bluuebunny/crossref_metadata_2025 huggingface dataset:
Containing influenza outbreaks with antiviral use in long‐term care facilities in Taiwan, 2008‐2014
Authors: Cheng Hao‐Yuan , Chen Wan‐Chin , Chou Yu‐Ju , Huang Angela Song‐En , Huang Wan‐Ting
Published: January 2018

Backgrounds

Influenza can spread rapidly in long‐term care facilities (LTCFs), and residents are usually at higher risk for influenza infections.

Objective

Our study aimed to evaluate the effectiveness of antiviral interventions on outbreak control.

Methods

Taiwan Centers for Disease Control used a syndromic surveillance system to monitor outbreaks in LTCFs. Local public health authorities verified those outbreaks and logged reports to the Epidemic Investigation Report Files Management System (EIRFMS). We conducted a retrospective cohort study by reviewing EIRFMS reports of influenza outbreaks in LTCFs during 2008‐2014. An influenza outbreak was defined as 3 or more cases of influenza‐like illness occurring within a 48‐hours period with ≥1 case of real‐time RT‐PCR‐confirmed influenza in the same LTCF. Antiviral interventions included providing antiviral treatment for patients and antiviral prophylaxis for contacts during outbreaks.

Results

Of 102 influenza outbreaks, median days from onset of the first patient to outbreak notification was 4 (range 0‐22). Median attack rate was 24% (range 2.2%‐100%). Median influenza vaccination coverage among residents was 81% (range 0%‐100%); 43% occurred during the summer months. Even though antiviral treatment was provided in 87% of the outbreaks, antiviral prophylaxis was implemented in only 40%. Starting antiviral treatment within 2 days of outbreak onset was associated with keeping attack rates at <25% (OR 0.29, 95% CI: 0.12‐0.71).

Conclusions

Early initiation of antiviral treatment may reduce the magnitude of influenza outbreaks. Clinicians should identify patients with influenza and start antiviral use early to prevent large outbreaks in LTCFs.
Constructive controversy and creative process engagement: The roles of positive conflict value, cognitive flexibility, and psychological safety
Authors: Ou Zhanying , Chen Tingting , Li Fuli , Tang Pokman
Published: January 2018

This research explores how and when constructive controversy enhances creative process engagement. We identify positive conflict value and cognitive flexibility as two mediating processes that transmit the effect of constructive controversy on creative process engagement. We further theorize that psychological safety shows opposing moderating effects: It strengthens the positive conflict value–creative process engagement link, whereas weakens the cognitive flexibility–creative process engagement link. Moreover, we propose that psychological safety strengthens and weakens the two mediating pathways through positive conflict value and cognitive flexibility, respectively. Results based on a multiwave data involving 239 employees from the research and development division of a large high‐technology company provide support for our hypotheses. Theoretical and practical implications are discussed.
‘In this Day and Age’: Social Facts, Common Sense and Cognition in Tort Law Judging in the United Kingdom
Authors: Burns Kylie
Published: January 2018

Tort law judging in the United Kingdom includes judicial ‘truth claims’ or ‘social facts’ about the world, society, and institutional and human behaviour. Although corrective justice and rights scholars assert tort law is autonomous and internally referential, social facts can be influential in tort decisions. While there is some evidence of judicial use of empirical research, many social facts are based on judicial notice, judicial common sense, and intuition. Social facts, often based on judicial common sense, play a role in tort judging. However, they can also be fertile ground for the introduction of cognitive bias and judicial error. The role of social facts in tort judging is not confined to ‘policy’ reasoning but includes social framework, context, and background. Emerging research on judicial cognition can help explain the nature and impact of common‐sense social facts. There is a need to consider potential responses to judicial use of social facts and judicial cognition.
A retrospective study of feline trauma patients admitted to a referral centre
Authors: Hernon T. , Gurney M. , Gibson S.
Published: January 2018

Objective

To identify prognostic information and provide recommendations for management of feline trauma patients.

Methods

Retrospective analysis of case records for 185 cats presented as emergency trauma cases to a referral hospital between February 2009 and December 2013. Each case was assigned a severity score from 1 (very minor injuries) to 6 (moribund, dying). The data were analysed using Mann–Whitney U and Spearman's rank correlation tests. Logistic regression was used to calculate odds ratios.

Results

Out of 185 cats, 22 (11%) did not survive to discharge. Those presenting with a higher severity score had a higher rate of mortality and a longer period of hospitalisation. Road traffic accidents were the most common cause of trauma (104/185) and had the highest mortality and complication rates. Cats with circulatory shock and multiple injuries were identified as having a higher rate of mortality.

Clinical significance

Cats involved in road traffic accidents and that present with signs of shock or multiple injuries following a traumatic event have an increased mortality rate. Cats with a higher severity score had an increased duration of hospitalisation.
Cannabis use is associated with reduced prevalence of progressive stages of alcoholic liver disease
Authors: Adejumo Adeyinka C. , Ajayi Tokunbo O. , Adegbala Oluwole M. , Adejumo Kelechi L. , Alliu Samson , Akinjero Akintunde M. , Onyeakusi Nnaemeka E. , Ojelabi Ogooluwa , Bukong Terence N.
Published: January 2018

Background

Abusive alcohol use has well‐established health risks including causing liver disease (ALD) characterized by alcoholic steatosis (AS), steatohepatitis (AH), fibrosis, cirrhosis (AC) and hepatocellular carcinoma (HCC). Strikingly, a significant number of individuals who abuse alcohol also use Cannabis, which has seen increased legalization globally. While cannabis has demonstrated anti‐inflammatory properties, its combined use with alcohol and the development of liver disease remain unclear.

