bluuebunny/crossref_metadata_2025 huggingface dataset:
Downscaling Aggregate Urban Metabolism Accounts to Local Districts
Authors: Horta Isabel M. , Keirstead James
Published: May 2016

Urban metabolism accounts of total annual energy, water, and other resource flows are increasingly available for a variety of world cities. For local decision makers, however, it may be important to understand the variations of resource consumption within the city. Given the difficulty of gathering suburban resource consumption data for many cities, this article investigates the potential of statistical downscaling methods to estimate local resource consumption using socioeconomic or other data sources. We evaluate six classes of downscaling methods: ratio‐based normalization; linear regression (both internally and externally calibrated); linear regression with spatial autocorrelation; multilevel linear regression; and a basic Bayesian analysis. The methods were applied to domestic energy consumption in London, UK, and our results show that it is possible to downscale aggregate resource consumption to smaller geographies with an average absolute prediction error of around 20%; however, performance varies widely by method, geography size, and fuel type. We also show how mapping these results can quickly identify districts with noteworthy resource consumption profiles. Further work should explore the design of local data collection strategies to enhance these methods and apply the techniques to other urban resources such as water or waste.
Adolescent Conflict Appraisals Moderate the Link Between Marital Conflict and Physiological Stress Reactivity
Authors: Lucas‐Thompson Rachel G. , Lunkenheimer Erika S. , Granger Douglas A.
Published: May 2016

The goal of this study was to advance understanding of how adolescent conflict appraisals contribute uniquely, and in combination with interparental conflict behavior, to individual differences in adolescent physiological reactivity. Saliva samples were collected from 153 adolescents (52% female; ages 10–17 years) before and after the Trier Social Stress Test. Saliva was assayed for cortisol and alpha‐amylase. Results revealed interactive effects between marital conflict and conflict appraisals. For youth who appraised parental conflict negatively (particularly as threatening), negative marital conflict predicted dampened reactivity; for youth who appraised parental conflict less negatively, negative marital conflict predicted heightened reactivity. These findings support the notion that the family context and youth appraisals of family relationships are linked with individual differences in biological sensitivity to context.
Enterovirus infection in febrile neonates: A hospital‐based prospective cohort study
Authors: Lv Xiao‐Qing , Qian Ling‐He , Wu Tai , Yuan Tian‐Ming
Published: May 2016

Aim

This study aims to investigate clinical characteristics and microbiological results and to assess the predictors for enterovirus infection in febrile neonates.

Methods

A prospective cohort study was conducted on 334 febrile patients (age: 0.33–28 days) in 2011–2012 years. Enterovirus RNA was detected by reverse transcription polymerase chain reaction on faeces or cerebrospinal fluid (CSF). Clinical characteristics were compared, and non‐conditional logistic regression analysis was performed to determine independent predictors for enterovirus infection.

Results

There were 131 episodes of neonatal enterovirus infection (39.22%). Forty‐eight (36.64%) developed respiratory symptoms, 69 (52.67%) had diarrhoea, 22 (16.79%) had poor feeding and 34 (25.95%) had rash. Eighteen (13.74%) had lower platelet counts, and CSF specimens were positive for enterovirus RNA in 44.27% (58/131) whose CSF revealed a mean white blood cell counts of 100.38 ± 147.97 cells/mm3 (range: 2–668 cells/mm3). The positivity of stool 38.92% (130/334) was significantly higher than that of CSF specimens 26.24% (58/221) for enterovirus RNA (P < 0.01). By logistic regression analysis, the following independently predicted enterovirus infection: abnormal CSF test (odds ratio (OR): 12.426, 95% confidence interval (CI): 5.633–27.413), thrombocytopenia (OR: 3.647, 95% CI: 1.312–10.136), duration of fever >3.25 (d) (OR: 2.293, 95% CI: 1.279–4.113), highest temperature >38.35 (°C) (OR: 2.094, 95% CI: 1.342–4.123) and negative bacterial culture (OR: 5.073, 95% CI: 1.504–17.114).

Conclusions

Our data indicated that enteroviruses should be routinely considered in the differential diagnosis of febrile neonates. The factors, which may predict the risk of neonatal enterovirus infection, were abnormal CSF test, thrombocytopenia, duration of fever >3.25 (d), highest temperature >38.35 (°C) and negative bacterial culture.
Human amygdala activation during rapid eye movements of rapid eye movement sleep: an intracranial study
Authors: Corsi‐Cabrera María , Velasco Francisco , del Río‐Portilla Yolanda , Armony Jorge L. , Trejo‐Martínez David , Guevara Miguel A. , Velasco Ana L.
Published: May 2016

The amygdaloid complex plays a crucial role in processing emotional signals and in the formation of emotional memories. Neuroimaging studies have shown human amygdala activation during rapid eye movement sleep (REM). Stereotactically implanted electrodes for presurgical evaluation in epileptic patients provide a unique opportunity to directly record amygdala activity. The present study analysed amygdala activity associated with REM sleep eye movements on the millisecond scale. We propose that phasic activation associated with rapid eye movements may provide the amygdala with endogenous excitation during REM sleep. Standard polysomnography and stereo‐electroencephalograph (SEEG) were recorded simultaneously during spontaneous sleep in the left amygdala of four patients. Time–frequency analysis and absolute power of gamma activity were obtained for 250 ms time windows preceding and following eye movement onset in REM sleep, and in spontaneous waking eye movements in the dark. Absolute power of the 44–48 Hz band increased significantly during the 250 ms time window after REM sleep rapid eye movements onset, but not during waking eye movements. Transient activation of the amygdala provides physiological support for the proposed participation of the amygdala in emotional expression, in the emotional content of dreams and for the reactivation and consolidation of emotional memories during REM sleep, as well as for next‐day emotional regulation, and its possible role in the bidirectional interaction between REM sleep and such sleep disorders as nightmares, anxiety and post‐traumatic sleep disorder. These results provide unique, direct evidence of increased activation of the human amygdala time‐locked to REM sleep rapid eye movements.
Effect of zonisamide on post‐traumatic Holmes’ tremor
Authors: Sekimoto Satoko , Oyama Genko , Izawa Nana , Ueno Sinichi , Jo Takayuki , Shimo Yasushi , Nakajima Asuka , Nakajima Madoka , Umemura Atsushi , Arai Hajime , Hattori Nobutaka
Published: May 2016

