: March 2015

Abstract
Basin classification rests on a plate tectonic foundation, highlighting lithospheric substrate, proximity to plate margin and relative motion of the nearest plate boundary. Major mechanisms for regional subsidence and uplift are subdivided into isostatic, flexural and dynamic groups. Basin-forming mechanisms and basin types do not exhibit simple cause-and-effect relationships, but rather reflect a matrix-type relationship. Different basin types have different spans of existence, with generally shorter life spans related to more tectonically active settings. Many ‘polyhistory’ basins, composed of two or more megasequences, reflect a long evolution dominated by different basin-forming and basin-modifying mechanisms. The supercontinent cycle is marked by distinct sets of basin types, developed during successive phases of the cycle. Major classification schemes are reviewed briefly, before surveying the range of basin types represented in the Proterozoic of several key cratonic areas. Basins examined encompass almost the entire Neoarchaean–Neoproterozoic period. All of these basins have a relatively long history of preservation, which can be tied to the essentially continental character of their basement rocks and concomitant enhanced ‘survivability’. Their preservation thus underlines the longevity and inherent stability of the continental lithosphere. The distinction between basin occurrence over geological time and preferential preservation is important when viewing the geological record.
Chapter 22 Precambrian metallic mineralization in India
Authors: Mishra Biswajit 
Published: March 2015

Abstract
Four Archaean cratons (Aravalli–Bundelkhand, Singhbhum, Bastar and Dharwar), together with the marginal Proterozoic mobile belts and sedimentary basins, constitute the geology of peninsular India. Huge resources of ferrous metals (Fe and Mn) and chromite, the lone granitoid-hosted Malanjkhand Cu–Mo deposit, a moderate occurrence of gold and promising platinum group element mineralization constitute the Archaean metal inventory of India. Additionally, the Proterozoic Aeon witnessed diverse mineralization in the mobile belts and craton–mobile belt contacts. These include vast resources of base metals in the northwestern Indian Shield and Mn in the central Indian block, apart from considerable U–Cu deposits in the Singhbhum Shear Zone. These ores formed as a consequence of an entire genetic spectrum, covering various orthomagmatic, volcanosedimentary and diverse hydrothermal processes, aided and abetted by supergene enrichment, as in the case of iron ores.
Chapter 4 Lithostratigraphic, geochronological and depositional framework of the Precambrian basins of the Aravalli Mountains and adjoining areas, Rajasthan, India
Authors: Roy A. B. , Purohit Ritesh 
Published: March 2015

Abstract

The Aravalli Mountains and neighbouring areas have well-preserved records of a protracted history of development of Precambrian basins, which spans about 2500 myr of the Earth's history. The oldest depositional basins are the greenstone belts that occur within the Archaean gneiss–granite terrain. Geochronological data indicate evolution of one such greenstone belt from 3300 to 2850 Ma. The younger Proterozoic cover successions include the Aravalli Supergroup, Delhi Supergroup and Sirohi Group, which evolved during three successive orogenic cycles spanning between
c.
2200 and
c.
1850 Ma,
c.
1700 and
c.
1450 Ma, and
c.
1000 and
c.
850 Ma, respectively. Each of these lithostratigraphic units evolved in separate basins having distinctive tectonic, metallogenic and evolutionary histories. The inversion of the youngest ‘orogenic’ basin marks the final cratonization of the Precambrian Aravalli crust at around 850 Ma. The succeeding depositional episodes include formation of ephemeral basins during the early phase of the plume-related Malani Group from 780 to 730 Ma, and the formation of the Marwar Supergroup deposited in stable platformal basins marks the terminal phase of the Precambrian crust-building history in the region.
Using RDMA efficiently for key-value services
Authors: Kalia Anuj , Kaminsky Michael , Andersen David G. 
Published: March 2015

This paper describes the design and implementation of HERD, a key-value system designed to make the best use of an RDMA network. Unlike prior RDMA-based key-value systems, HERD focuses its design on reducing network round trips while using efficient RDMA primitives; the result is substantially lower latency, and throughput that saturates modern, commodity RDMA hardware.
HERD has two unconventional decisions: First, it does not use RDMA reads, despite the allure of operations that bypass the remote CPU entirely. Second, it uses a mix of RDMA and messaging verbs, despite the conventional wisdom that the messaging primitives are slow. A HERD client writes its request into the server's memory; the server computes the reply. This design uses a single round trip for all requests and supports up to 26 million key-value operations per second with 5μs average latency. Notably, for small key-value items, our full system throughput is similar to native RDMA read throughput and is over 2X higher than recent RDMA-based key-value systems. We believe that HERD further serves as an effective template for the construction of RDMA-based datacenter services.
Fastpass
Authors: Perry Jonathan , Ousterhout Amy , Balakrishnan Hari , Shah Devavrat , Fugal Hans 
Published: March 2015

