bluuebunny/crossref_metadata_2025 huggingface dataset:
Cyclic nanoindentation studies of HgCdTe epitaxial films
Authors: Sharma Hemant Kumar , Sharma Rajesh Kumar , Saxena Raghvendra Sahai , Gokhale Aditya , Prasad Rajesh
Published: January 2020

Hg1−x
Cd
x
Te (x∼0.29) epitaxial films have been subjected to cyclic nanoindentation using spherical indenter from tribological aspects related to the development of polishing process for preparing defect free surface. Different loading/unloading rates of 0.5, 1 and the 4 mNs−1 with a peak load of 10 mN were used for 10 nanoindentation cycles. An open jaw shape was observed in the load-displacement curve for loading/unloading rate of 0.5 mNs−1, while hysteresis loops were observed for 1 and 4 mNs−1 loading/unloading rates. This phenomenon is explained in light of the regimes of elastic/anelastic deformation and smooth plastic flow. Pop-in during first loading cycle was observed at loading/unloading rates of 1 and 4 mNs−1, which was attributed to elasto-plastic transition. Multiple pop-in events of low extent were also found in the form of serrations in load-displacement curves for loading/unloading rates of 0.5 and 1 mNs−1. Based on these observations, the maximum load and minimum loading rate during polishing process for this material has been suggested. The mechanical properties of these films, such as contact stiffness and hardness have been extracted for different loading/unloading rates. The effect of indenter geometry on deformation behaviour using Berkovich indenter is also reported.
Effect of modified calcium sulphate whiskers on free-radical/cationic hybrid photopolymers for 3D printing
Authors: Jiao Ting , Lin Yucong , Liu Yang , Liu Jie , Lu Gang
Published: January 2020

This study presents and evaluates hybrid photopolymers applied to 3D printing. To obtain the hybrid system, epoxy acrylates (EA), epoxy resins and photoinitiators were compounded. As inorganic fillers are traditionally used to improve mechanical properties, calcium sulphate whiskers (CSW) coated with chitosan (CS) were modified by acryloyl chloride and the effects of the modification on hybrid photopolymers were investigated. The viscosity and volume shrinkage of the hybrid system were also evaluated. Fourier transform infrared measurements showed that hybrid photopolymers had a higher conversion. Meanwhile, the mechanical properties showed that the tensile strength of the cured samples containing 7% modified CSW was increased by 28% compared to that of pure resin. Additionally, the improvement of interface interaction between modified whiskers and hybrid photopolymers was observed by a scanning electron microscope. Dynamic mechanical analysis showed that the hybrid system, with the addition of 7% modified whiskers, exhibited a higher storage modulus and crosslinking density. This work, the first to use modified CSW on 3D printing to enhance the tensile strength of hybrid photopolymers, demonstrates that the photocured samples can contribute to high accuracy and resolution.
Mechanical properties of cortical bones related to temperature and orientation of Haversian canals
Authors: Ma Zhichao , Qiang Zhenfeng , Zhao Hongwei , Piao Hulin , Ren Luquan
Published: January 2020

The understanding of mechanical performances and microscopic failure mechanisms of cortical bones under service condition is necessary prerequisite of fracture prevention, which would support the development of bone tissue engineering and design of bionic bones. By using miniaturized horizontal in situ compression tester, the effects of both temperature and sampling orientations on the compressive strengths and fracture morphologies were investigated. The significant difference between fracture strengths and compressive strains at various temperatures indicated that the cortical bone was sensitive to temperature. Direct experimental evidences revealed the gradually fibrotic trend of fracture surfaces as a function of sampling orientation. Through the Haversian canals distribution analysis, the relationship between the distribution of Haversian canals and fracture path was established. Essentially, the competition between high density Haversian canals and stress concentration factor determines the initiation and propagation of cracks.
Electrical investigation of ITO films in Al-doped crystalline silicon solar cells
Authors: Abdul Hamid Siti Nor Fazlina , Mohd Sinin Nurul Aqidah , Mohd Ahir Zon Fazlila , Sepeai Suhaila , Sopian Kamaruzzaman , H Zaidi Saleem
Published: January 2020

Low temperature processing of crystalline Si solar cells is attractive due to lower wafer and manufacturing costs. For thinner silicon wafers, thermal mismatch between Al and Si at high temperatures leads to thermal stress and wafer bowing. In this paper, replacement of back surface Al BSF contact by ITO films has been investigated as a function of Al-doping level. ITO films were deposited on back Si surfaces with sheet resistances in ∼16–48Ω/□ range. ITO/Si contact resistance increases slightly as sheet resistance is reduced, however, the variation is not significant. At sheet resistance of 25Ω/□, solar cell performance comparable to conventional AL BSF configuration. Even at sheet resistance ∼50Ω/□, it is possible to form high quality ITO/Si contact. The role of surface defects has been deemed to be critical. Without etching of Al-doped surface, surface quality is poor due to defects originating from the Al-alloy formation. As these defects are removed with controlled etching, a more pristine surface emerges that forms superior contacts with ITO film.
Surface Ki-67 Expression Improves Reproducibility of Dysplasia Diagnosis in Barrett’s Esophagus
Authors: Yousaf Hira , Hayat Umar , Manivel Juan , Iwamoto Carlos , Peltola Justin , Hanson Brian , Larson Wendy , Dachel Susan , Gravely Amy , Mesa Hector
Published: January 2020

Objectives

Many studies have shown poor reproducibility among pathologists for diagnosing dysplasia in Barrett’s esophagus (BE). Immunohistochemical stains (IHC) are not widely used due to overlapping expression patterns in reactive and dysplastic processes. We hypothesized that markers involved in cell-cycle (cyclin D1, Ki-67, P16), differentiation/cell-cell interaction (β-catenin, SATB2 CD44, OCT4) and senescence (γH2AX) would produce different results in reactive and dysplastic processes.

