bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation Mechanism of the
ald
Gene Encoding Alanine Dehydrogenase in Mycobacterium smegmatis and Mycobacterium tuberculosis by the Lrp/AsnC Family Regulator AldR
Authors: Jeong Ji-A , Hyun Jaekyung , Oh Jeong-Il 
Published: July 2015

ABSTRACT

In the presence of alanine, AldR, which belongs to the Lrp/AsnC family of transcriptional regulators and regulates
ald
encoding alanine dehydrogenase in
Mycobacterium smegmatis
, changes its quaternary structure from a homodimer to an octamer with an open-ring conformation. Four AldR-binding sites (O2, O1, O4, and O3) with a consensus sequence of GA/T-N
2
-NWW/WWN-N
2
-A/TC were identified upstream of the
M. smegmatis
ald
gene by means of DNase I footprinting analysis. O2, O1, and O4 are required for the induction of
ald
expression by alanine, while O3 is directly involved in the repression of
ald
expression. In addition to O3, both O1 and O4 are also necessary for full repression of
ald
expression in the absence of alanine, due to cooperative binding of AldR dimers to O1, O4, and O3. Binding of a molecule of the AldR octamer to the
ald
control region was demonstrated to require two AldR-binding sites separated by three helical turns between their centers and one additional binding site that is in phase with the two AldR-binding sites. The cooperative binding of AldR dimers to DNA requires three AldR-binding sites that are aligned with a periodicity of three helical turns. The
aldR
gene is negatively autoregulated independently of alanine. Comparative analysis of
ald
expression of
M. smegmatis
and
Mycobacterium tuberculosis
in conjunction with sequence analysis of both
ald
control regions led us to suggest that the expression of the
ald
genes in both mycobacterial species is regulated by the same mechanism.

IMPORTANCE
In mycobacteria, alanine dehydrogenase (Ald) is the enzyme required both to utilize alanine as a nitrogen source and to grow under hypoxic conditions by maintaining the redox state of the NADH/NAD
+
pool. Expression of the
ald
gene was reported to be regulated by the AldR regulator that belongs to the Lrp/AsnC (feast/famine) family, but the underlying mechanism was unknown. This study revealed the regulation mechanism of
ald
in
Mycobacterium smegmatis
and
Mycobacterium tuberculosis
. Furthermore, a generalized arrangement pattern of
cis
-acting regulatory sites for Lrp/AsnC (feast/famine) family regulators is suggested in this study.
Binding of Cyclic Di-AMP to the Staphylococcus aureus Sensor Kinase KdpD Occurs via the Universal Stress Protein Domain and Downregulates the Expression of the Kdp Potassium Transporter
Authors: Moscoso Joana A. , Schramke Hannah , Zhang Yong , Tosi Tommaso , Dehbi Amina , Jung Kirsten , Gründling Angelika 
Published: July 2015

ABSTRACT

Nucleotide signaling molecules are important intracellular messengers that regulate a wide range of biological functions. The human pathogen
Staphylococcus aureus
produces the signaling nucleotide cyclic di-AMP (c-di-AMP). This molecule is common among Gram-positive bacteria and in many organisms is essential for survival under standard laboratory growth conditions. In this study, we investigated the interaction of c-di-AMP with the
S. aureus
KdpD protein. The sensor kinase KdpD forms a two-component signaling system with the response regulator KdpE and regulates the expression of the
kdpDE
genes and the
kdpFABC
operon coding for the Kdp potassium transporter components. Here we show that the
S. aureus
KdpD protein binds c-di-AMP specifically and with an affinity in the micromolar range through its universal stress protein (USP) domain. This domain is located within the N-terminal cytoplasmic region of KdpD, and amino acids of a conserved SXS-X
20
-FTAXY motif are important for this binding. We further show that KdpD2, a second KdpD protein found in some
S. aureus
strains, also binds c-di-AMP, and our bioinformatics analysis indicates that a subclass of KdpD proteins in c-di-AMP-producing bacteria has evolved to bind this signaling nucleotide. Finally, we show that c-di-AMP binding to KdpD inhibits the upregulation of the
kdpFABC
operon under salt stress, thus indicating that c-di-AMP is a negative regulator of potassium uptake in
S. aureus
.

