bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the DNA-binding mechanism of a LytTR-type transcription regulator
Authors: Behr Stefan , Heermann Ralf , Jung Kirsten 
Published: March 2016

Most bacterial response regulators (RRs) make contact with DNA through a recognition α-helix in their DNA-binding domains. An emerging class of RRs interacts with DNA via a relatively novel type of binding domain, called the LytTR domain, which is mainly composed of β-strands. YpdB belongs to this latter class, is part of a nutrient-sensing network in Escherichia coli and triggers expression of its only target gene, yhjX, in response to extracellular pyruvate. Expression of yhjX mainly occurs in the late exponential growth phase, and in a pulsed manner. Although the DNA-binding sites for YpdB are well defined, exactly how YpdB initiates pulsed gene expression has remained elusive. To address this question, we measured the binding kinetics of wild-type YpdB and the phosphomimetic variant YpdB-D53E to the yhjX promoter region (PyhjX) using surface plasmon resonance (SPR) spectroscopy combined with interaction map® (IM) analysis. Both YpdB and YpdB-D53E bound as monomers to the tandem-repeat sequences in the promoter, with YpdB-D53E displaying a higher maximal binding rate than YpdB. Furthermore, we identified a high-affinity (A-site) and a low-affinity binding site (B-site) within the yhjX promoter. Only YpdB-D53E utilizes an ‘AB-BA’ DNA-binding mechanism, involving sequential and cooperative promoter binding, and rapid, successive promoter clearance. We propose that response regulator phosphorylation, in combination with the cycle of cooperative DNA binding and rapid promoter clearance just described, can account for pulsed gene expression.
Can Application of Commercial Microbial Products Improve Fish Growth and Water Quality in Freshwater Polyculture?
Authors: Tang Jin-yu , Dai Yang-xin , Li You-ming , Qin Jian-guang , Wang Yan 
Published: March 2016

Abstract
A 31-d experiment was conducted to examine the effects of three commercial microbial products (Novozymes pond plus, Zhongshui BIO-AQUA, and Effective Microorganisms) on production performance and water quality in freshwater tanks stocked with Grass Carp Ctenopharyngodon idellus, Gibel Carp Carassius gibelio and Silver Carp Hypophthalmichthys molitrix. Four treatments were used: blank control (BL), adding Novozymes pond plus (NO), adding BIO-AQUA (PB), or adding Effective Microorganisms (EM). The fish were fed daily with a formulated feed, and each of the microbial products was added to the tanks every 10 d. No significant differences were found in survival, weight gain, and feed conversion ratio of the fishes, Secchi depth, chemical water quality, and phytoplankton between the blank control and any other treatments (NO, PB and EM). This study indicates that the addition of these three microbial products every 10 d has limited function to improve production performance and water quality in freshwater polyculture of Grass Carp, Gibel Carp, and Silver Carp within the first 31 d of application.
DUDes: a top-down taxonomic profiler for metagenomics
Authors: Piro Vitor C. , Lindner Martin S. , Renard Bernhard Y. 
Published: March 2016

Abstract
Motivation: Species identification and quantification are common tasks in metagenomics and pathogen detection studies. The most recent techniques are built on mapping the sequenced reads against a reference database (e.g. whole genomes, marker genes, proteins) followed by application-dependent analysis steps. Although these methods have been proven to be useful in many scenarios, there is still room for improvement in species and strain level detection, mainly for low abundant organisms.
Results: We propose a new method: DUDes, a reference-based taxonomic profiler that introduces a novel top-down approach to analyze metagenomic Next-generation sequencing (NGS) samples. Rather than predicting an organism presence in the sample based only on relative abundances, DUDes first identifies possible candidates by comparing the strength of the read mapping in each node of the taxonomic tree in an iterative manner. Instead of using the lowest common ancestor we propose a new approach: the deepest uncommon descendent. We showed in experiments that DUDes works for single and multiple organisms and can identify low abundant taxonomic groups with high precision.
Availability and Implementation: DUDes is open source and it is available at http://sf.net/p/dudes
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: renardB@rki.de
Measles Outbreak Associated With Low Vaccine Effectiveness Among Adults in Pohnpei State, Federated States of Micronesia, 2014
Authors: Hales Craig M. , Johnson Eliaser , Helgenberger Louisa , Papania Mark J. , Larzelere Maribeth , Gopalani Sameer V. , Lebo Emmaculate , Wallace Greg , Moturi Edna , Hickman Carole J. , Rota Paul A. , Alexander Hinden S. , Marin Mona 
Published: March 2016

