Metrics for measuring distances in configuration spaces

In order to characterize molecular structures we introduce configurational fingerprint vectors which are counterparts of quantities used experimentally to identify structures. The Euclidean distance between the configurational fingerprint vectors satisfies the properties of a metric and can therefore safely be used to measure dissimilarities between configurations in the high dimensional configuration space. We show that these metrics correlate well with the RMSD between two configurations if this RMSD is obtained from a global minimization over all translations, rotations and permutations of atomic indices. We introduce a Monte Carlo approach to obtain this global minimum of the RMSD between configurations

Minima Hopping Guided Path Search: An Efficient Method for Finding Complex Chemical Reaction Pathways

The Minima Hopping global optimization method uses physically realizable molecular dynamics moves in combination with an energy feedback that guarantees the escape from any potential energy funnel. For the purpose of finding reactions pathways, we argue that Minima Hopping is particularly suitable as a guide through the potential energy landscape and as a generator for pairs of minima that can be used as input structures for methods capable of finding transition states between two minima. For Lennard-Jones benchmark systems we compared this Minima Hopping guided path search method to a known approach for the exploration of potential energy landscapes that is based on deterministic mode-following. Although we used a stabilized mode-following technique that reliably allows to follow distinct directions when escaping from a local minimum, we observed that Minima Hopping guided path search is far superior in finding lowest-barrier reaction pathways. We therefore suggest that Minima Hopping guided path search can be used as a simple and efficient way to identify energetically low-lying chemical reaction pathways. Finally we applied the Minima Hopping guided path search approach to 75-atom and 102-atom Lennard Jones systems. For the 75-atom system we found pathways whose highest energies are significantly lower than the highest energy along the previously published lowest-barrier pathway. Furthermore, many of these pathways contain a smaller number of intermediate transition states than the previously publish lowest-barrier pathway. In case of the 102-atom system Minima Hopping guided path search found a previously unknown and energetically low-lying funnel.Comment: 15 pages, 8 figure

Aphasia and the Diagram Makers Revisited: an Update of Information Processing Models

Aphasic syndromes from diseases such as stroke and degenerative disorders are still common and disabling neurobehavioral disorders. Diagnosis, management and treatment of these communication disorders are often dependent upon understanding the neuropsychological mechanisms that underlie these disorders. Since the work of Broca it has been recognized that the human brain is organized in a modular fashion. Wernicke realized that the types of signs and symptoms displayed by aphasic patients reflect the degradation or disconnection of the modules that comprise this speech-language network. Thus, he was the first to propose a diagrammatic or information processing model of this modular language-speech network. Since he first published this model many new aphasic syndromes have been discovered and this has led to modifications of this model. This paper reviews some of the early (nineteenth century) models and then attempts to develop a more up-to-date and complete model

The End of the Rainbow: What Can We Say About the Extragalactic Sub-Megahertz Radio Sky?

The Galactic disc is opaque to radio waves from extragalactic sources with frequencies nu less than ~3 MHz. However, radio waves with kHz, Hz, and even lower frequencies may propagate through the intergalactic medium (IGM). I argue that the presence of these waves can be inferred by using the Universe as our detector. I discuss possible sub-MHz sources and set new non-trivial upper limits on the energy density of sub-MHz radio waves in galaxy clusters and the average cosmic background. Limits based on five effects are considered: (1) changes in the expansion of the Universe from the radiation energy density (2) heating of the IGM by free-free absorption; (3) radiation pressure squeezing of IGM clouds by external radio waves; (4) synchrotron heating of electrons in clusters; and (5) Inverse Compton upscattering of sub-MHz radio photons. Any sub-MHz background must have an energy density much smaller than the CMB at frequencies below 1 MHz. The free-free absorption bounds from the Lyman-alpha forest are potentially the strongest, but are highly dependent on the properties of sub-MHz radio scattering in the IGM. I estimate an upper limit of 6 * 10^4 L_sun Mpc^-3 for the emissivity within Lyman-alpha forest clouds in the frequency range 5 - 200 Hz. The sub-MHz energy density in the Coma cluster is constrained to be less than ~10^-15 erg cm^-3. At present, none of the limits is strong enough to rule out a maximal T_b = 10^12 K sub-MHz synchrotron background, but other sources may be constrained with a better knowledge of sub-MHz radio propagation in the IGM.Comment: Accepted by MNRAS, 4 figures, 20 pages

MAPKinase inhibition after failure of immune checkpoint blockade in patients with advanced melanoma – an evaluation of the multicenter prospective skin cancer registry ADOREG