Aim

The aim of this study was to determine the effects of cannabis use on the incidence of liver disease in individuals who abuse alcohol.

Methods

We analysed the 2014 Healthcare Cost and Utilization Project‐Nationwide Inpatient Sample (NIS) discharge records of patients 18 years and older, who had a past or current history of abusive alcohol use (n = 319 514). Using the International Classification of Disease, Ninth Edition codes, we studied the four distinct phases of progressive ALD with respect to three cannabis exposure groups: non‐cannabis users (90.39%), non‐dependent cannabis users (8.26%) and dependent cannabis users (1.36%). We accounted for the complex survey sampling methodology and estimated the adjusted odds ratio (AOR) for developing AS, AH, AC and HCC with respect to cannabis use (SAS 9.4).

Results

Our study revealed that among alcohol users, individuals who additionally use cannabis (dependent and non‐dependent cannabis use) showed significantly lower odds of developing AS, AH, AC and HCC (AOR: 0.55 [0.48‐0.64], 0.57 [0.53‐0.61], 0.45 [0.43‐0.48] and 0.62 [0.51‐0.76]). Furthermore, dependent users had significantly lower odds than non‐dependent users for developing liver disease.

Conclusions

Our findings suggest that cannabis use is associated with a reduced incidence of liver disease in alcoholics.
The Effect of PhD Funding on Postdegree Research Career and Publication Productivity
Authors: Nisticò Roberto
Published: January 2018

This paper explores the extent to which PhD funding encourages postdegree research career and leads to publications. Using novel data on Italian PhD graduates, I find positive modest effects of funding both on pursuing a research career and on publication productivity within a few years after graduation. The results are robust to a battery of checks and different model specifications. I also provide evidence that funded students invest more in research‐oriented activities and spend less time on outside (non‐research) work during the PhD, thus highlighting mechanisms that potentially account for the effect of funding.
Transparency‐enhancing technology allows three‐dimensional assessment of gastrointestinal mucosa: A porcine model
Authors: Mizutani Hiroya , Ono Satoshi , Ushiku Tetsuo , Kudo Yotaro , Ikemura Masako , Kageyama Natsuko , Yamamichi Nobutake , Fujishiro Mitsuhiro , Someya Takao , Fukayama Masashi , Koike Kazuhiko , Onodera Hiroshi
Published: January 2018

Although high‐resolution three‐dimensional imaging of endoscopically resected gastrointestinal specimens can help elucidating morphological features of gastrointestinal mucosa or tumor, there are no established methods to achieve this without breaking specimens apart. We evaluated the utility of transparency‐enhancing technology for three‐dimensional assessment of gastrointestinal mucosa in porcine models. Esophagus, stomach, and colon mucosa samples obtained from a sacrificed swine were formalin‐fixed and paraffin‐embedded, and subsequently deparaffinized for analysis. The samples were fluorescently stained, optically cleared using transparency‐enhancing technology: ilLUmination of Cleared organs to IDentify target molecules method (LUCID), and visualized using laser scanning microscopy. After observation, all specimens were paraffin‐embedded again and evaluated by conventional histopathological assessment to measure the impact of transparency‐enhancing procedures. As a result, microscopic observation revealed horizontal section views of mucosa at deeper levels and enabled the three‐dimensional image reconstruction of glandular and vascular structures. Besides, paraffin‐embedded specimens after transparency‐enhancing procedures were all assessed appropriately by conventional histopathological staining. These results suggest that transparency‐enhancing technology may be feasible for clinical application and enable the three‐dimensional structural analysis of endoscopic resected specimen non‐destructively. Although there remain many limitations or problems to be solved, this promising technology might represent a novel histopathological method for evaluating gastrointestinal cancers.
Piscicide impact extends beyond targets and toxicity
Authors: Donnelly Roarke
Published: January 2018

Restoration of fisheries often requires removal of invasive fishes. Although piscicides such as antimycin a and rotenone are reliable and cost‐effective tools for such removals, they may reduce the abundance of nontarget species directly via toxicity‐induced mortality (toxic effect) or indirectly via loss of prey (trophic effect). Toxic effects are well documented in some taxa, especially in benthic macroinvertebrates (BMIs). Yet, the corresponding trophic effects on nonpiscine, aquatic, and riparian species remain unstudied. I tested for a trophic effect of piscicides using a population of American Dippers (Cinclus mexicanus), songbirds that feed extensively on BMIs. I caught breeding birds and estimated body condition before, during, and after treatment of the stream with antimycin a or rotenone. Birds exhibited poorer body condition (3.0–3.7% lower body mass) during treatment than before or after treatment. These differences suggested that treatment reduced prey availability enough to impact birds at least 9 months after application. Therefore, continued use of piscicides for fish restoration would benefit from (1) site‐specific comparison of benefits of invasive fish removal to costs of potential or documented toxic and trophic effects of piscicides on nontarget organisms; (2) continued adherence to best practices for recovery of the BMI community after piscicide treatment; and (3) experimental study of piscicide impacts.
Microsatellite markers for evaluating the diversity of the natural killer complex and major histocompatibility complex genomic regions in domestic horses
Authors: Horecky C. , Horecka E. , Futas J. , Janova E. , Horin P. , Knoll A.
Published: January 2018