Holmes’ tremor is a rare symptom characterized by a complex combination of resting, postural and intention tremor. A 66‐year‐old right‐handed man post‐traumatically developed severe action tremor in his right hand, which had a component of the re‐emergent type and predominantly involved proximal muscles. He also presented mild resting tremor in his right hand. As the response of levodopa/carbidopa and arotinolol was limited, he started zonisamide, which resulted in dramatic improvement. The Fahn–Tolosa–Marin Tremor Rating Scale motor score improved from 52 points to 24 points. In conclusion, zonisamide could be a therapeutic option for post‐traumatic Holmes’ tremor. Further prospective studies are required.
Heat tolerance in a wild Oryza species is attributed to maintenance of Rubisco activation by a thermally stable Rubisco activase ortholog
Authors: Scafaro Andrew P. , Gallé Alexander , Van Rie Jeroen , Carmo‐Silva Elizabete , Salvucci Michael E. , Atwell Brian J.
Published: May 2016

The mechanistic basis of tolerance to heat stress was investigated in Oryza sativa and two wild rice species, Oryza meridionalis and Oryza australiensis. The wild relatives are endemic to the hot, arid Australian savannah.

Leaf elongation rates and gas exchange were measured during short periods of supra‐optimal heat, revealing species differences. The Rubisco activase (RCA) gene from each species was sequenced. Using expressed recombinant RCA and leaf‐extracted RCA, the kinetic properties of the two isoforms were studied under high temperatures.

Leaf elongation was undiminished at 45°C in O. australiensis. The net photosynthetic rate was almost 50% slower in O. sativa at 45°C than at 28°C, while in O. australiensis it was unaffected. Oryza meridionalis exhibited intermediate heat tolerance. Based on previous reports that RCA is heat‐labile, the Rubisco activation state was measured. It correlated positively with leaf elongation rates across all three species and four periods of exposure to 45°C. Sequence analysis revealed numerous polymorphisms in the RCA amino acid sequence from O. australiensis. The O. australiensis RCA enzyme was thermally stable up to 42°C, contrasting with RCA from O. sativa, which was inhibited at 36°C.

We attribute heat tolerance in the wild species to thermal stability of RCA, enabling Rubisco to remain active.
Analgesic management after thoracotomy for decortication in children: a retrospective audit of 83 children managed with a paravertebral infusion‐based regime
Authors: Murphy Tim , McCheyne Alan , Karlsson Jacob
Published: May 2016

Background

It is important that postoperative analgesic management after thoracotomy is very effective in order to optimize postoperative recovery. A regional technique such as an epidural or a paravertebral catheter with an infusion of local anesthetic may be supplemented with systemically administered analgesic drugs in order to achieve satisfactory analgesia.

Objective

The objective of this observational study was to evaluate whether a paravertebral infusion of local anesthetic delivered via a surgically placed catheter together with systemic analgesics is associated with low pain scores and satisfactory analgesia after thoracotomy for decortication in children.

Methods

We performed a retrospective analysis of the notes and charts of 83 children admitted with empyema thoracis and managed with thoracotomy and decortication. We collected data on the doses of analgesic drugs (morphine, paracetamol, and ibuprofen) and details of paravertebral infusions, together with postoperative pain scores for the first 48 h after surgery, or earlier if the paravertebral infusion was stopped within 48 h of surgery. Poor quality analgesia was defined as a score of 7 or more on the Visual Analog/Smiley Faces Scale (‘VAS/SF’).

Results

A total of 81 children were ASA 1 status and two were ASA 3 status. Analgesia comprised intravenous morphine at a mean dose of 20 μg·kg−1·h−1, together with oral paracetamol (62.5 mg·kg−1/24 h) and ibuprofen (14.2 mg·kg−1/24 h). The mean paravertebral bupivacaine dose was 0.29 mg·kg−1·h−1. Sixty‐four patients (77.1%) had good quality analgesia, 17 (20.5%) patients had moderate quality analgesia, and only two patients (2.4%) had poor quality analgesia.