AbstractBackground.  A measles outbreak in Pohnpei State, Federated States of Micronesia in 2014 affected many persons who had received ≥1 dose of measles-containing vaccine (MCV). A mass vaccination campaign targeted persons aged 6 months to 49 years, regardless of prior vaccination.Methods.  We evaluated vaccine effectiveness (VE) of MCV by comparing secondary attack rates among vaccinated and unvaccinated contacts after household exposure to measles.Results.  Among 318 contacts, VE for precampaign MCV was 23.1% (95% confidence interval [CI], −425 to 87.3) for 1 dose, 63.4% (95% CI, −103 to 90.6) for 2 doses, and 95.9% (95% CI, 45.0 to 100) for 3 doses. Vaccine effectiveness was 78.7% (95% CI, 10.1 to 97.7) for campaign doses received ≥5 days before rash onset in the primary case and 50.4% (95% CI, −52.1 to 87.9) for doses received 4 days before to 3 days after rash onset in the primary case. Vaccine effectiveness for most recent doses received before 2010 ranged from 51% to 57%, but it increased to 84% for second doses received in 2010 or later.Conclusions.  Low VE was a major source of measles susceptibility in this outbreak; potential reasons include historical cold chain inadequacies or waning of immunity. Vaccine effectiveness of campaign doses supports rapid implementation of vaccination campaigns in outbreak settings.
Decision Making Under the Gambler’s Fallacy: Evidence from Asylum Judges, Loan Officers, and Baseball Umpires
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Authors: Chen Daniel L. , Moskowitz Tobias J. , Shue Kelly 
Published: March 2016

Abstract
We find consistent evidence of negative autocorrelation in decision making that is unrelated to the merits of the cases considered in three separate high-stakes field settings: refugee asylum court decisions, loan application reviews, and Major League Baseball umpire pitch calls. The evidence is most consistent with the law of small numbers and the gambler’s fallacy—people underestimating the likelihood of sequential streaks occurring by chance—leading to negatively autocorrelated decisions that result in errors. The negative autocorrelation is stronger among more moderate and less experienced decision makers, following longer streaks of decisions in one direction, when the current and previous cases share similar characteristics or occur close in time, and when decision makers face weaker incentives for accuracy. Other explanations for negatively autocorrelated decisions such as quotas, learning, or preferences to treat all parties fairly are less consistent with the evidence, though we cannot completely rule out sequential contrast effects as an alternative explanation.
A Novel Algorithm to Derive Spread of Excitation Based on Deconvolution
Authors: Biesheuvel Jan Dirk , Briaire Jeroen J. , Frijns Johan H. M. 
Published: March 2016

Objective:
The width of the spread of excitation (SOE) curve has been widely thought to represent an estimate of SOE. Therefore, correlates between psychophysical parameters, such as pitch discrimination and speech perception, and the width of SOE curves, have long been investigated. However, to date, no relationships between these objective and subjective measurements have yet been determined. In a departure from the current thinking, the authors now propose that the SOE curve, recorded with forward masking, is the equivalent of a convolution operation. As such, deconvolution would be expected to retrieve the excitation areas attributable to either masker or probe, potentially more closely revealing the actual neural SOE. This study aimed to develop a new analytical tool with which to derive SOE using this principle.

Design:
Intraoperative SOE curve measurements of 16 subjects, implanted with an Advanced Bionics implant, were analyzed. Evoked compound action potential (ECAP)-based SOE curves were recorded on electrodes 3 to 16, using the forward masker paradigm, with variable masker. The measured SOE curves were then compared with predicted SOE curves, built by the convolution of basic excitation density profiles (EDPs). Predicted SOE curves were fitted to the measured SOEs by iterative adjustment of the EDPs for the masker and the probe.

