bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting phoneme and word recognition in noise using a computational model of the auditory periphery
Authors: Moncada-Torres Arturo , van Wieringen Astrid , Bruce Ian C. , Wouters Jan , Francart Tom
Published: January 2017

Several filterbank-based metrics have been proposed to predict speech intelligibility (SI). However, these metrics incorporate little knowledge of the auditory periphery. Neurogram-based metrics provide an alternative, incorporating knowledge of the physiology of hearing by using a mathematical model of the auditory nerve response. In this work, SI was assessed utilizing different filterbank-based metrics (the speech intelligibility index and the speech-based envelope power spectrum model) and neurogram-based metrics, using the biologically inspired model of the auditory nerve proposed by Zilany, Bruce, Nelson, and Carney [(2009), J. Acoust. Soc. Am. 126(5), 2390–2412] as a front-end and the neurogram similarity metric and spectro temporal modulation index as a back-end. Then, the correlations with behavioural scores were computed. Results showed that neurogram-based metrics representing the speech envelope showed higher correlations with the behavioural scores at a word level. At a per-phoneme level, it was found that phoneme transitions contribute to higher correlations between objective measures that use speech envelope information at the auditory periphery level and behavioural data. The presented framework could function as a useful tool for the validation and tuning of speech materials, as well as a benchmark for the development of speech processing algorithms.
Notched-noise precursors improve detection of low-frequency amplitude modulation
Authors: Almishaal Ali , Bidelman Gavin M. , Jennings Skyler G.
Published: January 2017

Amplitude modulation (AM) detection was measured with a short (50 ms), high-frequency carrier as a function of carrier level (Experiment I) and modulation frequency (Experiment II) for conditions with or without a notched-noise precursor. A longer carrier (500 ms) was also included in Experiment I. When the carrier was preceded by silence (no precursor condition) AM detection thresholds worsened for moderate-level carriers compared to lower- or higher-level carriers, resulting in a “mid-level hump.” AM detection thresholds with a precursor were better than those without a precursor, primarily for moderate-to-high level carriers, thus eliminating the mid-level hump in AM detection. When the carrier was 500 ms, AM thresholds improved by a constant (across all levels) relative to AM thresholds with a precursor, consistent with the longer carrier providing more “looks” to detect the AM signal. Experiment II revealed that improved AM detection with compared to without a precursor is limited to low-modulation frequencies (<60 Hz). These results are consistent with (1) a reduction in cochlear gain over the course of the precursor perhaps via the medial olivocochlear reflex or (2) a form of perceptual enhancement which may be mediated by adaptation of inhibition.
Follicular CD8 T cells accumulate in HIV infection and can kill infected cells in vitro via bispecific antibodies
Authors: Petrovas Constantinos , Ferrando-Martinez Sara , Gerner Michael Y. , Casazza Joseph P. , Pegu Amarendra , Deleage Claire , Cooper Arik , Hataye Jason , Andrews Sarah , Ambrozak David , Del Río Estrada Perla M. , Boritz Eli , Paris Robert , Moysi Eirini , Boswell Kristin L. , Ruiz-Mateos Ezequiel , Vagios Ilias , Leal Manuel , Ablanedo-Terrazas Yuria , Rivero Amaranta , Gonzalez-Hernandez Luz Alicia , McDermott Adrian B. , Moir Susan , Reyes-Terán Gustavo , Docobo Fernando , Pantaleo Giuseppe , Douek Daniel C. , Betts Michael R. , Estes Jacob D. , Germain Ronald N. , Mascola John R. , Koup Richard A.
Published: January 2017

LN inflammation in chronic HIV is associated with accumulation of follicular CD8 T cells that could be redirected to kill infected cells.
Tyrosine kinase blocking collagen IV–derived peptide suppresses ocular neovascularization and vascular leakage
Authors: Lima e Silva Raquel , Kanan Yogita , Mirando Adam C. , Kim Jayoung , Shmueli Ron B. , Lorenc Valeria E. , Fortmann Seth D. , Sciamanna Jason , Pandey Niranjan B. , Green Jordan J. , Popel Aleksander S. , Campochiaro Peter A.
Published: January 2017

An integrin-binding peptide derived from collagen IV prevents ligand-induced activation of multiple tyrosine kinase receptors and strongly suppresses ocular neovascularization and vascular leakage.
Good to the last “emulsified” drop
Authors: Castro Cesar M.
Published: January 2017

Nanoliter scale droplets sealed and encapsulated in solid PEFE polymer shells are combined with graphical coding to advance droplet microfluidics.
ERAD-icating mutant insulin promotes functional insulin secretion
Authors: Moore Daniel J.
Published: January 2017

Overexpression of a chaperone protein liberates functional insulin from a misfolded mutant partner to improve insulin secretion.
Perifosine Mechanisms of Action in Leishmania Species
Authors: López-Arencibia Atteneri , Martín-Navarro Carmen , Sifaoui Ines , Reyes-Batlle María , Wagner Carolina , Lorenzo-Morales Jacob , Maciver Sutherland K. , Piñero José E.
Published: January 2017