Methods

A micrograph album of 40 H&E and matching IHCs depicting optimally oriented lesions were evaluated independently by 3 pathologists. Expression was scored separately in the surface, isthmus, and base regions of the glands.

Results

Statistical analysis showed that surface Ki-67 expression showed the largest difference in expression and smallest P value (P < .001) for identifying dysplasia. At a cutoff level of 5% or less, negative predictive value (NPV) was 100%. κ correlation between pathologists improved from substantial to almost perfect (0.70-0.95) using ancillary surface Ki-67.

Conclusion

A case-control study with glass slides including all diagnostic categories using this parameter confirmed improved κ correlation among pathologists (0.29 vs 0.60), better correlation with outcomes (76% vs 69%), increased odd risks (15.3) for progression in positive cases, and an improvement in sensitivity (88% vs 64%) and NPV (88% vs 73%) compared to histology alone.
Developing an Executive Functioning Composite Score for Research and Clinical Trials
Authors: Iverson Grant L , Karr Justin E , Terry Douglas P , Garcia-Barrera Mauricio A , Holdnack James A , Ivins Brian J , Silverberg Noah D
Published: January 2020

Objective

Executive functioning encompasses interactive cognitive processes such as planning, organization, set-shifting, inhibition, self-monitoring, working memory, and initiating and sustaining motor and mental activity. Researchers therefore typically assess executive functioning with multiple tests, each yielding multiple scores. A single composite score of executive functioning, which summarizes deficits across a battery of tests, would be useful in research and clinical trials. This study examines multiple candidate composite scores of executive functioning using tests from the Delis–Kaplan Executive Function System (D-KEFS).

Method

Participants were 875 adults between the ages of 20 and 89 years from the D-KEFS standardization sample. Seven Total Achievement scores were used from three tests (i.e., Trail Making, Verbal Fluency, and Color–Word Interference) to form eight composite scores that were compared based on their psychometric properties and association with intelligence (IQ).

Results

The distributions of most composite scores were mildly to severely skewed, and some had a pronounced ceiling effect. The composite scores all showed a medium positive correlation with IQ. The composite scores were highly intercorrelated in the total sample and in four IQ subgroups (i.e., IQ <89, 90–99, 100–109, 110+), with some being so highly correlated that they appear redundant.

Conclusions

This study is part of a larger research program developing a cognition endpoint for research and clinical trials with sound psychometric properties and utility across discrepant test batteries. Future research is needed to examine the reliability and ecological validity of these composite scores.
Interaction screening by Kendall’s partial correlation for ultrahigh-dimensional data with survival trait
Authors: Wang Jie-Huei , Chen Yi-Hau
Published: January 2020

Motivation

In gene expression and genome-wide association studies, the identification of interaction effects is an important and challenging issue owing to its ultrahigh-dimensional nature. In particular, contaminated data and right-censored survival outcome make the associated feature screening even challenging.

Results

In this article, we propose an inverse probability-of-censoring weighted Kendall’s tau statistic to measure association of a survival trait with biomarkers, as well as a Kendall’s partial correlation statistic to measure the relationship of a survival trait with an interaction variable conditional on the main effects. The Kendall’s partial correlation is then used to conduct interaction screening. Simulation studies under various scenarios are performed to compare the performance of our proposal with some commonly available methods. In the real data application, we utilize our proposed method to identify epistasis associated with the clinical survival outcomes of non-small-cell lung cancer, diffuse large B-cell lymphoma and lung adenocarcinoma patients. Both simulation and real data studies demonstrate that our method performs well and outperforms existing methods in identifying main and interaction biomarkers.

Availability and implementation

R-package ‘IPCWK’ is available to implement this method, together with a reference manual describing how to perform the ‘IPCWK’ package.

Supplementary information

Supplementary data are available at Bioinformatics online.
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Authors: Drysdale Rachel , Cook Charles E , Petryszak Robert , Baillie-Gerritsen Vivienne , Barlow Mary , Gasteiger Elisabeth , Gruhl Franziska , Haas Jürgen , Lanfear Jerry , Lopez Rodrigo , Redaschi Nicole , Stockinger Heinz , Teixeira Daniel , Venkatesan Aravind ,   Elixir Core Data Resource Forum, Bateman Alex , Bridge Alan , Cochrane Guy , Finn Rob , Glöckner Frank Oliver , Hanauer Marc , Keane Thomas , Leach Andrew , Licata Luana , Oksvold Per , Orchard Sandra , Orengo Christine , Parkinson Helen , Persson Bengt , Porras Pablo , Rambla Jordi , Rath Ana , Rodwell Charlotte , Sarkans Ugis , Schomburg Dietmar , Sillitoe Ian , Spalding Dylan , Uhlén Mathias , Velankar Sameer , Vizcaíno Juan Antonio , von Feilitzen Kalle , von Mering Christian , Yates Andrew , Blomberg Niklas , Durinx Christine , McEntyre Johanna
Published: January 2020

