bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secure multiparty computation for privacy-preserving drug discovery
Authors: Ma Rong , Li Yi , Li Chenxing , Wan Fangping , Hu Hailin , Xu Wei , Zeng Jianyang 
Published: January 2020

AbstractMotivationQuantitative structure–activity relationship (QSAR) and drug–target interaction (DTI) prediction are both commonly used in drug discovery. Collaboration among pharmaceutical institutions can lead to better performance in both QSAR and DTI prediction. However, the drug-related data privacy and intellectual property issues have become a noticeable hindrance for inter-institutional collaboration in drug discovery.ResultsWe have developed two novel algorithms under secure multiparty computation (MPC), including QSARMPC and DTIMPC, which enable pharmaceutical institutions to achieve high-quality collaboration to advance drug discovery without divulging private drug-related information. QSARMPC, a neural network model under MPC, displays good scalability and performance and is feasible for privacy-preserving collaboration on large-scale QSAR prediction. DTIMPC integrates drug-related heterogeneous network data and accurately predicts novel DTIs, while keeping the drug information confidential. Under several experimental settings that reflect the situations in real drug discovery scenarios, we have demonstrated that DTIMPC possesses significant performance improvement over the baseline methods, generates novel DTI predictions with supporting evidence from the literature and shows the feasible scalability to handle growing DTI data. All these results indicate that QSARMPC and DTIMPC can provide practically useful tools for advancing privacy-preserving drug discovery.Availability and implementationThe source codes of QSARMPC and DTIMPC are available on the GitHub: https://github.com/rongma6/QSARMPC_DTIMPC.git.Supplementary informationSupplementary data are available at Bioinformatics online.
Structural and temporal modes of heterodichogamy and similar patterns across angiosperms
Authors: Endress Peter K 
Published: January 2020

AbstractDifferent kinds of synchronization of flowering, and of male and female function, have evolved in many angiosperms. The most complex patterns are heterodichogamy, pseudoheterodichogamy and duodichogamy. In this review, their occurrence across angiosperms is shown and the diversity in heterodichogamy and duodichogamy is outlined. Heterodichogamy is characterized by the occurrence of two temporally complementary genetic morphs, whereas in peudoheterodichogamy and duodichogamy only one morph occurs. In duodichogamy, the two phases result from alternating periods of several days of the same phase three or more times during a flowering season; however, they are of irregular length. In pseudoheterodichogamy, the two phases result from repeated flushes of flowering within individuals always with one or two flowerless days in between. In contrast to duodichogamy, the male and female phases alternate in a daily rhythm coordinated with the day-night rhythm. Heterodichogamy and similar patterns of synchronization are scattered across angiosperms; however, they are especially common in the Magnoliales, Laurales, Canellales, Zingiberales, Ranunculales, Trochodendrales, Fagales, Rosales, Malpighiales, Malvales, Sapindales, Caryophyllales and Apiales.
Clinical impact of an anti-biofilm Hydrofiber dressing in hard-to-heal wounds previously managed with traditional antimicrobial products and systemic antibiotics
Authors: Metcalf Daniel G , Bowler Philip G 
Published: January 2020

Abstract

Background
Hard-to-heal wounds are often compromised by the presence of biofilm. This presents an infection risk, yet traditional antimicrobial wound care products and systemic antibiotics are often used despite the uncertainty of therapeutic success and wound progression. The aim of this study was to investigate the clinical impact of a next-generation anti-biofilm Hydrofiber wound dressing (AQUACEL Ag+ Extra[AQAg+ E]) in hard-to-heal wounds that had previously been treated unsuccessfully with traditional silver-, iodine- or polyhexamethylene biguanide (PHMB)-containing dressings and products and/or systemic antibiotics.

Methods
Clinical case study evaluations of the anti-biofilm dressing were conducted, where deteriorating or stagnant wounds were selected by clinicians and primary dressings were replaced by the anti-biofilm dressing for up to 4 weeks, or as deemed clinically appropriate, with monitoring via case report forms. The data was stratified for cases where traditional silver-, iodine- or PHMB-containing products, or systemic antibiotics, had been used prior to the introduction of the anti-biofilm dressing.

Results
Sixty-five cases were identified for inclusion, wounds ranging in duration from 1 week to 20 years (median: 12 months). In 47 (72%) cases the wounds were stagnant, while 15 (23%) were deteriorating; 3 wounds were not recorded. After an average of 4.2 weeks of management with the anti-biofilm dressing (range: 1–11 weeks), in 11 (17%) cases the wounds had healed (i.e. complete wound closure), 40 (62%) wounds improved, 9 (14%) wounds remained the same and 5 (8%) wounds deteriorated.