IMPORTANCE
Staphylococcus aureus
is an important human pathogen and a major cause of food poisoning in Western countries. A common method for food preservation is the use of salt to drive dehydration. This study sheds light on the regulation of potassium uptake in
Staphylococcus aureus
, an important aspect of this bacterium's ability to tolerate high levels of salt. We show that the signaling nucleotide c-di-AMP binds to a regulatory component of the Kdp potassium uptake system and that this binding has an inhibitory effect on the expression of the
kdp
genes encoding a potassium transporter. c-di-AMP binds to the USP domain of KdpD, thus providing for the first time evidence for the ability of such a domain to bind a cyclic dinucleotide.
Quorum Sensing Protects Pseudomonas aeruginosa against Cheating by Other Species in a Laboratory Coculture Model
Authors: Smalley Nicole E. , An Dingding , Parsek Matthew R. , Chandler Josephine R. , Dandekar Ajai A. 
Published: July 2015

ABSTRACT

Many species of bacteria use a cell-cell communication system called quorum sensing (QS) to coordinate group activities. QS systems frequently regulate the production of exoproducts. Some of these products, such as proteases, are “public goods” that are shared among the population and vulnerable to cheating by nonproducing members of the population. Because the QS system of the opportunistic pathogen
Pseudomonas aeruginosa
regulates several public goods, it can serve as a model for studying cooperation. Bacteria also commonly regulate antimicrobial production through QS. In this study, we focused on the hypothesis that QS-regulated antimicrobials may be important for
P. aeruginosa
to protect against cheating by another bacterial species,
Burkholderia multivorans.
We assessed laboratory cocultures of
P. aeruginosa
and
B. multivorans
and investigated the importance of three
P. aeruginosa
QS-regulated antimicrobials, hydrogen cyanide, rhamnolipids, and phenazines, for competition. We found that
P. aeruginosa
dominates cocultures with
B. multivorans
and that the three antimicrobials together promote
P. aeruginosa
competitiveness, with hydrogen cyanide contributing the greatest effect. We show that these QS-regulated antimicrobials are also critical for
P. aeruginosa
to prevent
B. multivorans
from cheating under nutrient conditions where both species require a
P. aeruginosa
quorum-regulated protease for growth. Together our results highlight the importance of antimicrobials in protecting cooperating populations from exploitation by other species that can act as cheaters.

IMPORTANCE
Cooperative behaviors are threatened by social cheating, wherein individuals do not produce but nonetheless benefit from shared public goods. Bacteria have been shown to use several genetic mechanisms to restrain the emergence of cheaters from within the population, but public goods might also be used by other bacterial species in the vicinity. We demonstrate that a public good produced by
Pseudomonas aeruginosa
can be used by another species,
Burkholderia multivorans
, to obtain carbon and energy. We also show that
P. aeruginosa
antimicrobials that are coregulated with the public good prevent invasion by the cheating species. Our results demonstrate that cross-species cheating can occur and that coregulation of public goods with antimicrobials may stabilize cooperative behavior in mixed microbial communities.
Determining Surgical Complications in the Overweight (DISCOVER): a multicentre observational cohort study to evaluate the role of obesity as a risk factor for postoperative complications in general surgery
Authors: Nepogodiev Dmitri , Chapman Stephen J , Glasbey James , Kelly Michael , Khatri Chetan , Drake Thomas M , Kong Chia Yew , Mitchell Harriet , Harrison Ewen M , Fitzgerald J Edward , Bhangu Aneel 
Published: July 2015