Genotyping microsatellite markers represents a standard, relatively easy, and inexpensive method of assessing genetic diversity of complex genomic regions in various animal species, such as the major histocompatibility complex (MHC) and/or natural killer cell receptor (NKR) genes. MHC‐linked microsatellite markers have been identified and some of them were used for characterizing MHC polymorphism in various species, including horses. However, most of those were MHC class II markers, while MHC class I and III sub‐regions were less well covered. No tools for studying genetic diversity of NKR complex genomic regions are available in horses. Therefore, the aims of this work were to establish a panel of markers suitable for analyzing genetic diversity of the natural killer complex (NKC), and to develop additional microsatellite markers of the MHC class I and class III genomic sub‐regions in horses. Nine polymorphic microsatellite loci were newly identified in the equine NKC. Along with two previously reported microsatellites flanking this region, they constituted a panel of 11 loci allowing to characterize genetic variation in this functionally important part of the horse genome. Four newly described MHC class I/III‐linked markers were added to 11 known microsatellites to establish a panel of 15 MHC markers with a better coverage of the class I and class III sub‐regions. Major characteristics of the two panels produced on a group of 65 horses of 13 breeds and on five Przewalski's horses showed that they do reflect genetic variation within the horse species.
Characterization of the novel HLA‐B*40:01:31 allele
Authors: Zheng J. W. , Sun Y. , Xie J. H. , Xiang D.
Published: January 2018

The HLA‐B*40:01:31 allele differs from B*40:01:01 by one nucleotide substitution at position 216.
Designing a Sanitary Process System
Authors: Pastore Frank
Published: January 2018

Years ago a sanitary process system could be developed at the corporate and/or plant level by the engineering and operations staff and a few key vendors.

Today most engineering departments in the beverage industry have been drastically reduced in size or completely eliminated making it impossible for a company to complete a process system without outside help. Therefore, it is imperative for the end user to work closely with a recognized process equipment supplier to develop a system not limited to a line of equipment but utilizing complete process system engineering capabilities. This is especially true today as line sizes have increased in size and scope making it near impossible to design and build it in a small fabricating shop.

Prior to discussions with the process equipment supplier, the end user will have defined his or her final objectives.

Paper published with permission.
Overview of Mechanical Harvesting in Florida Citrus
Authors: Brown G. K.
Published: January 2018

Florida produces more citrus than all other states in the United States. In 1999, the total bearing area was estimated at 315,900 ha, and 245,000 ha were oranges (Anon, 2000). Recently, oranges averaged 77% of the total production and about 95% were processed. Orange production is projected to increase unless US weather, disease, labor, or economic forces act to depress production (Anon, 1993). Worldwide production and price competition in processed oranges are projected to decrease US grower returns, as free-trade conditions progress.

Paper published with permission.
The Power of Insulation in the Citrus Industry
Authors: King Ronald L.
Published: January 2018

Insulation is a forgotten technology that can provide an unrivaled return on investment. The Citrus Industry is not an exception. Insulation is the ‘Rodney Dangerfield’ of the construction industry: It receives very little respect and is taken for granted. Insulation is a powerful resource when designed, applied, and maintained properly. Yet, this technology is often forgotten or put on the bottom of the list and ignored.

A recent survey conducted by the National Insulation Association of more than 160 industrial plants, manufacturing, engineering, and architectural firms found that:

• Most had no idea of the payback period, rate of return, with the use of insulation, nor a method to quantify costs versus savings

• Many acknowledged that numerous areas of insulation were in serious need of repair

• The majority did not understand that insulation had any real environmental “tie in”

• Some did not consider additional insulation necessary: “the plant is working fine”

• Many could not relate corrosion under insulation to having anything to do with the insulation

• Most acknowledged their specifications were outdated

• Many confirmed they did not have a dedicated job function to address insulation specifications or anyone who was the “insulation champion”

• Many did not think of insulation as a system or requiring any special design review or technical consideration

That survey confirmed the ‘Rodney Dangerfield’ characterization and formed the basis for the foundation of a major industry educational and awareness initiative.

The benefits of insulation are in many cases invisible and long lasting. This technology is not some mysterious myth. Possibly it is misunderstood and under appreciated due to lack of knowledge. Calculating the operational benefits and the return on investment can be relatively simple. However, an insulation system does not have any moving parts, computer chips, or fancy gauges, and it is certainly not sexy. Maybe that is why in many circles insulation is not an exciting topic of discussion, even though it is a time tested and proven technology that can often provide an annual return on investment greater than 100%. There has not been a more important time in recent history than now to think about insulation differently. The Citrus Industry is not immune to that thought process.

Paper published with permission.
Innovative Mechanical Water Treatment for Evaporative Condensers at a Citrus Facility
Authors: Vella Philip
Published: January 2018

This paper will describe the use of non-chemical technology for the treatment of cooling water from evaporative condensers at a citrus facility. The technology used is Controlled Hydrodynamic Cavitation (CHC). CHC is one of the most innovative technologies employed today and is unlike all other non-chemical technologies currently available that provide scale, corrosion, and microbiological control in addition to water conservation.