Results:
It was possible to generate a good fit between the predicted and measured SOE curves, inclusive of their asymmetry. The rectangular EDP was of least value in terms of its ability to generate a good fit; smoother SOE curves were modeled using the exponential or Gaussian EDPs. In most subjects, the EDP width (i.e., the size of the excitation area) gradually changed from wide at the apex of the electrode array, to narrow at the base. A comparison of EDP widths to SOE curve widths, as calculated in the literature, revealed that the EDPs now provide a measure of the SOE that is qualitatively distinct from that provided using conventional methods.

Conclusions:
This study shows that an eCAP-based SOE curve, measured with forward masking, can be treated as a convolution of EDPs for masker and probe. The poor fit achieved for the measured and modeled data using the rectangular EDP, emphasizes the requirement for a sloping excitation area to mimic actual SOE recordings. Our deconvolution method provides an explanation for the frequently observed asymmetry of SOE curves measured along the electrode array, as this is a consequence of a wider excitation area in the apical part of the cochlea, in the absence of any asymmetry in the actual EDP. In addition, broader apical EDPs underlie the higher eCAP amplitudes found for apical stimulation.
Do articulating spacers or static spacers have more effect on the mental health status of patients undergoing two-stage revision total knee arthroplasty for periprosthetic joint infection?
Authors: Lee Su Chan , Gondalia Viral , Ahn Hye Sun , Kim Jong Won , Park Ha Young , Ong Alvin , Jung Kwang Am 
Published: March 2016

Background:
There are several studies that have focused on functional outcome and rate of recurrent infection for patients undergoing two-stage revision total knee arthroplasty (TKA) for the treatment of periprosthetic joint infection (PJI). However, there are very few studies assessing the mental health status of these patients, which is why we conducted a study to assess and compare the mental health status between patients who underwent first-stage revision with a static spacer and those who had an articulating spacer. Our hypothesis was that the patients with articulating spacers have a lesser degree of mental stress than those with static spacers.

Methods:
From 2011 to 2013, a total of 40 knees with a diagnosis of PJI were treated with a standard two-stage revision TKA. Hospital anxiety and depression scale (HADS)-A and D, Visual Analogue Scale (VAS), Short-form-36 mental health (SF-36) scores were compared between groups preoperatively and 4 weeks postoperatively.

Results:
There were no significant differences between the two groups. Similarly, P value did not show any significant differences between the groups for both VAS and SF-36 score even though it was significant within the groups for VAS score preoperatively and postoperatively (P<0.0001).

Conclusions:
Both articulating and static spacers significantly reduced the psychological stress on the patients undergoing two-stage revision for PJI. Based on our results, we concluded that improvement in mental health status of both articulating and static spacer groups were comparable with no statistically significant differences.
Efficacy, Safety, and Potential Biomarkers of Sunitinib and Transarterial Chemoembolization (TACE) Combination in Advanced Hepatocellular Carcinoma (HCC)
Authors: Pokuri Venkata K. , Tomaszewski Garin M. , Ait-Oudhia Sihem , Groman Adrienne , Khushalani Nikhil I. , Lugade Amit A. , Thanavala Yasmin , Ashton Edward A. , Grande Catherine , Fetterly Gerald J. , Iyer Renuka 
Published: March 2016

