Computing the homology of groups: the geometric way

In this paper we present several algorithms related with the computation of the homology of groups, from a geometric perspective (that is to say, carrying out the calculations by means of simplicial sets and using techniques of Algebraic Topology). More concretely, we have developed some algorithms which, making use of the effective homology method, construct the homology groups of Eilenberg-MacLane spaces K(G,1) for different groups G, allowing one in particular to determine the homology groups of G. Our algorithms have been programmed as new modules for the Kenzo system, enhancing it with the following new functionalities: - construction of the effective homology of K(G,1) from a given finite free resolution of the group G; - construction of the effective homology of K(A,1) for every finitely generated Abelian group A (as a consequence, the effective homology of K(A,n) is also available in Kenzo, for all n); - computation of homology groups of some 2-types; - construction of the effective homology for central extensions. In addition, an inverse problem is also approached in this work: given a group G such that K(G,1) has effective homology, can a finite free resolution of the group G be obtained? We provide some algorithms to solve this problem, based on a notion of norm of a group, allowing us to control the convergence of the process when building such a resolution

Single-molecule conductance of a chemically modified, {\pi}-extended tetrathiafulvalene and its charge-transfer complex with F4TCNQ

We describe the synthesis and single molecule electrical transport properties of a molecular wire containing a ${\pi}$-extended tetrathiafulvalene (exTTF) group and its charge-transfer complex with F4TCNQ. We form single molecule junctions using the in-situ break junction technique using a home-built scanning tunneling microscope with a range of conductance between 10 G$_{0}$ down to 10$^{-7}$ G$_{0}$. Within this range we do not observe a clear conductance signature of the neutral parent molecule, suggesting either that its conductance is too low or that it does not form stable junctions. Conversely, we do find a clear conductance signature in the experiments carried out on the charge-transfer complex. Due to the fact we expected this species to have a higher conductance than the neutral molecule, we believe this supports the idea that the conductance of the neutral molecule is very low, below our measurement sensitivity. This is further supported by our theoretical calculations. To the best of our knowledge, these are the first reported single molecule conductance measurements on a molecular charge-transfer species

Long-lived charged states of single porphyrin-tape junctions under ambient conditions

The ability to control the charge state of individual molecules wired in two-terminal single-molecule junctions is a key challenge in molecular electronics, particularly in relation to the development of molecular memory and other computational componentry. Here we demonstrate that single porphyrin molecular junctions can be reversibly charged and discharged at elevated biases under ambient conditions due to the presence of a localised molecular eigenstate close to the Fermi edge of the electrodes. In particular, we can observe long-lived charge-states with lifetimes upwards of 1–10 seconds after returning to low bias and large changes in conductance, in excess of 100-fold at low bias. Our theoretical analysis finds charge-state lifetimes within the same time range as the experiments. The ambient operation demonstrates that special conditions such as low temperatures or ultra-high vacuum are not essential to observe hysteresis and stable charged molecular junctions

Structural versus Electrical Functionalization of Oligo(phenyleneethynylene) Diamine Molecular Junctions

We explore both experimentally and theoretically the conductance and packing of molecular junctions based on oligo(phenyleneethynylene) (OPE) diamine wires, when a series of functional groups are incorporated into the wires. Using the scanning tunnelling microscopy break-junction (STM BJ) technique, we study these compounds in two environments (air and 1,2,4-trichlorobenzene) and explore different starting molecular concentrations. We show that the electrical conductance of the molecular junctions exhibits variations among different compounds, which are significant at standard concentrations but become unimportant when working at a low enough concentration. This shows that the main effect of the functional groups is to affect the packing of the molecular wires, rather than to modify their electrical properties. Our theoretical calculations consistently predict no significant changes in the conductance of the wires due to the electronic structure of the functional groups, although their ability to hinder ring rotations within the OPE backbone can lead to higher conductances at higher packing densities