Here the mechanism by which perifosine induced cell death in
Leishmania donovani
and
Leishmania amazonensis
is described. The drug reduced
Leishmania
mitochondrial membrane potential and decreased cellular ATP levels while increasing phosphatidylserine externalization. Perifosine did not increase membrane permeabilization. We also found that the drug inhibited the phosphorylation of Akt in the parasites. These results highlight the potential use of perifosine as an alternative to miltefosine against
Leishmania
.
Pharmacodynamics of Ceftaroline plus Ampicillin against Enterococcus faecalis in an
In Vitro
Pharmacokinetic/Pharmacodynamic Model of Simulated Endocardial Vegetations
Authors: Werth Brian J. , Shireman Laura M.
Published: January 2017

The combination of ampicillin plus ceftaroline has been suggested to be more reliably synergistic against
Enterococcus faecalis
than ampicillin plus ceftriaxone using time-kill methods. The purpose of this study was to determine if this trend persists in a two-compartment model of simulated endocardial vegetations (SEV) using clinically relevant pharmacokinetic exposures of these antimicrobials. Three clinically derived
E. faecalis
strains were included in the study. The MICs of study antimicrobials were determined by broth microdilution. Simulations of ampicillin (2 g every 4 h [q4h]; maximum concentration of drug in serum [
C
max
], 72.4 mg/liter; half-life [
t
1/2
], 1.9 h), ceftaroline-fosamil (600 mg q8h;
C
max
, 21.3 mg/liter;
t
1/2
, 2.66 h), ceftriaxone (
C
max
, 257 mg/liter;
t
1/2
, 8 h), and ampicillin plus ceftaroline and ampicillin plus ceftriaxone were evaluated against 3 strains of
E. faecalis
isolated from patients with endocarditis in an
in vitro
PK/PD SEV model over 72 h, with a starting inoculum of ∼9 log
10
CFU/g. All strains were susceptible to ampicillin (MIC, ≤2 mg/liter). Ceftaroline MICs varied from 2 to 16 mg/liter. All strains had ceftriaxone MICs of 256 mg/liter. W04 and W151 exhibited high-level aminoglycoside resistance but W07 did not. Ampicillin plus ceftaroline resulted in significantly greater reductions in CFU per gram by 72 h than ampicillin for all strains (
P
≤ 0.025) than ampicillin plus ceftriaxone for W04 (
P
= 0.019) but not W07 or W151 (
P
≥ 0.15). A 4-fold increase in ampicillin MIC was observed for W07 at 72 h, but this was prevented by the addition of ceftaroline or ceftriaxone. The combination of ampicillin plus ceftaroline appears to be at least as efficacious as ampicillin plus ceftriaxone and may lead to improved activity against some strains of
E. faecalis
, but these differences may be small and the clinical significance should not be overestimated.
Determinants of Antibacterial Spectrum and Resistance Potential of the Elongation Factor G Inhibitor Argyrin B in Key Gram-Negative Pathogens
Authors: Jones Adriana K. , Woods Angela L. , Takeoka Kenneth T. , Shen Xiaoyu , Wei Jun-Rong , Caughlan Ruth E. , Dean Charles R.
Published: January 2017

Argyrins are natural products with antibacterial activity against Gram-negative pathogens, such as
Pseudomonas aeruginosa
,
Burkholderia multivorans
, and
Stenotrophomonas maltophilia
. We previously showed that argyrin B targets elongation factor G (FusA). Here, we show that argyrin B activity against
P. aeruginosa
PAO1 (MIC = 8 μg/ml) was not affected by deletion of the MexAB-OprM, MexXY-OprM, MexCD-OprJ, or MexEF-OprN efflux pump. However, argyrin B induced expression of MexXY, causing slight but reproducible antagonism with the MexXY substrate antibiotic ciprofloxacin. Argyrin B activity against
Escherichia coli
increased in a strain with nine
tolC
efflux pump partner genes deleted. Complementation experiments showed that argyrin was effluxed by AcrAB, AcrEF, and MdtFX. Argyrin B was inactive against
Acinetobacter baumannii
. Differences between
A. baumannii
and
P. aeruginosa
FusA proteins at key residues for argyrin B interaction implied that natural target sequence variation impacted antibacterial activity. Consistent with this, expression of the sensitive
P. aeruginosa
FusA1 protein in
A. baumannii
conferred argyrin susceptibility, whereas resistant variants did not. Argyrin B was active against
S. maltophilia
(MIC = 4 μg/ml). Spontaneous resistance occurred at high frequency in the bacterium (circa 10
−7
), mediated by mutational inactivation of
fusA1
rather than by amino acid substitutions in the target binding region. This strongly suggested that resistance occurred at high frequency through loss of the sensitive FusA1, leaving an alternate argyrin-insensitive elongation factor. Supporting this, an additional
fusA
-like gene (
fusA2
) is present in
S. maltophilia
that was strongly upregulated in response to mutational loss of
fusA1
.
Resistance to Thiacetazone Derivatives Active against Mycobacterium abscessus Involves Mutations in the MmpL5 Transcriptional Repressor MAB_4384
Authors: Halloum Iman , Viljoen Albertus , Khanna Varun , Craig Derek , Bouchier Christiane , Brosch Roland , Coxon Geoffrey , Kremer Laurent
Published: January 2017