The objectives of this study conducted in 2003–2004 were to: (a) provide scale, corrosion, and microbiological control to a state-of-the-art facility which cools one of the largest refrigerated enclosures in North America, (b) improve condenser operating efficiency over the existing condenser systems, (c) conserve water by minimizing condenser makeup, (d) produce a reduced quantity of condenser bleed with reduced levels of contaminants, and (e) implement environmental improvements and worker safety wherever possible.

Based on the data obtained from the study, all objectives were met, operating expenditures were reduced, and the facility successfully continues to use the CHC technology.

Paper published with permission.
2010 Regulatory Update for Anhydrous Ammonia Refrigeration Processes
Authors: Ira Martha Mead
Published: January 2018

Refrigeration processes that contain more than 10,000 lb of anhydrous ammonia refrigerant are subject to a number of environmental and safety regulations, including the following:

▪ Occupational Safety and Health Administration’s (OSHA’s) Process Safety Management of Highly Hazardous Chemicals (the PSM Standard), 29 CFR 1910.119

▪ Environmental Protection Agency’s (EPA’s) Risk Management Plan (RMP) Rule, 40 CFR, Part 68

▪ EPA’s Emergency Planning and Community Right to Know Act (EPCRA), 40 CFR parts 350 to 372,

▪ Department of Homeland Security’s (DHS’s) Chemical Facility Anti-Terrorism Standard, 6 CFR Part 27.

These regulations require periodic reporting and other actions, such as employee training and the implementation of hazard prevention programs and emergency response plans. This paper provides a brief summary of the listed rules, as they apply to ammonia refrigeration processes, and describes the following regulatory changes and trends:

▪ OSHA 2009 PSM Covered Chemical Facilities National Emphasis Program, which will include a focus on ammonia refrigeration facilities

▪ EPA’s recently implemented RMP e*Submit procedure

▪ Recent changes to the Tier II reporting for Florida facilities

▪ Rulemaking related to the DHS chemical facility antiterrorism standard.

This paper should be helpful to ammonia refrigeration facility owners and operators who are struggling to stay in compliance with the many regulations applicable to their process. Additionally, the references and website links listed on the bibliography of this paper will serve as resources to further assist such owners and operators in the future, as regulations continue to change. All website addresses were checked on February 16, 2010.

Paper published with permission.
Juice Debittering: Basic Science, Optimization, and Recent Advances
Authors: Ghanem Fred
Published: January 2018

Bitterness such as Naringin in Grapefruits and Limonin in all Citrus fruits have a strong influence on consumers’ choices for their favorite juices. There have been many methods from ultrafiltration to biocatalysis used to lower such bitter compounds and make the juices more desirable by the consumer. One major tool for such debittering operation is the use of synthetic adsorbents which will be discussed in this paper.

Ion exchange resins and adsorbents have been used for over a century in various food applications to concentrate flavors, decolorize juices, and enhance the quality of the final product. These types of resins are being synthesized to specific parameters to distinguish them from other tools.

Mitsubishi Chemical’s work on optimizing their synthetic adsorbents for high bitterness removal from citrus juice was investigated. Parameters such as the base matrix structure, pore size and distribution, as well as the effect of surface area were studied. As the FDA has strict definitions about the appropriate resin chemistry that can be used in a food application (21 CFR 173.65), progress in new resin chemistry was limited by such regulations.

This paper discusses the use of the original Sepabeads SP70 which was introduced into the market about 20 years ago, to the high capacity resin, Sepabeads SP700, which was introduced 10 years ago, and finally, to the Sepabeads SP710, which is the current optimized version of 20 years of research work. Mitsubishi Chemical’s resins were compared to other resins in the industry for the removal of naringin, limonin, and 8-hydroxyfuranocoumarin (furanocoumarins are compounds that affects the proper absorption of certain medications). Proper regeneration and rejuvenation of these resins were outlined.

Paper published with permission.
Bacteria make their way to the brain
Authors: Dupnik Kathryn
Published: January 2018

Diverse bacterial species can be detected in the brains of mice with abdominal sepsis.
Personalized printing for stroke prevention, hand in glove
Authors: King Kevin R.
Published: January 2018

3D-printed patient-specific left atrial appendage occluders overcome anatomic variability to personalize stroke prevention.
Population Pharmacokinetics of Finafloxacin in Healthy Volunteers and Patients with Complicated Urinary Tract Infections
Authors: Taubert Max , Lückermann Mark , Vente Andreas , Dalhoff Axel , Fuhr Uwe
Published: January 2018

