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Background Most bacterial genomes contain integrated bacteriophages—prophages—in various states of decay. Many are active and able to excise from the genome and replicate, while others are cryptic prophages, remnants of their former selves. Over the last two decades, many computational tools have been developed to identify the prophage components of bacterial genomes, and it is a particularly active area for the application of machine learning approaches. However, progress is hindered and comparisons thwarted because there are no manually curated bacterial genomes that can be used to test new prophage prediction algorithms. Methods We present a library of gold-standard bacterial genomes with manually curated prophage annotations, and a computational framework to compare the predictions from different algorithms. We use this suite to compare all extant stand-alone prophage prediction algorithms and identify their strengths and weaknesses. We provide a FAIR dataset for prophage identification, and demonstrate the accuracy, precision, recall, and f 1 score from the analysis of ten different algorithms for the prediction of prophages. Results We identified strengths and weaknesses between the prophage prediction tools. Several tools exhibit exceptional f 1 scores, while others have better recall at the expense of more false positives. The tools vary greatly in runtime performance with few exhibiting all desirable qualities for large-scale analyses. Conclusions Our library of gold-standard prophage annotations and benchmarking framework provide a valuable resource for exploring strengths and weaknesses of current and future prophage annotation tools. We discuss caveats and concerns in this analysis, how those concerns may be mitigated, and avenues for future improvements. This framework will help developers identify opportunities for improvement and test updates. It will also help users in determining the tools that are best suited for their analysis.

AbstractMost bacterial genomes contain integrated bacteriophages—prophages—in various states of decay. Many are active and able to excise from the genome and replicate, while others are cryptic prophages, remnants of their former selves. Over the last two decades, many computational tools have been developed to identify the prophage components of bacterial genomes, and it is a particularly active area for the application of machine learning approaches. However, progress is hindered and comparisons thwarted because there are no manually curated bacterial genomes that can be used to test new prophage prediction algorithms.Here, we present a library of gold-standard bacterial genome annotations that include manually curated prophage annotations, and a computational framework to compare the predictions from different algorithms. We use this suite to compare all extant stand-alone prophage prediction algorithms to identify their strengths and weaknesses.We provide a FAIR dataset for prophage identification, and demonstrate the accuracy, precision, recall, and f1 score from the analysis of seven different algorithms for the prediction of prophages. We discuss caveats and concerns in this analysis and how those concerns may be mitigated.

Featured Application: Magnesium-doped carbonated hydroxyapatite and tricalcium phosphate anodized coatings are applied in alpha, beta, and duplex titanium alloys to improve osseointegration. The rising demand for dental and orthopedic implants and their frequent aseptic loosening failure mode necessitate the drive to continue modifying implant surfaces to improve osseointegration outcomes. Plasma-sprayed hydroxyapatite coatings are widely used but are prone to delamination. This study involves a single-step anodization process utilizing a novel electrolyte to produce Mg-doped carbonated hydroxyapatite and tricalcium phosphate-containing coatings on four titanium alloy surfaces. XRD confirmed hydroxyapatite and tricalcium phosphate formation, with FTIR examination revealing carbonate substitutions indicative of bone-like apatite formation in each oxide. SEM analyses revealed micro- and nano-scaled surface features on each oxide. SEM and EDS analyses of the oxide coating cross-sections showed each group to be bi-layered with an inner titanium dioxide-rich layer and an outer hydroxyapatite/tricalcium phosphate-rich layer. The oxide layer adhesion quality was shown to be good on CPTi, TAV, and TiMo α + β implant alloy surfaces. Unfortunately, the anodization process also resulted in an undesirable and embrittling omega phase at the substrate–oxide interface due to the migration of molybdenum into the inner oxide. Nonetheless, the anodized coatings on the CPTi and TAV alloy substrates, which are the most widely used titanium alloys for implant applications, show much potential for improving future patient outcomes. [ABSTRACT FROM AUTHOR]

