Automated reconstruction of ancient languages using probabilistic models of sound change.

One of the oldest problems in linguistics is reconstructing the words that appeared in the protolanguages from which modern languages evolved. Identifying the forms of these ancient languages makes it possible to evaluate proposals about the nature of language change and to draw inferences about human history. Protolanguages are typically reconstructed using a painstaking manual process known as the comparative method. We present a family of probabilistic models of sound change as well as algorithms for performing inference in these models. The resulting system automatically and accurately reconstructs protolanguages from modern languages. We apply this system to 637 Austronesian languages, providing an accurate, large-scale automatic reconstruction of a set of protolanguages. Over 85% of the system's reconstructions are within one character of the manual reconstruction provided by a linguist specializing in Austronesian languages. Being able to automatically reconstruct large numbers of languages provides a useful way to quantitatively explore hypotheses about the factors determining which sounds in a language are likely to change over time. We demonstrate this by showing that the reconstructed Austronesian protolanguages provide compelling support for a hypothesis about the relationship between the function of a sound and its probability of changing that was first proposed in 1955.

One-Shot GW Transport Calculations: A Charge-Conserving Solution.

Transport measurements are a common method of characterizing small systems in chemistry and physics. When interactions are negligible, the current through submicrometer structures can be obtained using the Landauer formula. Meir and Wingreen derived an exact expression for the current in the presence of interactions. This powerful tool requires knowledge of the exact Green's function. Alternatively, self-consistent approximations for the Green's function are frequently sufficient for calculating the current while crucially satisfying all conservation laws. We provide here yet another alternative, circumventing the high computational cost of these methods. We present expressions for the electric and thermal currents in which the lowest-order self-energy is summed to all orders (one-shot GW approximation). We account for both self-energy and vertex corrections such that current is conserved. Our formulas for the currents capture important features due to interactions and, hence, provide a powerful tool for cases in which the exact solution cannot be found.

The Cortical Representation of Language Timescales is Shared between Reading and Listening.

Language comprehension involves integrating low-level sensory inputs into a hierarchy of increasingly high-level features. Prior work studied brain representations of different levels of the language hierarchy, but has not determined whether these brain representations are shared between written and spoken language. To address this issue, we analyzed fMRI BOLD data recorded while participants read and listened to the same narratives in each modality. Levels of the language hierarchy were operationalized as timescales, where each timescale refers to a set of spectral components of a language stimulus. Voxelwise encoding models were used to determine where different timescales are represented across the cerebral cortex, for each modality separately. These models reveal that between the two modalities timescale representations are organized similarly across the cortical surface. Our results suggest that, after low-level sensory processing, language integration proceeds similarly regardless of stimulus modality.

Role of masks, testing and contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia.

OBJECTIVES: The early stages of the COVID-19 pandemic illustrated that SARS-CoV-2, the virus that causes the disease, has the potential to spread exponentially. Therefore, as long as a substantial proportion of the population remains susceptible to infection, the potential for new epidemic waves persists even in settings with low numbers of active COVID-19 infections, unless sufficient countermeasures are in place. We aim to quantify vulnerability to resurgences in COVID-19 transmission under variations in the levels of testing, tracing and mask usage. SETTING: The Australian state of New South Wales (NSW), a setting with prolonged low transmission, high mobility, non-universal mask usage and a well-functioning test-and-trace system. PARTICIPANTS: None (simulation study). RESULTS: We find that the relative impact of masks is greatest when testing and tracing rates are lower and vice versa. Scenarios with very high testing rates (90% of people with symptoms, plus 90% of people with a known history of contact with a confirmed case) were estimated to lead to a robustly controlled epidemic. However, across comparable levels of mask uptake and contact tracing, the number of infections over this period was projected to be 2-3 times higher if the testing rate was 80% instead of 90%, 8-12 times higher if the testing rate was 65% or 30-50 times higher with a 50% testing rate. In reality, NSW diagnosed 254 locally acquired cases over this period, an outcome that had a moderate probability in the model (10%-18%) assuming low mask uptake (0%-25%), even in the presence of extremely high testing (90%) and near-perfect community contact tracing (75%-100%), and a considerably higher probability if testing or tracing were at lower levels. CONCLUSIONS: Our work suggests that testing, tracing and masks can all be effective means of controlling transmission. A multifaceted strategy that combines all three, alongside continued hygiene and distancing protocols, is likely to be the most robust means of controlling transmission of SARS-CoV-2.