Finafloxacin is a novel fluoroquinolone with increased antibacterial activity at acidic pH and reduced susceptibility to several resistance mechanisms. A phase II study revealed a good efficacy/safety profile in patients with complicated urinary tract infections (cUTIs), while the pharmacokinetics was characterized by highly variable concentration-versus-time profiles, suggesting the need for an elaborated pharmacokinetic model. Data from three clinical trials were evaluated: 127 healthy volunteers were dosed orally (
n
= 77) or intravenously (
n
= 50), and 139 patients with cUTI received finafloxacin intravenously. Plasma (2,824 samples from volunteers and 414 samples from patients) and urine (496 samples from volunteers and 135 samples patients) concentrations were quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). NONMEM was used to build a population pharmacokinetic model, and pharmacokinetic/pharmacodynamic relationships were investigated via simulations and logistic regression. A two-compartment model with first-order elimination described the data best (central volume of distribution [
V
c
] and peripheral volume of distribution [
V
p
] of 47 liters [20%] and 43 liters [67%], respectively, and elimination clearance and intercompartmental clearance of 21 liters/h [54%] and 2.8 liters/h [57%], respectively [median bootstrap estimates {coefficients of variation}]).
V
c
increased with body surface area, and clearance was reduced in patients (−29%). Oral absorption was described best by parallel first- and zero-order processes (bioavailability of 75%). No pharmacodynamic surrogate parameter of clinical/microbiological outcome could be identified, which depended exclusively on the MIC of the causative pathogens. Despite the interindividual variability, the present data set does not support covariate-based dose adjustments. Based on the favorable safety and efficacy data, the clinical relevance of the observed variability appears to be limited. (This study has been registered at ClinicalTrials.gov under identifier NCT01928433.)
Clostridial Strain-Specific Characteristics Associated with Necrotizing Enterocolitis
Authors: Schönherr-Hellec Sophia , Klein Geraldine L. , Delannoy Johanne , Ferraris Laurent , Rozé Jean Christophe , Butel Marie José , Aires Julio
Published: January 2018

We aimed at identifying potential bacterial factors linking clostridia with necrotizing enterocolitis (NEC). We compared the phenotypic traits, stress responses, cellular cytotoxicity, and inflammatory capabilities of the largest collection of
Clostridium butyricum
and
Clostridium neonatale
strains isolated from fecal samples of NEC preterm neonates (PN) and control PNs. When strain characteristics were used as explanatory variables, a statistical discriminant analysis allowed the separation of NEC and control strains into separate groups. Strains isolated from NEC PN were characterized by a higher viability at 30°C (
P
= 0.03) and higher aerotolerance (
P
= 0.01), suggesting that NEC strains may have a competitive and/or survival advantage in the environmental gastrointestinal tract conditions of NEC PN. Heat-treated NEC bacteria induced higher production of interleukin-8 in Caco-2 cells (
P
= 0.03), suggesting proinflammatory activity.
In vitro
, bacteria, bacterial components, and fecal filtrates showed variable cytotoxic effects affecting the cellular network and/or cell viability, without specific association with NEC or control samples. Altogether, our data support the existence of a specific clostridial strain signature associated with NEC.

IMPORTANCE
Clostridia are part of the commensal microbiota in preterm neonates (PN). However, microbiota analyses by culture and metagenomics have linked necrotizing enterocolitis (NEC) and intestinal colonization with clostridial species. Nevertheless, little is known about the specific characteristics that may be shared by clostridia associated with NEC compared to commensal clostridia. Therefore, our goal was to identify specific bacterial factors linking clostridial strains with NEC. We report the existence of a specific bacterial signature associated with NEC and propose that activation of the innate immune response may be a unifying causative mechanism for the development of NEC independent of a specific pathogenic organism. The present study provides new insights into NEC pathophysiology that are needed for better diagnostics and strategies for implementing prevention of the disease.
Draft Genome Sequence of
Mycobacterium setense
CSUR47
Authors: Bouam Amar , Levasseur Anthony , Drancourt Michel
Published: January 2018

Mycobacterium setense
CSUR47 is a rapidly growing
Mycobacterium
species strain isolated from pus collected from a left maxillary sinus in Marseille, France. Here, we report the complete 6,278,097-bp genome sequence of
M. setense
CSUR47, which exhibits a 66.40% GC content and encodes 5,863 protein-coding genes, 48 tRNAs, and 9 rRNAs.
Draft Genome Sequence ofCoxiella burnetiiHistorical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia
Authors: Freylikhman Olga , Kiselev Artem , Kazakov Sergey , Sergushichev Alexey , Panferova Yulia , Tokarevich Nikolay , Kostareva Anna
Published: January 2018

This is the announcement of a draft genome sequence ofCoxiella burnetiistrain Leningrad-2, phase I. The strain, which is mildly virulent in infected guinea pigs, was isolated in 1957 from the blood of a patient with acute Q fever in Leningrad (now Saint Petersburg), Russia.
Draft Genome Sequence of
Streptococcus canis
Clinical Strain TA4, Harboring the M-Like Protein Gene and Isolated in Japan from a Patient with Bacteremia
Authors: Yoshida Haruno , Katayama Yukie , Fukushima Yasuto , Taniyama Daisuke , Murata Yoshiteru , Mizutani Tetsuya , Takahashi Takashi
Published: January 2018

Streptococcus canis
is an animal-origin β-hemolytic bacterium that can cause severe infections in animals and occasionally infects humans. Here, we report a draft genome sequence of an
S. canis
strain harboring the M-like protein gene. This strain was isolated from a patient with bacteremia (reported by Taniyama et al. [D. Taniyama, Y. Abe, T. Sakai, T. Kikuchi, and T. Takahashi, IDCases 7:48–52, 2017,
https://doi.org/10.1016/j.idcr.2017.01.002
]). The draft genome comprises 2,129,080 bp in 60 contigs.
Complete Genome Sequence of
Streptomyces
Bacteriophage Abt2graduatex2
Authors: Erill Ivan , Caruso Steven M.
Published: January 2018