Conclusions
The introduction of this anti-biofilm dressing into protocols of care that had previously involved wound management with traditional antimicrobial products and/or antibiotics was shown to facilitate improvements in the healing status of most of these hard-to-heal wounds. Dressings containing proven anti-biofilm technology, in combination with antimicrobial silver and exudate management technology, appear to be an effective alternative to traditional antimicrobial products and antibiotics in the cases presented here. The use of antimicrobial wound dressings that contain anti-biofilm technology may have a key role to play in more effective wound management and antibiotic stewardship.
Impact of Diabetes and Low Body Mass Index on Tuberculosis Treatment Outcomes
Authors: Kornfeld Hardy , Sahukar Shruthi B , Procter-Gray Elizabeth , Kumar Nathella P , West Kim , Kane Kevin , Natarajan Mohan , Li Wenjun , Babu Subash , Viswanathan Vijay 
Published: January 2020

Abstract

Background
Diabetes was identified as a tuberculosis (TB) risk factor mostly in retrospective studies with limited assessments of metabolic variables. The prospective Effects of Diabetes on Tuberculosis Severity study compared adults with pulmonary TB in Chennai, India, who were classified as having either diabetes or a normal glucose tolerance at enrollment.

Methods
Baseline TB severity, sputum conversion, and treatment outcomes (cure, failure, death, or loss to follow-up) were compared between groups with respect to glycemic status and body mass index (BMI).

Results
The cohort of 389 participants included 256 with diabetes and 133 with a normal glucose tolerance. Low BMIs (&lt;18.5 kg/m2) were present in 99 (74.4%) of nondiabetic participants and 85 (33.2%) of those with diabetes. Among participants with normal or high BMIs, rates of cure, treatment failure, or death did not vary by glycemic status. Participants with low BMIs had the highest radiographic severity of disease, the longest time to sputum culture conversion, and the highest rates of treatment failure and death. Among participants with low BMIs, poorly controlled diabetes (glycohemoglobin [HbA1c] ≥8.0%) was unexpectedly associated with better TB treatment outcomes. A high visceral adiposity index was associated with adverse outcomes and, despite an overall correlation with HbA1c, was elevated in some low-BMI individuals with normal glucose tolerance.

Conclusions
In this South Indian cohort, a low BMI was significantly associated with an increased risk for adverse TB treatment outcomes, while comorbid, poorly controlled diabetes lessened that risk. A high visceral adiposity index, either with or without dysglycemia, might reflect a novel TB susceptibility mechanism linked to adipose tissue dysfunction.
The sources of heterogeneity in firm performance: lessons from Italy1
Authors: Landini Fabio , Arrighetti Alessandro , Bartoloni Eleonora 
Published: January 2020

Abstract
An extensive body of literature documents large and persistent within-industry heterogeneity of firm performance. While some authors explain such evidence in terms of input misallocation, we provide an alternative analytical framework that integrates insights from resource-based and institutional approaches. We interpret firms’ behaviour as the result of the interaction among exogenous and endogenous factors. Exogenous factors, both supply and demand related, define the opportunity set that is available to firms. Endogenous factors reflect instead firm-specific interpretations of such set, which, combined with the available resources and capabilities, determine a firm’s strategic responses, which can be markedly heterogeneous. Whenever the diversity of firm conducts is associated with relatively small profit differentials, firm heterogeneity can persist. Evidence based on the evolution of labour productivity and profit dispersion in the Italian manufacturing sector between the 1990s and early 2000s provides support for our interpretative framework.
HSPMdb: a computational repository of heat shock protein modulators
Authors: Singh Prashant , Unik Breezy , Puri Anuradhika , Nagpal Gandharva , Singh Balvinder , Gautam Ankur , Sharma Deepak 
Published: January 2020