Conclusion

Analgesic outcomes with this regimen appear to be very satisfactory. It compares favorably with an epidural‐based regimen.
Cold chain and virus‐free chloroplast‐made booster vaccine to confer immunity against different poliovirus serotypes
Authors: Chan Hui‐Ting , Xiao Yuhong , Weldon William C. , Oberste Steven M. , Chumakov Konstantin , Daniell Henry
Published: May 2016

The WHO recommends complete withdrawal of oral polio vaccine (OPV) type 2 by April 2016 globally and replacing with at least one dose of inactivated poliovirus vaccine (IPV). However, high‐cost, limited supply of IPV, persistent circulating vaccine‐derived polioviruses transmission and need for subsequent boosters remain unresolved. To meet this critical need, a novel strategy of a low‐cost cold chain‐free plant‐made viral protein 1 (VP1) subunit oral booster vaccine after single IPV dose is reported. Codon optimization of the VP1 gene enhanced expression by 50‐fold in chloroplasts. Oral boosting of VP1 expressed in plant cells with plant‐derived adjuvants after single priming with IPV significantly increased VP1‐IgG1 and VP1‐IgA titres when compared to lower IgG1 or negligible IgA titres with IPV injections. IgA plays a pivotal role in polio eradication because of its transmission through contaminated water or sewer systems. Neutralizing antibody titres (~3.17–10.17 log2 titre) and seropositivity (70–90%) against all three poliovirus Sabin serotypes were observed with two doses of IPV and plant‐cell oral boosters but single dose of IPV resulted in poor neutralization. Lyophilized plant cells expressing VP1 stored at ambient temperature maintained efficacy and preserved antigen folding/assembly indefinitely, thereby eliminating cold chain currently required for all vaccines. Replacement of OPV with this booster vaccine and the next steps in clinical translation of FDA‐approved antigens and adjuvants are discussed.
Detection of intracellular IFN‐γ and IL‐4 cytokines in CD4+ and CD8+ T cells in the peripheral blood of dogs naturally infected with Leishmania infantum
Authors: Matralis D. , Papadogiannakis E. , Kontos V. , Papadopoulos E. , Ktenas E. , Koutinas A.
Published: May 2016

Canine leishmaniosis (CanL) is a systemic zoonotic disease the clinical manifestations of which can range from self‐healing cutaneous lesions to disseminated visceral disease. Effective activation of cellular immunity is the cornerstone of resistance against Leishmania infantum in infected dogs. The aim of this cross‐sectional, controlled study was the intracellular detection of interleukin 4 (IL‐4) and interferon‐γ (IFN‐γ) in CD4+ and CD8+ lymphocytes in the peripheral blood of 40 dogs naturally infected with L. infantum by applying flow cytometry. The percentage of CD4+IL‐4+ and CD8+IL‐4+ lymphocytes (with or without immunostimulation) was low in the clinically healthy and subclinically infected dogs in contrast to clinically affected ones. In the same groups of dogs, the percentage of CD4+IFN‐γ+ and CD8+IFN‐γ+ T cells in their resting phase and following specific immunostimulation with Leishmania soluble antigen (LSA) was also low. CD4+IL‐4+ and CD8+IL‐4+ T cell percentage was higher in sick compared to clinically healthy and subclinically infected dogs, after immunostimulation. The corresponding figure of CD8+IL‐4+ cells in sick dogs after LSA immunostimulation was also increased thus underlining the important role these cells may play in humoral immunity and perhaps the progression of CanL.
We Use Permcaths Instead of Peritoneal Catheters for Acute Kidney Injury and Urgent‐Start Dialysis
Authors: Dean Daniel , Cruz Dinna N.
Published: May 2016

The rising tide of severe acute kidney injury requiring dialysis (AKI‐D) and unplanned dialysis initiation for advanced CKD patients remains a major problem for the nephrology community worldwide. Hemodialysis (HD) through a central venous catheter remains the most common practice for both. Peritoneal dialysis (PD) remains greatly underutilized despite mounting evidence of equipoise with HD for a significant proportion of patients. PD is technically simpler, requires less infrastructure, and costs less. However, the structure of our healthcare system, hospital logistics, and the current state of nephrology training all contribute to the reflexive consult for a central venous catheter. As clinicians, we must ask ourselves if we are doing our patients and our healthcare system a disservice by not offering PD in AKI and urgent‐start situations.
We Give Too Much Intravenous Iron
Authors: Dwyer Jamie P.
Published: May 2016

Dialysis patients have absolute and functional iron deficiencies. Traditionally, oral iron preparations have been insufficient to maintain iron stores to support erythropoiesis, especially in the setting of the ubiquitous use of erythropoiesis‐stimulating agents. This has led to the widespread adoption of intravenous iron protocols designed to maintain iron stores at levels that are much higher than for patients not on dialysis. These protocols are often developed by dialysis providers and may be largely independent of the treating nephrologist. Concerns about multiple risks associated with the use of intravenous iron persist. Despite this, mean ferritin levels in the United States have risen, partly due to more intravenous iron use and partly due to reduced erythropoiesis‐stimulating agent use. Questions about the relationship of intravenous iron to infection, cardiac, and hepatobiliary risks remain. The failure of oral iron preparations to maintain iron stores continues to prompt the use of intravenous iron. Recently, studies with oral ferric citrate as a phosphate binder have shown improved iron stores and maintenance of hemoglobin, and studies with soluble ferric pyrophosphate added to dialysate have shown both maintenance of iron stores and hemoglobin. With new iron options that affect iron stores in dialysis patients, the use of intravenous iron and its potential risks may wane.
We Underdialyze Women and Smaller Patients
Authors: Daugirdas John T.
Published: May 2016

In women, children, and smaller adults, dialysis adequacy targets based solely on Kt/V might result not only in shorter treatments with inadequate fluid removal and undesirably rapid ultrafiltration rates, but also in less than optimal removal of small and middle molecular weight solutes if fractional removal is considered in relation to body surface area. The outcomes evidence for this is not definitive, but is suggested by a prespecified secondary analysis of the randomized HEMO trial results, and is supported by observational data. Also, there is evidence from normal renal physiology that in healthy humans of different body size, glomerular filtration rate (GFR) scales more closely to body surface area than to total body water. With these factors in mind, time on HD may need to be greater than that predicted by standard KT/V measurements to maximize survival in women and in smaller patients.
Long‐Run Impact of Biofuels on Food Prices
Authors: Chakravorty Ujjayant , Hubert Marie‐Hélène , Moreaux Michel , Nøstbakken Linda
Published: May 2016