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sildenafil triggers tumor lethality through altered expression of HSP90 and degradation of PKD2
Authors: Chen Lu , Liu Yang , Becher Alexander , Diepold Kristina , Schmid Evi , Fehn Adrian , Brunner Cornelia , Rouhi Arefeh , Chiosis Gabriela , Cronauer Marcus , Seufferlein Thomas , Azoitei Ninel
Published: January 2020

The repurposing of existing drugs has emerged as an attractive additional strategy to the development of novel compounds in the fight against cancerous diseases. Inhibition of phosphodiesterase 5 (PDE5) has been claimed as a potential approach to target various cancer subtypes in recent years. However, data on the treatment of tumors with PDE5 inhibitors as well as the underlying mechanisms are as yet very scarce. Here, we report that treatment of tumor cells with low concentrations of Sildenafil was associated with decreased cancer cell proliferation and augmented apoptosis in vitro and resulted in impaired tumor growth in vivo. Notably, incubation of cancer cells with Sildenafil was associated with altered expression of HSP90 chaperone followed by degradation of protein kinase D2, a client protein previously reported to be involved in tumor growth. Furthermore, the involvement of low doses of PU-H71, an HSP90 inhibitor currently under clinical evaluation, in combination with low concentrations of Sildenafil, synergistically and negatively impacted on the viability of cancer cells in vivo. Taken together, our study suggests that repurposing of already approved drugs, alone or in combination with oncology-dedicated compounds, may represent a novel cancer therapeutic strategy.
Motor Recruitment during Action Observation: Effect of Interindividual Differences in Action Strategy
Authors: Hilt P M , Cardellicchio P , Dolfini E , Pozzo T , Fadiga L , D’Ausilio A
Published: January 2020

Visual processing of other’s actions is supported by sensorimotor brain activations. Access to sensorimotor representations may, in principle, provide the top-down signal required to bias search and selection of critical visual features. For this to happen, it is necessary that a stable one-to-one mapping exists between observed kinematics and underlying motor commands. However, due to the inherent redundancy of the human musculoskeletal system, this is hardly the case for multijoint actions where everyone has his own moving style (individual motor signature—IMS). Here, we investigated the influence of subject’s IMS on subjects’ motor excitability during the observation of an actor achieving the same goal by adopting two different IMSs. Despite a clear dissociation in kinematic and electromyographic patterns between the two actions, we found no group-level modulation of corticospinal excitability (CSE) in observers. Rather, we found a negative relationship between CSE and actor-observer IMS distance, already at the single-subject level. Thus, sensorimotor activity during action observation does not slavishly replicate the motor plan implemented by the actor, but rather reflects the distance between what is canonical according to one’s own motor template and the observed movements performed by other individuals.
Understanding TIA: an ethnographic study of TIA consultations
Authors: Bridgwood Bernadeta M , Wilson Andrew , Clarke David , Eborall Helen
Published: January 2020

Background

Transient ischaemic attack (TIA) is a transient episode of neurological dysfunction. Rapid access TIA clinics have been set up as integrated ‘one-stop’ clinics that aim to investigate, diagnose, educate and implement treatment to reduce the risk of further TIA/stroke.

Objective

This study aimed to examine how TIA consultations were conducted by observing the consultations and then interviewing patients.

Methods

This ethnographic study observed fifteen patient-clinician consultations where a diagnosis of TIA was made within three different TIA outpatient clinics in the East Midlands. All fifteen patients, their accompanying family-members/carers and three stroke clinicians were interviewed. Data analysis was informed by the constant comparative approach.

Results

There was considerable variation in the conduct of these consultations across sites and clinicians. This resulted in variation in patient experience and knowledge after the consultation including the ability to recognize TIA-associated risk factors and their management. As TIA symptoms resolve, patients may reduce their need to seek health care services in addition to demonstrating reduced concordance with secondary stroke prevention. Health professionals recognize that this single appointment provides patients with a large amount of information which may be difficult to process. Importantly, there was little discussion about future symptoms and how to respond. A management plan, which considered a patient’s health belief, knowledge and encouraged the involvement of family members, improved information recall.

Conclusions

TIA is a complex medical diagnosis with multiple risk factors that may make the management complex and hence difficult for patients to undertake. Our findings found variability in the conduct, provision of information and patient understanding. Guidance on nationally agreed consultation framework may prove useful. Improved patient education may include individualized/sustained education utilizing multidisciplinary team members across family/primary and secondary care, video or greater online education and improved general public education.
Reclassification of Bacillus aryabhattai Shivaji et al. 2009 as a later heterotypic synonym of Bacillus megaterium de Bary 1884 (Approved Lists 1980)
Authors: Narsing Rao Manik Prabhu , Dong Zhou-Yan , Liu Guo-Hong , Li Li , Xiao Min , Li Wen-Jun
Published: January 2020