Abstract
Heat shock proteins (Hsp) are among highly conserved proteins across all domains of life. Though originally discovered as a cellular response to stress, these proteins are also involved in a wide range of cellular functions such as protein refolding, protein trafficking and cellular signalling. A large number of potential Hsp modulators are under clinical trials against various human diseases. As the number of modulators targeting Hsps is growing, there is a need to develop a comprehensive knowledge repository of these findings which is largely scattered. We have thus developed a web-accessible database, HSPMdb, which is a first of its kind manually curated repository of experimentally validated Hsp modulators (activators and inhibitors). The data was collected from 176 research articles and current version of HSPMdb holds 10 223 entries of compounds that are known to modulate activities of five major Hsps (Hsp100, Hsp90, Hsp70, Hsp60 and Hsp40) originated from 15 different organisms (i.e. human, yeast, bacteria, virus, mouse, rat, bovine, porcine, canine, chicken, Trypanosoma brucei and Plasmodium falciparum). HSPMdb provides comprehensive information on biological activities as well as the chemical properties of Hsp modulators. The biological activities of modulators are presented as enzymatic activity and cellular activity. Under the enzymatic activity field, parameters such as IC50, EC50, DC50, Ki and KD have been provided. In the cellular activity field, complete information on cellular activities (percentage cell growth inhibition, EC50 and GI50), type of cell viability assays and cell line used has been provided. One of the important features of HSPMdb is that it allows users to screen whether or not their compound of interest has any similarity with the previously known Hsp modulators. We anticipate that HSPMdb would become a valuable resource for the broader scientific community working in the area of chaperone biology and protein misfolding diseases. HSPMdb is freely accessible at http://bioinfo.imtech.res.in/bvs/hspmdb/index.php
Understanding the challenges of non-food industrial product contamination
Authors: Cunningham-Oakes Edward , Weiser Rebecca , Pointon Tom , Mahenthiralingam Eshwar 
Published: January 2020

ABSTRACT
Preventing microbial contamination of non-food products is a major area of industrial microbiology where preservatives are used to stop microbial growth. However, microorganisms occasionally overcome product preservation, causing recalls and the implementation of multiple procedures to prevent further contamination. Correct reporting of microbial contamination in non-food industrial products is vital, especially if spoilage organisms are antimicrobial resistant and pose a health threat. Gram-negative bacteria such as Pseudomonas, Burkholderia and Enterobacteriaceae are frequently reported as non-food product contaminants, including species that overlap current antimicrobial resistance priorities. Historical analysis of recall databases highlighted that for greater than 15% of contamination incidents, the causative microbial agents are reported as unidentified. Here we review the current antimicrobial resistant bacterial species associated with non-food product contamination and evaluate recall reporting in Europe from 2005 to 2018. Our review shows that 49% of microbial contaminants are reported as unidentified despite frequent detection of antimicrobial resistant pathogens; in contrast, 98% of food-related microbial contaminants are classified. Recommendations to fill this microbial identification gap in non-food product recalls are made. Overall, reporting standards for microbial contamination in non-food products must be improved to enable surveillance and for understanding the risks associated with antimicrobial resistant microorganisms
Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome
Authors: Barth Nicolai K H , Li Lifei , Taher Leila 
Published: January 2020

AbstractMany regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.
Spousal Influences on Monthly Disability in Late-Life Marriage in the Precipitating Events Project
Authors: Monin Joan K , Laws Holly , Gahbauer Evelyne , Murphy Terrence E , Gill Thomas M 
Published: January 2020

Abstract

Objectives
Few studies have examined spousal influences on disability in late-life marriage, and no prior study has examined these associations using monthly data. Drawing from interdependence theory, we hypothesized that one spouse currently having higher disability would be positively associated with their partner having higher disability in the next month. We also examined whether participants were at risk for increased disability when both spouses had higher prior disability. In addition, we examined gender differences in spousal associations.

Method
Data were from 37 married couples in the Precipitating Events Project, an ongoing longitudinal study of 754 initially nondisabled adults aged 70 years and older. Assessments included monthly disability (13 basic, instrumental, and mobility activities of daily living) and demographics.

Results
As hypothesized, higher disability in one spouse was positively associated with higher subsequent disability in their partner. Also, wives with higher disability were especially vulnerable to subsequent increased disability when husbands had higher disability.

Discussion
Incorporating a spouse’s current disability level in modeling older adults’ subsequent disability provides additional predictive information. Wives with greater disability may be at a particularly high risk of accelerated decline when their husbands have greater disability.
On the importance of benchmarking algorithms under realistic noise conditions
Authors: Birnie Claire , Chambers Kit , Angus Doug , Stork Anna L 
Published: January 2020

SUMMARYTesting with synthetic data sets is a vital stage in an algorithm’s development for benchmarking the algorithm’s performance. A common addition to synthetic data sets is White, Gaussian Noise (WGN) which is used to mimic noise that would be present in recorded data sets. The first section of this paper focuses on comparing the effects of WGN and realistic modelled noise on standard microseismic event detection and imaging algorithms using synthetic data sets with recorded noise as a benchmark. The data sets with WGN underperform on the trace-by-trace algorithm while overperforming on algorithms utilizing the full array. Throughout, the data sets with realistic modelled noise perform near identically to the recorded noise data sets. The study concludes by testing an algorithm that simultaneously solves for the source location and moment tensor of a microseismic event. Not only does the algorithm fail to perform at the signal-to-noise ratios indicated by the WGN results but the results with realistic modelled noise highlight pitfalls of the algorithm not previously identified. The misleading results from the WGN data sets highlight the need to test algorithms under realistic noise conditions to gain an understanding of the conditions under which an algorithm can perform and to minimize the risk of misinterpretation of the results.
The static and time-dependent signature of ocean–continent and ocean–ocean subduction: the case studies of Sumatra and Mariana complexes
Authors: Marotta A M , Restelli F , Bollino A , Regorda A , Sabadini R 
Published: January 2020

