bluuebunny/crossref_metadata_2025 huggingface dataset:
Data‐Based Decision‐Making: Developing a Method for Capturing Teachers’ Understanding of CBM Graphs
Authors: Espin Christine A. , Wayman Miya Miura , Deno Stanley L. , McMaster Kristen L. , de Rooij Mark
Published: January 2017

In this special issue, we explore the decision‐making aspect of data‐based decision‐making. The articles in the issue address a wide range of research questions, designs, methods, and analyses, but all focus on data‐based decision‐making for students with learning difficulties. In this first article, we introduce the topic of data‐based decision‐making and provide an overview of the special issue. We then describe a small, exploratory study designed to develop a method for studying teachers’ understanding and interpretation of Curriculum‐Based Measurement (CBM) graphs. Specifically, we examine whether think‐alouds scored for coherence, specificity, reflectivity, and accuracy differentiate teachers with more or less understanding of CBM data. We conclude the article by discussing the importance of, and the need for, research on teachers’ understanding, interpretation, and use of data for instructional decision‐making.
Wouldn't it be Nice? Moral Rules and Distant Worlds
Authors: Podgorski Abelard
Published: January 2017

Traditional rule consequentialism faces a problem sometimes called the ideal world objection—the worry that by looking only at the consequences in worlds where rules are universally adhered to, the theory fails to account for problems that arise because adherence to rules in the real world is inevitably imperfect. In response, recent theorists have defended sophisticated versions of rule consequentialism which are sensitive to the consequences in worlds with less utopian levels of adherence. In this paper, I argue that these attempts underestimate the problem they are designed to avoid—the worry about ideal worlds is only one manifestation of a deeper and more general problem, the distant world objection, which threatens not only the sophisticated revisions of rule consequentialism, but any view which determines what we ought to do by evaluating worlds that differ from ours in more than what is up to us.
Determinants of Heparin Dosing and Complications in Patients Undergoing Left Atrial Ablation on Uninterrupted Rivaroxaban
Authors: ENRIQUEZ ALAN D. , CHURCHILL TIMOTHY , GAUTAM SANDEEP , CHINITZ JASON S. , BARBHAIYA CHIRAG R. , KUMAR SAURABH , JOHN ROY M. , TEDROW USHA B. , KOPLAN BRUCE A. , STEVENSON WILLIAM G. , MICHAUD GREGORY F.
Published: January 2017

Background

Patients on rivaroxaban have variable international normalized ratios (INRs) but it is uncertain if INR impacts procedural heparin requirement during left atrial ablation. We sought to examine the determinants of heparin dosing in this patient population.

Methods

We reviewed consecutive patients who received rivaroxaban within 24 hours of left atrial ablation and compared them to patients on uninterrupted warfarin. The determinants of heparin requirement were evaluated using regression analysis. We then tested a weight‐based heparin dose prospectively in rivaroxaban patients.

Results

There were 258 patients on rivaroxaban and 213 on warfarin. The mean INR was 1.4 in the rivaroxaban group and 2.3 in the warfarin group (P < 0.01). To achieve an activated clotting time (ACT) >350 seconds, rivaroxaban patients required significantly more heparin (166.9 vs. 78.3 units/kg, P < 0.001). In the rivaroxaban group, body weight was the strongest predictor of heparin dose (r = 0.52), while INR was weakly correlated (r = −0.21). In the prospective group, 25 patients were given an initial heparin dose of 120 units/kg with 22/25 (88%) achieving an ACT > 300 seconds. There were seven and three cases of pericardial effusion in rivaroxaban and warfarin patients, respectively (P = 0.41). The average volume drained in the rivaroxaban group was elevated (988.6 vs. 275.0 mL, P = 0.21).

Conclusions

Body weight is the strongest predictor of procedural heparin requirement during left atrial ablation in patients on uninterrupted rivaroxaban, even in those with an elevated INR. A heparin dose of 120 units/kg achieves an ACT > 300 seconds in the majority of patients. In cases of pericardial effusion, bleeding may be prolonged.
Mapping for Acute Transvenous Phrenic Nerve Stimulation Study (MAPS Study)
Authors: DEKKER LUKAS R.C. , GERRITSE BART , SCHEINER AVRAM , KORNET LILIAN
Published: January 2017

Background

Central sleep apnea syndrome, correlated with the occurrence of heart failure, is characterized by periods of insufficient ventilation during sleep. This acute study in 15 patients aims to map the venous system and determine if diaphragmatic movement can be achieved by phrenic nerve stimulation at various locations within the venous system.

Methods

Subjects underwent a scheduled catheter ablation procedure. During the procedural waiting time, one multielectrode electrophysiology catheter was subsequently placed at the superior and inferior vena cava and the junctions of the left jugular and left brachiocephalic vein and right jugular and right brachiocephalic vein, for phrenic nerve stimulation (1–2 seconds ON/2–3 seconds OFF, 40 Hz, pulse width 210 μs). Diaphragmatic movement was assessed manually and by a breathing mask. During a follow‐up assessment between 2 and 4 weeks postprocedure, occurrence of adverse events was assessed.

Results

In all patients diaphragmatic movement was induced at one or more locations using a median threshold of at least 2 V and maximally 7.5 V (i.e., e 3.3 mA, 14.2 mA). The lowest median current to obtain diaphragmatic stimulation without discomfort was found for the right brachiocephalic vein (4.7 mA). In 12/15 patients diaphragmatic movement could be induced without any discomfort, but in three patients hiccups occurred.

