Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation

The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic contributions of the hydrophobic effect explicitly in an implicit solvent model. This allows us to capture two important effects: a length-scale dependence and a temperature dependence for the solvation of a hydrophobic particle. This consistent treatment of the hydrophobic effect explains cold denaturation and heat capacity measurements of solvated proteins.Comment: Added and corrected references for design procedure in main text (p. 2) and in Supplemental Information (p. 8

Effect of Preanalytical Processing of ThinPrep Specimens on Detection of High-Risk Human Papillomavirus by the Aptima HPV Assay

Two important preanalytical protocols performed on liquid-based cytological specimens, namely, automated cytology processing and glacial acetic acid (GAA) treatment, may occur prior to the arrival of specimens in a molecular diagnostics laboratory. Ninety-two ThinPrep vials previously positive for high-risk human papillomavirus (HPV) via the Cervista HPV HR test were preselected and alternated with 92 previously negative ThinPrep vials. The specimen set was processed in a consecutive fashion by an automated cytology processor without fastidious decontamination precautions. Carryover potential was subsequently assessed by performance of the Aptima HPV assay on aliquots from reprocessed ThinPrep vials. All previously negative ThinPrep vials yielded a negative result following routine automated cytology processing, despite close proximity to known-positive ThinPrep vials. In separate experiments, aliquots from 236 ThinPrep vials were forwarded for tandem analysis with and without GAA treatment. Data from GAA- and mock-treated specimens generated by Aptima HPV were compared to correlate data generated by Cervista. A 99.2% concordance of Aptima HPV results from GAA-treated and mock-treated specimens was noted. This result differed from the concordance result derived from Cervista (91.5%; P \u3c 0.0002). Of the initially positive Cervista results, 21.9% reverted to negative following GAA treatment; the correlate value was 2.7% for Aptima HPV (P = 0.01). While deleterious effects of GAA treatment on genomic DNA were noted with Cervista (P = 0.0015), GAA treatment had no significant effects on Aptima HPV specimen signal/cutoff ratios or amplification of internal control RNA (P ≥ 0.07). The validity of an Aptima HPV result is independent of GAA treatment and routine automated cytology processing

Interaction between regional temperature and shade level shapes saproxylic beetle communities

AimThe 'concept of relative constancy of habitats' assumes that species differ in their habitat preferences depending on the regional temperature so that all populations experience similar microclimatic conditions. Our aim was to assess the relevance of this concept by disentangling the effects of shade level and regional temperature on southern and northern distributed saproxylic (=dead wood dependent) beetle species.LocationSweden.MethodsWe established a field experiment by placing 435 logs of Norway spruce (Picea abies) along shade gradients in six regions differing in regional temperature (along a 1200 km latitudinal gradient). For each log, we sampled the saproxylic beetle community and calculated the Community Temperature Index (CTI), indicating to what extent the community is dominated by southern or northern species.ResultsSpecies richness and total abundance were better explained by shade level, whereas species composition was better explained by study region. In colder regions, CTI varied along the shade gradient, whereas in warmer regions, CTI was more similar along the shade gradient. Moreover, in colder regions, the number of southern species was higher in sun-exposed logs, whereas in warmer regions, the number of southern species was higher in shaded logs. This supports the concept of relative constancy of habitats. In contrast, northern species preferred shaded conditions regardless of the regional temperature.Main ConclusionsRegional temperature, shade level and resulting microclimate are important drivers of species richness, total abundance and composition. Occurrence patterns of saproxylic beetle species follow to some extent the concept of relative constancy of habitats since their habitat preferences vary with regional temperature. Northern species are of conservation concern due to disadvantages by climate warming and clear-cutting. They are favoured by preserving forests with rarely disturbed canopies

Identification of sex-specific compounds in the invasive four-eyed fir bark beetle Polygraphus proximus

Polygraphus proximus, a four-eyed fir bark beetle, is an invasive bark beetle species which has caused extensive damage to forests of Abies sibirica in southern and western Siberia and to Abies species in the European part of Russia. There is a high risk that the pest insect will spread to areas where it is currently not considered present, such as the European Union. In these areas, it threatens to attack conifer forests of various species which may result in major environmental and economic impact. The aim of this study was to identify pheromone components of P. proximus that can be used as pheromone baits. Males and females of P. proximus were allowed to bore into the bark of stem sections of Abies sibirica at the laboratory, and volatiles were collected with solid-phase microextraction (SPME). Analyses of these extracts with gas chromatography-mass spectrometry (GC-MS) revealed several sex-specific compounds. In total, twelve male-specific compounds and one female-specific compound were identified. The major male-specific compound determined by GC peak area was (Z)-2-(3,3-dimethylcyclohexylidene)-ethanol [(Z)-DMCHE] and the minor male-specific compounds were 3-methyl-3-buten-1-ol, 3-methyl-2-buten-1-ol, 3-methyl-2-butenal, benzyl alcohol, fragranol, 7-methyl-3-methylene-6-octen-1-ol, (Z)- and (E)-2-(3,3-dimethylcyclohexylidene)-acetaldehyde, geraniol, geranial and papayanol. The only female-specific compound was identified as 1-hexanol. Two of the male-specific compounds, (Z)-DMCHE and 3-methyl-2-buten-1-ol were shown to attract males and females of P. proximus in field studies. Thus, we now for the first time can present the structures of two male-specific components that are biologically active parts of P. proximus aggregation pheromone. However, some chemical communication overlap between P. proximus and P. subopacus needs to be further investigated as (Z)-DMCHE also attracted males and females of P. subopacus

