bluuebunny/crossref_metadata_2025 huggingface dataset:
Benchmarking doubles-corrected random-phase approximation methods for frequency dependent polarizabilities: Aromatic molecules calculated at the RPA, HRPA, RPA(D), HRPA(D), and SOPPA levels
Authors: Jørgensen Maria W. , Sauer Stephan P. A.
Published: June 2020

The performance of different polarization propagator methods, such as RPA, RPA(D), HRPA, HRPA(D), and SOPPA, have been tested against CC3 values for both static and dynamic polarizabilities. The test set consists of 14 (hetero-)aromatic medium-sized organic molecules, mostly with a high degree of symmetry. The benchmark of the methods remarkably reveals that RPA and HRPA(D) yield results comparable with the CC3 values and that they outperform SOPPA for these molecules. For a subset of the molecules, a comparison could be made to experimental values. The comparison for static polarizabilities proves that RPA and HRPA(D) as well as RPA(D) reproduce experimental values to a satisfying precision, whereas the SOPPA method compared to these three methods appears to perform only adequately. An investigation of the performance of Sadlej’s polarized triple zeta basis set against Dunning’s aug-cc-pVTZ basis set was also carried out. It is found that in contrast to other methods, Sadlej’s basis set did not perform sufficiently compared to the larger aug-cc-pVTZ basis set for the RPA based methods.
Effect of yeast culture (Saccharomyces cerevisiae) and garlic (Allium sativum) product mixture on growth performance, nutrient digestibility, faecal microflora, faecal noxious-gas emission and meat quality in finishing pigs
Authors: Sun Hao Yang , Kim In Ho
Published: June 2020

Context
Dietary supplementation with a single feed additive or a combination of different feed additives as growth promoters has been researched extensively. However, few studies have tested the combined use of probiotics (yeast culture) and phytogenics (garlic products) in pigs.

Aims
The present study was conducted to evaluate the effect of supplementation of a mixture of yeast culture, garlic extract and garlic essential oil (YGM) on growth performance, nutrient digestibility, faecal microflora, faecal noxious-gas emission and meat quality in finishing pigs.

Methods
Two hundred [(Landrace×Yorkshire)×Duroc] finishing pigs (50.37 ± 1.89 kg) were randomly allotted into two dietary treatments on the basis of bodyweight (BW) and sex for a 10-week feeding trial. Dietary treatments consisted of a basal diet (CON) and CON containing 0.1% of YGM. The YGM was composed of 54.5% of yeast culture, 40% of garlic extract powder and 5.5% of garlic essential oil. There were 20 replicated pens per treatment, with five pigs (3 barrows and 2 gilts) per pen. Pig BW was measured at the beginning and at the end of the experiment. Feed consumption was recorded daily during the experiment, on a pen basis, to calculate average daily gain (ADG).

Key results
Dietary YGM supplementation resulted in a higher (P < 0.05) final BW and ADG than in the control groups. Pigs fed YGM supplementation diet led to a higher (P < 0.05) digestibility of dry matter (DM) than in CON. The emission of hydrogen sulfide gas from faeces was significantly (P < 0.05) decreased in pigs fed YGM diets; however, ammonia and total mercaptan emissions were not influenced. There were no differences in meat-quality parameters between the two treatments.

Conclusions
Dietary YGM supplementation exerted beneficial effects on BW and ADG and DM digestibility, reduced hydrogen sulfide gas emission, and did not have any adverse effects on meat-quality parameters that are related to consumer acceptance.

Implications
The study has provided a basis and insight for future research on application of a combination of yeast culture, garlic extract and garlic essential oils, as an alternative to antibiotics in finishing pig diets.
Single-nucleotide polymorphisms for matrix metalloprotease-1 can affect perimysial strength and intramuscular fat content but not growth rate of cattle
Authors: Christensen S. , Monteavaro C. , Purslow P. P.
Published: June 2020

Context
Single-nucleotide polymorphisms (SNPs) in the gene coding for matrix metalloprotease-1 (MMP-1) are known to affect the level of intramuscular fat found in cattle. As well as a signalling molecule affecting adipogenesis, MMP-1 is a major collagenase involved in the turnover of connective tissue.

Aims
The aim of the work was to assess whether SNPs in the gene for MMP-1 may affect the mechanical properties of intramuscular connective tissue, and therefore meat texture.

Methods
Allelic frequencies of three SNPs for MMP-1 were determined in a group of black Aberdeen Angus cattle whose growth characteristics had been traced for 450 days before slaughter. Associations between the alleles of each of the three SNPs and growth rate, killing out percentage, half-carcass weight, intramuscular fat content, cooking loss, strength of perimysium in cooked M. semitendinosus and Warner–Bratzler peak force of cooked M. longissimus dorsi were studied.

Key results
None of the SNPs studied had any effect on growth curves, and only one SNP (ss77831914) showed differences in half-carcass weight between alleles. Carcass yield and killing out percentage showed a small difference between alleles of ss7783924. No effects were found on the Warner–Bratzler peak force of M. longissimus dorsi cooked to 70°C. Two SNPs (ss77831914 and ss77831924) showed significant differences between alleles in the raw strength of perimysium in M. semitendinosus and the amount of intramuscular fat.