Conclusion

Diaphragmatic stimulation from the brachiocephalic and caval veins is feasible. Potential side effects should be eliminated by adapting the stimulation pattern. This information could be used to design a catheter, combining cardiac pacing with enhancing diaphragm movement during a sleep apnea episode.
Drought coping strategies in cotton: increased crop per drop
Authors: Ullah Abid , Sun Heng , Yang Xiyan , Zhang Xianlong
Published: January 2017

The growth and yield of many crops, including cotton, are affected by water deficit. Cotton has evolved drought specific as well as general morpho‐physiological, biochemical and molecular responses to drought stress, which are discussed in this review. The key physiological responses against drought stress in cotton, including stomata closing, root development, cellular adaptations, photosynthesis, abscisic acid (ABA) and jasmonic acid (JA) production and reactive oxygen species (ROS) scavenging, have been identified by researchers. Drought stress induces the expression of stress‐related transcription factors and genes, such as ROS scavenging, ABA or mitogen‐activated protein kinases (MAPK) signalling genes, which activate various drought‐related pathways to induce tolerance in the plant. It is crucial to elucidate and induce drought‐tolerant traits via quantitative trait loci (QTL) analysis, transgenic approaches and exogenous application of substances. The current review article highlights the natural as well as engineered drought tolerance strategies in cotton.
There and Back Again: Loss and Reacquisition of Two‐Cys Photocycles in Cyanobacteriochromes
Authors: Rockwell Nathan C. , Martin Shelley S. , Lagarias John Clark
Published: January 2017

Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly related to phytochromes. Both families use linear tetrapyrrole (bilin) chromophores that are covalently attached to a conserved Cys residue. CBCRs are more spectrally diverse than phytochromes, with known examples detecting light from the near ultraviolet to the edge of the infrared (370‐750 nm). Detection of ultraviolet to blue light by CBCRs is mediated by a second Cys residue, which forms a covalent linkage to the bilin C10 atom. Second linkage formation is best understood in a subfamily possessing a conserved Asp‐Xaa‐Cys‐Phe (DXCF) motif. Some DXCF CBCRs can isomerize their phycocyanobilin (PCB) chromophores into phycoviolobilin (PVB), a property not reported for other lineages. Both the DXCF Cys and PVB formation have been lost during evolution of other CBCR subfamilies. Using phylogenetic analysis and characterization of recombinantly expressed CBCRs, we show that the DXCF Cys residue has also been reacquired during CBCR evolution. Guided by this knowledge, we successfully reintroduced a second cysteine into a red/green CBCR, restoring blue‐light sensing and PVB formation with two additional substitutions. Our results validate the roles of these residues in CBCR spectral tuning and thus provide new insight into the molecular basis of their spectral diversity.
Investigating the Relationship between the Social and Economic-financial Performance
Authors: Vaia Giovanni , Bisogno Marco , Tommasetti Aurelio
Published: January 2017

Hundreds of studies have explored and measured financial returns related to social performance (Margolis and Walsh, 2003), with controversial results. In addition to these studies’ outcomes, we found, in this body of literature, a lot of innovation in the integration and adaptation of financial analysis tools and models to the study of statistical relationships.In this paper, we investigate the relationship between corporate social performance and corporate financial (and economic) performance, using multiple measures of financial and social performance and by looking statistically at the movement of actual financial and social performance over time. We emphasize the worth of statistical analysis in traditional financial representations.Our findings show how ratio analysis and statistical cause-and-effect validation are not alternatives for developing the financial analysis of sustainability and reporting. We show, through constant testing and a double learning process, the critical relationship between the key factors of financial, economic and social performance.
The Blended Learning Environment: A Viable Alternative for Special Needs Students
Authors: Rivera Jennifer Hall
Published: January 2017

The traditional classroom provides a classical medium for educating students by allowing an open forum of communication between the pupil and teacher. The last twenty-five years have opened a new realm of possibilities in education through the use of technology and virtual supplemental resources, designed to engage learners in all academic levels. As general education and special needs teachers strive to provide the special education student with learning disabilities a constructive, enriching learning experience, the concept of a blended classroom has proven to be successful in achieving this goal. A blended learning environment provides special needs students with a two-fold benefit, a physical, face-to-face teacher of whom to ask questions and seek guidance, in addition to the assets of virtual resources.
Thermal Cycle Stability of Sealing Glass for 8YSZ Coated Cr-Containing Metal Interconnect
Authors: Peng Lian , Bai Yang , Zhu Qingshan
Published: January 2017

An 8 mol. % yttria stabilized zirconia (8YSZ) coating has been prepared on a Cr-containing stainless steel interconnect (SS410) to improve the chemical compatibility of a BaO–B2O3–SiO2 sealing glass with the SS410. Three different methods as, grinding the 8YSZ coating prior to the sealing (fixture A), putting an interlayer glass on the 8YSZ coating prior to the sealing (fixture B), and exerting an external compressive force of ∼10.28 kPa during the sealing (fixture C), have been used to improve the thermal cycle stability of the sealing glass. The fixture A (using the grinding method) and the fixture B (using the interlayer method) both show poor thermal cycle stability. For the fixture C, the external compressive force is found to help the self-healing of the sealing glass. Due to the good chemical compatibility of the sealing glass with the 8YSZ coating, the sealing glass of the fixture C exhibits super long-term thermal cycle stability. The leak rates of the sealing glass of the fixture C show nearly no increase up to 280 thermal cycles, after which the leak rates increase slowly with the thermal cycles and the leak rate is still less than the Solid Energy Convergence Alliance (SECA) limit at the 626th thermal cycle.
Use of Robotic Manipulators to Study Diarthrodial Joint Function
Authors: Debski Richard E. , Yamakawa Satoshi , Musahl Volker , Fujie Hiromichi
Published: January 2017