Objectives:To evaluate the safety/efficacy and explore biomarkers for a rationally designed combination of sunitinib and transarterial chemoembolization (TACE) in a prospective phase 2 study of advanced hepatocellular carcinoma (HCC).Methods:Inoperable HCC patients with Child-Pugh A disease received 37.5 mg sunitinib from days 1 to 7 followed by TACE on day 8. Sunitinib was resumed from days 15 to 36 followed by 2 weeks off. Patients received subsequent sunitinib cycles of 4 weeks on and 2 weeks off. Dynamic contrast-enhanced magnetic resonance imaging and circulating soluble biomarkers were assessed at baseline, day 8, day 10, and day 36.Results:Sixteen patients with liver only (n=10) and extrahepatic disease (n=6) were enrolled. After a median follow-up of 12.8 months, 2 partial responses, 11 stable disease, and 3 clinical deteriorations were seen for a clinical benefit rate of 81%. Median progression-free survival (PFS) was 8 months (95% CI, 4.3-9.3) and overall survival was 14.9 months (95% CI, 6.3-27.1). Eleven of 16 patients (69%) had grade 3/4 toxicities attributable to sunitinib, the most frequent being thrombocytopenia, amylase/lipase elevations, lymphopenia, and fatigue. Mean Ktrans(volume transfer constant) and viable tumor percent in consented patients decreased by 27% and 14.8%, respectively, with combination therapy. Soluble vascular endothelial growth factor receptor-2 (sVEGFR2) levels, cytokines (interleukin-8, interleukin-21), and monocytes decreased with combination therapy. Estimated sunitinib IC50 values of 15 and 10 ng/mL modulated Ktransand AUC90. sVEGFR2 levels decreased with Ktransand AUC90.Conclusions:Encouraging progression-free survival and overall survival were seen with acceptable toxicity in our study of sunitinib and TACE combination in advanced HCC. Potential imaging and serum biomarkers showed increased benefit with combination therapy.
The Posterior Approach Tarsal Switch Procedure for Myopathic Ptosis: A Modified Technique
Authors: Lenake Mpopi N. , McNab Alan A. 
Published: March 2016

Purpose:
The surgical management of myopathic ptosis remains a challenge. The authors report the results of a modified posterior approach tarsal switch technique, which raises both the upper and lower eyelids and reduces the risk of corneal exposure in these patients.

Methods:
A modified tarsal switch technique is described. A tarsoconjunctival and Muller’s muscle graft is harvested via a posterior approach from the upper eyelid, the defect closed, and the graft transferred to the lower eyelid.

Results:
The procedure was performed on 16 eyelids of 9 patients. No adjunctive procedures were performed. The patients ranged in age from 36 years to 79 years. All patients had bilateral myopathic ptosis, reduced levator function, and a poor Bell’s response. The margin reflex distance-1 increased by 1.5 to 4.5 mm (mean 2.3 mm) and the margin reflex distance-2 decreased by 0.5 to 2.5 mm (mean 1.6 mm). There were no intraoperative complications, no significant corneal exposure problems, and no patients required revision surgery over a follow-up period of 6 to 52 months (mean 16 months).

Conclusions:
This technique of harvesting the tarsoconjunctival-Muller’s muscle graft posteriorly, closing that defect and transferring the graft into the lower eyelid to elevate it, is an effective surgical procedure for the management of ptosis in patients with poor ocular protective mechanisms.
Factors Associated With the Efficacy of Probing for Adult Patients With Lacrimal Duct Obstruction
Authors: Ohtomo Kazuyoshi , Ueta Takashi 
Published: March 2016

Purpose:
To investigate the factors associated with the effectiveness of probing for epiphora in adults with lacrimal duct obstruction.

Methods:
This was a cross-sectional retrospective study involving 116 eyes of 82 patients (26 males and 56 females) with a primary acquired lacrimal duct obstruction who received a probing from June 2007 to October 2013. The influences of age, gender, the duration of the symptom before probing, the number of probing treatments during the follow-up period, locations of the obstructions, and the presence of mucopurulent discharge upon irrigation of the lacrimal sac on the efficacy of probing were evaluated.

Results:
Obstructions were observed in the nasolacrimal duct, common canaliculus, canaliculus, and punctum for 76% (88/116), 22% (26/116), 4% (5/116), and 3% (3/116), respectively. The overall efficacy of probing was 52% (60/116). Between the effective group and the noneffective group, 77% (20/26) of the common canaliculus obstructions were found in the effective group (p = 0.0039), whereas 67% (29/43) of the cases with discharge from the lacrimal sac were found in the noneffective group (p = 0.0020). On logistic regression analysis, the efficacy of probing was increased by the presence of common canaliculus obstruction (odds ratio = 6.0408; 95% confidence interval = 1.1255–48.9179, p = 0.0353), but was decreased by the presence of discharge from the lacrimal sac (odds ratio = 0.3508; 95% confidence interval = 0.1425–0.8345, p = 0.0176).

