Electron density-based GPT for optimization and suggestion of host-guest binders.

Here we present a machine learning model trained on electron density for the production of host-guest binders. These are read out as simplified molecular-input line-entry system (SMILES) format with >98% accuracy, enabling a complete characterization of the molecules in two dimensions. Our model generates three-dimensional representations of the electron density and electrostatic potentials of host-guest systems using a variational autoencoder, and then utilizes these representations to optimize the generation of guests via gradient descent. Finally the guests are converted to SMILES using a transformer. The successful practical application of our model to established molecular host systems, cucurbit[n]uril and metal-organic cages, resulted in the discovery of 9 previously validated guests for CB[6] and 7 unreported guests (with association constant Ka ranging from 13.5 M-1 to 5,470 M-1) and the discovery of 4 unreported guests for [Pd214]4+ (with Ka ranging from 44 M-1 to 529 M-1).

Radiotherapy as nose preservation treatment strategy for cancer of the nasal vestibule: The Dutch experience.

BACKGROUND AND PURPOSE: Primary radiotherapy is often preferred for early-stage cancer of the nasal vestibule (CNV), combining high disease control with preservation of nasal anatomy. However, due to practice variation and an absence of comparative trials, no consensus exists on preference for brachytherapy (BT) or external beam radiotherapy (EBRT). We compared these modalities in terms of disease control, nose preservation rates and toxicity. MATERIALS AND METHODS: Medical records of 225 patients with T1-T2 squamous cell carcinoma of the nasal vestibule treated with 3D image-guided primary radiotherapy between Jan 2010 and Dec 2016 in 6 Dutch institutions were reviewed retrospectively. RESULTS: 153 of 225 patients were treated with BT, 65 with EBRT and 7 with other modalities. Median follow-up was 46 months. Overall 3-year local control (LC) and regional control (RC) were 87% and 89%. Five-year disease-specific survival (DSS) and overall survival (OS) were 94% and 82%. Three-year survival with preserved nose (SPN) was 76%. BT provided higher 3-year LC (95% vs 71%, p < 0.01) and SPN compared with EBRT (82% vs 61%, p < 0.01). Multivariable and propensity-score-matched cohort analyses confirmed better outcomes after BT. No difference was seen in DSS or OS. Five-year incidence of CTCAE 5.0 grade ≥2 toxicity was higher after BT (20% vs 3%, p = 0.03) and consisted mostly of radiation ulcers. 50% of all late toxicity recovered. CONCLUSION: In this largest-to-date multicenter analysis of T1-T2 CNV, BT achieved superior LC and SPN compared with EBRT. Grade 1-2 radiation ulcers occurred more frequently after brachytherapy, but were transient in half the cases. Considering these results, BT can be recommended as first-line treatment for T1-T2 CNV.

Image Guided Brachytherapy for Cancer of the Nasal Vestibule: Local Control and Cosmesis.

PURPOSE: To evaluate the efficacy of modern image guided brachytherapy for squamous cell carcinoma of the nasal vestibule, to explore tumor volume as a prognostic factor for local and regional recurrence, and to assess patient satisfaction with nasal function and appearance after treatment. METHODS AND MATERIALS: In a retrospective analysis, we reviewed the medical records of 102 patients with Wang T1-T2 nasal vestibule cancer treated at a single institution with brachytherapy as the sole treatment. Median follow-up time was 42 months (range, 3-210 months). A patient satisfaction study using the validated Nasal Appearance and Function Evaluation Questionnaire was conducted among 42 patients more than 1 year after treatment. A statistically significant cutoff point for tumor volume as a prognostic factor of local control was established using Youden's index method. RESULTS: Seventy-seven of 102 patients were treated with interstitial implants, and 25 patients were treated by an intracavitary mould technique. The 5-year control rates were 95%, 91%, and 83% for local, regional, and locoregional control, respectively. Tumor volume ≥2.3 cm3 resulted in worse 3-year regional control compared to tumor volume <2.3 cm3 (62% vs 96%; P = .01). Ultimate regional control after salvage treatment was 96%, with no significant difference observed between subgroups by tumor volume (92% for ≥2.3 cm3 vs 96% for <2.3 cm3; P = .57). Three patients with regional failure developed distant metastases. Five-year disease-specific survival and overall survival were 94% and 74%, respectively. Patient-assessed cosmetic and functional satisfaction were both rated high (mean 3.7 and 4.0 of 5, respectively). CONCLUSION: We report the largest cohort to date treated with brachytherapy as the sole treatment for nasal vestibule carcinoma. Brachytherapy offers excellent local control for Wang T1-T2 tumors with high patient satisfaction. Tumor volume is an adequate predictive factor for patients at risk of regional recurrence, but ultimate control rates after salvage treatment are high. Therefore, we do not recommend elective treatment of the neck.

Propagation of Oscillating Chemical Signals through Reaction Networks.