Conclusions
Commonly occurring SNPs of the major collagenase MMP-1 can affect the strength of intramuscular connective tissue as well as intramuscular fat content. Although these differences in connective tissue strength do not influence Warner–Bratzler measures of toughness at a cooking temperature of 70°C, they may contribute to differences in toughness in low-temperature, long-time cooking.

Implications
Because none of the SNPs had effects on the growth curves of the cattle studied, selection of animals with the relevant alleles of SNPs ss77831914 ss77831924 could be used to produce more tender meat without affecting carcass yield.
Feeding lambs proportional mixtures of lucerne (
Authors: Nie Z. N. , Slocombe L. , Behrendt R. , Raeside M. , Clark S. , Jacobs J. L.
Published: June 2020

Context Metabolisable energy (ME) and crude protein (CP) concentrations of forages are key determinants of lamb performance during pasture-based finishing. However, forage species often have unbalanced proportions of ME and CP, which can lead to below-optimum performance of lambs. This may be a problem with maturing lucerne (Medicago sativa L.) swards during dry summer conditions, and is a major challenge faced by grazing industries in Mediterranean environments. Aim We investigated whether two summer forages, lucerne and forage brassica (Brassica napus L. cv. Winfred), with differing ME and CP concentration could improve the growth of maternal-composite lambs when offered in mixtures compared with either forage fed alone. Methods A randomised complete block experiment with five treatments and 10 replicate animals per treatment was conducted in an animal house at Hamilton, Victoria, from February to March 2014. The treatments were 100% lucerne, 75% lucerne : 25% brassica, 50% lucerne : 50% brassica, 25% lucerne : 75% brassica, and 100% brassica on a dry-matter basis and fed to lambs. The lucerne and brassica were harvested daily and chopped to ~3 cm length before mixing and feeding. The lambs were adapted for 4 weeks before the start of the experimental phase. Key results Fasted liveweight gain of lambs increased linearly with an increasing proportion of brassica and a decreasing proportion of lucerne in the diet; no mixture performed better than brassica alone. Conclusions Under the warm and dry conditions of this experiment, the ME of lucerne was more limiting to lamb growth than its CP concentration. Implications The results suggest that a small increase in ME supply could improve the performance of lambs grazing a maturing lucerne sward during dry summer conditions. Further research is warranted into improving lamb growth and feed efficiency from lush lucerne and brassica forages.
Dendronised Polymers as Templates for In Situ Quantum Dot Synthesis
Authors: Munshi Alaa M. , Kretzmann Jessica A. , Evans Cameron W. , Ranieri Anna M. , Schildkraut Zibeon , Massi Massimiliano , Norret Marck , Saunders Martin , Iyer K. Swaminathan
Published: June 2020

The utility of dendrimers as effective carriers for targeted drug delivery and imaging has been facilitated by a high degree of molecular uniformity, narrow molecular weight distribution, tunable size and shape characteristics, and multivalency. Dendrimer–quantum dot (QD) nanocomposites have traditionally been synthesised by electrostatic self-assembly of preformed dendrimers and QDs, but higher generations are associated with limited flexibility and increased cytotoxicity. In this paper, we report the fabrication of CdTe QD nanoparticles using a dendronised linear copolymer bearing thiolated fourth-generation poly(amido amine) (PAMAM) dendrons as the capping and stabilising agent. We demonstrate this approach enables synthesis of nanocomposites with aqueous and photophysical stability.
From participation to diagnostic assessment: a systematic scoping review of the role of the primary healthcare sector in the National Bowel Cancer Screening Program
Authors: Holden Carol A. , Frank Oliver , Caruso Joanna , Turnbull Deborah , Reed Richard L. , Miller Caroline L. , Olver Ian
Published: June 2020

Primary health care (PHC) plays a vital support role in organised colorectal cancer (CRC) screening programs by encouraging patient participation and ensuring timely referral for diagnostic assessment follow up. A systematic scoping review of the current evidence was conducted to inform strategies that better engage the PHC sector in organised CRC screening programs. Articles published from 2005 to November 2019 were searched across five databases. Evidence was synthesised and interventions that specifically require PHC involvement were mapped to stages of the CRC screening pathway. Fifty-seven unique studies were identified in which patient, provider and system-level interventions align with defined stages of the CRC screening pathway: namely, identifying/reminding patients who have not responded to CRC screening (non-adherence) (n=46) and follow up of a positive screen referral (n=11). Self-management support initiatives (patient level) and improvement initiatives (system level) demonstrate consistent benefits along the CRC screening pathway. Interventions evaluated as part of a quality-improvement process tended to report effectiveness; however, the variation in reporting makes it difficult to determine which elements contributed to the overall study outcomes. To maximise the benefits of population-based screening programs, better integration into existing primary care services can be achieved through targeting preventive and quality care interventions along the entire screening pathway.
Fragmentation of acetate-CoA ligase gives a clue to understand domain rearrangement history of NDP-forming acyl-CoA synthetase superfamily proteins
Authors: Chiba Yoko , Shitara Mariko , Takai Ken
Published: June 2020