Conclusion:
Probing can be a therapeutic choice for lacrimal duct obstructions, particularly when there is a common canaliculus obstruction and no discharge from the lacrimal sac.
The Bleph and the Brain: The Effect of Upper Eyelid Surgery on Chronic Headaches
Authors: Mokhtarzadeh Ali , McClelland Collin , Lee Michael S. , Smith Scott , Harrison Andrew R. 
Published: March 2016

Purpose:
To determine effect of upper eyelid surgery on headache symptoms.

Methods:
Consecutive adults undergoing upper eyelid surgery for obscuration of superior visual field, who also reported headache symptoms for greater than 1 year completed a pre- and postoperative Headache Impact Test-6 quality of life questionnaire (study group). A cohort of patients undergoing other oculoplastic procedures with headaches also completed the questionnaire pre- and postoperatively (control group). The study was conducted over a 2-year period. Neither the patients nor the study investigators were masked.

Results:
Twenty-eight patients met criteria for the study group, and 19 patients in the control group. Mean age was 58.7 and 60.7 years, respectively. There was no statistically significant difference in preoperative location of headaches. There was no significant difference in mean Headache Impact Test-6 scores preoperatively, 57.7 study group, 58.1 control group, p = 0.86. Mean postoperative scores were lower (improved) in the study arm, 45.3, as compared with the control arm, 58.6, p < 0.05. There was no statistically significant difference between individual preoperative survey questions between the study arm and control group, while every Headache Impact Test-6 question significantly improved in the study arm compared with the control arm. Mean Headache Impact Test-6 score improved 12.4 points in the study arm after surgery (p < 0.05), while the mean postoperative score worsened by 5 points in the control arm, but this was not significant (p = 0.48). Subjectively, 25 of 28 study patients, and 4 of 19 control patients noticed at least some improvement in headache symptoms after surgery.

Conclusions:
Correction of visually significant upper eyelid position may improve chronic headache symptoms.
Changes in and Determinants of Quality of Life in Patients With Advanced Non-Small-Cell Lung Cancer Undergoing Initial Chemotherapy
Authors: Dai Yu-Lee , Yang Cheng-Ta , Chen Kang-Hua , Tang Siew-Tzuh 
Published: March 2016

ABSTRACT

Background:
Few studies have evaluated completely the changes in quality of life (QOL) that occur from pretreatment through the first four consecutive cycles of chemotherapy or determined its determinants in patients with advanced non-small-cell lung cancer (NSCLC).

Purpose:
The aim of this study was to explore the changes to and determinants of QOL in patients with advanced NSCLC under initial chemotherapy from pretreatment through Cycle 4 of chemotherapy.

Methods:
The QOL of 139 patients with advanced NSCLC was assessed from prechemotherapy through Cycle 4 of chemotherapy. Changes to and determinants of QOL were evaluated using multivariate linear regression, which used generalized estimation equation models.

Results:
No significant changes were observed in the global QOL or the physical, role, emotional, or cognitive functional domains of QOL during the course of chemotherapy. However, the social functional domain of QOL improved significantly at Cycle 3 in comparison with the prechemotherapy values. Better global QOL was determined as better performance status, less frequent physical symptoms, and less severe anxiety and depressive symptoms. Important determinants of better QOL in the five functional domains included younger age, better performance status, less frequent physical symptoms, less severe anxiety and depressive symptoms, and weaker perceived social support. Furthermore, patients who achieved a partial response after chemotherapy enjoyed stronger improvements in global QOL and the QOL emotional functional domain than those who did not.

Conclusions:
To help patients with advanced NSCLC optimize their QOL, healthcare professionals should enhance their ability to identify patients who are at elevated risk of poor QOL throughout the course of chemotherapy and to appropriately detect and manage the related physical symptoms and side effects, strengthen patients’ social support, and lessen the anxiety and depressive symptoms of patients.