About 40 percent of US corn is now used to produce biofuels, which are used as substitutes for gasoline in transportation. In this paper, we use a Ricardian model with differential land quality to show that world food prices could rise by about 32 percent by 2022. About half of this increase is from the biofuel mandate and the rest is a result of demand‐side effects in the form of population growth and income‐induced changes in dietary preferences, from cereals to meat and dairy products. However, aggregate world carbon emissions would increase, because of significant land conversion to farming and leakage from lower oil prices.
Segregation in Friendship Networks
Authors: de Martí Joan , Zenou Yves
Published: May 2016

We analyze a network‐formation model where agents belong to different communities. Both individual benefits and costs depend on direct as well as indirect connections. Benefits of an indirect connection decrease with distance in the network, while the cost of a link depends on the type of agents involved. Two agents from the same community always face a low linking cost, while the cost of forming a relationship between two agents from different communities diminishes with the rate of exposure of each of them to the other community. We find that socialization among the same type of agent can be weak even if the cost of maintaining links within one's own type is very low. Our model also suggests that policies aimed at reducing segregation are socially desirable only if they reduce the within‐community cost differential by a sufficiently large amount.
Assessment of systemic inflammation by time‐trends of blood granulocyte count and plasma myeloperoxidase and elastase concentrations following colic surgery in horses
Authors: Salciccia Alexandra , Grulke Sigrid , de la Rebière de Pouyade Geoffroy , Franck Thierry , Detilleux Johann , Serteyn Didier , Sandersen Charlotte
Published: May 2016

Objective

To determine changes in blood granulocyte counts and in plasma myeloperoxidase (MPO) and elastase (ELT) concentrations in surgical colic cases, and to determine the relationship between these changes and the surgical procedure performed, occurrence of postoperative ileus, and final outcome.

Design

Prospective clinical study conducted over a 12‐month period.

Setting

University teaching hospital.

Animals

Fifty‐three horses undergoing emergency laparotomy and surviving at least 12 hours postoperatively.

Interventions

Blood samples were taken before surgery, during surgery, at the recovery from anesthesia, and then serially until the 150th hour after the first blood sampling. Granulocyte counts were performed by an automated cell hematology analyzer. Specific ELISAs were performed for the MPO and ELT measurements. Mixed models were used to compare the time‐trends of the 3 parameters.

Measurements and Main Results

Taking all horses together, the time‐trends of MPO and ELT were not significantly different from each other, but they were significantly different from the granulocyte time‐trend. The type of surgical procedure did not influence the time‐trends of the 3 parameters. Significant changes in the granulocyte time‐trends were associated with postoperative ileus and outcome. Significant changes in the MPO time‐trends were associated with outcome. The ELT time‐trends were not influenced by ileus or outcome.

Conclusions

Granulocyte counts and MPO change over time and are related to the severity of the inflammatory reaction in surgical colic cases. These time‐trends may allow evaluation of treatment efficacy in an effort to modulate excessive granulocyte activation and degranulation.
IMAGING DIAGNOSIS—CONCENTRIC PERIRADICULAR LIPOMA CAUSING LUMBAR NERVE ROOT COMPRESSION IN A DOG
Authors: Wahle Andrea M , Raith Karina , Posch Barbara , Eddicks Lina , Matiasek Kaspar , Jurina Konrad
Published: May 2016

An 11‐year‐old, male neutered Jack Russell Terrier was presented with a nerve root signature of the right pelvic limb. Magnetic resonance imaging revealed a well demarcated, ovoid, extramedullary mass at the level of the L7 vertebral body. This showed, compared to normal spinal cord, hyperintense signal on T1‐ and T2‐weighted images, which was suppressed on gradient echo short tau inversion recovery (GE‐STIR) images. Additionally, the mass was characterized by a fat density on computed tomography images. Histopathology of the surgically excised mass was consistent with concentric periradicular lipoma, which has not been described in domestic animals yet.
Pan–ice-sheet glacier terminus change in East Antarctica reveals sensitivity of Wilkes Land to sea-ice changes
Authors: Miles Bertie W. J. , Stokes Chris R. , Jamieson Stewart S. R.
Published: May 2016

Recent retreat of outlet glaciers in Wilkes Land, East Antarctica, is driven by changes in sea ice.
Arrays of microscopic organic LEDs for high-resolution optogenetics
Authors: Steude Anja , Witts Emily C. , Miles Gareth B. , Gather Malte C.
Published: May 2016

A novel optogenetics platform based on microscopic arrays of organic LEDs is used to control cells with light.
Rapid identification of health care–associated infections with an integrated fluorescence anisotropy system
Authors: Park Ki Soo , Huang Chen-Han , Lee Kyungheon , Yoo Yeong-Eun , Castro Cesar M. , Weissleder Ralph , Lee Hakho
Published: May 2016

A portable system for rapid bacterial profiling aims to rapidly diagnose health care–associated infections.
Tumor-homing peptides as tools for targeted delivery of payloads to the placenta
Authors: King Anna , Ndifon Cornelia , Lui Sylvia , Widdows Kate , Kotamraju Venkata R. , Agemy Lilach , Teesalu Tambet , Glazier Jocelyn D. , Cellesi Francesco , Tirelli Nicola , Aplin John D. , Ruoslahti Erkki , Harris Lynda K.
Published: May 2016

