Quantum Transition State Theory for proton transfer reactions in enzymes

We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative description of the temperature dependence and magnitude of kinetic isotope effects for two classes of enzymes which have been claimed to exhibit signatures of quantum tunneling. The only quantum effects are those associated with the transition state, both reflection at the barrier top and tunneling just below the barrier. We establish that the friction due to the environment is weak and only slightly modifies the reaction rate. Furthermore, at room temperature and for typical energy barriers environmental degrees of freedom with frequencies much less than 1000 cm$^{-1}$ do not have a significant effect on quantum corrections to the reaction rate.Comment: Aspects of the article are discussed at condensedconcepts.blogspot.co

Mental Health Admissions to Paediatric Wards Study (MAPS): a protocol for the analysis of Hospital Episode Statistics (HES) data.

INTRODUCTION: Children and young people (CYP) presenting with a mental health (MH) crisis are frequently admitted to general acute paediatric wards as a place of safety. Prior to the pandemic, a survey in England showed that CYP occupied 6% of general paediatric inpatient beds due to an MH crisis, and there have been longstanding concerns about the quality of care to support these patients in this setting. Mental Health Admissions to Paediatric Wards Study aims to generate a theory of change (ToC) model to improve the quality of care for CYP admitted to acute paediatric services after presenting in a MH crisis. METHODS AND ANALYSIS: We will undertake a national (England), sequential, mixed methods study to inform a ToC framework alongside a stakeholder group consisting of patients, families/carers and healthcare professionals (HCPs). Our study consists of four work packages (WP) undertaken over 30 months. WP1 is limited to using national routine administrative data to identify and characterise trends in MH admissions in acute paediatric wards in England between 2015- 2022. ETHICS AND DISSEMINATION: WP1 received ethical approval (Ref 23/NW/0192). We will publish the overall synthesis of data and the final ToC to improve care of CYP with MH crisis admitted to general acute paediatric settings. As coproducers of the ToC, we will work with our stakeholder group to ensure wide dissemination of findings. Potential impacts will be on service development, new models of care, training and workforce planning

Skeletal concentrations of lead, cadmium, zinc, and silver in ancient North American Pecos Indians.

Bone samples of 14 prehistoric North American Pecos Indians from circa 1400 A.D. were analyzed for lead, cadmium, zinc, and silver by graphite furnace atomic absorption spectrometry to establish the baseline levels of these elements in an ancient North American population. Measurements of outer and inner bone fractions indicate the former were contaminated postmortem for lead, zinc, and cadmium. The contamination-adjusted average (mean +/- SD) level of lead (expressed as the ratio of atomic lead to atomic calcium) in bones of the Indians was 8.4 +/- 4.4 x 10(-7)), which was similar to ratios in bones of ancient Peruvians (0.9 to 7.7 x 10(-7)) and significantly lower than ratios in bones of modern adults in England and the United States (210 to 350 x 10(-7]. The adjusted average concentrations (microgram per gram dry weight) of biologic cadmium, silver, and zinc in the Pecos Indian bones were 0.032 +/- 0.013, 0.094 +/- 0.044, and 130 +/- 66, as compared to concentrations of 1.8, 0.01 to 0.44, and 75 to 170 in the bones of modern people, respectively. Therefore, cadmium concentrations in Pecos Indian bones are also approximately 50-fold lower than those of contemporary humans. These data support earlier findings that most previously reported natural concentrations of lead in human tissues are erroneously high and indicate that natural concentrations of cadmium are also between one and two orders of magnitude lower than contemporary concentrations

Whose Science and whose Religion? Reflections on the Relations between Scientific and Religious Worldviews