IntroductionObesity is increasingly prevalent among patients undergoing surgery. Conflicting evidence exists regarding the impact of obesity on postoperative complications. This multicentre study aims to determine whether obesity is associated with increased postoperative complications following general surgery.Methods and analysisThis prospective, multicentre cohort study will be performed utilising a collaborative methodology. Consecutive adults undergoing open or laparoscopic, elective or emergency, gastrointestinal, bariatric or hepatobiliary surgery will be included. Day case patients will be excluded. The primary end point will be the overall 30-day major complication rate (Clavien-Dindo grade III–V complications). Data will be collected to risk-adjust outcomes for potential confounding factors, such as preoperative cardiac risk. This study will be disseminated through structured medical student networks using established collaborative methodology. The study will be powered to detect a two-percentage point increase in the major postoperative complication rate in obese versus non-obese patients.Ethics and disseminationFollowing appropriate assessment, an exemption from full ethics committee review has been received, and the study will be registered as a clinical audit or service evaluation at each participating hospital. Dissemination will take place through national and local research collaborative networks.
On the Use of Running Trends as Summary Statistics for Univariate Time Series and Time Series Association
Authors: Trottini Mario , Isabel Maria , Aguiar Vigo , Palazón Santiago Belda 
Published: July 2015

Abstract
Given a time series, running trends analysis (RTA) involves evaluating least squares trends over overlapping time windows of L consecutive time points, with overlap by all but one observation. This produces a new series called the “running trends series,” which is used as summary statistics of the original series for further analysis. In recent years, RTA has been widely used in climate applied research as summary statistics for time series and time series association. There is no doubt that RTA might be a useful descriptive tool, but, despite its general use in applied research, precisely what it reveals about the underlying time series is unclear and, as a result, its interpretation is unclear too. This paper contributes to such interpretation in two ways: 1) an explicit formula is obtained for the set of time series with a given series of running trends, making it possible to show that running trends, alone, perform very poorly as summary statistics for univariate time series and time series association; and 2) an equivalence is established between RTA and the estimation of a (possibly nonlinear) trend component of the underlying time series using a weighted moving average filter. Such equivalence provides a solid ground for RTA implementation and interpretation/validation. In this respect, the authors propose as diagnostic tools for RTA 1) the plot of the original series, with RTA trend estimation superposed, 2) the average R2 value and the percentage of statistically significant running trends across windows, and 3) the plot of the running trends series with the corresponding confidence intervals.
The impact of change in albumin assay on reference intervals, prevalence of ‘hypoalbuminaemia’ and albumin prescriptions
Authors: Coley-Grant Deon , Herbert Mike , Cornes Michael P , Barlow Ian M , Ford Clare , Gama Rousseau 
Published: July 2015

Background We studied the impact on reference intervals, classification of patients with hypoalbuminaemia and albumin infusion prescriptions on changing from a bromocresol green (BCG) to a bromocresol purple (BCP) serum albumin assay. Methods Passing-Bablok regression analysis and Bland-Altman plot were used to compare Abbott BCP and Roche BCG methods. Linear regression analysis was used to compare in-house and an external laboratory Abbott BCP serum albumin results. Reference intervals for Abbott BCP serum albumin were derived in two different laboratories using pathology data from adult patients in primary care. Prescriptions for 20% albumin infusions were compared one year before and one year after changing the albumin method. Results Abbott BCP assay had a negative bias of approximately 6 g/L compared with Roche BCG method. There was good agreement ( y = 1.04  x − 1.03; R2 = 0.9933) between in-house and external laboratory Abbott BCP results. Reference intervals for the serum albumin Abbott BCP assay were 31–45 g/L, different to those recommended by Pathology Harmony and the manufacturers (35–50 g/L). Following the change in method there was a large increase in the number of patients classified as hypoalbuminaemic using Pathology Harmony references intervals (32%) but not when retrospectively compared to locally derived reference intervals (16%) compared with the previous year (12%). The method change was associated with a 44.6% increase in albumin prescriptions. This equated to an annual increase in expenditure of £35,234. Conclusions We suggest that serum albumin reference intervals be method specific to prevent misclassification of albumin status in patients. Change in albumin methodology may have significant impact on hospital resources.
Formulating and elaborating a model for the measurement of intellectual capital in Spanish public universities
Authors: Ramírez Yolanda , Manzaneque Montserrat , Priego Alba María 
Published: July 2015