Available chemotherapeutic options are very limited against
Mycobacterium abscessus
, which imparts a particular challenge in the treatment of cystic fibrosis (CF) patients infected with this rapidly growing mycobacterium. New drugs are urgently needed against this emerging pathogen, but the discovery of active chemotypes has not been performed intensively. Interestingly, however, the repurposing of thiacetazone (TAC), a drug once used to treat tuberculosis, has increased following the deciphering of its mechanism of action and the detection of significantly more potent analogues. We therefore report studies performed on a library of 38 TAC-related derivatives previously evaluated for their antitubercular activity. Several compounds, including D6, D15, and D17, were found to exhibit potent activity
in vitro
against
M. abscessus
,
Mycobacterium massiliense
, and
Mycobacterium bolletii
clinical isolates from CF and non-CF patients. Similar to TAC in
Mycobacterium tuberculosis
, the three analogues act as prodrugs in
M. abscessus
, requiring bioactivation by the EthA enzyme, MAB_0985. Importantly, mutations in the transcriptional TetR repressor MAB_4384, with concomitant upregulation of the divergently oriented adjacent genes encoding an MmpS5/MmpL5 efflux pump system, accounted for high cross-resistance levels among all three compounds. Overall, this study uncovered a new mechanism of drug resistance in
M. abscessus
and demonstrated that simple structural optimization of the TAC scaffold can lead to the development of new drug candidates against
M. abscessus
infections.
Bacterium-Derived Cell-Penetrating Peptides Deliver Gentamicin To Kill Intracellular Pathogens
Authors: Gomarasca Marta , F. C. Martins Thaynan , Greune Lilo , Hardwidge Philip R. , Schmidt M. Alexander , Rüter Christian
Published: January 2017

Commonly used antimicrobials show poor cellular uptake and often have limited access to intracellular targets, resulting in low antimicrobial activity against intracellular pathogens. An efficient delivery system to transport these drugs to the intracellular site of action is needed. Cell-penetrating peptides (CPPs) mediate the internalization of biologically active molecules into the cytoplasm. Here, we characterized two CPPs, α1H and α2H, derived from the
Yersinia enterocolitica
YopM effector protein. These CPPs, as well as Tat (
trans
-activator of transcription) from HIV-1, were used to deliver the antibiotic gentamicin to target intracellular bacteria. The YopM-derived CPPs penetrated different endothelial and epithelial cells to the same extent as Tat. CPPs were covalently conjugated to gentamicin, and CPP-gentamicin conjugates were used to target infected cells to kill multiple intracellular Gram-negative pathogenic bacteria, including
Escherichia coli
K1,
Salmonella enterica
serovar Typhimurium, and
Shigella flexneri
. Taken together, CPPs show great potential as delivery vehicles for antimicrobial agents and may contribute to the generation of new therapeutic tools to treat infectious diseases caused by intracellular pathogens.
Plasmidic
qnr
Genes Confer Clinical Resistance to Ciprofloxacin under Urinary Tract Physiological Conditions
Authors: Martín-Gutiérrez Guillermo , Rodríguez-Martínez José Manuel , Pascual Álvaro , Rodríguez-Beltrán Jerónimo , Blázquez Jesús
Published: January 2017

Escherichia coli
variants expressing plasmid-mediated
qnr
genes are usually susceptible to fluoroquinolones by standard susceptibility testing. Here we show that, under specific urinary tract physiological conditions, susceptible laboratory and clinical strains harboring
qnr
determinants become fully resistant to ciprofloxacin (CIP). Therefore, physiological conditions, mainly urine pH values, should be considered when performing susceptibility testing of CIP activity against
E. coli
in treating urinary tract infection (UTI) and for selecting appropriate antibiotics for UTI treatment.
Specific Glucoside Transporters Influence Septal Structure and Function in the Filamentous, Heterocyst-Forming Cyanobacterium Anabaena sp. Strain PCC 7120
Authors: Nieves-Morión Mercedes , Lechno-Yossef Sigal , López-Igual Rocío , Frías José E. , Mariscal Vicente , Nürnberg Dennis J. , Mullineaux Conrad W. , Wolk C. Peter , Flores Enrique
Published: January 2017

When deprived of combined nitrogen, some filamentous cyanobacteria contain two cell types: vegetative cells that fix CO
2
through oxygenic photosynthesis and heterocysts that are specialized in N
2
fixation. In the diazotrophic filament, the vegetative cells provide the heterocysts with reduced carbon (mainly in the form of sucrose) and heterocysts provide the vegetative cells with combined nitrogen. Septal junctions traverse peptidoglycan through structures known as nanopores and appear to mediate intercellular molecular transfer that can be traced with fluorescent markers, including the sucrose analog esculin (a coumarin glucoside) that is incorporated into the cells. Uptake of esculin by the model heterocyst-forming cyanobacterium
Anabaena
sp. strain PCC 7120 was inhibited by the α-glucosides sucrose and maltose. Analysis of
Anabaena
mutants identified components of three glucoside transporters that move esculin into the cells: GlsC (Alr4781) and GlsP (All0261) are an ATP-binding subunit and a permease subunit of two different ABC transporters, respectively, and HepP (All1711) is a major facilitator superfamily (MFS) protein that was shown previously to be involved in formation of the heterocyst envelope. Transfer of fluorescent markers (especially calcein) between vegetative cells of
Anabaena
was impaired by mutation of glucoside transporter genes. GlsP and HepP interact in bacterial two-hybrid assays with the septal junction-related protein SepJ, and GlsC was found to be necessary for the formation of a normal number of septal peptidoglycan nanopores and for normal subcellular localization of SepJ. Therefore, beyond their possible role in nutrient uptake in
Anabaena
, glucoside transporters influence the structure and function of septal junctions.