An ideal datacenter network should provide several properties, including low median and tail latency, high utilization (throughput), fair allocation of network resources between users or applications, deadline-aware scheduling, and congestion (loss) avoidance. Current datacenter networks inherit the principles that went into the design of the Internet, where packet transmission and path selection decisions are distributed among the endpoints and routers. Instead, we propose that each sender should delegate control---to a centralized arbiter---of when each packet should be transmitted and what path it should follow.
This paper describes Fastpass, a datacenter network architecture built using this principle. Fastpass incorporates two fast algorithms: the first determines the time at which each packet should be transmitted, while the second determines the path to use for that packet. In addition, Fastpass uses an efficient protocol between the endpoints and the arbiter and an arbiter replication strategy for fault-tolerant failover. We deployed and evaluated Fastpass in a portion of Facebook's datacenter network. Our results show that Fastpass achieves high throughput comparable to current networks at a 240x reduction is queue lengths (4.35 Mbytes reducing to 18 Kbytes), achieves much fairer and consistent flow throughputs than the baseline TCP (5200x reduction in the standard deviation of per-flow throughput with five concurrent connections), scalability from 1 to 8 cores in the arbiter implementation with the ability to schedule 2.21 Terabits/s of traffic in software on eight cores, and a 2.5x reduction in the number of TCP retransmissions in a latency-sensitive service at Facebook.
One tunnel is (often) enough
Authors: Peter Simon , Javed Umar , Zhang Qiao , Woos Doug , Anderson Thomas , Krishnamurthy Arvind 
Published: March 2015

A longstanding problem with the Internet is that it is vulnerable to outages, black holes, hijacking and denial of service. Although architectural solutions have been proposed to address many of these issues, they have had difficulty being adopted due to the need for widespread adoption before most users would see any benefit. This is especially relevant as the Internet is increasingly used for applications where correct and continuous operation is essential.
In this paper, we study whether a simple, easy to implement model is sufficient for addressing the aforementioned Internet vulnerabilities. Our model, called ARROW (Advertised Reliable Routing Over Waypoints), is designed to allow users to configure reliable and secure end to end paths through participating providers. With ARROW, a highly reliable ISP offers tunneled transit through its network, along with packet transformation at the ingress, as a service to remote paying customers. Those customers can stitch together reliable end to end paths through a combination of participating and non-participating ISPs in order to improve the fault-tolerance, robustness, and security of mission critical transmissions. Unlike efforts to redesign the Internet from scratch, we show that ARROW can address a set of well-known Internet vulnerabilities, for most users, with the adoption of only a single transit ISP. To demonstrate ARROW, we have added it to a small-scale wide-area ISP we control. We evaluate its performance and failure recovery properties in both simulation and live settings.
An experimental study of the learnability of congestion control
Authors: Sivaraman Anirudh , Winstein Keith , Thaker Pratiksha , Balakrishnan Hari 
Published: March 2015

When designing a distributed network protocol, typically it is infeasible to fully define the target network where the protocol is intended to be used. It is therefore natural to ask: How faithfully do protocol designers really need to understand the networks they design for? What are the important signals that endpoints should listen to? How can researchers gain confidence that systems that work well on well-characterized test networks during development will also perform adequately on real networks that are inevitably more complex, or future networks yet to be developed? Is there a tradeoff between the performance of a protocol and the breadth of its intended operating range of networks? What is the cost of playing fairly with cross-traffic that is governed by another protocol?
We examine these questions quantitatively in the context of congestion control, by using an automated protocol-design tool to approximate the best possible congestion-control scheme given imperfect prior knowledge about the network. We found only weak evidence of a tradeoff between operating range in link speeds and performance, even when the operating range was extended to cover a thousand-fold range of link speeds. We found that it may be acceptable to simplify some characteristics of the network---such as its topology---when modeling for design purposes. Some other features, such as the degree of multiplexing and the aggressiveness of contending endpoints, are important to capture in a model.
Mahimahi
Authors: Netravali Ravi , Sivaraman Anirudh , Winstein Keith , Das Somak , Goyal Ameesh , Balakrishnan Hari 
Published: March 2015

This demo presents a measurement toolkit, Mahimahi, that records websites and replays them under emulated network conditions. Mahimahi is structured as a set of arbitrarily composable UNIX shells. It includes two shells to record and replay Web pages, RecordShell and ReplayShell, as well as two shells for network emulation, DelayShell and LinkShell. In addition, Mahimahi includes a corpus of recorded websites along with benchmark results and link traces (https://github.com/ravinet/sites).
Mahimahi improves on prior record-and-replay frameworks in three ways. First, it preserves the multi-origin nature of Web pages, present in approximately 98% of the Alexa U.S. Top 500, when replaying. Second, Mahimahi isolates its own network traffic, allowing multiple instances to run concurrently with no impact on the host machine and collected measurements. Finally, Mahimahi is not inherently tied to browsers and can be used to evaluate many different applications.
A demo of Mahimahi recording and replaying a Web page over an emulated link can be found at http://youtu.be/vytwDKBA-8s. The source code and instructions to use Mahimahi are available at http://mahimahi.mit.edu/.
Individual differences in subjective and objective alertness during sleep deprivation are stable and unrelated
Authors: Leproult Rachel , Colecchia Egidio F. , Berardi Anna Maria , Stickgold Robert , Kosslyn Stephen M. , Van Cauter Eve 
Published: March 2015

This study examines the individual reproducibility of alterations of subjective, objective, and EEG measures of alertness during 27 h of continuous wakefulness and analyzes their interrelationships. Eight subjects were studied twice under similar constant-routine conditions. Scales and performance tasks were administered at hourly intervals to define temporal changes in subjective and objective alertness. The wake EEG was recorded every 2 h, 2 min with eyes open and 2 min with eyes closed. Plasma glucose and melatonin levels were measured to estimate brain glucose utilization and individual circadian phase, respectively. Decrements of subjective alertness and performance deficits were found to be highly reproducible for a given individual. Remarkably, there was no relationship between the impairments of subjective and objective alertness. With increased duration of wakefulness, EEG activity with eyes closed increased in the delta range and decreased in the alpha range, but the magnitudes of these changes were also unrelated. These findings indicate that sleep deprivation has highly reproducible, but independent, effects on brain mechanisms controlling subjective and objective alertness.