Akin to electronic systems that can tune to and process signals of select frequencies, systems/networks of chemical reactions also "propagate" time-varying concentration inputs in a frequency-dependent manner. Whereas signals of low frequencies are transmitted, higher frequency inputs are dampened and converted into steady-concentration outputs. Such behavior is observed in both idealized reaction chains as well as realistic signaling cascades, in the latter case explaining the experimentally observed responses of such cascades to input calcium oscillations. These and other results are supported by numerical simulations within the freely available Kinetix web application we developed to study chemical systems of arbitrary architectures, reaction kinetics, and boundary conditions.

Discovery and Enumeration of Organic-Chemical and Biomimetic Reaction Cycles within the Network of Chemistry.

Analysis of the chemical-organic knowledge represented as a giant network reveals that it contains millions of reaction sequences closing into cycles. Without realizing it, independent chemists working at different times have jointly created examples of cyclic sequences that allow for the recovery of useful reagents and for the autoamplification of synthetically important molecules, those that mimic biological cycles, and those that can be operated one-pot.

Self-Terminating Confinement Approach for Large-Area Uniform Monolayer Graphene Directly over Si/SiOx by Chemical Vapor Deposition.

To synthesize graphene by chemical vapor deposition (CVD) both in large area and with uniform layer number directly over Si/SiOx has proven challenging. The use of catalytically active metal substrates, in particular Cu, has shown far greater success and therefore is popular. That said, for electronics applications it requires a transfer procedure, which tends to damage and contaminate the graphene. Thus, the direct fabrication of uniform graphene on Si/SiOx remains attractive. Here we show a facile confinement CVD approach in which we simply "sandwich" two Si wafers with their oxide faces in contact to form uniform monolayer graphene. A thorough examination of the material reveals it comprises faceted grains despite initially nucleating as round islands. Upon clustering, they facet to minimize their energy. This behavior leads to faceting in polygons, as the system aims to ideally form hexagons, the lowest energy form, much like the hexagonal cells in a beehive, which requires the minimum wax. This process also leads to a near minimal total grain boundary length per unit area. This fact, along with the high graphene quality, is reflected in its electrical performance, which is highly comparable with graphene formed over other substrates, including Cu. In addition, the graphene growth is self-terminating. Our CVD approach is easily scalable and will make graphene formation directly on Si wafers competitive against that from metal substrates, which suffer from transfer. Moreover, this CVD route should be applicable for the direct synthesis of other 2D materials and their van der Waals heterostructures.

Hypermethylation of E-cadherin is an independent predictor of improved survival in head and neck squamous cell carcinoma.

BACKGROUND: The loss of E-cadherin (ECAD) protein expression has been linked to aggressive head and neck squamous cell carcinoma (HNSCC). Promoter hypermethylation of the cadherin 1, type 1 (CDH1) gene (encoding ECAD) is 1 mechanism by which this protein can be inactivated, although this epigenetic alteration of the gene has not been linked conclusively to poorer patient outcome and, in fact, may be associated with better patient prognosis. METHODS: The authors investigated the prevalence of CDH1 promoter hypermethylation in a population-based case series of 340 primary HNSCC tumors using methylation-specific polymerase chain reaction. They also studied the association between CDH1 hypermethylation and patient demographic characteristics using multivariate analysis and examined the impact of CDH1 hypermethylation on patient survival using both univariate and multivariate methods. RESULTS: Hypermethylation of CDH1 was significantly more prevalent (P < .03) among individuals with a low smoking history independent of whether they were seropositive for human papillomavirus type 16 (HPV-16). Patients who had tumors with CDH1 hypermethylation had significantly better overall survival compared with patients who had tumors without hypermethylation (P < .02; log-rank test). This effect was independent of HPV-16 status and demonstrated a significant hazard ratio of 0.5 (95% confidence interval, 0.3-0.9) in a model that controlled for HPV-16 serology, age, sex, and tumor stage. CONCLUSIONS: The current results suggested that hypermethylation of CDH1 occurs more commonly in patients with HNSCC who are low smokers, suggesting that an additional factor may be driving this epigenetic alteration. Clinically, CDH1 hypermethylation may hold powerful prognostic potential in addition to that observed with HPV serology, and the authors concluded that it should be pursued in additional studies.

Agreement between contemporaneously recorded and subsequently recalled time spent outdoors: implications for environmental exposure studies.