Tumor-homing peptides have been exploited to create nanocarriers for targeted delivery of therapeutic agents to the placenta.
Metabolic Pathway Involved in 6-Chloro-2-Benzoxazolinone Degradation by Pigmentiphaga sp. Strain DL-8 and Identification of the Novel Metal-Dependent Hydrolase CbaA
Authors: Dong Weiliang , Wang Fei , Huang Fei , Wang Yicheng , Zhou Jie , Ye Xianfeng , Li Zhoukun , Hou Ying , Huang Yan , Ma Jiangfeng , Jiang Min , Cui Zhongli
Published: May 2016

6-Chloro-2-benzoxazolinone (CDHB) is a precursor of herbicide, insecticide, and fungicide synthesis and has a broad spectrum of biological activity.
Pigmentiphaga
sp. strain DL-8 can transform CDHB into 2-amino-5-chlorophenol (2A5CP), which it then utilizes as a carbon source for growth. The CDHB hydrolase (CbaA) was purified from strain DL-8, which can also hydrolyze 2-benzoxazolinone (BOA), 5-chloro-2-BOA, and benzamide. The specific activity of purified CbaA was 5,900 U · mg protein
−1
for CDHB, with

K
m

and
k
cat
values of 0.29 mM and 8,500 s
−1
, respectively. The optimal pH for purified CbaA was 9.0, the highest activity was observed at 55°C, and the inactive metal-free enzyme could be reactivated by Mg
2+
, Ni
2+
, Ca
2+
, or Zn
2+
. Based on the results obtained for the CbaA peptide mass fingerprinting and draft genome sequence of strain DL-8,
cbaA
(encoding 339 amino acids) was cloned and expressed in
Escherichia coli
BL21(DE3). CbaA shared 18 to 21% identity with some metal-dependent hydrolases of the PF01499 family and contained the signature metal-binding motif Q
127
XXXQ
131
XD
133
XXXH
137
. The conserved amino acid residues His288 and Glu301 served as the proton donor and acceptor.
E. coli
BL21(DE3-pET-
cbaA
) resting cells could transform 0.2 mM CDHB into 2A5CP. The mutant strain DL-8Δ
cbaA
lost the ability to degrade CDHB but retained the ability to degrade 2A5CP, consistent with strain DL-8. These results indicated that
cbaA
was the key gene responsible for CDHB degradation by strain DL-8.

IMPORTANCE
2-Benzoxazolinone (BOA) derivatives are widely used as synthetic intermediates and are also an important group of allelochemicals acting in response to tissue damage or pathogen attack in gramineous plants. However, the degradation mechanism of BOA derivatives by microorganisms is not clear. In the present study, we reported the identification of CbaA and metabolic pathway responsible for the degradation of CDHB in
Pigmentiphaga
sp. DL-8. This will provide microorganism and gene resources for the bioremediation of the environmental pollution caused by BOA derivatives.
Implications of Limited Thermophilicity of Nitrite Reduction for Control of Sulfide Production in Oil Reservoirs
Authors: Fida Tekle Tafese , Chen Chuan , Okpala Gloria , Voordouw Gerrit
Published: May 2016

Nitrate reduction to nitrite in oil fields appears to be more thermophilic than the subsequent reduction of nitrite. Concentrated microbial consortia from oil fields reduced both nitrate and nitrite at 40 and 45°C but only nitrate at and above 50°C. The abundance of the
nirS
gene correlated with mesophilic nitrite reduction activity.
Thauera
and
Pseudomonas
were the dominant mesophilic nitrate-reducing bacteria (mNRB), whereas
Petrobacter
and
Geobacillus
were the dominant thermophilic NRB (tNRB) in these consortia. The mNRB
Thauera
sp. strain TK001, isolated in this study, reduced nitrate and nitrite at 40 and 45°C but not at 50°C, whereas the tNRB
Petrobacter
sp. strain TK002 and
Geobacillus
sp. strain TK003 reduced nitrate to nitrite but did not reduce nitrite further from 50 to 70°C. Testing of 12 deposited pure cultures of tNRB with 4 electron donors indicated reduction of nitrate in 40 of 48 and reduction of nitrite in only 9 of 48 incubations. Nitrate is injected into high-temperature oil fields to prevent sulfide formation (souring) by sulfate-reducing bacteria (SRB), which are strongly inhibited by nitrite. Injection of cold seawater to produce oil creates mesothermic zones. Our results suggest that preventing the temperature of these zones from dropping below 50°C will limit the reduction of nitrite, allowing more effective souring control.

IMPORTANCE
Nitrite can accumulate at temperatures of 50 to 70°C, because nitrate reduction extends to higher temperatures than the subsequent reduction of nitrite. This is important for understanding the fundamentals of thermophilicity and for the control of souring in oil fields catalyzed by SRB, which are strongly inhibited by nitrite.
Paralogous Regulators ArsR1 and ArsR2 of Pseudomonas putida KT2440 as a Basis for Arsenic Biosensor Development
Authors: Fernández Matilde , Morel Bertrand , Ramos Juan L. , Krell Tino
Published: May 2016