The
Streptomyces
bacteriophage Abt2graduatex2 is a double-stranded DNA (dsDNA)
Siphoviridae
isolated from soil collected in Baltimore, MD, and harvested using
Streptomyces griseus
subsp.
griseus
. Abt2graduatex2, a cluster BG phage, encodes an HicA-like toxin.
Complete Genome Sequence of
Paracoccus yeei
TT13, Isolated from Human Skin
Authors: Lim Jae Yun , Hwang Ingyu , Ganzorig Munkhtsatsral , Pokhriyal Shivalika , Singh Rajni , Lee Kyoung
Published: January 2018

Paracoccus yeei
TT13 was isolated from human skin because of its ability to degrade propylene glycol. Here, we present the whole-genome sequence of this strain; it possesses one 3.58-Mb chromosome and six plasmids. TT13 genome analysis indicated that this bacterium has denitrification potential.
Increased Epitope Complexity Correlated with Antibody Affinity Maturation and a Novel Binding Mode Revealed by Structures of Rabbit Antibodies against the Third Variable Loop (V3) of HIV-1 gp120
Authors: Pan Ruimin , Qin Yali , Banasik Marisa , Lees William , Shepherd Adrian J. , Cho Michael W. , Kong Xiang-Peng
Published: January 2018

The third variable (V3) loop of HIV-1 gp120 is an immunodominant region targeted by neutralizing antibodies (nAbs). Despite limited breadth, better characterization of the structural details of the interactions between these nAbs and their target epitopes would enhance our understanding of the mechanism of neutralization and facilitate designing better immunogens to induce nAbs with greater breadth. Recently, we isolated two anti-V3 neutralizing monoclonal antibodies (MAbs), 10A3 and 10A37, from a rabbit immunized with gp120 of the M group consensus sequence. In this study, crystal structures of these MAbs bound to target epitopes were determined. 10A3 binds to the V3 crown (303TRKSIHIGPGRAF317) using the cradle binding mode, similar to human V3 MAbs encoded by IGHV5-51 germ line genes, and its epitope structure resembles that bound to the human antibodies. In contrast, 10A37, which exhibits greater breadth and potency than 10A3, binds the V3 crown and the succeeding stem region (308HIGPGRAFYTTGEI323). Unexpectedly, the315RAFYTT320portion of the epitope existed as helical turns, a V3 structure that has not been observed previously. Its main chain-dominated antigen-antibody interactions not only explain the broad neutralization of 10A37 but also show that its epitope is a potential vaccine target to be further evaluated. In conclusion, our study provides novel insights about neutralization-susceptible epitope structures of the V3 loop of HIV-1 gp120 and demonstrates that, despite low amino acid sequence similarity to human antibody germ line genes, rabbits can serve as a useful animal model to evaluate human vaccine candidates.

IMPORTANCEThe apex crown of V3 of HIV-1 gp120 is the most immunogenic region of the surface glycoprotein, and many MAbs targeting this region have been developed. Structural understanding of V3 crown MAbs not only can help understand how antibody responses target this unique region but also contribute to immunogen design for vaccine development. We present here crystal structures of two neutralizing V3 MAbs, 10A3 and 10A37, developed from a rabbit immunized with gp120. Our analysis of 10A3 in complex with V3 provided a detailed example of how epitope complexity can evolve with affinity maturation, while that of 10A37 revealed a novel V3 binding mode targeting the C-terminal side of the V3 crown and showed that this region can form a helical structure. Our study provides novel insights about neutralization-susceptible V3 epitope structures and demonstrates that rabbits can serve as a useful animal model to evaluate human vaccine candidates.
How fast can low-angle normal faults slip? Insights from cosmogenic exposure dating of the active Mai’iu fault, Papua New Guinea
Authors: Webber S. , Norton K.P. , Little T.A. , Wallace L.M. , Ellis S.
Published: January 2018

Is there an upper limit to normal fault slip rates? The Mai’iu fault, located within the rapidly extending Woodlark Rift, Papua New Guinea, is one of few active continental low-angle normal faults (LANFs) globally. There is ongoing debate regarding how commonly normal faults slip at shallow (<30°) dips, and at what rates. We present a global compilation of reported slip rates on active and inactive extensional detachments that suggests that such faults may slip at >10–20 mm/yr—faster than any reported high-angle normal fault. Cosmogenic nuclide exposure dating (10Be in quartz) of the lowermost Mai’iu fault scarp supports this finding, indicating slip at 11.7 ± 3.5 mm/yr over the past ∼5.5 k.y. Our results highlight the long-term viability of LANFs, and show that the Mai’iu fault represents one of Earth’s fastest active continental normal faults. Rapid and large-displacement slip is likely enabled by extremely low fault frictional strength.
Visual outcomes after chemotherapy for optic pathway glioma in children with and without neurofibromatosis type 1: results of the International Society of Paediatric Oncology (SIOP) Low-Grade Glioma 2004 trial UK cohort
Authors: Falzon Kevin , Drimtzias Evangelos , Picton Susan , Simmons Ian
Published: January 2018

Aims

To report visual acuity (VA) outcomes following chemotherapy for optic pathway glioma (OPG) in children with or without neurofibromatosis type-1 (NF1) and to analyse associated risk factors.