Diarthrodial joint function is mediated by a complex interaction between bones, ligaments, capsules, articular cartilage, and muscles. To gain a better understanding of injury mechanisms and to improve surgical procedures, an improved understanding of the structure and function of diarthrodial joints needs to be obtained. Thus, robotic testing systems have been developed to measure the resulting kinematics of diarthrodial joints as well as the in situ forces in ligaments and their replacement grafts in response to external loading conditions. These six degrees-of-freedom (DOF) testing systems can be controlled in either position or force modes to simulate physiological loading conditions or clinical exams. Recent advances allow kinematic, in situ force, and strain data to be measured continuously throughout the range of joint motion using velocity-impedance control, and in vivo kinematic data to be reproduced on cadaveric specimens to determine in situ forces during physiologic motions. The principle of superposition can also be used to determine the in situ forces carried by capsular tissue in the longitudinal direction after separation from the rest of the capsule as well as the interaction forces with the surrounding tissue. Finally, robotic testing systems can be used to simulate soft tissue injury mechanisms, and computational models can be validated using the kinematic and force data to help predict in vivo stresses and strains present in these tissues. The goal of these analyses is to help improve surgical repair procedures and postoperative rehabilitation protocols. In the future, more information is needed regarding the complex in vivo loads applied to diarthrodial joints during clinical exams and activities of daily living to serve as input to the robotic testing systems. Improving the capability to accurately reproduce in vivo kinematics with robotic testing systems should also be examined.
Reliability improvements of TiN/Al2O3/TiN for linear high voltage metal–insulator–metal capacitors using an optimized thermal treatment
Authors: Lefevre Aude , Ferreira Delphine , Veillerot Marc , Barnes Jean-Paul , Parat Guy , Czernohorsky Malte , Lallemand Florent
Published: January 2017

Metal–insulator–metal (MIM) capacitors with TiN and high thickness of Al2O3 above 50 nm were fabricated to address high voltage (>30 V) and linear capacitor applications. Atomic layer deposition is used to deposit both TiN and Al2O3 to guarantee a good composition and thickness control. The impact of the deposition process and post-treatment condition on the MIM capacitor's breakdown voltage is studied and correlated with time of flight-secondary ion mass spectrometry (ToF-SIMS). Higher deposition temperature and thermal treatment of TiN and Al2O3 after deposition increase breakdown voltage and improve uniformity. ToF-SIMS demonstrates that Al2O3 higher deposition temperature or rapid thermal processing annealing reduce the diffusion of TiN in Al2O3 leading to thinner TiN/Al2O3 interface layers that influence breakdown voltage and uniformity.
Transmission microwave spectroscopy for local characterization of dielectric materials
Authors: Lucibello Andrea , Joseph Christopher Hardly , Proietti Emanuela , Sardi Giovanni Maria , Capoccia Giovanni , Marcelli Romolo
Published: January 2017

In this work, the authors present a technique for the local characterization of the dielectric properties of materials. More in details, a setup will be described, and the related measurement modeling will be discussed. In this way, it is possible to obtain a calibrated and nondestructive determination of the dielectric constant in a submicrometric region; the detection of any surface or buried metallization is a straightforward application for microelectronics. The analysis is performed as a function of the frequency in the microwave range and, further on, the data can be transformed in time domain for one dimensional tomography. The authors will show that microwave spectroscopy can be performed by means of standard coaxial pins employed as probes for measurements both in reflection and transmission mode, giving the information of the frequency dependent properties of the exploited material or structure by means of the measured impedance. Experiments are performed in the range between 1 and 18 GHz, and different dielectric samples are tested. In order to evaluate the surface and subsurface measuring capability, samples obtained by thin metallic film deposition on a silicon wafer and buried by a polymeric layer are realized and characterized.
Germany to probe Nazi-era medical science
Authors: Gannon Megan
Published: January 2017

Overlooked brain tissue slides prompt another look at “euthanasia” victims.
Eocene lantern fruits from Gondwanan Patagonia and the early origins of Solanaceae
Authors: Wilf Peter , Carvalho Mónica R. , Gandolfo María A. , Cúneo N. Rubén
Published: January 2017

Shedding light on fossil lantern fruit

The Solanaceae (or nightshades) are one of the best-studied plant families, yet their evolutionary origins have thus far been relatively obscure. Corroborative fossil evidence of molecular phylogenetic divergence dates has been lacking. Wilf
et al.
present 52-million-year-old fossils of lantern fruits from Argentina, which they ascribe to the modern genus
Physalis.
These fossil finds suggest a much earlier origin of the lantern fruit lineage and indicate that the Solanaceae may have diversified before the final breakup of the Gondwanan supercontinent.