The remarkable metal resistance of many microorganisms is related to the presence of multiple metal resistance operons.
Pseudomonas putida
KT2440 can be considered a model for these microorganisms since its arsenic resistance is due to the action of proteins encoded by the two paralogous arsenic resistance operons ARS1 and ARS2. Both operons contain the genes encoding the transcriptional regulators ArsR1 and ArsR2 that control operon expression. We show here that purified ArsR1 and ArsR2 bind the trivalent salt of arsenic (arsenite) with similar affinities (~30 μM), whereas no binding is observed for the pentavalent salt (arsenate). Furthermore, trivalent salts of bismuth and antimony showed binding to both paralogues. The positions of cysteines, found to bind arsenic in other homologues, indicate that ArsR1 and ArsR2 employ different modes of arsenite recognition. Both paralogues are dimeric and possess significant thermal stability. Both proteins were used to construct whole-cell,
lacZ
-based biosensors. Whereas responses to bismuth were negligible, significant responses were observed for arsenite, arsenate, and antimony. Biosensors based on the
P. putida
arsB1 arsB2
arsenic efflux pump double mutant were significantly more sensitive than biosensors based on the wild-type strain. This sensitivity enhancement by pump mutation may be a convenient strategy for the construction of other biosensors. A frequent limitation found for other arsenic biosensors was their elevated background signal and interference by inorganic phosphate. The constructed biosensors show no interference by inorganic phosphate, are characterized by a very low background signal, and were found to be suitable to analyze environmental samples.

IMPORTANCE
Arsenic is at the top of the priority list of hazardous compounds issued by the U.S. Agency for Toxic Substances and Disease. The reason for the stunning arsenic resistance of many microorganisms is the existence of paralogous arsenic resistance operons.
Pseudomonas putida
KT2440 is a model organism for such bacteria, and their duplicated
ars
operons and in particular their ArsR transcription regulators have been studied in depth by
in vivo
approaches. Here we present an analysis of both purified ArsR paralogues by different biophysical techniques, and data obtained provide valuable insight into their structure and function. Particularly insightful was the comparison of ArsR effector profiles determined by
in vitro
and
in vivo
experimentation. We also report the use of both paralogues to construct robust and highly sensitive arsenic biosensors. Our finding that the deletion of both arsenic efflux pumps significantly increases biosensor sensitivity is of general relevance in the biosensor field.
Detection of Zoonotic Enteropathogens in Children and Domestic Animals in a Semirural Community in Ecuador
Authors: Vasco Karla , Graham Jay P. , Trueba Gabriel
Published: May 2016

Animals are important reservoirs of zoonotic enteropathogens, and transmission to humans occurs more frequently in low- and middle-income countries (LMICs), where small-scale livestock production is common. In this study, we investigated the presence of zoonotic enteropathogens in stool samples from 64 asymptomatic children and 203 domestic animals of 62 households in a semirural community in Ecuador between June and August 2014. Multilocus sequence typing (MLST) was used to assess zoonotic transmission of
Campylobacter jejuni
and atypical enteropathogenic
Escherichia coli
(aEPEC), which were the most prevalent bacterial pathogens in children and domestic animals (30.7% and 10.5%, respectively). Four sequence types (STs) of
C. jejuni
and four STs of aEPEC were identical between children and domestic animals. The apparent sources of human infection were chickens, dogs, guinea pigs, and rabbits for
C. jejuni
and pigs, dogs, and chickens for aEPEC. Other pathogens detected in children and domestic animals were
Giardia lamblia
(13.1%),
Cryptosporidium parvum
(1.1%), and Shiga toxin-producing
E. coli
(STEC) (2.6%).
Salmonella enterica
was detected in 5 dogs and
Yersinia enterocolitica
was identified in 1 pig. Even though we identified 7 enteric pathogens in children, we encountered evidence of active transmission between domestic animals and humans only for
C. jejuni
and aEPEC. We also found evidence that
C. jejuni
strains from chickens were more likely to be transmitted to humans than those coming from other domestic animals. Our findings demonstrate the complex nature of enteropathogen transmission between domestic animals and humans and stress the need for further studies.

IMPORTANCE
We found evidence that
Campylobacter jejuni
,
Giardia
, and aEPEC organisms were the most common zoonotic enteropathogens in children and domestic animals in a region close to Quito, the capital of Ecuador. Genetic analysis of the isolates suggests transmission of some genotypes of
C. jejuni
and aEPEC from domestic animals to humans in this region. We also found that the genotypes associated with
C. jejuni
from chickens were present more often in children than were those from other domestic animals. The potential environmental factors associated with transmission of these pathogens to humans then are discussed.
Cutting to the Core of the Issue: Emerging Strategies To Reduce Prostate Biopsy-Related Infections
Authors: Chamberland Robin R.
Published: May 2016

Over 1 million men undergo biopsy in the United States each year to evaluate for prostate cancer (S. Loeb, H. B. Carter, S. I. Berndt, W. Ricker, and E. M. Schaeffer, J Urol 186:1830–1834, 2011,
http://dx.doi.org/10.1016/j.juro.2011.06.057
). In recent years, there has been a rise in infectious complications related to these procedures. This review aims to provide an overview of the guidelines that direct transrectal prostate biopsy, to describe associated infection, and to evaluate the published data driving the current trend toward prebiopsy screening for resistant organisms.
Malassezia arunalokei sp. nov., a Novel Yeast Species Isolated from Seborrheic Dermatitis Patients and Healthy Individuals from India
Authors: Honnavar Prasanna , Prasad Gandham S. , Ghosh Anup , Dogra Sunil , Handa Sanjeev , Rudramurthy Shivaprakash M.
Published: May 2016