NDP-forming type acyl-CoA synthetase superfamily proteins are known to have six essential subdomains (1, 2, 3, a, b, c) of which partition and order are varied, suggesting yet-to-be-defined subdomain rearrangement happened in its evolution. Comparison in physicochemical and biochemical characteristics between the recombinant proteins which we made from fragmented subdomains and wild-type protein, acetate-CoA ligase in a hyperthermophilic archaeon, consisting of two distinct subunits (α1-2-3 and βa-b-c) provided a clue to the mystery of its molecular evolutionary passage. Although solubility and thermostability of each fragmented subdomain turned out to be lower than that of wild-type, mixture of the three synthetic subunits of α1-2, α3, and βa-b-c had quaternary structure, thermostability, and enzymatic activity comparable to those of the wild-type. This suggests that substantial independence and mobility of subdomain 3 have enabled rearrangement of the subdomains; and thermostability of the subdomains has constrained the composition of the subunits.
The cell biology of inflammation: From common traits to remarkable immunological adaptations
Authors: Weavers Helen , Martin Paul
Published: June 2020

Tissue damage triggers a rapid and robust inflammatory response in order to clear and repair a wound. Remarkably, many of the cell biology features that underlie the ability of leukocytes to home in to sites of injury and to fight infection—most of which are topics of intensive current research—were originally observed in various weird and wonderful translucent organisms over a century ago by Elie Metchnikoff, the “father of innate immunity,” who is credited with discovering phagocytes in 1882. In this review, we use Metchnikoff’s seminal lectures as a starting point to discuss the tremendous variety of cell biology features that underpin the function of these multitasking immune cells. Some of these are shared by other cell types (including aspects of motility, membrane trafficking, cell division, and death), but others are more unique features of innate immune cells, enabling them to fulfill their specialized functions, such as encapsulation of invading pathogens, cell–cell fusion in response to foreign bodies, and their self-sacrifice as occurs during NETosis.
Magnetic field generation in a laser-irradiated thin collisionless plasma target by return current electrons carrying orbital angular momentum
Authors: Shi Y , Weichman K , Kingham R J , Arefiev A V
Published: June 2020

Magnetized high energy density physics offers new opportunities for observing magnetic field-related physics for the first time in the laser–plasma context. We focus on one such phenomenon, which is the ability of a laser-irradiated magnetized plasma to amplify a seed magnetic field. We performed a series of fully kinetic 3D simulations of magnetic field amplification by a picosecond-scale relativistic laser pulse of intensity 4.2 × 1018 W cm−2 incident on a thin overdense target. We observe axial magnetic field amplification from an initial 0.1 kT seed to 1.5 kT over a volume of several cubic microns, persisting hundreds of femtoseconds longer than the laser pulse duration. The magnetic field amplification is driven by electrons in the return current gaining favorable orbital angular momentum from the seed magnetic field. This mechanism is robust to laser polarization and delivers order-of-magnitude amplification over a range of simulation parameters.
A high performance adaptive on-time controlled valley-current-mode DC–DC buck converter
Authors: Jiang Chanrong , Chai Changchun , Han Chenxi , Yang Yintang
Published: June 2020

This paper presents an AOT-controlled (adaptive-on-time, AOT) valley-current-mode buck converter for portable application. The buck converter with synchronous rectifier not only uses valley-current-mode control but also possesses hybrid-mode control functions at the same time. Due to the presence of the zero-current detection circuit, the converter can switch freely between the two operating modes without the need for an external mode selection circuit, which further reduces the design difficulty and chip area. The converter for the application of high power efficiency and wide current range is used to generate the voltage of 0.6–3.0 V with a battery source of 3.3–5.0 V, while the load current range is 0.05–2 A. The circuit can work in continuous conduction mode with constant frequency in high load current range. In addition, a stable output voltage can be obtained with small voltage ripple. In pace with the load current decreases to a critical value, the converter transforms into the discontinuous conduction mode smoothly. As the switching period increases, the switching loss decreases, which can significantly improve the conversion efficiency. The proposed AOT controlled valley current mode buck converter is integrated with standard 0.18 μm process and the simulation results show that the converter provides well-loaded regulations with power efficiency over 95%. When the circuit switches between the two conduction modes drastically, the response time can be controlled within 30 μs. The undershoot voltage is controlled within 25 mV under a large current hopping range.
Mathematical analysis of organic-pass transistor using pseudo-p-OTFTs
Authors: Pal Shagun , Kumar Brijesh
Published: June 2020

