wfl Python toolkit for creating machine learning interatomic potentials and related atomistic simulation workflows.

Predictive atomistic simulations are increasingly employed for data intensive high throughput studies that take advantage of constantly growing computational resources. To handle the sheer number of individual calculations that are needed in such studies, workflow management packages for atomistic simulations have been developed for a rapidly growing user base. These packages are predominantly designed to handle computationally heavy ab initio calculations, usually with a focus on data provenance and reproducibility. However, in related simulation communities, e.g., the developers of machine learning interatomic potentials (MLIPs), the computational requirements are somewhat different: the types, sizes, and numbers of computational tasks are more diverse and, therefore, require additional ways of parallelization and local or remote execution for optimal efficiency. In this work, we present the atomistic simulation and MLIP fitting workflow management package wfl and Python remote execution package ExPyRe to meet these requirements. With wfl and ExPyRe, versatile atomic simulation environment based workflows that perform diverse procedures can be written. This capability is based on a low-level developer-oriented framework, which can be utilized to construct high level functionality for user-friendly programs. Such high level capabilities to automate machine learning interatomic potential fitting procedures are already incorporated in wfl, which we use to showcase its capabilities in this work. We believe that wfl fills an important niche in several growing simulation communities and will aid the development of efficient custom computational tasks.

Machine-learned acceleration for molecular dynamics in CASTEP.

Machine learning (ML) methods are of rapidly growing interest for materials modeling, and yet, the use of ML interatomic potentials for new systems is often more demanding than that of established density-functional theory (DFT) packages. Here, we describe computational methodology to combine the CASTEP first-principles simulation software with the on-the-fly fitting and evaluation of ML interatomic potential models. Our approach is based on regular checking against DFT reference data, which provides a direct measure of the accuracy of the evolving ML model. We discuss the general framework and the specific solutions implemented, and we present an example application to high-temperature molecular-dynamics simulations of carbon nanostructures. The code is freely available for academic research.

Rectal and colon cancer: Not just a different anatomic site.

Due to differences in anatomy, primary rectal and colon cancer require different staging procedures, different neo-adjuvant treatment and different surgical approaches. For example, neoadjuvant radiotherapy or chemoradiotherapy is administered solely for rectal cancer. Neoadjuvant therapy and total mesorectal excision for rectal cancer might be responsible in part for the differing effect of adjuvant systemic treatment on overall survival, which is more evident in colon cancer than in rectal cancer. Apart from anatomic divergences, rectal and colon cancer also differ in their embryological origin and metastatic patterns. Moreover, they harbor a different composition of drug targets, such as v-raf murine sarcoma viral oncogene homolog B (BRAF), which is preferentially mutated in proximal colon cancers, and the epidermal growth factor receptor (EGFR), which is prevalently amplified or overexpressed in distal colorectal cancers. Despite their differences in metastatic pattern, composition of drug targets and earlier local treatment, metastatic rectal and colon cancer are, however, commonly regarded as one entity and are treated alike. In this review, we focused on rectal cancer and its biological and clinical differences and similarities relative to colon cancer. These aspects are crucial because they influence the current staging and treatment of these cancers, and might influence the design of future trials with targeted drugs.

Evaluation of short-course radiotherapy followed by neoadjuvant bevacizumab, capecitabine, and oxaliplatin and subsequent radical surgical treatment in primary stage IV rectal cancer.

BACKGROUND: To evaluate the efficacy and tolerability of preoperative short-course radiotherapy followed by capecitabine and oxaliplatin treatment in combination with bevacizumab and subsequent radical surgical treatment of all tumor sites in patients with stage IV rectal cancer. PATIENTS AND METHODS: Adults with primary metastasized rectal cancer were enrolled. They received radiotherapy (5 × 5 Gy) followed by bevacizumab (7.5 mg/kg, day 1) and oxaliplatin (130 mg/m(2), day 1) intravenously and capecitabine (1000 mg/m(2) twice daily orally, days 1-14) for up to six cycles. Surgery was carried out 6-8 weeks after the last bevacizumab dose. The percentage of radical surgical treatment, 2-year survival and recurrence rates, and treatment-related toxicity was evaluated. RESULTS: Of 50 included patients, 42 (84%) had liver metastases, 5 (10%) lung metastases, and 3 (6%) both liver and lung metastases. Radical surgical treatment was possible in 36 (72%) patients. The 2-year overall survival rate was 80% [95% confidence interval (CI) 66.3%-90.0%]. The 2-year recurrence rate was 64% (95% CI 49.8%-84.5%). Toxic effects were tolerable. No treatment-related deaths occurred. CONCLUSIONS: Radical surgical treatment of all tumor sites carried out after short-course radiotherapy, and bevacizumab-capecitabine-oxaliplatin combination therapy is a feasible and potentially curative approach in primary metastasized rectal cancer.

[Polysomnography in the prevention of crib death]. / A polysomnographia helye a bölcsóhalál megelözésében.

The authors stress the importance of polysomnography--a new electrophysiologic method--in the prevention of SIDS (cot death). SIDS is the most important and frequent cause of infant mortality between 1 and 12 months of age in western countries (nowadays between 1-2/1000!). In Hungary the frequency is not so high. In the last few years the incidence declined after the "back to sleep" campaigns, but to reach further success, it is very important to seek the so called "risk" babies. The unique cause of cot death is not yet understood exactly, but some instability in respiration (mostly during the sleep) is one of the accepted principal basic factors. The mentioned new method helps in choosing the SIDS risk infants from the "normal" population, allows to examine their respiratory irregularity or even disorders during the sleep and gives possibility for the prevention of lethal apneas. The authors describe the details of the prevention in case of abnormal polysomnography in their other publications.

[Paracetamol poisoning in infancy--is paracetamol safe?]. / Csecsemökori paracetamol mérgezés--veszélytelen-e a paracetamol?

A 5-month-old baby was observed. At the severely ill infant accidental misadministration of Paracetamol was verified. After surveying the literature the authors discussed the possible pathobiochemical ways and draw attention to the dangers of the misuse of antipyretics.