Science
, this issue p.
71
Rb1
and
Trp53
cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance
Authors: Ku Sheng Yu , Rosario Spencer , Wang Yanqing , Mu Ping , Seshadri Mukund , Goodrich Zachary W. , Goodrich Maxwell M. , Labbé David P. , Gomez Eduardo Cortes , Wang Jianmin , Long Henry W. , Xu Bo , Brown Myles , Loda Massimo , Sawyers Charles L. , Ellis Leigh , Goodrich David W.
Published: January 2017

Evading cancer drugs by identity fraud

Prostate cancer growth is fueled by male hormones called androgens. Drugs targeting the androgen receptor (AR) are initially efficacious, but most tumors eventually become resistant (see the Perspective by Kelly and Balk). Mu
et al.
found that prostate cancer cells escaped the effects of androgen deprivation therapy through a change in lineage identity. Functional loss of the tumor suppressors TP53 and RB1 promoted a shift from AR-dependent luminal epithelial cells to AR-independent basal-like cells. In related work, Ku
et al.
found that prostate cancer metastasis, lineage switching, and drug resistance were driven by the combined loss of the same tumor suppressors and were accompanied by increased expression of the epigenetic regulator Ezh2. Ezh2 inhibitors reversed the lineage switch and restored sensitivity to androgen deprivation therapy in experimental models.

Science
, this issue p.
84
, p.
78
; see also p.
29
A plan for U.K. science after the European Union referendum
Authors: Galsworthy Mike , McKee Martin
Published: January 2017

Funding, regulation, immigration, and investment should be points of focus
A conundrum for density functional theory
Authors: Hammes-Schiffer Sharon
Published: January 2017

DFT studies may sometimes get the right results for the wrong reasons
Perception drives the evolution of observable traits
Authors: Farris Hamilton
Published: January 2017

Bats choose flowers on the basis of nectar volume and concentration, affecting how the flowers evolve
Reprogramming to resist
Authors: Kelly Kathleen , Balk Steven P.
Published: January 2017

Prostate cancer cells alter identity to resist therapy
Population Pharmacokinetics of Piperacillin in Nonobese, Obese, and Morbidly Obese Critically Ill Patients
Authors: Alobaid Abdulaziz S. , Wallis Steven C. , Jarrett Paul , Starr Therese , Stuart Janine , Lassig-Smith Melissa , Mejia Jenny Lisette Ordóñez , Roberts Michael S. , Roger Claire , Udy Andrew A. , Lipman Jeffrey , Roberts Jason A.
Published: January 2017

The treatment of infections in critically ill obese and morbidly obese patients is challenging because of the combined physiological changes that result from obesity and critical illness. The aim of this study was to describe the population pharmacokinetics of piperacillin in a cohort of critically ill patients, including obese and morbidly obese patients. Critically ill patients who received piperacillin-tazobactam were classified according to their body mass index (BMI) as nonobese, obese, and morbidly obese. Plasma samples were collected, and piperacillin concentrations were determined by a validated chromatographic method. Population pharmacokinetic analysis and Monte Carlo dosing simulations were performed using Pmetrics software. Thirty-seven critically ill patients (including 12 obese patients and 12 morbidly obese patients) were enrolled. The patients' mean ± standard deviation age, weight, and BMI were 50 ± 15 years, 104 ± 35 kg, and 38.0 ± 15.0 kg/m
2
, respectively. The concentration-time data were best described by a two-compartment linear model. The mean ± SD parameter estimates for the final covariate model were a clearance of 14.0 ± 7.1 liters/h, a volume of distribution of the central compartment of 49.0 ± 19.0 liters, an intercompartmental clearance from the central compartment to the peripheral compartment of 0.9 ± 0.6 liters · h
−1
, and an intercompartmental clearance from the peripheral compartment to the central compartment of 2.3 ± 2.8 liters · h
−1
. A higher measured creatinine clearance and shorter-duration infusions were associated with a lower likelihood of achieving therapeutic piperacillin exposures in patients in all BMI categories. Piperacillin pharmacokinetics are altered in the presence of obesity and critical illness. As with nonobese patients, prolonged infusions increase the likelihood of achieving therapeutic concentrations.
Subcellular Partitioning and Intramacrophage Selectivity of Antimicrobial Compounds against Mycobacterium tuberculosis
Authors: Schump Michael D. , Fox Douglas M. , Bertozzi Carolyn R. , Riley Lee W.
Published: January 2017

The efficacy of antimicrobial drugs against
Mycobacterium tuberculosis
, an intracellular bacterial pathogen, is generally first established by testing compounds against bacteria in axenic culture. However, inside infected macrophages, bacteria encounter an environment which differs substantially from broth culture and are subject to important host-dependent pharmacokinetic phenomena which modulate drug activity. Here, we describe how pH-dependent partitioning drives asymmetric antimicrobial drug distribution in
M. tuberculosis-
infected macrophages. Specifically, weak bases with moderate activity against
M. tuberculosis
(fluoxetine, sertraline, and dibucaine) were shown to accumulate intracellularly due to differential permeability and relative abundance of their ionized and nonionized forms. Nonprotonatable analogs of the test compounds did not show this effect. Neutralization of acidic organelles directly with ammonium chloride or indirectly with bafilomycin A1 partially abrogated the growth restriction of these drugs. Using high-performance liquid chromatography, we quantified the degree of accumulation and reversibility upon acidic compartment neutralization in macrophages and observed that accumulation was greater in infected than in uninfected macrophages. We further demonstrate that the efficacy of a clinically used compound, clofazimine, is augmented by pH-based partitioning in a macrophage infection model. Because the parameters which govern this effect are well understood and are amenable to chemical modification, this knowledge may enable the rational development of more effective antibiotics against tuberculosis.
Pseudomonas aeruginosa Oligoribonuclease Contributes to Tolerance to Ciprofloxacin by Regulating Pyocin Biosynthesis
Authors: Chen Fei , Chen Gukui , Liu Yiwei , Jin Yongxin , Cheng Zhihui , Liu Yang , Yang Liang , Jin Shouguang , Wu Weihui
Published: January 2017