IMPORTANCE
Heterocyst-forming cyanobacteria have the ability to perform oxygenic photosynthesis and to assimilate atmospheric CO
2
and N
2
. These organisms grow as filaments that fix these gases specifically in vegetative cells and heterocysts, respectively. For the filaments to grow, these types of cells exchange nutrients, including sucrose, which serves as a source of reducing power and of carbon skeletons for the heterocysts. Movement of sucrose between cells in the filament takes place through septal junctions and has been traced with a fluorescent sucrose analog, esculin, that can be taken up by the cells. Here, we identified α-glucoside transporters of
Anabaena
that mediate uptake of esculin and, notably, influence septal structure and the function of septal junctions.
The Gut Microbiome of the Vector
Lutzomyia longipalpis
Is Essential for Survival of
Leishmania infantum
Authors: Kelly Patrick H. , Bahr Sarah M. , Serafim Tiago D. , Ajami Nadim J. , Petrosino Joseph F. , Meneses Claudio , Kirby John R. , Valenzuela Jesus G. , Kamhawi Shaden , Wilson Mary E.
Published: January 2017

The vector-borne disease leishmaniasis, caused by
Leishmania
species protozoa, is transmitted to humans by phlebotomine sand flies. Development of
Leishmania
to infective metacyclic promastigotes in the insect gut, a process termed metacyclogenesis, is an essential prerequisite for transmission. Based on the hypothesis that vector gut microbiota influence the development of virulent parasites, we sequenced midgut microbiomes in the sand fly
Lutzomyia longipalpis
with or without
Leishmania infantum
infection. Sucrose-fed sand flies contained a highly diverse, stable midgut microbiome. Blood feeding caused a decrease in microbial richness that eventually recovered. However, bacterial richness progressively decreased in
L. infantum-
infected sand flies.
Acetobacteraceae
spp. became dominant and numbers of
Pseudomonadaceae
spp. diminished coordinately as the parasite underwent metacyclogenesis and parasite numbers increased. Importantly, antibiotic-mediated perturbation of the midgut microbiome rendered sand flies unable to support parasite growth and metacyclogenesis. Together, these data suggest that the sand fly midgut microbiome is a critical factor for
Leishmania
growth and differentiation to its infective state prior to disease transmission.

IMPORTANCE
Leishmania infantum
, a parasitic protozoan causing fatal visceral leishmaniasis, is transmitted to humans through the bite of the sand fly
Lutzomyia longipalpis
. Development of the parasite to its virulent metacyclic state occurs in the sand fly gut. In this study, the microbiota within the
Lu. longipalpis
midgut was delineated by 16S ribosomal DNA (rDNA) sequencing, revealing a highly diverse community composition that lost diversity as parasites developed to their metacyclic state and increased in abundance in infected flies. Perturbing sand fly gut microbiota with an antibiotic cocktail, which alone had no effect on either the parasite or the fly, arrested both the development of virulent parasites and parasite expansion. These findings indicate the importance of bacterial commensals within the insect vector for the development of virulent pathogens, and raise the possibility that impairing the microbial composition within the vector might represent a novel approach to control of vector-borne diseases.
Induced Packaging of Cellular MicroRNAs into HIV-1 Virions Can Inhibit Infectivity
Authors: Bogerd Hal P. , Kennedy Edward M. , Whisnant Adam W. , Cullen Bryan R.
Published: January 2017

Analysis of the incorporation of cellular microRNAs (miRNAs) into highly purified HIV-1 virions revealed that this largely, but not entirely, mirrored the level of miRNA expression in the producer CD4
+
T cells. Specifically, of the 58 cellular miRNAs detected at significant levels in the producer cells, only 5 were found in virions at a level 2- to 4-fold higher than that predicted on the basis of random cytoplasmic sampling. Of note, these included two miRNAs, miR-155 and miR-92a, that were reported previously to at least weakly bind HIV-1 transcripts. To test whether miRNA binding to the HIV-1 genome can induce virion incorporation, artificial miRNA target sites were introduced into the viral genome and a 10- to 40-fold increase in the packaging of the cognate miRNAs into virions was then observed, leading to the recruitment of up to 1.6 miRNA copies per virion. Importantly, this high level of incorporation significantly inhibited HIV-1 virion infectivity. These results suggest that target sites for cellular miRNAs can inhibit RNA virus replication at two distinct steps, i.e., during infection and during viral gene expression, thus explaining why a range of different RNA viruses appear to have evolved to avoid cellular miRNA binding to their genome.