PURPOSE: The aim of the study is to evaluate the agreement between contemporaneously recorded and subsequently recalled time spent outdoors during 1 week among members of an occupational cohort. METHODS: One hundred twenty-five radiologic technologists from northern and southern geographic areas in the United States recorded time spent outdoors for 7 consecutive days in a daily diary. Six months later, study participants completed a mailed self-administered questionnaire of the number of outdoor hours during the same 7-day period. We tested the agreement between questionnaire responses and diary entries. Logistic regression models were used to identify variables significantly affecting agreement. RESULTS: Time spent outdoors comprised one fifth of the total time recorded in the diaries. Agreement (weighted kappa [kappa(w)]) between reported outdoor time during weekdays (kappa(w) = 0.49; 95% confidence interval [CI], 0.39-0.59) was significantly (p < 0.05) higher than for weekends (kappa(w) = 0.23; 95% CI, 0.12-0.34). Similarly, agreement was lower for weekends compared with weekdays in multivariate analyses, reaching statistical significance (p = 0.05) in only the southern regions. CONCLUSIONS: Although our investigation was carried out among volunteers from the US radiologic technologist cohort, we believe retrospective questionnaires may be more accurate in reporting time spent outdoors for weekdays compared with weekends in any group of indoor workers. These differences have implications for the wording in future questionnaires about time spent outdoors and level and sources of uncertainty characterizing estimated time spent outdoors on weekdays versus weekend days.

Selection in a cycling population: differential response among skeletal traits.

Population density cycles influence phenotypic evolution through both density-dependent selection during periods of high density and through enhanced genetic drift during periods of low density. We investigated the response of different phenotypic traits to the same density cycles in a population of the yellow-necked mouse, Apodemus flavicollis, from Bialowieza National Park in Poland. We examined nonmetric skull traits, skull and mandible size, skull and mandible shape, and transferrin allele frequencies. We found that all of the traits changed significantly over the seven-year study period. The greatest changes in nonmetric traits and mandible size occurred during periods of increasing density, and the magnitude of changes in skull and mandible shape was correlated with the magnitude of density changes. Frequencies of transferrin alleles changed the most when population density was in decline. Changes among the five phenotypic traits were generally uncorrelated with one another, except for skull and mandible shape. Nonmetric traits were selectively neutral when assessed with Q(ST)/F(ST) analysis, whereas mandible size, mandible shape, and skull shape showed evidence of fairly strong selection. Selection on skull size was weak or nonexistent. We discuss how different assumptions about the genetic components of variance affect Q(ST) estimates when phenotypic variances are substituted for genetic ones. We also found that change in mandible size, mandible shape, skull size, and skull shape were greater than expected under a neutral model given reasonable assumptions about heritability and effective population size.

Gains and losses of DNA sequences in childhood brain tumors analyzed by comparative genomic hybridization.

Primary central nervous system neoplasms are the most common solid tumors in children. Genetic changes underlying childhood brain-tumor development and progression are incompletely characterized. To get an overview of the genetic events leading to the development of brain tumors and to identify chromosomal regions that may contain genes important in brain-tumor progression, we employed a comparative genomic hybridization technique. Twenty-four pediatric primary brain tumors were analyzed in this study. DNA copy number changes were observed in most of the samples (79%), and almost all chromosomes were involved. The total number of genetic aberrations (copy-number gains and losses per tumor) was significantly higher in the cerebellar primitive neuroectodermal tumor subgroup than in the gliomas. The high-grade tumors had more DNA changes than did the low-grade tumors. The most often gained chromosomes were: 6q (45%), 4q (34.5%), and chromosome 1 (24% of the cases). The minimal common regions involved in DNA gains were narrowed down to 6q14-16 and 4q26-28. Losses of a specific chromosome (partly or as a whole) occurred on average in 7% of the cases. Chromosomal regions that were most often lost included chromosome 1 (17%), chromosome 16 (17%), and chromosome 2 (14%). These findings suggest that genes localized to these minimal common chromosomal regions play a role in the tumorogenesis of childhood brain tumors. Our results indicate: (1) a great degree of genomic imbalance in these tumors; (2) that a high number of aberrations correlate with aggressive tumor biology; (3) and that nonrandom genetic changes may be associated with particular tumor types.

Taming the "no-show" tiger: decreasing the rate of absenteeism at educational programs.

A multidisciplinary staff development department developed a continuous quality improvement project to study the consistently high absentee rate for scheduled training and its relationship to the class registration process. Data were collected using a 9-question survey of students who failed to attend scheduled training. Findings show that changes to the class registration process resulted in a decrease in the number of absentees under the control of the staff development department from an average of 43% to 6% by the end of the year-long review period. The overall absentee rate stabilized at 20% and has been established as the benchmark for this setting.

Automated external defibrillators: prehospital use in advanced cardiac life support.

It is evident that AEDs may be used by minimally trained first responders to terminate VF safely and rapidly in victims of out-of-hospital cardiac arrest. To enhance patient survival of out-of-hospital VF, there must be coordination between AED-trained first responders and ACLS providers.

Nursing management of hypothermia in the multiple-trauma patient.

Hypothermia is a common complication occurring in seriously injured patients. Emergency department and prehospital protocols governing the care of trauma patients should include the assessment of core temperature and the management of hypothermia so that it does not go unrecognized and untreated.