Objectives: Forty to sixty percent of patients with advanced melanoma show primary resistance to PD-1-based immunotherapy, 30-40% of initial responders also progress. Here, we evaluated the outcome of second-line targeted therapy (TT) after progression on PD-1-based immune checkpoint inhibition (ICI) in BRAFV600-mutated melanoma. In addition, we report data on the activity of re-exposure with PD-1-based regimes. Methods: Patients with advanced (non- resectable stage III or IV, AJCC 2017, 8th edition) melanoma progressing on PD-1-based ICI (nivolumab, pembrolizumab or ipilimumab plus nivolumab) and receiving second-line BRAF plus MEK inhibition were identified from the prospective multicenter skin cancer registry ADOREG. Results: We identified 108 patients with unresectable stage III or stage IV melanoma progressing on first-line ICI (nivolumab, pembrolizumab or ipilimumab plus nivolumab) and receiving second-line combined BRAF/MEK inhibition. Seventy- three percent of the cohort presented with primary PD-1 resistant disease. Median progression-free survival ( PFS) on ICI was 2.6 (95% CI 2.2-2.9) months. Median PFS on subsequent TT was 6.6 (95% CI 5.4 -7.8) months. Median OS from start of second-line TT was 16.0 (95% CI 11.2-20.8) months. The 3-year PFS and OS rates on second-line TT were 16% and 30%. The objective response rate (ORR) and disease control rate (DCR) to TT were 42.6% and 55.6%. In patients with brain metastases, the ORR and DCR were 31.4% and 43.1%. Patients without brain metastases showed an ORR and DCR of 52.6% and 66.7%, respectively. Response to first-line ICI was associated with a numerically higher ORR and DCR to second-line TT and improved OS on TT. Twenty-three patients received third-line ICI of whom two patients showed an objective response. Conclusions: BRAF plus MEK inhibition shows meaningful activity and outcome in patients with advanced melanoma resistant to anti-PD-1- based immunotherapy. Rates of long- term benefit and survival in our study were similar to those reported for treatment-naive patients receiving first-line MAPKi

Fire ant social chromosomes: Differences in number, sequence and expression of odorant binding proteins.

Variation in social behavior is common yet our knowledge of the mechanisms underpinning its evolution is limited. The fire ant Solenopsis invicta provides a textbook example of a Mendelian element controlling social organization: alternate alleles of a genetic element first identified as encoding an odorant binding protein (OBP) named Gp-9 determine whether a colony accepts one or multiple queens. The potential roles of such a protein in perceiving olfactory cues and evidence of positive selection on its amino acid sequence made it an appealing candidate gene. However, we recently showed that recombination is suppressed between Gp-9 and hundreds of other genes as part of a >19 Mb supergene-like region carried by a pair of social chromosomes. This finding raises the need to reassess the potential role of Gp-9. We identify 23 OBPs in the fire ant genome assembly, including nine located in the region of suppressed recombination with Gp-9. For six of these, the alleles carried by the two variants of the supergene-like region differ in protein-coding sequence and thus likely in function, with Gp-9 showing the strongest evidence of positive selection. We identify an additional OBP specific to the Sb variant of the region. Finally, we find that 14 OBPs are differentially expressed between single- and multiple-queen colonies. These results are consistent with multiple OBPs playing a role in determining social structure

Brain metastasis and survival outcomes after first-line therapy in metastatic melanoma: a multicenter DeCOG study on 1704 patients from the prospective skin cancer registry ADOREG