Rising out-of-pocket costs threaten an already vulnerable population: an introduction to the PAN Foundation and AJMC collaborative supplement.

This supplement showcases the winning papers from the PAN Challenge, which aimed to foster conversations about how to rein in out-of-pocket costs to eliminate barriers between patients and their critical medical treatments.

The increasing need for the safety net: an introduction to the Patient Access Network Foundation and AJMC collaborative supplement.

This supplement showcases the winning papers and case studies from the PAN Challenge, which aimed to stimulate a dialogue on ways to reduce or eliminate the barriers and disparities that Medicare and ACA enrollees face in obtaining medications to treat life-threatening, chronic, and rare diseases.

Cleaning and Disinfection of Bacillus cereus Biofilm.

Methodology has been evolving for the testing of disinfectants against bacterial single-species biofilms, as the difficulty of biofilm remediation continues to gain much-needed attention. Bacterial single-species biofilm contamination presents a real risk to good manufacturing practice-regulated industries. However, mixed-species biofilms and biofilms containing bacterial spores remain an even greater challenge for cleaning and disinfection. Among spore-forming microorganisms frequently encountered in pharmaceutical manufacturing areas, the spores of Bacillus cereus are often determined to be the hardest to disinfect and eradicate. One of the reasons for the low degree of susceptibility to disinfection is the ability of these spores to be encapsulated within an exopolysachharide biofilm matrix. In this series of experiments, we evaluated the disinfectant susceptibility of B. cereus biofilms relative to disassociated B. cereus spores and biofilm from a non-spore-forming species. Further, we assessed the impact that pre-cleaning has on increasing that susceptibility. LAY ABSTRACT: Methodology has been evolving for the testing of disinfectants against bacterial single-species biofilms, as the difficulty of biofilm remediation continues to gain much-needed attention. Bacterial single-species biofilm contamination presents a real risk to good manufacturing practice-regulated industries. However, mixed-species biofilms and biofilms containing bacterial spores remain an even greater challenge for cleaning and disinfection. Among spore-forming microorganisms frequently encountered in pharmaceutical manufacturing areas, the spores of Bacillus cereus are often determined to be the hardest to disinfect and eradicate. One of the reasons for the low degree of susceptibility to disinfection is the ability of these spores to be encapsulated within an exopolysachharide biofilm matrix. In this series of experiments, we evaluated the disinfectant susceptibility of B. cereus biofilms relative to disassociated B. cereus spores and biofilm from a non-spore-forming species. Further, we assessed the impact that pre-cleaning has on increasing that susceptibility.

Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

OBJECTIVE: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. DESIGN: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. RESULTS: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. CONCLUSION: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

The effects of psychotherapy, nefazodone, and their combination on subjective assessment of disturbed sleep in chronic depression.