Steady state behavior analysis of organic thin film transistor (OTFTs) has been thoroughly researched in the past few decades. Yet, this static logic analysis has drawbacks of high power dissipation and high power consumption, and a large number of prerequisites in the number of transistors for the digital logic circuit application. Hence, to overcome these basic fundamental drawbacks of static logic, the dynamic logic study of organic thin film transistor has been analyzed in this paper. The fundamental basic of dynamic logic is a pass transistor for which logic high and logic low model is designed at an operating voltage of 5 V and frequency of 5 kHz. Additionally, the novel approach of analytical model for organic pass transistor (OPT) circuit is included and verified using MATLAB. The transient individualities of organic pass transistor OPT are examined through Atlas 2-D numerical device simulator. The reduction in the power dissipation along with additional voltage scaling and reduction in the clock frequency such as pipelining may further enable the applications into more complex VLSI ICs.
Numerical study of mono-crystalline silicon solar cells with passivated emitter and rear contact configuration for the efficiency beyond 24% based on mass production technology
Authors: Wang Peng , Li Gaofei , Wang Miao , Li Hong , Zheng Jing , Yang Liyou , Chen Yigang , Li Dongdong , Lu Linfeng
Published: June 2020

Mono-crystalline silicon solar cells with a passivated emitter rear contact (PERC) configuration have attracted extensive attention from both industry and scientific communities. A record efficiency of 24.06% on p-type silicon wafer and mass production efficiency around 22% have been demonstrated, mainly due to its superior rear side passivation. In this work, the PERC solar cells with a p-type silicon wafer were numerically studied in terms of the surface passivation, quality of silicon wafer and metal electrodes. A rational way to achieve a 24% mass-production efficiency was proposed. Free energy loss analyses were adopted to address the loss sources with respect to the limit efficiency of 29%, which provides a guideline for the design and manufacture of a high-efficiency PERC solar cell.
CO2 emissions from forest degradation in Brazilian Amazon
Authors: Assis Talita Oliveira , de Aguiar Ana Paula Dutra , von Randow Celso , Melo de Paula Gomes Diego , Kury Juliana Nunes , Ometto Jean Pierre H B , Nobre Carlos A
Published: June 2020

Forest degradation is widespread around the world, due to multiple factors such as unsustainable logging, agriculture, invasive species, fire, fuelwood gathering, and livestock grazing. In the Brazilian Amazon forest degradation from August 2006 to July 2016 reached 1,1 869 800 ha. The processes of forest degradation are still poorly understood, being a missing component in anthropogenic CO2 emission estimates in tropical forests. In this work, we analyzed temporal trajectories of forest degradation from August 2006 to July 2016 in the Brazilian Amazon and assessed their impact on the regional carbon balance. We combined the degradation process with deforestation-related processes (clear-cut deforestation and secondary vegetation dynamics), using the spatially-explicit INPE-EM carbon emission model. The trajectory analysis showed that 13% of the degraded area ended up being cleared and converted in the period and 61% of the total degraded area experienced only one event of degradation throughout the whole period. Net emissions added up to 5.4 GtCO2, considering the emissions from forest degradation and deforestation, absorption from degraded forest recovery, and secondary vegetation dynamics. The results show an increase in the contribution of forest degradation to net emissions towards the end of the period, related to the decrease in clear-cut deforestation rates, decoupled from the forest degradation rates. The analysis also indicates that the regeneration of degraded forests absorbed 1.8 GtCO2 from August 2006 and July 2016—a component typically overlooked in the regional carbon balance.
Get Parkinson’s medications on time: the Leeds QI project
Authors: Corrado Joanna , Jackson Oliver , Baxandall David , Robson Jeremy , Duggan-Carter Philippa , Throssell Jane , Westgarth Tracy , Chhokar Gurjit , Alty Jane , Cracknell Alison
Published: June 2020

Parkinson’s disease (PD) is a common neurodegenerative disease. Delayed administration of PD medications is associated with increased risk of life-threatening complications including choking, aspiration pneumonia and neuroleptic malignant syndrome.

In 2016, the spouse of a patient with PD wrote to Leeds Teaching Hospitals Trust (LTHT) to highlight that multiple medication delays and omissions had occurred during his recent admission. In response, LTHT formed a PD quality improvement (QI) Collaborative of multidisciplinary members committed to ensuring timely PD medication administration.

The faculty used Institute for Healthcare Improvement Model for Improvement QI methodology. Interventions were tested on pilot wards and the most successful were scaled up and spread across all 90 adult inpatient wards as an ‘intervention bundle’.

Between January 2016 and June 2020 mean delays in the time from admission to first dose of medication dropped from over 7 to under 1 h. The mean percentage of omitted PD medications reduced from 15.1 to 0.6%.

Project success was multifactorial but due to: Simplicity of interventions.Multiprofessional ownership by frontline teams to make changes and take prompt action.The spouse of the patient taking a leading role in the Collaborative, bringing her unique personal insight and experience, which facilitated behavioural change.
Towards precision medicine: Therapeutic drug monitoring–guided dosing of vancomycin and β-lactam antibiotics to maximize effectiveness and minimize toxicity
Authors: Cusumano Jaclyn A , Klinker Kenneth P , Huttner Angela , Luther Megan K , Roberts Jason A , LaPlante Kerry L
Published: June 2020

Purpose

The goal of this review is to explore the role of antimicrobial therapeutic drug monitoring (TDM), especially in critically ill, obese, and older adults, with a specific focus on β-lactams and vancomycin.