IMPORTANCE
The genomes of RNA viruses have the potential to interact with cellular miRNAs, which could lead to their incorporation into virions, with unknown effects on virion function. Here, it is demonstrated that wild-type HIV-1 virions essentially randomly incorporate low levels of the miRNAs expressed by infected cells. However, the specific incorporation of high levels of individual cellular miRNAs can be induced by insertion of cognate target sites into the viral genome. Of note, this results in a modest but significant inhibition of virion infectivity. These data imply that cellular miRNAs have the potential to inhibit viral replication by interfering with not only viral mRNA function but also virion infectivity.
Balance Trees Reveal Microbial Niche Differentiation
Authors: Morton James T. , Sanders Jon , Quinn Robert A. , McDonald Daniel , Gonzalez Antonio , Vázquez-Baeza Yoshiki , Navas-Molina Jose A. , Song Se Jin , Metcalf Jessica L. , Hyde Embriette R. , Lladser Manuel , Dorrestein Pieter C. , Knight Rob
Published: January 2017

By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained athttps://github.com/biocore/gneiss.
Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling
Authors: Asnicar Francesco , Manara Serena , Zolfo Moreno , Truong Duy Tin , Scholz Matthias , Armanini Federica , Ferretti Pamela , Gorfer Valentina , Pedrotti Anna , Tett Adrian , Segata Nicola
Published: January 2017

Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species,
per se
, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.
Multiple pregnancy in a primigravida with uncorrected Pentalogy of Fallot
Authors: Partana Pamela , Tan Jarrod Kah Hwee , Tan Ju Le , Tan Lay Kok
Published: January 2017

Pentalogy of Fallot is a cyanotic congenital heart disease that has guarded prognosis without surgical intervention in infancy. Women with uncorrected defects rarely survive into childbearing age and pregnancy in this group is associated with a high rate of perinatal loss. Physiological cardiovascular changes in pregnancy can lead to maternal haemodynamic instability with subsequent adverse cardiac sequelae with or without fetal decompensation. Optimum management and pregnancy outcomes in mother with uncorrected Pentalogy of Fallot and twin pregnancy have not been described in the literature. We describe a successful case of monochorionic diamniotic twin pregnancy in an affected woman who has not undergone surgical repair. Her pregnancy progressed without any adverse cardiopulmonary complications. Her caesarean delivery and postpartum recovery were favourable, with successful birth of two healthy babies at 35.7 weeks. This case emphasises the importance of a multidisciplinary team, especially of obstetricians with expertise in high-risk pregnancies, adult congenital heart disease cardiologists and anaesthesiologist.
Primary squamous cell carcinoma of the thyroid with complete response to radical radiotherapy and concurrent cisplatin-based chemotherapy
Authors: Del Rosario Michael , Dasanu Constantin , Tsai Henry , Johnson Robert
Published: January 2017

Chemoradiotherapy and/or surgery are both potentially radical treatments for squamous cell carcinomas. Squamous cell carcinomas are considered chemosensitive tumours compared to adenocarcinomas or anaplastic thyroid malignancies. A 76-year-old man was found to have T4bN0M0 primary squamous cell carcinoma of the thyroid with encasement of the internal carotid artery. The disease was deemed unresectable. Therefore, he was treated with radical radiotherapy with concurrent cisplatin-based chemotherapy. We discuss herein the aetiology, diagnosis and management of primary squamous cell carcinoma of the thyroid. We demonstrate success of chemoradiotherapy in an unresectable case of a rare and aggressive disease.
Late spontaneous decapsulation of the kidney graft in a patient with hepatitis C and treated with sirolimus: possible pathophysiological association in a rare complication
Authors: Leal Rita , Pinto Helena , Alves Rui , Figueiredo Arnaldo
Published: January 2017

Late decapsulation with fluid collection is a rare complication of renal transplantation with deleterious effects on kidney function. Its physiopathology is unclear but there might be an association with mammalian target of rapamycin (m-TOR) inhibitors, especially in patients with chronic hepatitis C. We report a case of late spontaneous decapsulation 12 years after kidney transplant in a patient infected with hepatitis C under treatment with sirolimus. He underwent marsupialisation of the collection, sirolimus was converted to cyclosporine and hepatitis C treatment was performed with success. This is the first successful case report of late spontaneous decapsulation of the kidney graft in a patient with hepatitis C.
Generic prognostic factors for musculoskeletal pain in primary care: a systematic review
Authors: Artus Majid , Campbell Paul , Mallen Christian D , Dunn Kate M , van der Windt Danielle A W
Published: January 2017

Objectives

To summarise the evidence for generic prognostic factors across a range of musculoskeletal (MSK) conditions.

Setting

primary care.

Methods and outcomes

Comprehensive systematic literature review. MEDLINE, CINAHL, PsychINFO and EMBASE were searched for prospective cohort studies, based in primary care (search period—inception to December 2015). Studies were included if they reported on adults consulting with MSK conditions and provided data on associations between baseline characteristics (prognostic factors) and outcome. A prognostic factor was identified as generic when significantly associated with any outcome for 2 or more different MSK conditions. Evidence synthesis focused on consistency of findings and study quality.

Results

14 682 citations were identified and 78 studies were included (involving more than 48 000 participants with 18 different outcome domains). 51 studies were on spinal pain/back pain/low back pain, 12 on neck/shoulder/arm pain, 3 on knee pain, 3 on hip pain and 9 on multisite pain/widespread pain. Total quality scores ranged from 5 to 14 (mean 11) and 65 studies (83%) scored 9 or more. Out of a total of 78 different prognostic factors for which data were provided, the following factors are considered to be generic prognostic factors for MSK conditions: widespread pain, high functional disability, somatisation, high pain intensity and presence of previous pain episodes. In addition, consistent evidence was found for use of pain medications not to be associated with outcome, suggesting that this factor is not a generic prognostic factor for MSK conditions.