Bacterial oligoribonuclease (Orn) is a conserved 3′-to-5′ exonuclease. In
Pseudomonas aeruginosa
, it has been demonstrated that Orn plays a major role in the hydrolysis of pGpG, which is required for cyclic-di-GMP homeostasis. Meanwhile, Orn is involved in the degradation of nanoRNAs, which can alter global gene expression by serving as transcription initiation primers. Previously, we found that Orn is required for the type III secretion system and pathogenesis of
P. aeruginosa
, indicating a role of Orn in the bacterial response to environmental stimuli. Here we report that Orn is required for the tolerance of
P. aeruginosa
to ciprofloxacin. Transcriptome analysis of an
orn
mutant revealed the upregulation of pyocin biosynthesis genes. Mutation of genes involved in pyocin biosynthesis in the background of an
orn
mutant restored bacterial tolerance to ciprofloxacin. We further demonstrate that the upregulation of pyocin biosynthesis genes is due to RecA-mediated autoproteolysis of PrtR, which is the major negative regulator of pyocin biosynthesis genes. In addition, the SOS response genes were upregulated in the
orn
mutant, indicating a DNA damage stress. Therefore, our results revealed a novel role of Orn in bacterial tolerance to ciprofloxacin.
Population Pharmacokinetic Model of Doxycycline Plasma Concentrations Using Pooled Study Data
Authors: Hopkins Ashley M. , Wojciechowski Jessica , Abuhelwa Ahmad Y. , Mudge Stuart , Upton Richard N. , Foster David J. R.
Published: January 2017

The literature presently lacks a population pharmacokinetic analysis of doxycycline. This study aimed to develop a population pharmacokinetic model of doxycycline plasma concentrations that could be used to assess the power of bioequivalence between Doryx delayed-release tablets and Doryx MPC. Doxycycline pharmacokinetic data were available from eight phase 1 clinical trials following single/multiple doses of conventional-release doxycycline capsules, Doryx delayed-release tablets, and Doryx MPC under fed and fasted conditions. A population pharmacokinetic model was developed in a stepwise manner using NONMEM, version 7.3. The final covariate model was developed according to a forward inclusion (
P
< 0.01) and then backward deletion (
P
< 0.001) procedure. The final model was a two-compartment model with two-transit absorption compartments. Structural covariates in the base model included formulation effects on relative bioavailability (
F
), absorption lag (ALAG), and the transit absorption rate (KTR) under the fed status. An absorption delay (lag) for the fed status (FTLAG2 = 0.203 h) was also included in the model as a structural covariate. The fed status was observed to decrease
F
by 10.5%, and the effect of female sex was a 14.4% increase in clearance. The manuscript presents the first population pharmacokinetic model of doxycycline plasma concentrations following oral doxycycline administration. The model was used to assess the power of bioequivalence between Doryx delayed-release tablets and Doryx MPC, and it could potentially be used to critically examine and optimize doxycycline dose regimens.
Local Delivery of the Toll-Like Receptor 9 Ligand CpG Downregulates Host Immune and Inflammatory Responses, Ameliorating Established Leishmania (Viannia) panamensis Chronic Infection
Authors: Ehrlich Allison K. , Fernández Olga L. , Rodriguez-Pinto Daniel , Castilho Tiago M. , Corral Caridad Maria J. , Goldsmith-Pestana Karen , Saravia Nancy Gore , McMahon-Pratt Diane
Published: January 2017

Infection byLeishmania(Viannia)panamensis, the predominant etiologic agent for cutaneous leishmaniasis in Colombia, is characterized by a chronic mixed inflammatory response. Current treatment options are plagued by toxicity, lengthy treatment regimens, and growing evidence of drug resistance. Immunotherapy, modulating the immune system to mount a protective response, may provide an alternate therapeutic approach. We investigated the ability of the Toll-like receptor 9 (TLR9) ligand CpG to modulate established disease in theL. (V.)panamensismouse model. Treatment of established infection with a high dose (50 μg) of CpG ameliorated disease and lowered parasite burden. Interestingly, immediately after treatment there was a significant increase in transforming growth factor β (TGF-β) and concomitantly an increase in T regulatory cell (Treg) function. Although a general reduction in cell-mediated immune cytokine and chemokine (gamma interferon [IFN-γ], interleukin 10 [IL-10], IL-13, IL-6, granulocyte-macrophage colony-stimulating factor [GM-CSF], IL-4, and MIP-1α) responses of the treated mice was observed, certain chemokines (RANTES, monocyte chemoattractant protein 1[MCP-1], and IP-10) were increased. Further, in peripheral blood mononuclear cells (PBMCs) from patients with cutaneous leishmaniasis, CpG treatment similarly exhibited a dose-response effect on the production of IFN-γ, IL-17, IL-10, and IL-13, with reductions observed at higher doses. To further understand the underlying mechanisms and cell populations driving the CpG mediated response, we examined theex vivodose effects mediated by the TLR9+cell populations (dendritic cells, macrophages, and B cells) found to accumulate labeled CpGin vivo. Notably, B cells altered the production of IL-17, IL-13, and IFN-γ, supporting a role for B cells functioning as antigen-presenting cells (APCs) and/or regulatory cells during infection. Interestingly, B cells have been previously demonstrated as a primary type of APC in patients infected withL. (V.)panamensisand thus may be useful targets of immunotherapy. Collectively, our results show that CpG-induced immune regulation leads to a dampening of the host immune response and healing in the mouse model, and it may provide an alternate approach to treatment of cutaneous leishmaniasis caused byL. (V.)panamensis.
The functional domain of adenylate cyclase associated with entry into meiosis in Saccharomyces cerevisiae
Authors: Uno I , Oshima T , Hirata A , Ishikawa T
Published: January 2017