The continued rise of antimicrobial resistance prompts the need to optimize antimicrobial dosing. The aim of TDM is to individualize antimicrobial dosing to achieve antibiotic exposures associated with improved patient outcomes. Initially, TDM was developed to minimize adverse effects during use of narrow therapeutic index agents. Today, patient and organism complexity are expanding the need for precision dosing through TDM services. Alterations of pharmacokinetics and pharmacodynamics (PK/PD) in the critically ill, obese, and older adult populations, in conjunction with declining organism susceptibility, complicate attainment of therapeutic targets. Over the last decade, antimicrobial TDM has expanded with the emergence of literature supporting β-lactam TDM and a shift from monitoring vancomycin trough concentrations to monitoring of the ratio of area under the concentration (AUC) curve to minimum inhibitory concentration (MIC). PK/PD experts should be at the forefront of implementing precision dosing practices.

Conclusion

Precision dosing through TDM is expanding and is especially important in populations with altered PK/PD, including critically ill, obese, and older adults. Due to wide PK/PD variability in these populations, TDM is vital to maximize antimicrobial effectiveness and decrease adverse event rates. However, there is still a need for studies connecting TDM to patient outcomes. Providing patient-specific care through β-lactam TDM and transitioning to vancomycin AUC/MIC monitoring may be challenging, but with experts at the forefront of this initiative, PK-based optimization of antimicrobial therapy can be achieved.
Clinical pharmacy programmatic perspectives on use of direct-acting antivirals for acquired hepatitis C infection in solid organ transplant recipients
Authors: Crona Lana , Berry Holly , Byrns Jennifer , Campbell Udobi
Published: June 2020

Purpose

An institutional workflow developed by clinical pharmacists for initiation of directing-acting antiviral (DAA) therapy for patients who receive solid organ transplants from hepatitis C (HCV)–positive donors is described; programmatic challenges in providing pharmaceutical care to these patients are reviewed.

In recent years the introduction of new oral DAAs, coupled with faster screening of donor organs for HCV infection through use of a nucleic acid test (NAT), has facilitated transplants of organs from HCV-seropositive donors to HCV-seronegative recipients. The solid organ transplant program of a North Carolina health system began performing such transplants in December 2017. In the pharmacist-developed workflow, patients are initiated on DAA therapy in the outpatient clinic setting, and clinic pharmacists are consulted regarding drug selection. Prescriptions for DAA therapy are sent to an on-site specialty pharmacy, where pharmacists and pharmacy technicians work to obtain prior authorization and, if necessary, payment assistance through manufacturer-sponsored programs. The medical team is notified at the time of patient approval to begin treatment. Pharmacists provide counseling at the time of DAA therapy initiation and follow up with patients every 2 weeks to confirm adherence. As of June 2019, about 100 transplants of HCV NAT–positive organs had been performed (approximately 50% were kidney transplants; 15%, lung transplants; 20%, heart transplants; and 15%, liver transplants). Many challenges are encountered in the process of providing pharmaceutical care to this patient population, including challenges in patient selection and counseling, overcoming financial barriers and insurance restrictions, and coordinating with an internal specialty pharmacy to ensure timely delivery of medication to patients.

Conclusion

Within a solid organ transplantation program, clinical pharmacists and other pharmacy personnel can play vital roles in ensuring safe and effective DAA therapy for recipients of transplanted HCV NAT–positive organs.
Impact of PhORCAS references on overall application score for postgraduate year 1 pharmacy residency candidates
Authors: Atyia Sara A , Paloucek Frank P , Butts Allison R , Oyler Douglas R , Martin Craig A , Schadler Aric D , Cook Aaron M
Published: June 2020

Purpose

The disparity between the number of applicants for postgraduate year 1 (PGY1) pharmacy residency positions and the number of available residency positions increases the need to optimize how applicants are evaluated. The purpose of the study described here was to evaluate the correlation of ratings of residency candidate characteristics by academic and professional references listed on residency applications with overall application score, applicant ranking, and the likelihood of candidates receiving an invitation to interview.

Methods

A multicenter, retrospective study was conducted to evaluate the correlation of reference writers’ ratings of 13 candidate characteristics and their overall recommendations with program-determined outcomes (eg, final application score, applicant ranking, and invitation to interview) through analysis of PGY1 applications submitted through the Pharmacy Online Residency Centralized Application System (PhORCAS) from 2015 through 2018. Keywords and themes within the open-ended section of letters of reference were also analyzed for correlation with overall application score.

Results

A total of 5,923 references listed on 1,867 applications to 4 PGY1 pharmacy residency programs processed by PhORCAS were included in the analysis. For the majority of applicant characteristic ratings (ie, 74% of 56,872 ratings overall), reference writers rated candidates as exceeding expectations, and applicants were “highly recommended” by these evaluators in 91% of cases. References’ average characteristic ratings and overall recommendations were poorly correlated with final application score (R2 = 0.12 [P < 0.0001] and R2 = 0.08 [P < 0.0001], respectively), final ranking (R2 = 0.02 [P < 0.0001] and R2 = 0.03 [P < 0.0001], respectively), and invitation to interview (R2 = 0.07 [P < 0.0001] and R2 = 0.04 [P < 0.0001], respectively). For the themes evaluated, references’ use of teaching words best correlated with normalized final application score, although the correlation was poor (R2 = 0.007, P = 0.0001).