Bias-driven conductance increase with length in porphyrin tapes

A key goal in molecular electronics has been to find molecules that facilitate efficient charge transport over long distances. Normally molecular wires become less conductive with increasing length. Here we report a series of fused porphyrin oligomers for which the conductance increases substantially with length by > 10-fold at a bias of 0.7 V. This exceptional behavior can be attributed to the rapid decrease of the HOMO-LUMO gap with the length of fused porphyrins. In contrast, for butadiyne-linked porphyrin oligomers with moderate inter-ring coupling, a normal conductance decrease with length is found for all bias voltages explored (± 1 V), although the attenuation factor (β) decreases from ca. 2 nm-1 at low bias to < 1 nm-1 at 0.9 V, highlighting that β is not an intrinsic molecular property. Further theoretical analysis using density functional theory underlines the role of inter-site coupling and indicates that this large increase in conductance with length at increasing voltages can be generalized to other molecular oligomers

Detecting mechanochemical atropisomerization within an STM break junction

We have employed the scanning tunneling microscope break-junction technique to investigate the single-molecule conductance of a family of 5,15-diaryl porphyrins bearing thioacetyl (SAc) or methylsulfide (SMe) binding groups at the ortho position of the phenyl rings (S2 compounds). These ortho substituents lead to two atropisomers, cis and trans, for each compound, which do not interconvert in solution under ambient conditions; even at high temperatures, isomerization takes several hours (half-life 15 h at 140 °C for SAc in C2Cl4D2). All the S2 compounds exhibit two conductance groups, and comparison with a monothiolated (S1) compound shows the higher group arises from a direct Au−porphyrin interaction. The lower conductance group is associated with the S-to-S pathway. When the binding group is SMe, the difference in junction length distribution reflects the difference in S−S distance (0.3 nm) between the two isomers. In the case of SAc, there are no significant differences between the plateau length distributions of the two isomers, and both show maximal stretching distances well exceeding their calculated junction lengths. Contact deformation accounts for part of the extra length, but the results indicate that cis-to-trans conversion takes place in the junction for the cis isomer. The barrier to atropisomerization is lower than the strength of the thiolate Au−S and Au−Au bonds, but higher than that of the Au−SMe bond, which explains why the strain in the junction only induces isomerization in the SAc compound

European experts consensus: BRCA/homologous recombination deficiency testing in first-line ovarian cancer

Background: Homologous recombination repair (HRR) enables fault-free repair of double-stranded DNA breaks. HRR deficiency is predicted to occur in around half of high-grade serous ovarian carcinomas. Ovarian cancers harbouring HRR deficiency typically exhibit sensitivity to poly-ADP ribose polymerase inhibitors (PARPi). Current guidelines recommend a range of approaches for genetic testing to identify predictors of sensitivity to PARPi in ovarian cancer and to identify genetic predisposition. Design: To establish a European-wide consensus for genetic testing (including the genetic care pathway), decision making and clinical management of patients with recently diagnosed advanced ovarian cancer, and the validity of biomarkers to predict the effectiveness of PARPi in the first-line setting. The collaborative European experts’ consensus group consisted of a steering committee (n = 14) and contributors (n = 84). A (modified) Delphi process was used to establish consensus statements based on a systematic literature search, conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines. Results: A consensus was reached on 34 statements amongst 98 caregivers (including oncologists, pathologists, clinical geneticists, genetic researchers, and patient advocates). The statements concentrated on (i) the value of testing for BRCA1/2 mutations and HRR deficiency testing, including when and whom to test; (ii) the importance of developing new and better HRR deficiency tests; (iii) the importance of germline non-BRCA HRR and mismatch repair gene mutations for predicting familial risk, but not for predicting sensitivity to PARPi, in the first-line setting; (iv) who should be able to inform patients about genetic testing, and what training and education should these caregivers receive. Conclusion: These consensus recommendations, from a multidisciplinary panel of experts from across Europe, provide clear guidance on the use of BRCA and HRR deficiency testing for recently diagnosed patients with advanced ovarian cancer

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field