STUDY OBJECTIVES: The purpose of the study was to compare the effects of psychotherapy, nefazodone, and their combination on subjective measures of sleep in patients with chronic forms of major depression. DESIGN: Participants were randomized to receive 12 weeks of treatment with one of the three interventions. SETTING: The study was conducted in parallel at 12 academic institutions and was approved by the Human Subjects Committee at each site. PARTICIPANTS: 484 adult outpatients (65.29% female) who met DSM-IV criteria for one of three chronic forms of major depression. INTERVENTIONS: Psychotherapy (16-20 sessions) was provided by certified therapists following a standardized treatment manual for Cognitive Behavioral Analysis System of Psychotherapy (CBASP), a variant of cognitive psychotherapy developed for chronic depression. Pharmacotherapy consisted of open-label nefazodone, 300-600 mg per day in two divided doses prescribed by psychiatrists. The clinical management visits were limited to 15-20 minutes and followed a standardized protocol. Combination treatment consisted of both therapies. MEASUREMENTS AND RESULTS: Depression outcome was determined by the 24-item Hamilton Rating Scale for Depression and the 30-item Inventory of Depressive Symptomatology-Self Rating. Sleep outcome was measured prospectively with daily sleep diaries that were completed a week prior to HRSD assessments at baseline and after 1, 2, 3, 4, 8, and 12 weeks of treatment. Although nefazodone alone and CBASP alone had comparable impact on global measures of depression outcome, only monotherapy with nefazodone improved early morning awakening and total sleep time. Significant improvements in sleep quality, time awake after sleep onset, latency to sleep onset, and sleep efficiency were present in each of the three treatment groups. These improvements, however, occurred earlier in the course of treatment for participants receiving nefazodone, alone or in combination with CBASP. CONCLUSIONS: Nefazodone therapy may have a direct impact on disturbed sleep associated with depression beyond what would be expected if the improvements were all a consequence of improved depression.

Analyzing the rate at which languages lose the influence of a common ancestor.

Analyzing the rate at which languages change can clarify whether similarities across languages are solely the result of cognitive biases or might be partially due to descent from a common ancestor. To demonstrate this approach, we use a simple model of language evolution to mathematically determine how long it should take for the distribution over languages to lose the influence of a common ancestor and converge to a form that is determined by constraints on language learning. We show that modeling language learning as Bayesian inference of n binary parameters or the ordering of n constraints results in convergence in a number of generations that is on the order of n log n. We relax some of the simplifying assumptions of this model to explore how different assumptions about language evolution affect predictions about the time to convergence; in general, convergence time increases as the model becomes more realistic. This allows us to characterize the assumptions about language learning (given the models that we consider) that are sufficient for convergence to have taken place on a timescale that is consistent with the origin of human languages. These results clearly identify the consequences of a set of simple models of language evolution and show how analysis of convergence rates provides a tool that can be used to explore questions about the relationship between accounts of language learning and the origins of similarities across languages.

Inactivation of chlorhexidine gluconate on skin by incompatible alcohol hand sanitizing gels.

Incompatibility of leave-on products with an antimicrobial residual can negate the efficacy benefits of chlorhexidine gluconate (CHG) persistence. Two marketed alcohol products containing Carbomer were tested using a pigskin substrate model against Staphylococcus aureus. The CHG residual achieved a 4.22 log(10) reduction (standard deviation [SD] = 0.32) in this study, which was dramatically reduced to a 0.54 (SD = 0.50) and 0.46 (SD = 0.56) after subsequent treatment with incompatible alcohol gel products. A marketed alcohol product containing a nonionic thickener maintained the efficacy of the CHG chemical reservoir (log(10) reduction = 4.26, SD = 0.00). Similar findings were demonstrated when alcohol solutions containing the individual thickening agents were tested as simple formulations. An in vivo test using human forearms and Serratia marcescens similarly demonstrated that the activity of a CHG reservoir (log(10) reduction = 3.73, SD = 0.86) was not reduced by a nonionic thickened product (log(10) reduction = 3.98, SD = 0.72) but was significantly reduced by treatment with alcohol products containing anionic thickeners carbomer (log(10) reduction = -0.32, SD = 0.34) or acrylates/C10-30 alkyl acrylate crosspolymer (log(10) reduction = -0.20, SD = 0.32). The use of anionic thickeners or emulsifiers in leave-on products, including alcohol hand sanitizers, may inactivate the persistent antibacterial activity of CHG.