In the present study, the taxonomic position of Bacillus aryabhattai and Bacillus megaterium was evaluated using morphological, biochemical, phylogenomic and genome analysis. The morphological and biochemical of these two species were almost similar with few exceptions. The major fatty acids in B. megaterium DSM 32T and B. aryabhattai 21047T were anteiso-C15:0 and iso-C15:0. In the phylogenomic tree, both species clade together and shared high 16S rRNA gene sequence similarity (99.6%). The average nucleotide identity values between Bacillus aryabhattai and Bacillus megaterium were above the threshold values for bacterial species delineation. Based upon morphological, biochemical, chemotaxonomic and comparative genome analysis, we propose to reclassify Bacillus aryabhattai Shivaji et al. 2009 as a later heterotypic synonym of Bacillus megaterium de Bary 1884 (Approved Lists 1980).
Dynamic coupling of allometric ratios to a process-based forest growth model for estimating the impacts of stand density changes
Authors: Grote Rüdiger , Kraus David , Weis Wendelin , Ettl Rasmus , Göttlein Axel
Published: January 2020

Process-based models are increasingly applied for simulating long-term forest developments in order to capture climate change impacts and to investigate suitable management responses. Regarding dimensional development, however, allometric relations such as the height/diameter ratio, branch and coarse root fractions or the dependency of crown dimension on stem diameter often do not account for environmental influences. While this may be appropriate for even-aged, monospecific forests, serious biases can be expected if stand density or forest structure changes rapidly. Such events occur in particular when forests experience disturbances such as intensive thinning or during early development stages of planted or naturally regenerated trees. We therefore suggest a calculation of allometric relationships that depends primarily on neighbourhood competition. Respective equations have been implemented into a physiology-based ecosystem model that considers asymmetric competition by explicit simulation of resource acquisition and depletion per canopy layer. The new implementation has been tested at two sites in Germany where beech (Fagus sylvatica) saplings have either been planted below a shelterwood of old spruces (Picea abies) or grown under clear-cut conditions. We show that the modified model is able to realistically describe tree development in response to stand density changes and is able to represent regeneration growth beneath a gradually decreasing overstorey of mature trees. In particular, the model could represent the faster crown size development in saplings until full ground coverage is established and a faster height growth afterwards. The effect enhances leaf area and thus assimilation per tree and increases carbon availability for stem growth at early development stages. Finally, the necessity to consider dynamic allometric relations with respect to climate change impacts is discussed, and further improvements are suggested.
CAMITAX: Taxon labels for microbial genomes
Authors: Bremges Andreas , Fritz Adrian , McHardy Alice C
Published: January 2020

Background

The number of microbial genome sequences is increasing exponentially, especially thanks to recent advances in recovering complete or near-complete genomes from metagenomes and single cells. Assigning reliable taxon labels to genomes is key and often a prerequisite for downstream analyses.

Findings

We introduce CAMITAX, a scalable and reproducible workflow for the taxonomic labelling of microbial genomes recovered from isolates, single cells, and metagenomes. CAMITAX combines genome distance–, 16S ribosomal RNA gene–, and gene homology–based taxonomic assignments with phylogenetic placement. It uses Nextflow to orchestrate reference databases and software containers and thus combines ease of installation and use with computational reproducibility. We evaluated the method on several hundred metagenome-assembled genomes with high-quality taxonomic annotations from the TARA Oceans project, and we show that the ensemble classification method in CAMITAX improved on all individual methods across tested ranks.

Conclusions

While we initially developed CAMITAX to aid the Critical Assessment of Metagenome Interpretation (CAMI) initiative, it evolved into a comprehensive software package to reliably assign taxon labels to microbial genomes. CAMITAX is available under Apache License 2.0 at https://github.com/CAMI-challenge/CAMITAX.
Eigenvector models for solving the seismic inverse problem for the Helmholtz equation
Authors: Faucher Florian , Scherzer Otmar , Barucq Hélène
Published: January 2020

We study the seismic inverse problem for the recovery of subsurface properties in acoustic media. In order to reduce the ill-posedness of the problem, the heterogeneous wave speed parameter is represented using a limited number of coefficients associated with a basis of eigenvectors of a diffusion equation, following the regularization by discretization approach. We compare several choices for the diffusion coefficient in the partial differential equations, which are extracted from the field of image processing. We first investigate their efficiency for image decomposition (accuracy of the representation with respect to the number of variables). Next, we implement the method in the quantitative reconstruction procedure for seismic imaging, following the full waveform inversion method, where the difficulty resides in that the basis is defined from an initial model where none of the actual structures is known. In particular, we demonstrate that the method may be relevant for the reconstruction of media with salt-domes. We use the method in 2-D and 3-D experiments, and show that the eigenvector representation compensates for the lack of low-frequency information, it eventually serves us to extract guidelines for the implementation of the method.
Effects of flanking sequences and cellular context on subcellular behavior and pathology of mutant HTT
Authors: Chongtham Anjalika , Bornemann Douglas J , Barbaro Brett A , Lukacsovich Tamas , Agrawal Namita , Syed Adeela , Worthge Shane , Purcell Judith , Burke John , Chin Theodore M , Marsh J Lawrence
Published: January 2020