Arguments about the relationship between science and religion often proceed by identifying a set of essential characteristics of scientific and religious worldviews and arguing on the basis of these characteristics for claims about a relationship of conflict or compatibility between them. Such a strategy is doomed to failure because science, to some extent, and religion, to a much larger extent, are cultural phenomena that are too diverse in their expressions to be characterized in terms of a unified worldview. In this paper I follow a different strategy. Having offered a loose characterization of the nature of science, I pose five questions about specific areas where religious and scientific worldviews may conflict - questions about the nature of faith, the belief in a God or Gods, the authority of sacred texts, the relationship between scientific and religious conceptions of the mind/soul, and the relationship between scientific and religious understandings of moral behavior. My review of these questions will show that they cannot be answered unequivocally because there is no agreement amongst religious believers as to the meaning of important religious concepts. Thus, whether scientific and religious worldviews conflict depends essentially upon whose science and whose religion one is considering. In closing, I consider the implications of this conundrum for science education

Insights from Amphioxus into the Evolution of Vertebrate Cartilage

Central to the story of vertebrate evolution is the origin of the vertebrate head, a problem difficult to approach using paleontology and comparative morphology due to a lack of unambiguous intermediate forms. Embryologically, much of the vertebrate head is derived from two ectodermal tissues, the neural crest and cranial placodes. Recent work in protochordates suggests the first chordates possessed migratory neural tube cells with some features of neural crest cells. However, it is unclear how and when these cells acquired the ability to form cellular cartilage, a cell type unique to vertebrates. It has been variously proposed that the neural crest acquired chondrogenic ability by recruiting proto-chondrogenic gene programs deployed in the neural tube, pharynx, and notochord. To test these hypotheses we examined the expression of 11 amphioxus orthologs of genes involved in neural crest chondrogenesis. Consistent with cellular cartilage as a vertebrate novelty, we find that no single amphioxus tissue co-expresses all or most of these genes. However, most are variously co-expressed in mesodermal derivatives. Our results suggest that neural crest-derived cartilage evolved by serial cooption of genes which functioned primitively in mesoderm

Dogs Discriminate Identical Twins

Earlier studies have shown variation among experimental attempts to establish whether human monozygotic twins that are genetically identical also have identical individual scents. In none of the cases were the dogs able to distinguish all the individual scents of monozygotic twins living in the same environment if the scents were presented to them separately. Ten specially trained police German Shepherd dogs of three Czech Republic Police Regional Headquarters were used for scent identification in our study. The dogs were supposed to match scents of two monozygotic pairs (5 and 7 years old) and two dizygotic twin pairs (8 and 13 years old). Scents were collected on cotton squares stored in glass jars. Dog handlers were blind to the experiment details. In each trial (line-up), one scent was used as a starting scent and the dog was then sent to determine if any of the 7 presented glass jars contained a matching scent. Scents of children of similar ages were used as distractors. In the matching procedure, the dogs matched correctly the scent of one twin with the other, as well as two scents collected from every single identical and non-identical twin to prove their efficacy and likewise, the presence of the matching twin scent in any given glass jar. All dogs in all trials distinguished correctly the scents of identical as well as non-identical twins. All dogs similarly matched positively two scents collected from the same individuals. Our findings indicated that specially trained German Shepherd dogs are able to distinguish individual scents of identical twins despite the fact that they live in the same environment, eat the same food and even if the scents are not presented to them simultaneously

An extension of the benefit segmentation base for the consumption of organic foods : a time perspective

Benefit segmentation is a long-standing marketing approach that emphasises the ‘what’ and ‘how’ dimensions of consumer benefits; that is, what benefits consumers perceive in product/service consumption, and how such benefits are perceived. This research proposes a fresh time-based approach to benefit segmentation – namely, focusing on the ‘when’ element or when in time benefits take effect. Drawing upon a survey of UK consumers, it explains and discusses consumption motivations through examining antecedents of temporally dominated benefits in application to organic food. Specifically, the study investigates why some consumers predominantly seek present-based benefits vis-à-vis future-based benefits or vice versa in organic food purchase and consumption behaviour. Using correlation and regression analyses, the research findings establish significant associations of level of involvement, prior knowledge level, and product usage level, and some association of time orientation with the temporally emphasised consumption benefits consumers ultimately pursue. Overall, the research highlights the added contribution of a time perspective in a benefit segmentation approach which can assist marketers in understanding better and communicating more effectively with consumers through drawing up consumer profiles based on when in time their dominantly pursued benefit for an offering is perceived to take effect