Intellectual capital approaches become critical at universities mainly due to the fact that knowledge is the main output as well as input in these institutions. Although some attempts to measure intellectual capital have been made so far, there is still a long way to go. The purpose of the present article is to provide a model for the measurement of intellectual capital in higher education institutions. The results of a study done at Spanish public universities are used to indicate which intangible elements need to be measured, and a new framework for the measurement and management of intellectual capital is presented. Points for practitioners The main contribution of this article is the validation of the consensus on the key intangible elements and indicators that should comprise a university intellectual capital model. Our proposed intellectual capital model helps universities on the path to presenting information that is useful to their stakeholders, contributing to greater transparency, accountability and comparability in the higher education sector. This article offers useful and specific guidelines for intellectual capital reporting practice in universities. The creation of a framework of intellectual capital reporting facilitates benchmarking analysis and comparative studies in order to help decision-making processes, improve the articulation of public policies and increase transparency in the whole system.
Interest-Based Bargaining: Labor and Management Working Together in Ramsey County, Minnesota
Authors: Brainerd Richard 
Published: July 2015

In a local example, where a new approach to bargaining got started, we find Ramsey County, Minnesota. After a bitter strike and experiments with outside negotiators, the parties turned to interest-based bargaining as a way to improve the bargaining relationship. Even though the brief period that the county contracted out negotiations seemed peaceful compared to the preceding tumultuous years, the parries found that an interest-based bargaining relationship produced results beyond expectations. Construing bargaining as part of a mutual interest relationship, the parties rely on each other's on-going service and quality of work-life concerns. Now, contracts are renegotiated in record time, before expiration, in contrast to the lengthy delays under the traditional collective bargaining model. Issues are addressed by joint groups between bargaining rounds. Grievances have been reduced, thus causing less disruption. Better service is now provided, and customer service has been enhanced. The parties also applied the interest-based approach to the always complicated problem of merging departments. Correcting the anachronism of separate city and county health departments, this new relationship and approach was used to handle the personnel and labor issues involved in such a merger. Here, Ramsey County shows how to move in a municipal context from a traditional to a cooperative relationship and how quickly the benefits spread out and emerge.
Employee Involvement in Seattle: Reengineering Government in a City Lacking a Financial Crisis
Authors: Lyons Lizanne , Vivenzio Anthony D. 
Published: July 2015

Without fiscal pressure, but with a clamor for re-engineering and service reform reverberating, the usually progressive Seattle began an improved labor-management relations effort through a series of project teams sponsored by departmental joint-labor management committees. The aim was to save costs and improve service. Unlike the other examples in this issue, Seattle didn't start with bargaining improvement or conflict resolution in mind, nor did it begin with a large and visible project like health care or a civic arena. Seattle started with a simple but ambitious plan, sponsored by labor and management, to create the capacity to set up well-structured ad hoc joint teams to attack potential savings and improvements under the umbrella of joint committees in each department. Cost savings and improvements came from such diverse services as the electric utility, the parks department, fleet maintenance, the municipal court and animal control. The resulting Employee Involvement Committees can discuss any issue, other than wage and benefits, that relates to services improvement. A citywide oversight committee helps to share lessons and to help put issues relevant to bargaining into play in the proper forum. With the help of a U.S. Federal Mediation and Conciliation Service (FMCS) grant, Seattle and the coalition of unions jointly built training and administrative capacity to ensure success. The grant and the city support expanded the number of management and union leaders involved with constructive problem solving. Over two dozen involvement committees were launched and made progress within a year, and many departmental joint committees were started or revitalized. The results of the EICs and related arrangements led to and created enthusiasm for expansive changes in the labor-management relationship. These innovative arrangements were also expected to affect the bargaining climate and a broader range of workplace, service and cost items. In a dramatic broadening of these early efforts, the city formed a city-level Labor Management Leadership Committee with key representatives from the city council, the mayor's office and cabinet department. The Seattle example, partly an alternative to managed competition, shows the possibilities in starting small, building capacity, focusing on service through joint efforts, and seeing the expanded trust moving to other aspects of the relationship and creating greater opportunities for improvement. This jointly authored perspective brings insight to understanding how the EICs became a successful event and an effective catalyst for broader change.
Police Officer Candidate Background Investigation Law Enforcement Management's Most Effective Tool for Employing the Most Qualified Candidate
Authors: Bradford David 
Published: July 2015