The majority of species within the genus
Malassezia
are lipophilic yeasts that colonize the skin of warm-blooded animals. Two species,
Malassezia globosa
and
Malassezia restricta
, are implicated in the causation of seborrheic dermatitis/dandruff (SD/D). During our survey of SD/D cases, we isolated several species of
Malassezia
and noticed vast variations within a few lipid-dependent species. Variations observed in the phenotypic characteristics (colony morphology, absence of catalase activity, growth at 37°C, and precipitation surrounding wells containing Tween 20 or Cremophor EL) suggested the possible presence of a novel species. Sequence divergence observed in the internal transcribed spacer (ITS) region, the D1/D2 domain, and the intergenic spacer 1 (IGS1) region of rDNA and the
TEF1
gene, PCR-restriction fragment length polymorphism (RFLP) analysis of the ITS2 region, and fluorescent amplified fragment length polymorphism analysis support the existence of a novel species. Based on phenotypic and molecular characterization of these strains, we propose a new species, namely,
M. arunalokei
sp. nov., and we designate NCCPF 127130 (= MTCC 12054 = CBS 13387) as the type strain.
The Emerging Duck Flavivirus Is Not Pathogenic for Primates and Is Highly Sensitive to Mammalian Interferon Antiviral Signaling
Authors: Wang Hong-Jiang , Li Xiao-Feng , Liu Long , Xu Yan-Peng , Ye Qing , Deng Yong-Qiang , Huang Xing-Yao , Zhao Hui , Qin E-De , Shi Pei-Yong , Gao George F. , Qin Cheng-Feng
Published: May 2016

Flaviviruses pose a significant threat to both animals and humans. Recently, a novel flavivirus, duck Tembusu virus (DTMUV), was identified to be the causative agent of a serious duck viral disease in Asia. Its rapid spread, expanding host range, and uncertain transmission routes have raised substantial concerns regarding its potential threats to nonavian hosts, including humans. Here, we demonstrate that DTMUV is not pathogenic for nonhuman primates and is highly sensitive to mammal type I interferon (IFN) signaling.
In vitro
assays demonstrated that DTMUV infected and replicated efficiently in various mammalian cell lines. Further tests in mice demonstrated high neurovirulence and the age-dependent neuroinvasiveness of the virus. In particular, the inoculation of DTMUV into rhesus monkeys did not result in either viremia or apparent clinical symptoms, although DTMUV-specific humoral immune responses were detected. Furthermore, we revealed that although avian IFN failed to inhibit DTMUV in avian cells, DTMUV was more sensitive to the antiviral effects of type I interferon than other known human-pathogenic flaviviruses. Knockout of the type I IFN receptor in mice caused apparent viremia, viscerotropic disease, and mortality, indicating a vital role of IFN signaling in protection against DTMUV infection. Collectively, we provide direct experimental evidence that this novel avian-origin DTMUV possesses a limited capability to establish infection in immunocompetent primates due to its decreased antagonistic activity in the mammal IFN system. Furthermore, our findings highlight the potential risk of DTMUV infection in immunocompromised individuals and warrant studies on the cross-species transmission and pathogenesis of this novel flavivirus.

IMPORTANCE
Mosquito-borne flaviviruses comprise a large group of pathogenic and nonpathogenic members. The pathogenic flaviviruses include dengue, West Nile, and Japanese encephalitis viruses, and the nonpathogenic flaviviruses normally persist in a natural cycle and rarely cause disease in humans. A novel flavivirus, DTMUV (also known as duck egg drop syndrome flavivirus [DEDSV]) was identified in 2012 in ducks and then rapidly spread to several Asian countries. This new flavivirus was then shown to infect multiple avian species, resulting in neurological symptoms with unknown routes of transmission. There is public concern regarding its potential transmission from birds to humans and other nonavian hosts. Our present study shows that the mammalian IFN system can efficiently eliminate DTMUV infection and that the emergence of severe DTMUV-associated disease in mammals, especially humans, is unlikely. Currently, DTMUV infection mostly affects avian species.
Nipah Virus C and W Proteins Contribute to Respiratory Disease in Ferrets
Authors: Satterfield Benjamin A. , Cross Robert W. , Fenton Karla A. , Borisevich Viktoriya , Agans Krystle N. , Deer Daniel J. , Graber Jessica , Basler Christopher F. , Geisbert Thomas W. , Mire Chad E.
Published: May 2016

Nipah virus (NiV) is a highly lethal paramyxovirus that recently emerged as a causative agent of febrile encephalitis and severe respiratory disease in humans. The ferret model has emerged as the preferred small-animal model with which to study NiV disease, but much is still unknown about the viral determinants of NiV pathogenesis, including the contribution of the C protein in ferrets. Additionally, studies have yet to examine the synergistic effects of the various P gene products on pathogenesis in animal models. Using recombinant NiVs (rNiVs), we examine the sole contribution of the NiV C protein and the combined contributions of the C and W proteins in the ferret model of NiV pathogenesis. We show that an rNiV void of C expression resulted in 100% mortality, though with limited respiratory disease, like our previously reported rNiV void of W expression; this finding is in stark contrast to the attenuated phenotype observed in previous hamster studies utilizing rNiVs void of C expression. We also observed that an rNiV void of both C and W expression resulted in limited respiratory disease; however, there was severe neurological disease leading to 60% mortality, and the surviving ferrets demonstrated sequelae similar to those for human survivors of NiV encephalitis.

