A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Testing a global standard for quantifying species recovery and assessing conservation impact

Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a “Green List of Species” (now the IUCN Green Status of Species). A draft Green Status framework for assessing species’ progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species’ viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species’ recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard

Trends in template/fragment-free protein structure prediction

Predicting the structure of a protein from its amino acid sequence is a long-standing unsolved problem in computational biology. Its solution would be of both fundamental and practical importance as the gap between the number of known sequences and the number of experimentally solved structures widens rapidly. Currently, the most successful approaches are based on fragment/template reassembly. Lacking progress in template-free structure prediction calls for novel ideas and approaches. This article reviews trends in the development of physical and specific knowledge-based energy functions as well as sampling techniques for fragment-free structure prediction. Recent physical- and knowledge-based studies demonstrated that it is possible to sample and predict highly accurate protein structures without borrowing native fragments from known protein structures. These emerging approaches with fully flexible sampling have the potential to move the field forward

Leptin and HDL-cholesterol in non-diabetic normotensive subjects.

BACKGROUND: We investigated the relationships between body mass index (BMI), serum leptin and serum HDL-cholesterol. MATERIAL AND METHODS: A retrospective study was carried out in 80 patients who did not have type 2 diabetes mellitus and/or high blood pressure. RESULTS: Both serum leptin and HDL-cholesterol serum levels correlated with BMI (r = 0.616 and r = -0.269, respectively), but when the BMI values were kept constant no correlation was found between serum leptin and HDL-cholesterol both in simple and in multiple regression. CONCLUSION: The findings suggest that serum leptin concentration is completely independent of lipid metabolism

A new approach to the fashioning of the gastroenteroanastomosis in laparoscopicstandard biliopancreatic diversion.

A retrocolic submesocolic approach was used for creating the gastroenteroanastomosis in 42 consecutive patients who underwent laparoscopic biliopancreatic diversion for obesity. The surgical technique is described in detail. The laparoscopic gastroenteroanastomosis was successfully performed on all the operated patients, with no intraoperative complications requiring conversion to open surgery and no immediate or late postoperative morbidity related to the anastomosis

Laparoscopic standard biliopancreatic diversion: technique and preliminaryresults.

BACKGROUND: A technique for standard laparoscopic BPD was developed. METHODS: Standard laparoscopic BPD was performed in 26 morbidly obese patients with mean BMI 43. Details of the technique, using 6 trocars, and instrumentation are described. Intestinal limb lengths were measured fully stretched, and the gastric remnant volume was also measured. Both enteroenteral and gastrointestinal anastomoses were fashioned with a side-to-side technique using the endoGIA, the conjoined defect being closed with a manual running seromuscular suture. RESULTS: 6 and 12 month weight loss results were similar to those obtained in open BPD. CONCLUSION: Laparoscopic standard BPD is a feasible alternative to the open operative procedure, the major advantage being the likely near total avoidance of wound hernia