Diploid yeast cells that carry a part of the CYR1 gene deficient in a region coding for the N-terminal domain of adenylate cyclase were growth arrested and accumulated unbudded cells after inoculation into complete medium or nitrogen-free medium, but produced many cells which had one or more buds after incubation in sporulation medium. The cells incubated in sporulation medium had abnormal spindles which were free from the spindle pole bodies, larger in size, or frequently distributed in cytoplasm. The levels of cyclic AMP in these cells did not decrease to the wild-type level after transfer to the sporulation medium and remained at a constant level. The results suggest that the N-terminal domain of adenylate cyclase is associated with the regulatory function for sporulation. The environmental signals for sporulation may be transferred to the adenylate cyclase system through a factor that negatively interacts with the N-terminal domain of this enzyme.
Biotransformations of carboxylated aromatic compounds by the acetogen Clostridium thermoaceticum: generation of growth-supportive CO2 equivalents under CO2-limited conditions
Authors: Hsu T , Daniel S L , Lux M F , Drake H L
Published: January 2017

Clostridium thermoaceticum ATCC 39073 converted vanillate to catechol. Although carboxylated aromatic compounds which did not contain methoxyl groups were not by themselves growth supportive, protocatechuate and p-hydroxybenzoate (nonmethoxylated aromatic compounds) were converted to catechol and phenol, respectively, during carbon monoxide-dependent growth. Syringate is not subject to decarboxylation by C. thermoaceticum (Z. Wu, S. L. Daniel, and H. L. Drake, J. Bacteriol. 170:5705-5708, 1988), and sustained growth at the expense of syringate-derived methoxyl groups was dependent on supplemental CO2. In contrast, vanillate was growth supportive in the absence of supplemental CO2, and 14CO2 was the major 14C-labeled product during [carboxyl-14C]vanillate-dependent growth. Furthermore, the decarboxylation of protocatechuate and p-hydroxybenzoate supported methanol- and 1,2,3-trimethoxybenzene-dependent growth (CO2 is required for growth at the expense of these substrates) when supplemental CO2 was depleted from the growth medium, and the decarboxylation of protocatechuate was concomitant with improved cell yields of methanol cultures. These findings demonstrate that (i) C. thermoaceticum is competent in the decarboxylation of certain aromatic compounds and (ii) under certain conditions, decarboxylation may be integrated to the flow of carbon and energy during acetogenesis.
Agmenellum quadruplicatum M.AquI, a novel modification methylase
Authors: Karreman C , de Waard A
Published: January 2017

The complete type II modification methylase of Agmenellum quadruplicatum was cloned in Escherichia coli as an R.Sau3A fragment of approximately 4.5 kilobases. The coding sequence was contained in a stretch of 1,156 base pairs which was organized into two parallel, partly overlapping open reading frames of 248 and 139 codons. In vivo complementation experiments showed that the synthesis of both predicted peptides was required for full methylase activity. The amino acid sequences were considerably similar to regions of other deoxycytidylate methylases.
Chemotactic control of the two flagellar systems of Vibrio parahaemolyticus
Authors: Sar N , McCarter L , Simon M , Silverman M
Published: January 2017

Vibrio parahaemolyticus synthesizes two distinct flagellar organelles, the polar flagellum (Fla), which propels the bacterium in a liquid environment (swimming), and the lateral flagella (Laf), which are responsible for movement over surfaces (swarming). Chemotactic control of each of these flagellar systems was evaluated separately by analyzing the behavioral responses of strains defective in either motility system, i.e., Fla+ Laf- (swimming only) or Fla- Laf+ (swarming only) mutants. Capillary assays, modified by using viscous solutions to measure swarming motility, were used to quantitate chemotaxis by the Fla+ Laf- or Fla- Laf+ mutants. The behavior of the mutants was very similar with respect to the attractant compounds and the concentrations which elicited responses. The effect of chemotaxis gene defects on the operation of the two flagellar systems was also examined. A locus previously shown to encode functions required for chemotactic control of the polar flagellum was cloned and mutated by transposon Tn5 insertion in Escherichia coli, and the defects in this locus, che-4 and che-5, were then transferred to the Fla+ Laf- or Fla- Laf+ strains of V. parahaemolyticus. Introduction of the che mutations into these strains prevented chemotaxis into capillary tubes and greatly diminished movement of bacteria over the surface of agar media or through semisolid media. We conclude that the two flagellar organelles, which consist of independent motor-propeller structures, are directed by a common chemosensory control system.
Disruption of a rhodaneselike gene results in cysteine auxotrophy in Saccharopolyspora erythraea
Authors: Donadio S , Shafiee A , Hutchinson C R
Published: January 2017