Huntington’s disease (HD) is caused by an expansion of a poly glutamine (polyQ) stretch in the huntingtin protein (HTT) that is necessary to cause pathology and formation of HTT aggregates. Here we ask whether expanded polyQ is sufficient to cause pathology and aggregate formation. By addressing the sufficiency question, one can identify cellular processes and structural parameters that influence HD pathology and HTT subcellular behavior (i.e. aggregation state and subcellular location). Using Drosophila, we compare the effects of expressing mutant full-length human HTT (fl-mHTT) to the effects of mutant human HTTexon1 and to two commonly used synthetic fragments, HTT171 and shortstop (HTT118). Expanded polyQ alone is not sufficient to cause inclusion formation since full-length HTT and HTTex1 with expanded polyQ are both toxic although full-length HTT remains diffuse while HTTex1 forms inclusions. Further, inclusions are not sufficient to cause pathology since HTT171-120Q forms inclusions but is benign and co-expression of HTT171-120Q with non-aggregating pathogenic fl-mHTT recruits fl-mHTT to aggregates and rescues its pathogenicity. Additionally, the influence of sequences outside the expanded polyQ domain is revealed by finding that small modifications to the HTT118 or HTT171 fragments can dramatically alter their subcellular behavior and pathogenicity. Finally, mutant HTT subcellular behavior is strongly modified by different cell and tissue environments (e.g. fl-mHTT appears as diffuse nuclear in one tissue and diffuse cytoplasmic in another but toxic in both). These observations underscore the importance of cellular and structural context for the interpretation and comparison of experiments using different fragments and tissues to report the effects of expanded polyQ.
The Effects of Gamma Irradiation on Chemical Biomarker Recovery from Mixed Chemical/Biological Threat Exposure Specimens
Authors: Isenberg Samantha L , Carter Melissa D , Moon Jonathan L , Laughlin Sarah , Petway Marla , Mojica Mike A , Rood Julia E , Gursky Alexis K , Sheppard Cody I , Bagarozzi Dennis A , Pirkle James L , Johnson Rudolph C
Published: January 2020

Background

Irradiative sterilization of clinical specimens prior to chemical laboratory testing provides a way to not only sterilize pathogens and ensure laboratorian safety but also preserve sample volume and maintain compatibility with quantitative chemical diagnostic protocols. Since the compatibility of clinical biomarkers with gamma irradiation is not well characterized, a subset of diagnostic biomarkers ranging in molecular size, concentration, and clinical matrix was analyzed to determine recovery following gamma irradiation.

Methods

Sample irradiation of previously characterized quality control materials (QCs) at 5 Mrad was carried out at the Gamma Cell Irradiation Facility at the Centers for Disease Control and Prevention (CDC) in Atlanta, GA. Following irradiation, the QCs were analyzed alongside non-irradiated QCs to determine analyte recovery between dosed and control samples.

Results

Biomarkers for exposure to abrin, ricin, and organophosphorus nerve agents (OPNAs) were analyzed for their stability following gamma irradiation. The diagnostic biomarkers included adducts to butyrylcholinesterase, abrine, and ricinine, respectively, and were recovered at over 90% of their initial concentration.

Conclusions

The results from this pilot study support the implementation of an irradiative sterilization protocol for possible mixed-exposure samples containing both chemical and biological threat agents (mixed CBTs). Furthermore, irradiative sterilization significantly reduces a laboratorian’s risk of infection from exposure to an infectious agent without compromising chemical diagnostic testing integrity, particularly for diagnostic assays in which the chemical analyte has been shown to be fully conserved following a 5 Mrad irradiative dose.
CompactDry “Nissui” ETC for Enumeration of Enterococci in a Variety of Foods: AOAC Performance Tested MethodSM 111902
Authors: Mizuochi Shingo
Published: January 2020

Background

The CompactDry “Nissui” ETC is a ready-to-use dry media sheet using a chromogenic medium with selective agents for the detection and enumeration of Enterococcus spp. After a 20–24 h incubation at 37 ± 1°C, Enterococcus colonies appear blue.

Objective

The performance of the CompactDry “Nissui” ETC was compared to that of the Nordic Committee on Food Analysis (NMKL) reference method 68, Enterococcus, Determination in Foods and Feeds, for 10 matrixes including cream, custard, lettuce, parsley, pasta salad, frozen ground beef patties, fresh cooked prawns, sandwiches, raw beef, and tuna pate.

Methods

Performance indicators included repeatability, difference of means (DOM), robustness and inclusivity/exclusivity.

Results

For all 30 materials (10 matrixes each inoculated at three levels), the relative standard deviation of repeatability (RSDr) was <10% for both methods. Most materials yielded RSDr <5%, with five materials between 5 and 10% for the CompactDry “Nissui” ETC method and ten materials between 5 and 10% for the NMKL 68 method. The DOM ranged from –0.240 (95% CI–0.363, –0.118) to 0.228 (95% CI 0.041, 0.415) log10 CFU/g, well within the –0.5 to 0.5 log10 CFU/g range generally accepted as microbiologically insignificant. Both the reference method and this method have limitations of the species detected.