Methods

A prospective, multicentre, cohort study involving 155 children treated between September 2004 and December 2012. Initial and final VA was used for per-eye and per-subject analysis. Correlation tests were performed to determine whether initial VA predicted final VA. Logistic regression was used to determine whether age and tumour location were associated risk factors.

Results

90 children had complete ophthalmological data. At initiation of chemotherapy, 26% and 49% of eyes with NF1-OPG and sporadic OPG, respectively, had VA of ≥0.7 log of the minimum angle of resolution (logMAR). At final visit, per eye, 49% had ≤0.2, 23% had 0.30–0.60 and 28% had VA≥0.70 logMAR in the NF1-OPG group. In the sporadic OPG group, per eye, 32% had ≤0.2, 11% had VA 0.30–0.60 and 57% had ≥0.70 logMAR. Children with sporadic OPG, per eye, were significantly less likely to have VA outcomes ≤0.60 logMAR compared with children with NF1-OPG (OR=0.30; 95% CI 0.16 to 0.56; P<0.0001). Per subject, VA improved in 24%, remained stable in 35% and worsened in 41% of children with NF1-OPG and improved in 18%, remained stable in 43% and worsened in 39% of children with sporadic OPG.

Conclusions

Children with and without NF1 demonstrated the same rate of VA improvement, stabilisation or worsening; however, children with sporadic OPG had a poorer VA outcome. Better initial VA, older age, absence of postchiasm tumour and presence of NF1 were associated with improved or stable VA outcomes.
Peripapillary vascular changes in radiation optic neuropathy: an optical coherence tomography angiography grading
Authors: Parrozzani Raffaele , Frizziero Luisa , Londei Davide , Trainiti Sara , Modugno Rocco Luigi , Leonardi Francesca , Pulze Serena , Miglionico Giacomo , Pilotto Elisabetta , Midena Edoardo
Published: January 2018

Aims

To investigate peripapillary vascular changes secondary to radiation optic neuropathy (RON) using optical coherence tomography angiography (OCT-A) and to propose a clinical grading of RON based on OCT-A findings.

Methods

Thirty-four patients affected by RON were consecutively included. Each patient underwent best corrected visual acuity measurement (ETDRS score) and OCT-A (Nidek RS-3000 Advance device, Nidek, Gamagori, Japan). The radial peripapillary capillary plexus (RPCP) and the entire peripapillary capillary bed (EPCB) were analysed. Quantitative analysis of the OCT-A images was performed using open-source available ImageJ software (National Institutes of Health, Bethesda, Maryland, USA). Qualitative analysis based on the proposed clinical grading (Grades 0–4) was also performed by two masked graders.

Results

RON clinical (qualitative) classification based on RPCP correlated with the quantitative RPCP perfusion analysis (P=0.0001). RON clinical classification based on RPCP statistically correlated with ETDRS score (P=0.001). RON clinical classification based on EPCB also correlated with the quantitative EPCB perfusion analysis and ETDRS score (P=0.02 and P=0.01, respectively). Compared with the clinical classification based on EPCB, the qualitative classification based on RPCP reached a higher intergrader agreement (0.96 and 0.86, respectively).

Conclusion

OCT-A can be used to detect RPCP abnormalities and to clinically classify RON with a high interexaminer agreement. The proposed clinical classification is supported by the quantitative analysis based on the use of specific images elaboration techniques and correlates with visual acuity of the examined eyes.
Enrichment of antibiotic resistance genes in soil receiving composts derived from swine manure, yard wastes, or food wastes, and evidence for multiyear persistence of swine Clostridium spp.
Authors: Scott Andrew , Tien Yuan-Ching , Drury Craig F. , Reynolds W. Daniel , Topp Edward
Published: January 2018

The impact of amendment with swine manure compost (SMC), yard waste compost (YWC), or food waste compost (FWC) on the abundance of antibiotic resistance genes in soil was evaluated. Following a commercial-scale application of the composts in a field experiment, soils were sampled periodically for a decade, and archived air-dried. Soil DNA was extracted and gene targets quantified by qPCR. Compared with untreated control soil, all 3 amendment types increased the abundance of gene targets for up to 4 years postapplication. The abundance of several gene targets was much higher in soil amended with SMC than in soil receiving either YWC or FWC. The gene target ermB remained higher in the SMC treatment for a decade postapplication. Clostridia were significantly more abundant in the SMC-amended soil throughout the decade following application. Eight percent of Clostridium spp. isolates from the SMC treatment carried ermB. Overall, addition of organic amendments to soils has the potential to increase the abundance of antibiotic resistance genes. Amendments of fecal origin, such as SMC, will in addition entrain bacteria carrying antibiotic resistance genes. Environmentally recalcitrant clostridia, and the antibiotic resistance genes that they carry, will persist for many years under field conditions following the application of SMC.
An Inquisitive Perspective on Modals and Quantifiers
Authors: Ciardelli Ivano , Roelofsen Floris
Published: January 2018