A manager's prior experience may affect an organization's resource allocation decisions and its performance. I examine this issue in the context of National Football League (NFL) franchises. I find that teams with coaches from an offensive background spend 5.5% points more of their salary cap space on offensive personnel, while a defensive background does not significantly affect the share of resources allocated to defensive personnel. While additional salary resources committed to offensive and defensive personnel do improve team performance in those respective areas, marginal improvements in offensive and defensive performance associated with greater spending are generally unaffected by the coach's background, a finding suggesting that a coach's background does not confer an informational advantage on certain types of personnel. I further find no evidence of significant differences in the effects that spending on offence and defence respectively have on team performance, suggesting efficiency within this labour market. [ABSTRACT FROM AUTHOR]

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Periapical radiographs are routinely used in dental practice for diagnosis and treatment planning purposes. However, they often suffer from artifacts, distortions, and superimpositions, which can lead to potential misinterpretations. Thus, an automated detection system is required to overcome these challenges. Artificial intelligence (AI) has been revolutionizing various fields, including medicine and dentistry, by facilitating the development of intelligent systems that can aid in performing complex tasks such as diagnosis and treatment planning. The purpose of the present study was to verify the diagnostic performance of an AI system for the automatic detection of teeth, caries, implants, restorations, and fixed prosthesis on periapical radiographs. A dataset comprising 1000 periapical radiographs collected from 500 adult patients was analyzed by an AI system and compared with annotations provided by two oral and maxillofacial radiologists. A strong correlation (R > 0.5) was observed between AI perception and observers 1 and 2 in carious teeth (0.7–0.73), implants (0.97–0.98), restored teeth (0.85–0.89), teeth with fixed prosthesis (0.92–0.94), and missing teeth (0.82–0.85). The automatic detection by the AI system was comparable to the oral radiologists and may be useful for automatic identification in periapical radiographs. [ABSTRACT FROM AUTHOR]

West Tasmania has a complex geological history, including a Cambrian tectonic collision and related orogenesis, which formed ore deposits in a volcanic hosted massive sulfide (VHMS) setting. While the topography and dense vegetation covering the area presents challenges for on-ground investigations, the area is relatively well-studied such that 3D geological models are available. This contribution presents results of a broadband magnetotelluric (MT) 2D transect across the area (∼30 stations over a $ \sim 80\,{\rm km} $ ∼ 80 km line, deployed in early 2016) that enables a combined interpretation of regional-scale geoelectric and geological structures. After accounting for noise, distortion and geoelectric strike; we produce 2D resistivity models using OCCAM2D inversion. We infer low resistivity anomalies in the shallow ( $ \lt 3\,{\rm km} $ < 3 km ), mid (3–8 km) and deeper crust. Along this MT transect the shallow and mid crust low resistivity zones correspond to major crustal faults. Deep low resistivity features in the east of the transect suggest fluid pathways associated with metamorphism along the western boundary of the Tyennan block during the Cambrian Tyennan Orogeny, while others potentially represent the metasomatism of lower crustal rocks and fluid pathways converging into the mid crust. [ABSTRACT FROM AUTHOR]

Heat flow data obtained in connection with geothermal resource exploration suggests anomalous upper crustal structure and processes in parts of central east Tasmania. The regional scale crustal geology of the Midlands of Tasmania is, however, mostly obscured at the surface by the Permo-Triassic sedimentary sequences of the Tasmania Basin together with extensive exposures of Jurassic dolerite. We investigate controls on undercover crustal processes in this region by combining long period and broadband magnetotelluric (MT) datasets in 3D inversions for the geoelectric structure; followed by an interpretation that is informed by aspects of the pre-existing 3D regional geological and geophysical model. The new 3D model allows improved resolution of low resistivity anomalies together with a qualitative appraisal of spatially variable model sensitivity. The most robust features ( $ \lt 1\,\Omega {\rm m} $ < 1 Ω m ) in the 2–3 km depth interval occur where N–S and E–W faults intersect with a high point in the topography of the upper surface of a deep seated granite body. Enhancement of conductivity in this zone by clay, graphite or mineralisation, or a combination thereof, is likely. Other low resistivity features suggest that conductive pathways exist where major or multiple faults are present. These interpretations provide support for continued exploration in the Midlands of Tasmania for a variety of resources related to crustal fluids and fracturing. [ABSTRACT FROM AUTHOR]