Conclusion

Reference writers’ ratings of PGY1 residency candidate characteristics in PhORCAS are poorly correlated with application score, applicant ranking, and invitation to interview. The results of this study suggest that the existing PhORCAS standardized form for submitting references is of limited utility in its current state.
XIII—Dutch Book and Accuracy Theorems
Authors: Mahtani Anna
Published: June 2020

Dutch book and accuracy arguments are used to justify certain rationality constraints on credence functions. Underlying these Dutch book and accuracy arguments are associated theorems, and I show that the interpretation of these theorems can vary along a range of dimensions. Given that the theorems can be interpreted in a variety of different ways, what is the status of the associated arguments? I consider three possibilities: we could aggregate the results of the differently interpreted theorems in some way, and motivate rationality constraints based on this aggregation; we could be permissive, and accept the conclusions of the Dutch book and accuracy arguments under all interpretations of the associated theorems; or we could select one uniquely correct interpretation of the Dutch book or accuracy theorem, and use that to justify certain rationality constraints. I show that each possibility faces problems, and conclude that Dutch book and accuracy theorems cannot be used to justify any principle of rationality.
BioModels Parameters: a treasure trove of parameter values from published systems biology models
Authors: Glont Mihai , Arankalle Chinmay , Tiwari Krishna , Nguyen Tung V N , Hermjakob Henning , Malik-Sheriff Rahuman S
Published: June 2020

Motivation

One of the major bottlenecks in building systems biology models is identification and estimation of model parameters for model calibration. Searching for model parameters from published literature and models is an essential, yet laborious task.

Results

We have developed a new service, BioModels Parameters, to facilitate search and retrieval of parameter values from the Systems Biology Markup Language models stored in BioModels. Modellers can now directly search for a model entity (e.g. a protein or drug) to retrieve the rate equations describing it; the associated parameter values (e.g. degradation rate, production rate, Kcat, Michaelis–Menten constant, etc.) and the initial concentrations. Currently, BioModels Parameters contains entries from over 84,000 reactions and 60 different taxa with cross-references. The retrieved rate equations and parameters can be used for scanning parameter ranges, model fitting and model extension. Thus, BioModels Parameters will be a valuable service for systems biology modellers.

Availability and implementation

The data are accessible via web interface and API. BioModels Parameters is free to use and is publicly available at https://www.ebi.ac.uk/biomodels/parameterSearch.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Jaw Epidemic: Recognition, Origins, Cures, and Prevention
Authors: Kahn Sandra , Ehrlich Paul , Feldman Marcus , Sapolsky Robert , Wong Simon
Published: June 2020

Contemporary humans are living very different lives from those of their ancestors, and some of the changes have had serious consequences for health. Multiple chronic “diseases of civilization,” such as cardiovascular problems, cancers, ADHD, and dementias are prevalent, increasing morbidity rates. Stress, including the disruption of traditional sleep patterns by modern lifestyles, plays a prominent role in the etiology of these diseases, including obstructive sleep apnea. Surprisingly, jaw shrinkage since the agricultural revolution, leading to an epidemic of crooked teeth, a lack of adequate space for the last molars (wisdom teeth), and constricted airways, is a major cause of sleep-related stress. Despite claims that the cause of this jaw epidemic is somehow genetic, the speed with which human jaws have changed, especially in the last few centuries, is much too fast to be evolutionary. Correlation in time and space strongly suggests the symptoms are phenotypic responses to a vast natural experiment—rapid and dramatic modifications of human physical and cultural environments. The agricultural and industrial revolutions have produced smaller jaws and less-toned muscles of the face and oropharynx, which contribute to the serious health problems mentioned above. The mechanism of change, research and clinical trials suggest, lies in orofacial posture, the way people now hold their jaws when not voluntarily moving them in speaking or eating and especially when sleeping. The critical resting oral posture has been disrupted in societies no longer hunting and gathering. Virtually all aspects of how modern people function and rest are radically different from those of our ancestors. We also briefly discuss treatment of jaw symptoms and possible clinical cures for individuals, as well as changes in society that might lead to better care and, ultimately, prevention.
Pronounced differences in visitation by potential pollinators to co-occurring species of Fabaceae in the Southwest Australian biodiversity hotspot
Authors: Scaccabarozzi Daniela , Dixon Kingsley W , Tomlinson Sean , Milne Lynne , Bohman Björn , Phillips Ryan D , Cozzolino Salvatore
Published: June 2020