Conclusions

The CompactDry “Nissui” ETC was validated for the enumeration of Enterococcus species in cream, custard, lettuce, parsley, pasta salad, frozen ground beef patties, fresh cooked prawns, sandwiches, raw beef, and tuna pate.
Facultative Viviparity in a Flesh Fly (Diptera: Sarcophagidae): Forensic Implications of High Variability in Rates of Oviparity in Blaesoxipha plinthopyga (Diptera: Sarcophagidae)
Authors: Lesne Pierre , Srivastav Satyam P , El-Hefnawy Ahmed , Parrott Jonathan J , Sanford Michelle R , Tarone Aaron M
Published: January 2020

Flesh flies are major primary consumers of carrion and are commonly found on human remains. Due to this latter feeding habit, their development rates can be used to provide temporal information in forensic investigations. This is usually done by referencing published flesh fly development datasets. Flesh flies are typically assumed to be strictly viviparous and datasets reporting their development rates therefore start at the first larval instar. However, an increasing number of studies has identified oviposition by flesh flies, including the forensically relevant species Blaesoxipha plinthopyga Wiedemann. To assess the impact of egg-laying behavior on casework, oviparity rates and time before larval hatching were assessed under controlled laboratory conditions that reflect common casework conditions in Harris County, Texas. We demonstrated systematic deposition of viable eggs but at a very variable rate between samples. Similarly, the duration between oviposition and larval hatching was highly variable, with some eggs taking more than a day to hatch after deposition. These results highlight the need to account for embryonic development in forensic investigations including B. plinthopyga and advocates for the re-evaluation of the assumed strict viviparity of the Sarcophagidae.
Groupthink Bias in International Adjudication
Authors: Günther Philipp
Published: January 2020

One of the most common assumptions about decision-making is that groups usually enhance the quality of the outcomes of deliberative processes. The research on groupthink behaviour challenges this belief by hypothesizing that certain group constellations excessively seek concurrence and thereby increase the probability of faulty decision-making. Since the decision-making process in international adjudication almost always involves group choices, it is crucial to consider the group environment of collegial court decision-making. This article utilizes the General Group Problem Solving model (GGPS) to ascertain how strong the different group conformity antecedents are pronounced in five international courts (the ICJ, the ITLOS, the WTO AB, the ECtHR and the ICC). The results of the GGPS analysis indicate that the WTO AB and the ICC are most likely susceptible to groupthink effects while the other courts are relatively resilient.
Modal logics with hard diamond-free fragments
Authors: Achilleos Antonis
Published: January 2020

We investigate the complexity of modal satisfiability for a family of multi-modal logics with interdependencies among the modalities. In particular, we examine four characteristic multi-modal logics with dependencies and demonstrate that, even if we restrict the formulae to be diamond-free and to have only one propositional variable, these logics still have a high complexity. This result identifies and isolates two sources of complexity: the presence of axiom $D$ for some of the modalities and certain modal interdependencies. We then further investigate and characterize the complexity of the diamond-free, 1-variable fragments of multi-modal logics in a general setting.
Exploiting morphological data from Pulsar Wind Nebulae via a spatiotemporal leptonic transport code
Authors: van Rensburg C , Venter C , Seyffert A S , Harding Alice K
Published: January 2020

The next era of ground-based Cherenkov telescope development will see a great increase in both quantity and quality of γ-ray morphological data. This initiated the development of a spatiotemporal leptonic transport code to model pulsar wind nebulae. We present results from this code that predicts the evolution of the leptonic particle spectrum and radiation at different radii in a spherically symmetric source. We simultaneously fit the overall broad-band spectral energy distribution, the surface brightness profile, and the X-ray photon index versus radius for PWN 3C 58, PWN G21.5 − 0.9, and PWN G0.9 + 0.1. Such concurrent fitting of disparate data sets is non-trivial and we thus investigate the utility of different goodness-of-fit statistics, specifically the traditional χ2 test statistic and a newly developed scaled-flux-normalized test statistic to obtain best-fitting parameters. We find reasonable fits to the spatial and spectral data of all three sources, but note some remaining degeneracies that will have to be broken by future observations.
First demonstration of OH suppression in a high-efficiency near-infrared spectrograph
Authors: Ellis S C , Bland-Hawthorn J , Lawrence J S , Horton A J , Content R , Roth M M , Pai N , Zhelem R , Case S , Hernandez E , Leon-Saval S G , Haynes R , Min S S , Giannone D , Madhav K , Rahman A , Betters C , Haynes D , Couch W , Kewley L J , McDermid R , Spitler L , Sharp R G , Veilleux S
Published: January 2020

Ground-based near-infrared (NIR) astronomy is severely hampered by the forest of atmospheric emission lines resulting from the rovibrational decay of OH molecules in the upper atmosphere. The extreme brightness of these lines, as well as their spatial and temporal variability, makes accurate sky subtraction difficult. Selectively filtering these lines with OH suppression instruments has been a long standing goal for NIR spectroscopy. We have shown previously the efficacy of fibre Bragg gratings (FBGs) combined with photonic lanterns for achieving OH suppression. Here we report on PRAXIS, a unique NIR spectrograph that is optimized for OH suppression with FBGs. We show for the first time that OH suppression (of any kind) is possible with high overall throughput (18 per cent end-to-end), and provide examples of the relative benefits of OH suppression.
A blinding solution for inference from astronomical data
Authors: Sellentin Elena
Published: January 2020