Improving access to endogenous DNA in ancient bones and teeth

Poor DNA preservation is the most limiting factor in ancient genomic research. In the majority of ancient bones and teeth, endogenous DNA molecules represent a minor fraction of the whole DNA extract, rendering shot-gun sequencing inefficient for obtaining genomic data. Based on ancient human bone samples from temperate and tropical environments, we show that an EDTA-based enzymatic ‘pre-digestion’ of powdered bone increases the proportion of endogenous DNA several fold. By performing the pre-digestion step between 30 min and 6 hours on five bones, we observe an asymptotic increase in endogenous DNA content, with a 2.7-fold average increase reached at 1 hour. We repeat the experiment using a brief pre-digestion (15 or 30 mins) on 21 ancient bones and teeth from a variety of archaeological contexts and observe an improvement in 16 of these. We here advocate the implementation of a brief pre-digestion step as a standard procedure in ancient DNA extractions. Finally, we demonstrate on 14 ancient teeth that by targeting the outer layer of the roots we obtain up to 14 times more endogenous DNA than when using the inner dentine. Our presented methods are likely to increase the proportion of ancient samples that are suitable for genome-scale characterization.Full Tex

Pyroelectricity of silicon-doped hafnium oxide thin films

Ferroelectricity in hafnium oxide thin films is known to be induced by various doping elements and in solid-solution with zirconia. While a wealth of studies is focused on their basic ferroelectric properties and memory applications, thorough studies of the related pyroelectric properties and their application potential are only rarely found. This work investigates the impact of Si doping on the phase composition and ferro- as well as pyroelectric properties of thin film capacitors. Dynamic hysteresis measurements and the field-free Sharp-Garn method were used to correlate the reported orthorhombic phase fractions with the remanent polarization and pyroelectric coefficient. Maximum values of 8.21 µC cm−2 and −46.2 µC K−1 m−2 for remanent polarization and pyroelectric coefficient were found for a Si content of 2.0 at%, respectively. Moreover, temperature-dependent measurements reveal nearly constant values for the pyroelectric coefficient and remanent polarization over the temperature range of 0 °C to 170 °C, which make the material a promising candidate for IR sensor and energy conversion applications beyond the commonly discussed use in memory applications

AI unboxed and jobs: A novel measure and firm-level evidence from three countries

We unbox developments in artificial intelligence (AI) to estimate how exposure to these developments affect firm-level labour demand, using detailed register data from Denmark, Portugal and Sweden over two decades. Based on data on AI capabilities and occupational work content, we develop and validate a time-variant measure for occupational exposure to AI across subdomains of AI, such as language modelling. According to the model, white collar occupations are most exposed to AI, and especially white collar work that entails relatively little social interaction. We illustrate its usefulness by applying it to near-universal data on firms and individuals from Sweden, Denmark, and Portugal, and estimating firm labour demand regressions. We find a positive (negative) association between AI exposure and labour demand for high-skilled white (blue) collar work. Overall, there is an up-skilling effect, with the share of white-collar to blue collar workers increasing with AI exposure. Exposure to AI within the subdomains of image and language are positively (negatively) linked to demand for high-skilled white collar (blue collar) work, whereas other AI-areas are heterogeneously linked to groups of workers

Draft Genome Sequencing of Three Glutaraldehyde-Tolerant Bacteria from Produced Water from Hydraulic Fracturing

Here, we report the draft genome sequence of three glutaraldehyde-resistant isolates from produced water from hydraulic fracturing operations. The three strains were identified as sp. strain G11, sp. strain G15, and sp. strain G16. The genome sequences of these isolates will provide insights into biocide resistance in hydraulic fracturing operations

Epidural Hematoma Following Cervical Spine Surgery.

STUDY DESIGN: A multicentered retrospective case series. OBJECTIVE: To determine the incidence and circumstances surrounding the development of a symptomatic postoperative epidural hematoma in the cervical spine. METHODS: Patients who underwent cervical spine surgery between January 1, 2005, and December 31, 2011, at 23 institutions were reviewed, and all patients who developed an epidural hematoma were identified. RESULTS: A total of 16 582 cervical spine surgeries were identified, and 15 patients developed a postoperative epidural hematoma, for a total incidence of 0.090%. Substantial variation between institutions was noted, with 11 sites reporting no epidural hematomas, and 1 site reporting an incidence of 0.76%. All patients initially presented with a neurologic deficit. Nine patients had complete resolution of the neurologic deficit after hematoma evacuation; however 2 of the 3 patients (66%) who had a delay in the diagnosis of the epidural hematoma had residual neurologic deficits compared to only 4 of the 12 patients (33%) who had no delay in the diagnosis or treatment (P = .53). Additionally, the patients who experienced a postoperative epidural hematoma did not experience any significant improvement in health-related quality-of-life metrics as a result of the index procedure at final follow-up evaluation. CONCLUSION: This is the largest series to date to analyze the incidence of an epidural hematoma following cervical spine surgery, and this study suggest that an epidural hematoma occurs in approximately 1 out of 1000 cervical spine surgeries. Prompt diagnosis and treatment may improve the chance of making a complete neurologic recovery, but patients who develop this complication do not show improvements in the health-related quality-of-life measurements