Inquisitive semantics enriches the standard truth-conditional notion of meaning, in order to facilitate an integrated semantic analysis of statements and questions. Taking this richer view on meaning as a starting point, this review presents a new perspective on modal operators and quantifiers, one that has the potential to address a number of challenges for standard semantic analyses of such operators. To illustrate the new perspective, we present an inquisitive take on the semantics of attitude verbs and on quantifiers taking scope out of questions.
Variation in behavioral engagement during an active learning activity leads to differential knowledge gains in college students
Authors: LaDage Lara D. , Tornello Samantha L. , Vallejera Jennilyn M. , Baker Emily E. , Yan Yue , Chowdhury Anik
Published: January 2018

There are many pedagogical techniques used by educators in higher education; however, some techniques and activities have been shown to be more beneficial to student learning than others. Research has demonstrated that active learning and learning in which students cognitively engage with the material in a multitude of ways result in better understanding and retention. The aim of the present study was to determine which of three pedagogical techniques led to improvement in learning and retention in undergraduate college students. Subjects partook in one of three different types of pedagogical engagement: hands-on learning with a model, observing someone else manipulate the model, and traditional lecture-based presentation. Students were then asked to take an online quiz that tested their knowledge of the new material, both immediately after learning the material and 2 wk later. Students who engaged in direct manipulation of the model scored higher on the assessment immediately after learning the material compared with the other two groups. However, there were no differences among the three groups when assessed after a 2-wk retention interval. Thus active learning techniques that involve direct interaction with the material can lead to learning benefits; however, how these techniques benefit long-term retention of the information is equivocal.
Podocyte-specific knockin of PTEN protects kidney from hyperglycemia
Authors: Wang Huizhen , Feng Ziwei , Xie Jianteng , Wen Feng , Jv Menglei , Liang Tiantian , Li Jing , Wang Yanhui , Zuo Yangyang , Li Sheng , Li Ruizhao , Li Zhilian , Zhang Bin , Liang Xinling , Liu Shuangxin , Shi Wei , Wang Wenjian
Published: January 2018

Phosphatase and tensin homolog deleted on chromosome 10 (PTEN) has proven to be downregulated in podocytes challenged with high glucose (HG), and knockout of PTEN in podocytes aggravated the progression of diabetic kidney disease (DKD). However, whether podocyte-specific knockin of PTEN protects the kidney against hyperglycemia in vivo remains unknown. The inducible podocyte-specific PTEN knockin (PPKI) mice were generated by crossing newly created transgenic loxP-stop- loxP-PTEN mice with podocin-iCreERT2 mice. Diabetes mellitus was induced in mice by intraperitoneal injection of streptozotocin at a dose of 150 mg/kg. In vitro, small interfering RNA and adenovirus interference were used to observe the role of PTEN in HG-treated podocytes. Our data demonstrated that PTEN was markedly reduced in the podocytes of patients with DKD and focal segmental glomerulosclerosis, as well as in those of db/db mice. Interestingly, podocyte-specific knockin of PTEN significantly alleviated albuminuria, mesangial matrix expansion, effacement of podocyte foot processes, and incrassation of glomerular basement membrane in diabetic PPKI mice compared with wild-type diabetic mice, whereas no alteration was observed in the level of blood glucose. The potential renal protection of overexpressed PTEN in podocytes was partly attributed with an improvement in autophagy and motility and the inhibition of apoptosis. Our results showed that podocyte-specific knockin of PTEN protected the kidney against hyperglycemia in vivo , suggesting that targeting PTEN might be a novel and promising therapeutic strategy against DKD.
Mechanisms and controversies in mutantCul3-mediated familial hyperkalemic hypertension
Authors: Ferdaus Mohammed Z. , McCormick James A.
Published: January 2018

Autosomal dominant mutations in cullin-3 ( Cul3) cause the most severe form of familial hyperkalemic hypertension (FHHt). Cul3 mutations cause skipping of exon 9, which results in an internal deletion of 57 amino acids from the CUL3 protein (CUL3-∆9). The precise mechanism by which this altered form of CUL3 causes FHHt is controversial. CUL3 is a member of the cullin-RING ubiquitin ligase family that mediates ubiquitination and thus degradation of cellular proteins, including with-no-lysine [K] kinases (WNKs). In CUL3-∆9-mediated FHHt, proteasomal degradation of WNKs is abrogated, leading to overactivation of the WNK targets sterile 20/SPS-1 related proline/alanine-rich kinase and oxidative stress-response kinase-1, which directly phosphorylate and activate the thiazide-sensitive Na+-Cl−cotransporter. Several groups have suggested different mechanisms by which CUL3-∆9 causes FHHt. The majority of these are derived from in vitro data, but recently the Kurz group (Schumacher FR, Siew K, Zhang J, Johnson C, Wood N, Cleary SE, Al Maskari RS, Ferryman JT, Hardege I, Figg NL, Enchev R, Knebel A, O’Shaughnessy KM, Kurz T. EMBO Mol Med 7: 1285–1306, 2015) described the first mouse model of CUL3-∆9-mediated FHHt. Analysis of this model suggested that CUL3-∆9 is degraded in vivo, and thus Cul3 mutations cause FHHt by inducing haploinsufficiency. We recently directly tested this model but found that other dominant effects of CUL3-∆9 must contribute to the development of FHHt. In this review, we focus on our current knowledge of CUL3-∆9 action gained from in vitro and in vivo models that may help unravel this complex problem.