Background Despite the availability of effective systemic therapies, a significant number of advanced melanoma patients develops brain metastases. This study investigated differences in incidence and time to diagnosis of brain metastasis and survival outcomes dependent on the type of first-line therapy.Methods Patients with metastatic, non-resectable melanoma (AJCCv8 stage IIIC–V) without brain metastasis at start of first-line therapy (1L-therapy) were identified from the prospective multicenter real-world skin cancer registry ADOREG. Study endpoints were incidence of brain metastasis, brain metastasis-free survival (BMFS), progression-free survival (PFS), and overall survival (OS).Results Of 1704 patients, 916 were BRAF wild-type (BRAFwt) and 788 were BRAF V600 mutant (BRAFmut). Median follow-up time after start of 1L-therapy was 40.4 months. BRAFwt patients received 1L-therapy with immune checkpoint inhibitors (ICI) against CTLA-4+PD-1 (n=281) or PD-1 (n=544). In BRAFmut patients, 1L-therapy was ICI in 415 patients (CTLA-4+PD-1, n=108; PD-1, n=264), and BRAF+MEK targeted therapy (TT) in 373 patients. After 24 months, 1L-therapy with BRAF+MEK resulted in a higher incidence of brain metastasis compared with PD-1±CTLA-4 (BRAF+MEK, 30.3%; CTLA-4+PD-1, 22.2%; PD-1, 14.0%). In multivariate analysis, BRAFmut patients developed brain metastases earlier on 1L-therapy with BRAF+MEK than with PD-1±CTLA-4 (CTLA-4+PD-1: HR 0.560, 95% CI 0.332 to 0.945, p=0.030; PD-1: HR 0.575, 95% CI 0.372 to 0.888, p=0.013). Type of 1L-therapy, tumor stage, and age were independent prognostic factors for BMFS in BRAFmut patients. In BRAFwt patients, tumor stage was independently associated with longer BMFS; ECOG Performance status (ECOG-PS), lactate dehydrogenase (LDH), and tumor stage with OS. CTLA-4+PD-1 did not result in better BMFS, PFS, or OS than PD-1 in BRAFwt patients. For BRAFmut patients, multivariate Cox regression revealed ECOG-PS, type of 1L-therapy, tumor stage, and LDH as independent prognostic factors for PFS and OS. 1L-therapy with CTLA-4+PD-1 led to longer OS than PD-1 (HR 1.97, 95% CI 1.122 to 3.455, p=0.018) or BRAF+MEK (HR 2.41, 95% CI 1.432 to 4.054, p=0.001), without PD-1 being superior to BRAF+MEK.Conclusions In BRAFmut patients 1L-therapy with PD-1±CTLA-4 ICI resulted in a delayed and less frequent development of brain metastasis compared with BRAF+MEK TT. 1L-therapy with CTLA-4+PD-1 showed superior OS compared with PD-1 and BRAF+MEK. In BRAFwt patients, no differences in brain metastasis and survival outcomes were detected for CTLA-4+PD-1 compared with PD-1

The German National Registry of Primary Immunodeficiencies (2012-2017)

Introduction: The German PID-NET registry was founded in 2009, serving as the first national registry of patients with primary immunodeficiencies (PID) in Germany. It is part of the European Society for Immunodeficiencies (ESID) registry. The primary purpose of the registry is to gather data on the epidemiology, diagnostic delay, diagnosis, and treatment of PIDs. Methods: Clinical and laboratory data was collected from 2,453 patients from 36 German PID centres in an online registry. Data was analysed with the software Stata® and Excel. Results: The minimum prevalence of PID in Germany is 2.72 per 100,000 inhabitants. Among patients aged 1–25, there was a clear predominance of males. The median age of living patients ranged between 7 and 40 years, depending on the respective PID. Predominantly antibody disorders were the most prevalent group with 57% of all 2,453 PID patients (including 728 CVID patients). A gene defect was identified in 36% of patients. Familial cases were observed in 21% of patients. The age of onset for presenting symptoms ranged from birth to late adulthood (range 0–88 years). Presenting symptoms comprised infections (74%) and immune dysregulation (22%). Ninety-three patients were diagnosed without prior clinical symptoms. Regarding the general and clinical diagnostic delay, no PID had undergone a slight decrease within the last decade. However, both, SCID and hyper IgE- syndrome showed a substantial improvement in shortening the time between onset of symptoms and genetic diagnosis. Regarding treatment, 49% of all patients received immunoglobulin G (IgG) substitution (70%—subcutaneous; 29%—intravenous; 1%—unknown). Three-hundred patients underwent at least one hematopoietic stem cell transplantation (HSCT). Five patients had gene therapy. Conclusion: The German PID-NET registry is a precious tool for physicians, researchers, the pharmaceutical industry, politicians, and ultimately the patients, for whom the outcomes will eventually lead to a more timely diagnosis and better treatment

Examining the generalizability of research findings from archival data

This initiative examined systematically the extent to which a large set of archival research findings generalizes across contexts. We repeated the key analyses for 29 original strategic management effects in the same context (direct reproduction) as well as in 52 novel time periods and geographies; 45% of the reproductions returned results matching the original reports together with 55% of tests in different spans of years and 40% of tests in novel geographies. Some original findings were associated with multiple new tests. Reproducibility was the best predictor of generalizability—for the findings that proved directly reproducible, 84% emerged in other available time periods and 57% emerged in other geographies. Overall, only limited empirical evidence emerged for context sensitivity. In a forecasting survey, independent scientists were able to anticipate which effects would find support in tests in new samples