Despite their diversity and the potential for specialized pollination systems, Australian Fabaceae have received little attention in pollination studies. In the Southwest Australian Floristic Region (SWAFR), a recognized biodiversity hotspot, co-occurring and abundant species of Faboideae exhibit a range of floral colours and forms, suggestive of adaptation to different groups of pollinators. For four communities of Fabaceae in the SWAFR we investigated whether co-occurring species overlap in pollinator genera, whether these pollinators show differences in behaviour on the pea flower and whether variations in stamen length and nectar composition among species are associated with different pollinator types. Species of Fabaceae were visited by one to four genera of native bees, suggesting varying levels of ecological specialisation. In Fabaceae with more specialized interactions, co-occurring species showed marked differences in the bee genera attracted. Unexpectedly, some Fabaceae frequently attracted beetles, which may play an important role in their pollination. There was no evidence for an association between stamen length or nectar composition and the type of pollinator. The introduced honeybee, visited all studied species of Fabaceae, suggesting that they may act both as a pollinator and a potential competitor with native pollinators.
Spatiotemporal changes in substantia nigra neuromelanin content in Parkinson’s disease
Authors: Biondetti Emma , Gaurav Rahul , Yahia-Cherif Lydia , Mangone Graziella , Pyatigorskaya Nadya , Valabrègue Romain , Ewenczyk Claire , Hutchison Matthew , François Chantal , Arnulf Isabelle , Corvol Jean-Christophe , Vidailhet Marie , Lehéricy Stéphane
Published: June 2020

This study aimed to investigate the spatiotemporal changes in neuromelanin-sensitive MRI signal in the substantia nigra and their relation to clinical scores of disease severity in patients with early or progressing Parkinson’s disease and patients with idiopathic rapid eye movement sleep behaviour disorder (iRBD) exempt of Parkinsonian signs compared to healthy control subjects. Longitudinal T1-weighted anatomical and neuromelanin-sensitive MRI was performed in two cohorts, including patients with iRBD, patients with early or progressing Parkinson’s disease, and control subjects. Based on the aligned substantia nigra segmentations using a study-specific brain anatomical template, parametric maps of the probability of a voxel belonging to the substantia nigra were calculated for patients with various degrees of disease severity and controls. For each voxel in the substantia nigra, probability map of controls, correlations between signal-to-noise ratios on neuromelanin-sensitive MRI in patients with iRBD and Parkinson’s disease and clinical scores of motor disability, cognition and mood/behaviour were calculated. Our results showed that in patients, compared to the healthy control subjects, the volume of the substantia nigra was progressively reduced for increasing disease severity. The neuromelanin signal changes appeared to start in the posterolateral motor areas of the substantia nigra and then progressed to more medial areas of this region. The ratio between the volume of the substantia nigra in patients with Parkinson’s disease relative to the controls was best fitted by a mono-exponential decay. Based on this model, the pre-symptomatic phase of the disease started at 5.3 years before disease diagnosis, and 23.1% of the substantia nigra volume was lost at the time of diagnosis, which was in line with previous findings using post-mortem histology of the human substantia nigra and radiotracer studies of the human striatum. Voxel-wise patterns of correlation between neuromelanin-sensitive MRI signal-to-noise ratio and motor, cognitive and mood/behavioural clinical scores were localized in distinct regions of the substantia nigra. This localization reflected the functional organization of the nigrostriatal system observed in histological and electrophysiological studies in non-human primates (motor, cognitive and mood/behavioural domains). In conclusion, neuromelanin-sensitive MRI enabled us to assess voxel-wise modifications of substantia nigra’s morphology in vivo in humans, including healthy controls, patients with iRBD and patients with Parkinson’s disease, and identify their correlation with nigral function across all motor, cognitive and behavioural domains. This insight could help assess disease progression in drug trials of disease modification.
Clinical Features and Gut Microbiome of Asymptomatic Entamoeba histolytica Infection
Authors: Yanagawa Yasuaki , Nagata Naoyoshi , Yagita Kenji , Watanabe Kazuhiro , Okubo Hidetaka , Kikuchi Yoshimi , Gatanaga Hiroyuki , Oka Shinichi , Watanabe Koji
Published: June 2020

Background

Entamoeba histolytica infection is a sexually transmitted disease in some developed countries. Asymptomatic infection often occurs and can be a source of transmission; however, limited data are available regarding the pathogenesis of E. histolytica.

Methods

This was a single-center, cross-sectional study. Specimens were prospectively collected from patients with clinically suspected cases. Entamoeba histolytica infection was defined as a case in which the identification of E. histolytica was confirmed by polymerase chain reaction (PCR) of a clinical specimen. Data from asymptomatic cases were compared with those from symptomatic invasive cases.

Results

Sixty-four E. histolytica–infected cases, including 13 asymptomatic cases, were identified during the study period. Microbiological diagnosis was made by endoscopic sampling in 26.6% of these cases (17/64). Endoscopy identified macroscopically visible lesions in all cases; however, the sensitivity of histopathology on biopsy samples was low (45.5%) compared with PCR (94.7%). In asymptomatic cases, infection sites were limited around the proximal colon; moreover, trophozoites were frequently identified at infection sites whereas cystic forms were commonly detected in stools. Gut microbiome analyses showed more uniform composition in asymptomatic cases than in symptomatic invasive cases, which were represented by a relatively high abundance of Ruminococcaceae, Coriobacteriaceae, and Clostridiaceae, and a low abundance of Streptococcaceae.