This paper presents a joint blinding and deblinding strategy for inference of physical laws from astronomical data. The strategy allows for up to three blinding stages, where the data may be blinded, the computations of theoretical physics may be blinded, and –assuming Gaussianly distributed data – the covariance matrix may be blinded. We found covariance blinding to be particularly effective, as it enables the blinder to determine close to exactly where the blinded posterior will peak. Accordingly, we present an algorithm which induces posterior shifts in predetermined directions by hiding untraceable biases in a covariance matrix. The associated deblinding takes the form of a numerically lightweight post-processing step, where the blinded posterior is multiplied with deblinding weights. We illustrate the blinding strategy for cosmic shear from KiDS-450, and show that even though there is no direct evidence of the KiDS-450 covariance matrix being biased, the famous cosmic shear tension with Planck could easily be induced by a mischaracterization of correlations between ξ− at the highest redshift and all lower redshifts. The blinding algorithm illustrates the increasing importance of accurate uncertainty assessment in astronomical inferences, as otherwise involuntary blinding through biases occurs.
Deep Imaging Analysis in VISUAL Reveals the Role of YABBY Genes in Vascular Stem Cell Fate Determination
Authors: Nurani Alif Meem , Ozawa Yasuko , Furuya Tomoyuki , Sakamoto Yuki , Ebine Kazuo , Matsunaga Sachihiro , Ueda Takashi , Fukuda Hiroo , Kondo Yuki
Published: January 2020

Stem cells undergo cell division and differentiation to ensure organized tissue development. Because plant cells are immobile, plant stem cells ought to decide their cell fate prior to differentiation, to locate specialized cells in the correct position. In this study, based on a chemical screen, we isolated a novel secondary cell wall indicator BF-170, which binds to lignin and can be used to image in vitro and in situ xylem development. Use of BF-170 to observe the vascular differentiation pattern in the in vitro vascular cell induction system, VISUAL, revealed that adaxial mesophyll cells of cotyledons predominantly generate ectopic xylem cells. Moreover, phloem cells are abundantly produced on the abaxial layer, suggesting the involvement of leaf adaxial–abaxial polarity in determining vascular cell fate. Analysis of abaxial polarity mutants highlighted the role of YAB3, an abaxial cell fate regulator, in suppressing xylem and promoting phloem differentiation on the abaxial domains in VISUAL. Furthermore, YABBY family genes affected in vivo vascular development during the secondary growth. Our results denoted the possibility that such mediators of spatial information contribute to correctly determine the cell fate of vascular stem cells, to conserve the vascular pattern of land plants.
The Impact of an Experimental Guaranteed Income on Crime and Violence
Authors: Calnitsky David , Gonalons-Pons Pilar
Published: January 2020

Would unconditional cash payments reduce crime and violence? This paper examines data on crime and violence in the context of an understudied social experiment from the late 1970s called the Manitoba Basic Annual Income Experiment, or Mincome. We combine town-level crime statistics for all medium-sized Canadian Prairie towns with town-level socio-demographic data from the census to study how an experimental guaranteed income affected both violent crime and total crime. We find a significant negative relationship between Mincome and both outcomes. We also decompose total crime and analyze its main components, property crime and “other” crime, and find a significant negative relationship between Mincome and property crime. While the impact on property crime is theoretically straightforward, we close by speculating on the mechanisms that might link the availability of guaranteed annual income payments to a decline in violence, focusing on the mechanisms that shape patterns of inter-partner violence.
Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism
Authors: Starostik Margaret R. , Sosina Olukayode A. , McCoy Rajiv C.
Published: January 2020

Less than half of human zygotes survive to live birth, primarily due to aneuploidies of meiotic or mitotic origin. Mitotic errors lead to chromosomal mosaicism, defined by multiple cell lineages with distinct chromosome complements. The incidence and fitness consequences of chromosomal mosaicism in human embryos remain controversial, with most previous studies based on bulk DNA assays or comparisons of multiple biopsies of a few embryonic cells. Single-cell genomic data provide an opportunity to quantify mosaicism on an embryo-wide scale. To this end, we extended an approach to infer aneuploidies based on chromosome dosage-associated changes in gene expression by integrating signatures of allelic imbalance. We applied this method to published single-cell RNA sequencing data from 74 disaggregated human embryos, spanning the morula to blastocyst stages. Our analysis revealed widespread mosaic aneuploidies across preimplantation development, with 59 of 74 (80%) embryos harboring at least one aneuploid cell (1% FDR). By clustering copy number calls, we reconstructed histories of chromosome mis-segregation, distinguishing meiotic and early mitotic errors from those occurring after lineage differentiation. We observed no significant enrichment of aneuploid cells in the trophectoderm compared to the inner cell mass, though we do detect such an enrichment in published data from later post-implantation stages. Finally, we observed that aneuploid cells exhibit upregulation of immune response genes, as well as downregulation of genes involved in proliferation, metabolism, and protein processing, consistent with stress responses previously documented in other stages and systems. Together, our work provides a high-resolution view of aneuploidy in preimplantation embryos and supports the conclusion that low-level mosaicism is a common feature of early human development.
Tiled Reconstruction Improves Structured Illumination Microscopy
Authors: Hoffman David P. , Betzig Eric
Published: January 2020