Conclusions

This large review provides new evidence for generic prognostic factors for MSK conditions in primary care. Such factors include pain intensity, widespread pain, high functional disability, somatisation and movement restriction. This information can be used to screen and select patients for targeted treatment in clinical research as well as to inform the management of MSK conditions in primary care.
GPRASP2, a novel causative gene mutated in an X-linked recessive syndromic hearing loss
Authors: Xing Guangqian , Yao Jun , Liu Chunyu , Wei Qinjun , Qian Xuli , Wu Lingxin , Lu Yajie , Cao Xin
Published: January 2017

Background

A substantial amount of nuclear genes have been identified to be implicated in genetic hearing loss, while X-linked hearing loss is genetically heterogeneous and relatively infrequent.

Objective

To identify the causative gene mutation in a five-generation Chinese family with an X-linked recessive syndromic hearing loss (SHL).

Methods

Targeted X-chromosome exome sequencing was conducted, and cosegregation analysis was performed in the members of the affected family. The in silico and expression studies were also performed.

Results

A 2-bp missense mutation (c.1717_1718GC>AA, p.A573N) in the G protein-coupled receptor associated sorting protein 2 (GPRASP2) gene was identified in four hemizygous male patients and two heterozygous female carriers, which was cosegregated with the clinical phenotypes in this family. In silico analysis supported that this gene mutation is functionally deleterious, and it was detected that homologousGprasp2was highly expressed in multiple structures of the mouse cochlea, which suggested thatGPRASP2might be the genetic cause for the described disease phenotypes.

Conclusions

This study presented a novel X-linked SHL combined with unique and unrecognised clinical features, and a missense variation ofGPRASP2was first identified to be implicated in X-linked SHL.
‘He would by no means risque his Reputation’: patient and doctor shame in Daniel Turner'sDe Morbis Cutaneis(1714) andSyphilis(1717)
Authors: Cock Emily
Published: January 2017

This article offers a historical corollary to the examination of shame in medical practice by considering the negotiation of shame in the treatment of a stigmatised disease at a time in which surgeons themselves occupied a highly ambivalent social position. It will focus on case studies provided by Daniel Turner (1667–1741), prominent surgeon and later member of the College of Physicians, in his textbooksDe Morbis Cutaneis. A Treatise of Diseases Incident to the Skin(1714) andSyphilis. A Practical Dissertation on the Venereal Disease(1717). Turner demonstrates an awareness of the precarious position of both the surgeon and the syphilitic, and devotes significant portions of his text to advising the trainee surgeon on how to manage patients' reticence over disclosure of symptoms, expectations for cure and impudence towards medical authority. In turn, the trainee must manage his own reputation as a moral and medical authority who can treat all distempers, yet without condoning or facilitating the shameful behaviours associated with a sexual disease. Furthermore, shaming plays a key role in enabling Turner to fashion an ideal patient whose successful cure will both respond to and build the surgeon's medical authority and that of the medical field in general.
Geophysical, geological, and hydrogeological characterization of a tributary buried bedrock valley in southern Ontario
Authors: Steelman Colby M. , Arnaud Emmanuelle , Pehme Peeter , Parker Beth L.
Published: January 2017

Buried bedrock valleys infilled with Quaternary-aged sediment have the potential to become productive aquifers owing to prevalent sand and gravel deposits often associated with these topographic lows. In areas where groundwater is drawn from the underlying bedrock aquifer, buried bedrock channels may significantly affect the spatial distribution of recharge and localized contaminant pathways. Therefore, understanding the form, distribution, and the nature of Quaternary infill sediments within these buried bedrock river valleys, and their relationship to hydraulically transmissive bedrock features is an important aspect of groundwater resource management. Here, we evaluate the effectiveness of electrical resistivity and seismic refraction collected over a partially urbanized 150 ha area with variable vegetation, roads, and structures, to map the spatial distribution of sediments and delineation of a channel segment associated with a regional bedrock valley. Electrical resistivity and seismic refraction was performed along 13 (covering ∼11.6 km) and seven transects (covering ∼0.9 km), respectively, to map and characterize the bedrock surface morphology beneath a variable thickness of unconsolidated deposits. Three continuously cored holes and downhole geophysical logs, supplemented with four nearby water well records captured the in-channel as well as adjacent Quaternary stratigraphy (∼15–40 m). Cores recorded multiple glacial till deposits and ice-marginal processes associated with ice advances and retreats. Hydraulic transmissivity of the bedrock around the valley feature was evaluated using a FLUTe hydraulic transmissivity profiling technique. This study demonstrates the potential of combining several surface geophysical methods with sedimentological analysis of continuous cores and hydraulic data for characterizing tributary bedrock channel morphology and Quaternary infill at a scale relevant to localized studies of municipal production well recharge zones and contaminant transport and fate.
A spatiotemporal model for snow crab (Chionoecetes opilio) stock size in the southern Gulf of St. Lawrence
Authors: Cadigan Noel G. , Wade Elmer , Nielsen Anders
Published: January 2017