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

<p>Abstract</p> <p>Background</p> <p>Assays of multiple tumor samples frequently reveal recurrent genomic aberrations, including point mutations and copy-number alterations, that affect individual genes. Analyses that extend beyond single genes are often restricted to examining pathways, interactions and functional modules that are already known.</p> <p>Methods</p> <p>We present a method that identifies functional modules without any information other than patterns of recurrent and mutually exclusive aberrations (RME patterns) that arise due to positive selection for key cancer phenotypes. Our algorithm efficiently constructs and searches networks of potential interactions and identifies significant modules (RME modules) by using the algorithmic significance test.</p> <p>Results</p> <p>We apply the method to the TCGA collection of 145 glioblastoma samples, resulting in extension of known pathways and discovery of new functional modules. The method predicts a role for <it>EP300 </it>that was previously unknown in glioblastoma. We demonstrate the clinical relevance of these results by validating that expression of <it>EP300 </it>is prognostic, predicting survival independent of age at diagnosis and tumor grade.</p> <p>Conclusions</p> <p>We have developed a sensitive, simple, and fast method for automatically detecting functional modules in tumors based solely on patterns of recurrent genomic aberration. Due to its ability to analyze very large amounts of diverse data, we expect it to be increasingly useful when applied to the many tumor panels scheduled to be assayed in the near future.</p

Like-minded sources on Facebook are prevalent but not polarizing

Many critics raise concerns about the prevalence of ‘echo chambers’ on social media and their potential role in increasing political polarization. However, the lack of available data and the challenges of conducting large-scale field experiments have made it difficult to assess the scope of the problem 1,2. Here we present data from 2020 for the entire population of active adult Facebook users in the USA showing that content from ‘like-minded’ sources constitutes the majority of what people see on the platform, although political information and news represent only a small fraction of these exposures. To evaluate a potential response to concerns about the effects of echo chambers, we conducted a multi-wave field experiment on Facebook among 23,377 users for whom we reduced exposure to content from like-minded sources during the 2020 US presidential election by about one-third. We found that the intervention increased their exposure to content from cross-cutting sources and decreased exposure to uncivil language, but had no measurable effects on eight preregistered attitudinal measures such as affective polarization, ideological extremity, candidate evaluations and belief in false claims. These precisely estimated results suggest that although exposure to content from like-minded sources on social media is common, reducing its prevalence during the 2020 US presidential election did not correspondingly reduce polarization in beliefs or attitudes

Hypervirulent Clostridium difficile PCR-Ribotypes Exhibit Resistance to Widely Used Disinfectants

The increased prevalence of Clostridium difficile infection (CDI) has coincided with enhanced transmissibility and severity of disease, which is often linked to two distinct clonal lineages designated PCR-ribotype 027 and 017 responsible for CDI outbreaks in the USA, Europe and Asia. We assessed sporulation and susceptibility of three PCR-ribotypes; 012, 017 and 027 to four classes of disinfectants; chlorine releasing agents (CRAs), peroxygens, quaternary ammonium compounds (QAC) and biguanides. The 017 PCR-ribotype, showed the highest sporulation frequency under these test conditions. The oxidizing biocides and CRAs were the most efficacious in decontamination of C. difficile vegetative cells and spores, the efficacy of the CRAs were concentration dependent irrespective of PCR-ribotype. However, there were differences observed in the susceptibility of the PCR-ribotypes, independent of the concentrations tested for Virkon®, Newgenn®, Proceine 40® and Hibiscrub®. Whereas, for Steri7® and Biocleanse® the difference observed between the disinfectants were dependent on both PCR-ribotype and concentration. The oxidizing agent Perasafe® was consistently efficacious across all three PCR ribotypes at varying concentrations; with a consistent five Log10 reduction in spore titre. The PCR-ribotype and concentration dependent differences in the efficacy of the disinfectants in this study indicate that disinfectant choice is a factor for llimiting the survival and transmission of C. difficile spores in healthcare settings