Medication-related osteonecrosis of the jaw (MRONJ) is an adverse reaction caused by the use of antiresorptive antiangiogenic medication. The most commonly affected areas are posterior regions of mandible and maxilla. However, a simultaneous occurrence in both jaws is rarely observed. We present an interesting case of MRONJ affecting both jaws. A 47-year-old female presented with pain and swelling in the left posterior region of the mandible. The patient’s medical history was significant for breast cancer with ongoing bisphosphonate therapy. Cone-beam computerized tomography (CBCT) confirmed the presence of an extraction socket at the site of complaint. There was evidence of a diffuse sclerotic bone reaction in the maxillary posterior region bilaterally. The mandible showed presence of diffuse sclerotic bone only in the left para-symphysis and posterior region in addition to association with a periosteal bone reaction in the left para-symphysis region. Considering these findings and a history of exposure to bisphosphonate medication, the final diagnosis was conclusive of MRONJ. Management was aimed at suppressing the symptoms of pain and infection. The present case study reinforces the importance of correlating clinical and radiographic findings. Early diagnosis of MRONJ may lead to a more conservative treatment approach, greatly improving the patient’s prognosis. [ABSTRACT FROM AUTHOR]

Early stage technology startups rely critically on talented scientists and engineers to commercialize new technologies. And yet these startups compete with established technology firms to hire the best workers. Theories of ability sorting predict that high-ability workers will choose jobs in established firms that offer greater complementary assets and higher pay, leaving low-ability workers to take lower paying and riskier jobs in startups. We propose an alternative view in which heterogeneity in both worker ability and preferences enable startups to hire talented workers who have a taste for a startup work environment even at lower pay. Using a longitudinal survey that follows 2,394 science and engineering PhDs from graduate school into their first industrial employment, we overcome common empirical challenges by observing ability and stated preferences prior to entry into the labor market. We find that both ability and career preferences strongly predict startup employment with high-ability workers who prefer startup employment being the most likely to work in a startup. We show that this partly reflects dual selection effects whereby worker preferences result in a large pool of startup job applicants and startups make job offers to the most talented workers. Additional analyses confirm that startup employees earn approximately 17% lower pay. This gap is greatest for high-ability workers and persists over workers' early careers, suggesting that they accept a negative compensating differential in exchange for the nonpecuniary benefits of startup employment. Data on job attributes and stated reasons for job choice further support this interpretation. This paper was accepted by Toby Stuart, entrepreneurship and innovation. Funding: This work was supported by the National Science Foundation SciSIP Award [Grant 1262270] and the Ewing Marion Kauffman Foundation (Junior Faculty Fellowship). Supplemental Material: The online appendix and data are available at https://doi.org/10.1287/mnsc.2023.4868. [ABSTRACT FROM AUTHOR]

Titanium has a long history of clinical use, but the naturally forming oxide is not ideal for bacterial resistance. Anodization processes can modify the crystallinity, surface topography, and surface chemistry of titanium oxides. Anatase, rutile, and mixed phase oxides are known to exhibit photocatalytic activity (PCA)-driven bacterial resistance under UVA irradiation. Silver additions are reported to enhance PCA and reduce bacterial attachment. This study investigated the effects of silver-doping additions to three established anodization processes. Silver doping showed no significant influence on oxide crystallinity, surface topography, or surface wettability. Oxides from a sulfuric acid anodization process exhibited significantly enhanced PCA after silver doping, but silver-doped oxides produced from phosphoric-acid-containing electrolytes did not. Staphylococcus aureus attachment was also assessed under dark and UVA-irradiated conditions on each oxide. Each oxide exhibited a photocatalytic antimicrobial effect as indicated by significantly decreased bacterial attachment under UVA irradiation compared to dark conditions. However, only the phosphorus-doped mixed anatase and rutile phase oxide exhibited an additional significant reduction in bacteria attachment under UVA irradiation as a result of silver doping. The antimicrobial success of this oxide was attributed to the combination of the mixed phase oxide and higher silver-doping uptake levels. [ABSTRACT FROM AUTHOR]