We develop a high-resolution spatiotemporal model of stock size and harvest rates for snow crab (Chionoecetes opilio) in the southern Gulf of St. Lawrence, which supports an economically important fishery off the east coast of Canada. It is a spatial and weekly model during 1997–2014 that utilizes within-season depletion based on catch per unit of effort (CPUE; kg·pot–1) and also biomass values from a survey designed specifically for this stock. The model is formulated in a state-space framework. The main contribution of the model is to provide a better understanding of fishery-dependent factors that affect CPUE. There is strong evidence of density dependence in the relationship with CPUE and stock biomass, in addition to a general increase in CPUE catchability over time that may be related to changes in gear soak time and spatial variation in catchability. We also find that a natural mortality rate of 0.4 provides a better fit to survey results. Model results suggest that there is no evidence of effort saturation in the fishery.
Prevalence and diversity of waterborneArcobacter butzleriin southwestern Alberta, Canada
Authors: Webb Andrew L. , Taboada Eduardo N. , Selinger L. Brent , Boras Valerie F. , Inglis G. Douglas
Published: January 2017

Arcobacter butzleri is a potential enteric pathogen to human beings, but its reservoirs and modes of transmission are largely unverified. Microbiological and molecular detection and subtyping techniques can facilitate surveillance of A. butzleri in hosts and environmental reservoirs. We isolated A. butzleri from 173 surface water samples (25.6%) and 81 treated wastewater samples (77.9%) collected in southwestern Alberta over a 1-year period. Arcobacter butzleri isolates (n = 500) were genotyped and compared to determine diversity of A. butzleri in southwestern Alberta. Culture methods affected the frequency of detection and genotype diversity of A. butzleri, and isolation comprehensiveness was different for surface waters and treated wastewaters. Detection of A. butzleri in the Oldman River Watershed corresponded with season, river flow rates, and fecal coliform densities. Arcobacter butzleri was detected most frequently in treated wastewater, in the Oldman River downstream from treated wastewater outfalls, and in tributaries near areas of intensive confined feeding operations. All sample sources possessed high genotype diversity, and A. butzleri isolates from treated wastewaters were genetically similar to isolates from the Oldman River downriver from treated wastewater outfall sites. In southwestern Alberta, municipal and agricultural activities contribute to the density and genotype diversity of A. butzleri in surface waters.
Direct Torque Control of Induction Motor Using Enhanced Firefly Algorithm — ANFIS
Authors: Chandra Sekhar J. N. , Marutheswar G. V.
Published: January 2017

In this paper, the hybrid direct torque control (DTC) technique is proposed for controlling the speed of the induction motor (IM). The hybrid technique is the combination of an enhanced firefly algorithm (FA) and the adaptive neuro fuzzy inference system (ANFIS) technique. The performance of the FA is improved by updating the randomized parameter. Here, the genetic algorithm (GA) is utilized for updating the parameter and improved the performance of the FA. Initially, the actual torque and the change of toque are applied to the input of the enhanced FA and form the electromagnetic torque as a dataset. The output of the enhanced FA is given to the input of the ANFIS which is determined from the output of interference system. The dynamic behavior of the IM is analyzed in terms of the parameters such as the speed, torque, flux, etc. Based on the parameters, the motor speed is controlled by utilizing the proposed technique. Then the output of the ANFIS is translated into the stator voltage which is given to the input of the support vector machine (SVM). After that, the control signal is generated for controlling the speed of the IM. The proposed hybrid technique is implemented in the Matlab/Simulink platform. The performance analysis of the proposed method is demonstrated and contrasted with the existing techniques such as without controller, particle swarm optimization (PSO)-based ANFIS and FA-ANFIS controller.
Spinodal instabilities in baryon-rich quark matter
Authors: Ko Che Ming , Li Feng
Published: January 2017

For quark matter at finite baryon chemical potential, its density develops large fluctuations when it undergoes a first-order phase transition. Based on the Nambu–Jona–Lasinio (NJL) model, we have used the linear response theory to study the growth rate of density fluctuations and its dependence on the wavelength of unstable modes. Using the transport equation derived from the NJL model, we have also studied the time evolution of the unstable modes and the density fluctuations in a baryon-rich quark matter that is confined in a finite volume. Allowing the expansion of the quark matter, we have further studied the survivability of the density fluctuations as the density and temperature of the quark matter decrease. Possible experimental signatures of the density fluctuations have been suggested.
The nuclear force: Meson theory versus chiral effective field theory
Authors: Machleidt R.
Published: January 2017

Gerry Brown has played a major role in initiating and stimulating systematic work on the theories of nuclear forces. It is the purpose of this paper to review those theories — in his memory.
Agile Methods for Boosting the Commercialization Process of New Technology
Authors: Tura Nina , Hannola Lea , Pynnönen Mikko
Published: January 2017

Challenges in innovation processes have influenced the development of agile methods, which are lighter and nimbler tools for development projects. This study elucidates the possibilities of agile methods for enhancing the effectiveness of innovation processes with the aim of quickly and successfully commercializing new technology. The focus is on different process phases of commercialization, from identifying the business potential to finalizing the innovation commercialization plan. As a result of the study, a novel, rapid, and agile process was created to improve the effectiveness of the technology-based innovation process, supporting the creation of more sustainable and valuable business models.
Sticky Cantor sets in ℝd
Authors: Krushkal Vyacheslav
Published: January 2017