A 3,373-base-pair DNA segment from a clone fortuitously isolated from Saccharopolyspora erythraea by hybridization to an oligodeoxynucleotide probe was sequenced. Computer-assisted analysis of the nucleotide sequence reveals three closely linked Streptomyces open reading frames plus a fourth converging on the others. The deduced product of one of them, ORF2, shows considerable similarity to bovine liver rhodanese. orf2, and the closely linked orf3 located just downstream of it, were disrupted by insertion of an apramycin resistance cassette into the orf2 coding sequence along with inversion of the fragment carrying most of orf2 and orf3 via two successive recombinational events in the wild-type strain. The mutant strain thus created contains wild-type levels of rhodanese activity but cannot grow on minimal medium. It is a cysteine auxotroph, capable of utilizing efficiently only thiosulfate among the inorganic sulfur sources tested. orf2 has been designated cysA. The possible role of the rhodaneselike cysA gene product in thiosulfate formation is discussed.
Cloned aerolysin of Aeromonas hydrophila is exported by a wild-type marine Vibrio strain but remains periplasmic in pleiotropic export mutants
Authors: Wong K R , McLean D M , Buckley J T
Published: January 2017

With a wide host range vector, the structural gene aerA for the hole-forming extracellular protein aerolysin of Aeromonas hydrophila was cloned into the marine Vibrio sp. strain 60 and into three pleiotropic export mutants (epr mutants). The parent strain and all of the mutants were able to express the protein with the aerA promoter in the plasmid. The parent strain exported proaerolysin into the medium, while all of the mutants accumulated the protoxin in their periplasms. Two of the mutants also accumulated protease; however, as we have found earlier with A. hydrophila, the periplasmic form of proaerolysin in the Vibrio sp. must somehow be protected from proteolysis because it was not converted to active toxin until the cells were shocked. Conversion could be prevented by adding o-phenanthroline to the solutions used in shocking. These results show that the export pathway in the marine Vibrio sp. is very similar to the pathway in A. hydrophila.
Chromosomal organization and expression of Escherichia coli pabA
Authors: Tran P V , Bannor T A , Doktor S Z , Nichols B P
Published: January 2017

The pabA gene in Escherichia coli and Salmonella typhimurium encodes the glutamine amidotransferase subunit of para-aminobenzoate synthase, which catalyzes the first reaction in the conversion of chorismate to para-aminobenzoate (PABA). We have determined the nucleotide sequences of 1,362 base pairs preceding E. coli pabA and of 981 base pairs preceding S. typhimurium pabA. The nucleotide sequences suggest the presence of two protein-coding regions immediately upstream of pabA, designated orf1 and fic. Transcription analysis indicates that E. coli pabA is encoded by two overlapping transcriptional units. The polycistronic transcriptional unit includes orf1-fic-pabA and is initiated by the promoter designated P2. The monocistronic unit includes only pabA and is initiated by the promoter designated P1, which is located in the fic-coding region. Both promoters transcribe pabA to about the same steady-state level. However, expression analysis using chromosomal pabA-lacZ translational fusions indicated that P1 expressed PabA at least 50-fold more efficiently than P2. pabA-dependent growth rate analysis indicates that P1 is essential and P2 is dispensable for PABA metabolism. In the absence of P1, growth was reduced as a result of insufficient PabA expressed from P2. The significance of these results and possible posttranscriptional control mechanisms which affect PabA expression from the P2-initiated polycistronic unit are discussed.
In vivo degradation of secreted fusion proteins by the Escherichia coli outer membrane protease OmpT
Authors: Baneyx F , Georgiou G
Published: January 2017

The Escherichia coli outer membrane protease OmpT (protease VII) has been shown to degrade several proteins in vitro, but its function in vivo is uncertain. We demonstrate that OmpT participates in the degradation of a fusion protein secreted into the periplasmic space. A strain with mutations in degP (K.L. Strauch and J. Beckwith, Proc. Natl. Acad. Sci. USA 85:1576-1580, 1988) and ompT exhibits a cumulative decrease in protein degradation and should be useful for the expression of proteolytically sensitive secreted proteins.
Characterization and Diagnostic Application of Trypanosoma cruzi Trypomastigote Excreted-Secreted Antigens Shed in Extracellular Vesicles Released from Infected Mammalian Cells
Authors: Bautista-López Norma L. , Ndao Momar , Camargo Fabio Vasquez , Nara Takeshi , Annoura Takeshi , Hardie Darryl B. , Borchers Christoph H. , Jardim Armando
Published: January 2017

Chagas disease, caused byTrypanosoma cruzi, although endemic in many parts of Central and South America, is emerging as a global health threat through the potential contamination of blood supplies. Consequently, in the absence of a gold standard assay for the diagnosis of Chagas disease, additional antigens or strategies are needed. A proteomic analysis of the trypomastigote excreted-secreted antigens (TESA) associated with exosomal vesicles shed byT. cruziidentified ∼80 parasite proteins, with the majority beingtrans-sialidases. Mass spectrometry analysis of immunoprecipitation products performed using Chagas immune sera showed a marked enrichment in a subset of TESA proteins. Of particular relevance for diagnostic applications were the retrotransposon hot spot (RHS) proteins, which are absent inLeishmaniaspp., parasites that often confound diagnosis of Chagas disease. Interestingly, serological screens using recombinant RHS showed a robust immunoreactivity with sera from patients with clinical stages of Chagas ranging from asymptomatic to advance cardiomyopathy and this immunoreactivity was comparable to that of crude TESA. More importantly, no cross-reactivity with RHS was detected with sera from patients with malaria, leishmaniasis, toxoplasmosis, or African sleeping sickness, making this protein an attractive reagent for diagnosis of Chagas disease.
Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm
Authors: Harju Inka , Lange Christoph , Kostrzewa Markus , Maier Thomas , Rantakokko-Jalava Kaisu , Haanperä Marjo
Published: January 2017