The Crime Bill of 1994 has generated a large cash flow of federal funds into state and local coffers for hiring additional personnel. In the rush to get the federal funding, many agencies have altered their hiring practices for police personnel in order to meet deadlines and quotas. Agencies have experienced a vast array of libelous situations, occupational problems, non-productive employees, and worst of all, bad cops charged with criminal activities when pre-employment screening practices have been shortcut. This article examines what can happen when hiring practices are accelerated and thorough background investigations condensed or eliminated. The article presents three elements of a quality background investigation and five policy development guidelines for producing a background investigation manual and procedure. The article also presents a sample Background Investigation Manual and Procedure and related forms developed by the author for use in his agency utilizing the concepts and principles presented.
Effect of statins on preventing infectious complications after surgery: Systematic review and meta-analysis
Authors: Ma Bao-Xin , Li Hua , Li Jing-Sen , Wu Sui-Sheng 
Published: July 2015

Objective * These authors contributed equally to this work. A meta-analysis to investigate the association between preoperative statin use and the risk of postoperative infectious complications in patients undergoing surgery. Methods PubMed® and Embase® databases were searched for relevant studies. Data were extracted using a standardized data collection form. The primary effect measure was the odds ratio (OR) of postoperative infectious complications. Summary OR were calculated. Results The analysis included 10 cohort studies with a total of 147 263 participants. Statin use was associated with a lower incidence of postoperative infectious complications in all studies (summary OR 0.917, 95% conﬁdence intervals [CI] 0.862, 0.975, fixed-effects model; summary OR 0.731, 95% CI 0.584, 0.870, random-effects model); cardiac surgery (summary OR 0.673; 95% CI 0.535, 0.847); treatment in the USA (summary OR 0.678; 95% CI 0.597, 0.770); retrospective cohort studies (summary OR 0.664; 95% CI 0.521, 0.846). Conclusion Preoperative statin use is associated with a reduced risk of postoperative infectious complications.
A qualitative meta-synthesis about challenges experienced in occupational therapy practice
Authors: Murray Carolyn , Turpin Merrill , Edwards Ian , Jones Mark 
Published: July 2015

Introduction Information about challenges for occupational therapists is typically provided in small-scale studies from different perspectives. The purpose of this meta-synthesis was to synthesise and report about challenges in occupational therapy practice that appear to penetrate across the profession. Method Databases searched were Ovid Medline, EMBASE, AMED and CINAHL. Search terms were selected after gaining understanding of the topic: occupational therap* AND Exp burnout / OR Exp morals / OR retention OR clinical reasoning OR new graduate OR novice OR transition-to-practice. Studies were critically appraised using the criteria of credibility, transferability, confirmability and dependability. Findings, along with direct quotes, were extracted and data compared and contrasted through first, second and third order analysis. Findings Twenty-four studies were included in the meta-synthesis and three constructs were identified: ‘challenges in context’; ‘personal challenges’ and ‘social and cultural challenges’. These findings inform knowledge about constraining factors on clinical reasoning and the alignment of practice with the occupational therapy philosophy, and give insight into satisfaction with practice, ethical and professional behaviours. Conclusion These findings could inform provision of professional support, education for students and enhance agency to reform practice. More research is needed about professional socialisation, clinical reasoning and ethical issues.