A subset of [Formula: see text] is called “sticky” if it cannot be isotoped off of itself by a small ambient isotopy. Sticky wild Cantor sets are constructed in [Formula: see text] for each [Formula: see text].
Resonant and Switching Fields for a Weakly Coupled Magnetic Tunnel Junction System
Authors: Layadi A.
Published: January 2017

The ferromagnetic resonance (FMR) and the magnetization switching fields have been analytically determined for weakly coupled Magnetic Tunnel Junction or spin valve systems. Such systems consist of an antiferromagnetic (AF) and two ferromagnetic (F) thin films separated by a nonmagnetic one. Both bilinear [Formula: see text] and biquadratic [Formula: see text] coupling parameters are used to describe the interlayer exchange coupling, while the exchange anisotropy field [Formula: see text] characterizes the interfacial ([Formula: see text]/AF) interaction. It will be shown how [Formula: see text], [Formula: see text], [Formula: see text] and the in-plane anisotropy fields can be derived for the experimental measure of the FMR field and the different magnetization switching fields.
Damping and Magnetic Anisotropy of Epitaxial Fe1.7Ge Ultrathin Films Grown on Ge(111) Substrates
Authors: Belmeguenai M. , Berling D. , Zighem F. , Chérif S. M.
Published: January 2017

6, 10 and 20[Formula: see text]nm thick hexagonal Fe[Formula: see text]Ge thin films have been grown on face-centered-cubic Ge(111) substrates by molecular beam epitaxy. X-ray diffraction investigations revealed an excellent epitaxy of the Fe[Formula: see text]Ge films, with crystallographic [Formula: see text] and [Formula: see text] axes lying in the sample plane. Ferromagnetic resonance, magneto-optical Kerr effect and transverse bias initial inverse susceptibility and torque (TBIIST) measurements reveal that the in-plane anisotropy results from the superposition of a uniaxial and a sixfold symmetry terms. The sixfold anisotropy field, which is in agreement with the crystal structure of the samples, increases with the film thickness suggesting an enhancement of the sample quality, while the small uniaxial anisotropy field does not show regular thickness dependence. Frequency and angular dependences of the FMR linewidth show two-magnon scattering and inhomogeneities contributions which depend on the film thickness. A Gilbert damping parameter as low as 0.0064 is found.
Income and Wealth Distributions from Stochastic Strategy Minority Game
Authors: Ghosh Asim , Biswas Soumyajyoti
Published: January 2017

We propose a version of the Minority Game where the agents at each time make investments either in terms of money or stock from their possessions. The amount of investments at each time step, and not the number of people opting for a choice, determines the ‘minority’. The invested money is returned to the stock investors and the invested stock is returned to the money investors in proportion of their respective investments at each time. In this way, agents in the less investment side faces higher demand, and hence are in ‘minority’, receiving higher pay-off for their investments. This dynamics lead the ‘market’ to a self-organized state. We measure the distributions of income of the agents at every step and also the accumulated wealth, both of which have a stationary distribution. The distribution functions follow Pareto’s law when the agents invest random fractions of their wealth. This reflects the role of heterogeneity in economic interactions.
Feasibility of a 785 nm diode laser in Raman spectroscopy for characterizing hydrocarbon-bearing fluid inclusions in Mumbai Offshore Basin, India
Authors: Jayanthi J. L. , Nandakumar V. , Anoop S. S.
Published: January 2017

Detection of the chemical constituents of hydrocarbons in the hydrocarbon-bearing fluid inclusions in diagenetic mineral cements, secondary fractures and overgrowths could be a useful indicator of the nature of oil in a basin. Microscope-based Raman spectroscopy is a non-destructive, optical vibrational spectroscopic technique that can precisely isolate and analyse hydrocarbon fluid inclusions (HCFIs). The main challenge with Raman spectral studies on natural HCFIs is the common presence of fluorescence emission from minerals and aromatic compounds in HCFIs leading to the masking of Raman signals. The present study is a demonstration of how best the Raman signals from natural hydrocarbon-bearing fluid inclusions could be detected using an excitation wavelength of 785 nm with suitable optical parameters and with special wafer preparation techniques to negate the background fluorescence. Using the laser Raman technique we were able to detect peaks corresponding to cyclohexane (786 and 3245 cm
−1
), benzene and bromobenzene (606, 1010, 1310, 1486 and 1580 cm
−1
), carbon monoxide (2143 cm
−1
), nitrogen (2331 cm
−1
), ethylene (1296 cm
−1
), sulphur oxide (524 cm
−1
), carbonyl sulphide (2055 cm
−1
), hydrogen sulphide in liquid form (2580 cm
−1
) along with the presence of a broad peak of liquid water at 3100–3500 cm
−1
, peaks of calcium carbonate (710, 854 cm
−1
) and calcium sulphate (1135 cm
−1
). The study samples were specially prepared with fluorescence-quenching dyes added with a resin-hardener mixture to eliminate background fluorescence. Nine fluid-inclusion assemblages in minerals like quartz, feldspar and calcite from the RV-1 well of the Ratnagiri Block, Mumbai Offshore Basin, India were investigated.