Reliable distinction ofStreptococcus pneumoniaeand viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation betweenS. pneumoniaeand closely relatedSreptococcusmitisspecies group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation betweenS. pneumoniaeandS. mitisspecies group streptococci. One hundred one clinicalS. mitisspecies group streptococcal strains and 188 clinicalS. pneumoniaestrains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation ofS. pneumoniaeandS. mitisspecies group streptococci: when the new database version containing 5,627 strains was used, only one of the 101S. mitisspecies group isolates was misidentified asS. pneumoniae, whereas 66 of them were misidentified asS. pneumoniaewhen the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of theS. mitisspecies group strains asS. pneumoniae. AllS. pneumoniaestrains were correctly identified asS. pneumoniaewith both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and otherS. mitisspecies group streptococci with the MALDI Biotyper.
The Bactec FX Blood Culture System Detects Brucella melitensis Bacteremia in Adult Patients within the Routine 1-Week Incubation Period
Authors: Sagi Moshe , Nesher Lior , Yagupsky Pablo
Published: January 2017

The performance of the Bactec FX blood culture system for detecting
Brucella
bacteremia within the routine 1-week incubation period was assessed in a prospective study conducted in an area in southern Israel in which
Brucella melitensis
is endemic. Aerobic vials (BD Bactec Plus Aerobic/F medium) inoculated with blood specimens obtained from adult patients with positive Rose-Bengal screening test results were monitored for 4 consecutive weeks, and blind subcultures of negative vials were performed on solid media on days 7 and 28. During a 16-month period, a total of 31 (35.2%) of 88 cultures, obtained from 19 (38.0%) of 50 patients, were positive for
Brucella melitensis
. The blood culture instrument identified 30 (96.8%) of 31 positive vials within 7 days of incubation; the single positive vial that was missed by the automated readings was detected only by the blind subculture performed on day 28. It is concluded that the Bactec FX system is able to detect the vast majority of episodes of
Brucella
bacteremia within the 1-week incubation protocol instituted in most clinical microbiology laboratories and without the need to perform blind subcultures of negative vials, enabling early diagnosis and saving labor and incubation time and space.
Human Cytomegalovirus (HCMV)-Specific CD4
+
T Cells Are Polyfunctional and Can Respond to HCMV-Infected Dendritic Cells
In Vitro
Authors: Jackson Sarah E. , Sedikides George X. , Mason Gavin M. , Okecha Georgina , Wills Mark R.
Published: January 2017

Human cytomegalovirus (HCMV) infection and periodic reactivation are generally well controlled by the HCMV-specific T cell response in healthy people. While the CD8
+
T cell response to HCMV has been extensively studied, the HCMV-specific CD4
+
T cell effector response is not as well understood, especially in the context of direct interactions with HCMV-infected cells. We screened the gamma interferon (IFN-γ) and interleukin-10 (IL-10) responses to 6 HCMV peptide pools (pp65, pp71, IE1, IE2, gB, and US3, selected because they were the peptides most frequently responded to in our previous studies) in 84 donors aged 23 to 74 years. The HCMV-specific CD4
+
T cell response to pp65, IE1, IE2, and gB was predominantly Th1 biased, with neither the loss nor the accumulation of these responses occurring with increasing age. A larger proportion of donors produced an IL-10 response to pp71 and US3, but the IFN-γ response was still dominant. CD4
+
T cells specific to the HCMV proteins studied were predominantly effector memory cells and produced both cytotoxic (CD107a expression) and cytokine (macrophage inflammatory protein 1β secretion) effector responses. Importantly, when we measured the CD4
+
T cell response to cytomegalovirus (CMV)-infected dendritic cells
in vitro
, we observed that the CD4
+
T cells produced a range of cytotoxic and secretory effector functions, despite the presence of CMV-encoded immune evasion molecules. CD4
+
T cell responses to HCMV-infected dendritic cells were sufficient to control the dissemination of virus in an
in vitro
assay. Together, the results show that HCMV-specific CD4
+
T cell responses, even those from elderly individuals, are highly functional and are directly antiviral.

IMPORTANCE
Human cytomegalovirus (HCMV) infection is carried for a lifetime and in healthy people is kept under control by the immune system. HCMV has evolved many mechanisms to evade the immune response, possibly explaining why the virus is never eliminated during the host's lifetime. The dysfunction of immune cells associated with the long-term carriage of HCMV has been linked with poor responses to new pathogens and vaccines when people are older. In this study, we investigated the response of a subset of immune cells (CD4
+
T cells) to HCMV proteins in healthy donors of all ages, and we demonstrate that the functionality of CD4
+
T cells is maintained. We also show that CD4
+
T cells produce effector functions in response to HCMV-infected cells and can prevent virus spread. Our work demonstrates that these HCMV-specific immune cells retain many important functions and help to prevent deleterious HCMV disease in healthy older people.