Structured illumination microscopy (SIM) is widely used for fast, long-term, live-cell super-resolution imaging. However, SIM images can contain substantial artifacts if the sample does not conform to the underlying assumptions of the reconstruction algorithm. Here we describe a simple, easy to implement, process that can be combined with any reconstruction algorithm to alleviate many common SIM reconstruction artifacts and briefly discuss possible extensions.
Ecological Relationships in the Serengeti National Park
Authors: Brownstein Kole
Published: January 2020

The use of camera traps in animal ecology has transformed the field by allowing a greater quantity of detailed observations with limited human interference. One of largest camera trap studies published to date is from the Serengeti National Park (SNP) in Tanzania, East Africa which deployed 225 camera traps and obtained over 1.2 million pictures. This paper will focus primarily on the top predator of the Serengeti, the lion, and how it affects and is affected by prey, subordinate predators and the dramatic shift in the seasons. I asked the following three questions to better understand species relationships in the SNP: 1) Do the seasons in the SNP have an effect on the RAB of lions? 2) Does the presence or absence of lions have an effect on the RAB of hyenas in the wet season? 3) Does the presence/absence of Thompson gazelles (Eudorcas thomsonii) and impalas (Aepyceros melampus) in the wet season have an effect on the RAB of lions? During the dry and wet season of 2012 in the SNP there did not appear to be a change in the relative abundance of lions (Fig. 1), nor did lion relative abundance affect hyenas. The lions might possibly alter their diet during the dry seasons to include non-migratory species and choose not to change their territory on a season to season basis. Based on these findings research should focus on how the lions adapt to the changes in prey abundance during the wet and dry season. This preliminary analysis of the ecological dynamics of lions and associated species in the SNP is intriguing and yet raises significantly more questions than it has answered. Additional research surrounding the effects of yearly migration on the lions home territory, diet, and species interactions should be investigated more thoroughly, to greater understand the ecological relationships in the SNP.
Protein Sequence Design with a Learned Potential
Authors: Anand-Achim Namrata , Eguchi Raphael R. , Mathews Irimpan I. , Perez Carla P. , Derry Alexander , Altman Russ B. , Huang Po-Ssu
Published: January 2020

Abstract

The task of protein sequence design is central to nearly all rational protein engineering problems, and enormous effort has gone into the development of energy functions to guide design. We investigate the capability of a deep neural network model to automate design of sequences onto protein backbones, having learned directly from crystal structure data and without any human-specified priors. The model generalizes to native topologies not seen during training, producing experimentally stable designs. We evaluate the generalizability of our method to a de novo TIM-barrel scaffold. The model produces novel sequences, and high-resolution crystal structures of two designs show excellent agreement with the in silico models. Our findings demonstrate the tractability of an entirely learned method for protein sequence design.
Alterations of human lung and gut microbiome in non-small cell lung carcinomas and distant metastasis
Authors: Lu Hui , Gao Na L. , Wei Chunhua , Wang Jiaojiao , Tong Fan , Li Huanhuan , Zhang Ruiguang , Ma Hong , Yang Nong , Zhang Yongchang , Wang Ye , Liang Zhiwen , Zeng Hao , Chen Wei-Hua , Dong Xiaorong
Published: January 2020

Background

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Although dysbiosis of lung and gut microbiota have been associated with NSCLC, their relative contributions are unclear; in addition, their roles in distant metastasis (DM) are still illusive.

Results

We surveyed the fecal and sputum (as a proxy for lung) microbiota in healthy controls and NSCLC patients of various stages, and found significant perturbations of gut- and sputum-microbiota in patients with NSCLC and DM. Machine-learning models combining both microbiota (mixed models) performed better than either dataset in patient stratification, with the highest area under the curve (AUC) value of 0.842. Sputum-microbiota contributed more than the gut in the mixed models; in addition, sputum-only models performed similarly to the mixed models in most cases. Several microbial-biomarkers were shared by both microbiota, indicating their similar roles at distinct body sites. Microbial-biomarkers of distinct disease stages were mostly shared, suggesting biomarkers for distant metastasis could be acquired early. Furthermore,Pseudomonas aeruginosa, a species previously associated with wound infections, was significantly more abundant in brain metastasis, indicating distinct types of DMs could have different microbial-biomarkers.

Conclusion

Our results indicate that alterations of sputum-microbiota have stronger relationships with NSCLC and distant metastasis than the gut, and strongly support the feasibility of metagenome-based non-invasive disease diagnosis and risk evaluation.
Late onset of Syt2a expression at synapses relevant to social behavior
Authors: Goode Collette , Voeun Mae , Ncube Denver , Eisen Judith , Washbourne Philip , Tallafuss Alexandra
Published: January 2020

As they form, synapses go through various stages of maturation and refinement. These steps are linked to significant changes in synaptic function, potentially resulting in changes in behavior. Here, we examined the distribution of the synaptic vesicle protein Synaptotagmin 2a (Syt2a) during development of the zebrafish nervous system. Syt2a is widely distributed throughout the midbrain and hindbrain early during larval development but very weakly expressed in the forebrain. Later in development, Syt2a expression levels increase, particularly in regions associated with social behavior, and most intriguingly, around the time social behavior becomes apparent. We provide evidence that Syt2a localizes to synapses on socially-relevant neurons in the ventral forebrain, co-localizing with tyrosine hydroxylase, a biosynthetic enzyme in the dopamine pathway. Our results suggest a maturation step for synapses in the forebrain that are spatiotemporally related to social behavior.