IMPORTANCE
Nipah virus (NiV) is a human pathogen capable of causing lethal respiratory and neurological disease. Many human survivors have long-lasting neurological impairment. Using a ferret model, this study demonstrated the roles of the NiV C and W proteins in pathogenesis, where lack of either the C or the W protein independently decreased the severity of clinical respiratory disease but did not decrease lethality. Abolishing both C and W expression, however, dramatically decreased the severity of respiratory disease and the level of destruction of splenic germinal centers. These ferrets still suffered severe neurological disease: 60% succumbed to disease, and the survivors experienced long-term neurological impairment, such as that seen in human survivors. This new ferret NiV C and W knockout model may allow, for the first time, the examination of interventions to prevent or mitigate the neurological damage and sequelae experienced by human survivors.
Feline Calicivirus Infection Disrupts Assembly of Cytoplasmic Stress Granules and Induces G3BP1 Cleavage
Authors: Humoud Majid N. , Doyle Nicole , Royall Elizabeth , Willcocks Margaret M. , Sorgeloos Frederic , van Kuppeveld Frank , Roberts Lisa O. , Goodfellow Ian G. , Langereis Martijn A. , Locker Nicolas
Published: May 2016

In response to stress such as virus infection, cells can stall translation by storing mRNAs away in cellular compartments called stress granules (SGs). This defense mechanism favors cell survival by limiting the use of energy and nutrients until the stress is resolved. In some cases it may also block viral propagation as viruses are dependent on the host cell resources to produce viral proteins. Human norovirus is a member of the
Caliciviridae
family responsible for gastroenteritis outbreaks worldwide. Previous studies on caliciviruses have identified mechanisms by which they can usurp the host translational machinery, using the viral protein genome-linked VPg, or regulate host protein synthesis through the mitogen-activated protein kinase (MAPK) pathway. Here, we examined the effect of feline calicivirus (FCV) infection on SG accumulation. We show that FCV infection impairs the assembly of SGs despite an increased phosphorylation of eukaryotic initiation factor eIF2α, a hallmark of stress pathway activation. Furthermore, SGs did not accumulate in FCV-infected cells that were stressed with arsenite or hydrogen peroxide. FCV infection resulted in the cleavage of the SG-nucleating protein Ras-GTPase activating SH3 domain-binding protein (G3BP1), which is mediated by the viral 3C-like proteinase NS6
Pro
. Using mutational analysis, we identified the FCV-induced cleavage site within G3BP1, which differs from the poliovirus 3C proteinase cleavage site previously identified. Finally, we showed that NS6
Pro
-mediated G3BP1 cleavage impairs SG assembly. In contrast, murine norovirus (MNV) infection did not impact arsenite-induced SG assembly or G3BP1 integrity, suggesting that related caliciviruses have distinct effects on the stress response pathway.

IMPORTANCE
Human noroviruses are a major cause of viral gastroenteritis, and it is important to understand how they interact with the infected host cell. Feline calicivirus (FCV) and murine norovirus (MNV) are used as models to understand norovirus biology. Recent studies have suggested that the assembly of stress granules is central in orchestrating stress and antiviral responses to restrict viral replication. Overall, our study provides the first insight on how caliciviruses impair stress granule assembly by targeting the nucleating factor G3BP1 via the viral proteinase NS6
Pro
. This work provides new insights into host-pathogen interactions that regulate stress pathways during FCV infection.
In Vivo
Analysis of Infectivity, Fusogenicity, and Incorporation of a Mutagenic Viral Glycoprotein Library Reveals Determinants for Virus Incorporation
Authors: Salamango Daniel J. , Alam Khalid K. , Burke Donald H. , Johnson Marc C.
Published: May 2016

Enveloped viruses utilize transmembrane surface glycoproteins to gain entry into target cells. Glycoproteins from diverse viral families can be incorporated into nonnative viral particles in a process termed pseudotyping; however, the molecular mechanisms governing acquisition of these glycoproteins are poorly understood. For murine leukemia virus envelope (MLV Env) glycoprotein, incorporation into foreign viral particles has been shown to be an active process, but it does not appear to be caused by direct interactions among viral proteins. In this study, we coupled
in vivo
selection systems with Illumina next-generation sequencing (NGS) to test hundreds of thousands of MLV Env mutants for the ability to be enriched in viral particles and to perform other glycoprotein functions. NGS analyses on a subset of these mutants predicted that the residues important for incorporation are in the membrane-proximal external region (MPER), particularly W127 and W137, and the residues in the membrane-spanning domain (MSD) and also immediately flanking it (T140 to L163). These predictions were validated by directly measuring the impact of mutations in these regions on fusogenicity, infectivity, and incorporation. We suggest that these two regions dictate pseudotyping through interactions with specific lipid environments formed during viral assembly.

IMPORTANCE
Researchers from numerous fields routinely exploit the ability to manipulate viral tropism by swapping viral surface proteins. However, this process, termed pseudotyping, is poorly understood at the molecular level. For murine leukemia virus envelope (MLV Env) glycoprotein, incorporation into foreign viral particles is an active process, but it does not appear to occur through direct viral protein-protein interactions. In this study, we tested hundreds of thousands of MLV Env mutants for the ability to be enriched in viral particles as well as perform other glycoprotein functions. Our analyses on a subset of these mutants predict that the glycoprotein regions embedded in and immediately flanking the viral membrane dictate active incorporation into viral particles. We suggest that pseudotyping occurs through specific lipid-protein interactions at the viral assembly site.
Doctor, where is my iris?
Authors: Sophocleous Sophocles
Published: May 2016

Phacoemulsification cataract surgery with small clear corneal incision (CCI) is the standard of care for cataract treatment. Self-sealing, clear corneal wounds have been found to be stable and able to withstand high pressures. Nevertheless, there are a few cases published describing patients with previous cataract surgery and manually performed CCI who sustained blunt trauma with associated wound dehiscence, iris disinsertion and expulsion through the wound. The case described here demonstrates an eye that had traumatic aniridia post-blunt trauma, while the intraocular lens and the rest of the ocular structures remained intact.