Conclusions

These results indicate that the encystation and attenuation of E. histolytica are highly affected by the intestinal contents, including the gut microbiome.
Outbreak of Norovirus Gastroenteritis Associated With Ice Cream Contaminated by Frozen Raspberries From China—Minnesota, United States, 2016
Authors: Saupe Amy A , Rounds Joshua , Sorenson Alida , Hedeen Nicole , Bagstad Erica , Reinberg Roee , Wagley A Gail , Cebelinski Elizabeth , Smith Kirk
Published: June 2020

Background

Norovirus is the etiology for about 60% of foodborne outbreaks identified in Minnesota. Contamination of food during preparation by food handlers is by far the most common cause of these outbreaks. Norovirus outbreaks due to commercially distributed foods are rarely reported in the United States, and only 2 have been previously identified in Minnesota, both due to oysters.

Methods

In August 2016, we investigated an outbreak of norovirus gastroenteritis in Minnesota that was linked to consumption of commercially distributed ice cream at multiple venues. Sanitarians from local public health agencies visited the facilities involved for follow-up, and case-control studies were conducted. The outbreak was identified by linking multiple independent illness reports to a centralized foodborne illness complaint system and subsequently confirmed though genotyping of stool specimens.

Results

A total of 15 cases from 4 venues were reported. Raspberry chocolate chip ice cream was statistically associated with illness in 2 analytic studies (6 of 7 cases vs 0 of 7 controls; odds ratio, undefined; P = .005). Norovirus GII.17[P17] (GII.17 Kawasaki) strains from case stool specimens matched norovirus found in frozen raspberries imported from China that were used to make the implicated ice cream.

Conclusions

To our knowledge, this is the first norovirus outbreak due to commercially distributed frozen berries identified in the United States. To detect norovirus outbreaks associated with commercially distributed food vehicles, investigators should thoroughly investigate all norovirus outbreaks (including stool testing and genotyping), coordinate complaint and response activities across agencies and jurisdictions, and consider testing food for norovirus when appropriate.
The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020
Authors:   The dMIQE Group, Whale Alexandra S , De Spiegelaere Ward , Trypsteen Wim , Nour Afif Abdel , Bae Young-Kyung , Benes Vladimir , Burke Daniel , Cleveland Megan , Corbisier Philippe , Devonshire Alison S , Dong Lianhua , Drandi Daniela , Foy Carole A , Garson Jeremy A , He Hua-Jun , Hellemans Jan , Kubista Mikael , Lievens Antoon , Makrigiorgos Mike G , Milavec Mojca , Mueller Reinhold D , Nolan Tania , O’Sullivan Denise M , Pfaffl Michael W , Rödiger Stefan , Romsos Erica L , Shipley Gregory L , Taly Valerie , Untergasser Andreas , Wittwer Carl T , Bustin Stephen A , Vandesompele Jo , Huggett Jim F
Published: June 2020

Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.
Systematic Review: Gastrointestinal Ultrasound Scoring Indices for Inflammatory Bowel Disease
Authors: Goodsall Thomas M , Nguyen Tran M , Parker Claire E , Ma Christopher , Andrews Jane M , Jairath Vipul , Bryant Robert V
Published: June 2020

Background and Aims

Serial measurements of luminal disease activity may facilitate inflammatory bowel disease management. Gastrointestinal ultrasound is an easily performed, non-invasive alternative to other assessment modes. However, its widespread use is limited by concerns regarding validity, reliability, and responsiveness. We systematically identified ultrasound scoring indices used to evaluate inflammatory bowel disease activity and examine their operating characteristics.

Methods

Electronic databases were searched from inception to June 14, 2019 using pre-defined terms. Studies that reported on gastrointestinal ultrasound index operating properties in an inflammatory bowel disease population were eligible for inclusion. Study characteristics, index components, and operating property data [ie, validity, reliability, responsiveness, sensitivity, specificity, accuracy, positive predictive value, and negative predictive value] were extracted. The QUADAS-2 tool was used to examine study-level risk of bias.

Results

Of the 2610 studies identified, 26 studies reporting on 21 ultrasound indices were included. The most common index components included bowel wall thickness, colour Doppler imaging, and bowel wall stratification. The correlation between ultrasound indices and references standards ranged r = 0.62–0.95 and k = 0.40–0.96. Sensitivity, specificity, accuracy, positive predictive value, and negative predictive values ranged 39–100%, 63–100%, 73–100%, 57–100%, and 40–100%, respectively. Reliability and responsiveness data were limited. Most [92%, 24/26] studies received at least one unclear or high risk of bias rating.

Conclusions

Several gastrointestinal ultrasound indices for use in inflammatory bowel disease have been developed. Future research should focus on fully validating existing or novel gastrointestinal ultrasound scoring instruments for assessment of Crohn’s disease and ulcerative colitis.