SUMMARYThe anomalous density structure at subduction zones, both in the wedge and in the upper mantle, is analysed to shed light on the processes that are responsible for the characteristic gravity fingerprints of two types of subduction: ocean–continent and ocean–ocean. Our modelling is then performed within the frame of the EIGEN-6C4 gravitational disturbance pattern of two subductions representative of the above two types, the Sumatra and Mariana complexes, finally enabling the different characteristics of the two patterns to be observed and understood on a physical basis, including some small-scale details. A 2-D viscous modelling perpendicular to the trench accounts for the effects on the gravity pattern caused by a wide range of parameters in terms of convergence velocity, subduction dip angle and lateral variability of the crustal thickness of the overriding plate, as well as compositional differentiation, phase changes and hydration of the mantle. Plate coupling, modelled within a new scheme where the relative velocity at the plate contact results self-consistently from the thermomechanical evolution of the system, is shown to have an important impact on the gravity signature. Beyond the already understood general bipolar fingerprint of subduction, perpendicular to the trench, we obtain the density and gravity signatures of the processes occurring within the wedge and mantle that are responsible for the two different gravity patterns. To be compliant with the geodetic EIGEN-6C4 gravitational disturbance and to compare our predictions with the gravity at Sumatra and Mariana, we define a model normal Earth. Although the peak-to-peak gravitational disturbance is comparable for the two types of subductions, approximately 250 mGal, from both observations and modelling, encompassing the highest positive maximum on the overriding plates and the negative minimum on the trench, the trough is wider for the ocean–ocean subduction: approximately 300 km compared to approximately 180 km for the ocean–continent subduction. Furthermore, the gravitational disturbance pattern is more symmetric for the ocean–ocean subduction compared to the ocean–continent subduction in terms of the amplitudes of the two positive maxima over the overriding and subducting plates. Their difference is, for the ocean–ocean type, approximately one half of the ocean–continent one. These different characteristics of the two types of subductions are exploited herein in terms of the different crustal thicknesses of the overriding plate and of the different dynamics in the wedge and in the mantle for the two types of subduction, in close agreement with the gravity data.
The earliest arbitration treaty? A reassessment of the Anglo-Norman treaty of 991*
Authors: Benham Jenny 
Published: January 2020

Abstract
Concluded at Rouen in March 991, the Anglo-Norman treaty has traditionally occupied a very small corner of the huge historiography for King Æthelred’s reign as one of the first of the king’s failures to deal with the threat of renewed viking raids. This article is an attempt to rethink the place and importance of this treaty in the scholarly literature by looking at it from the perspective of how diplomacy was practised in the earlier middle ages. It reveals the treaty as the earliest arbitration treaty in the medieval West and offers alternative ways of viewing the immediate context and circumstances of the negotiations, as well as the persistence of important diplomatic practices across a long period.
Retinal degeneration in mice expressing the constitutively active G90D rhodopsin mutant
Authors: Colozo Alejandro T , Vasudevan Sreelakshmi , Park Paul S-H 
Published: January 2020

Abstract
Rhodopsin is the G protein-coupled receptor in rod photoreceptor cells that initiates vision upon photon capture. The light receptor is normally locked in an inactive state in the dark by the covalently bound inverse agonist 11-cis retinal. Mutations can render the receptor active even in the absence of light. This constitutive activity can desensitize rod photoreceptor cells and lead to night blindness. A G90D mutation in rhodopsin causes the receptor to be constitutively active and leads to congenital stationary night blindness, which is generally thought to be devoid of retinal degeneration. The constitutively active species responsible for the night blindness phenotype is unclear. Moreover, the classification as a stationary disease devoid of retinal degeneration is also misleading. A transgenic mouse model for congenital stationary night blindness that expresses the G90D rhodopsin mutant was examined to better understand the origin of constitutive activity and the potential for retinal degeneration. Heterozygous mice for the G90D mutation did not exhibit retinal degeneration whereas homozygous mice exhibited progressive retinal degeneration. Only a modest reversal of retinal degeneration was observed when transducin signaling was eliminated genetically, indicating that some of the retinal degeneration occurred in a transducin-independent manner. Biochemical studies on purified rhodopsin from mice indicated that multiple species can potentially contribute to the constitutive activity causing night blindness.