Flexible Ansatz for N-Body Perturbation Theory.

We propose a new perturbation theory framework that can be used to help with the projective solution of the Schrödinger equation for arbitrary wave functions. This Flexible Ansatz for N-body Perturbation Theory (FANPT) is based on our previously proposed Flexible Ansatz for the N-body Configuration Interaction (FANCI). We derive recursive FANPT expressions, including arbitrary orders in the perturbation hierarchy. We show that the FANPT equations are well-behaved across a wide range of conditions, including static correlation-dominated configurations and highly nonlinear wave functions.

Coupled cluster-inspired geminal wavefunctions.

Electron pairs have an illustrious history in chemistry, from powerful concepts to understanding structural stability and reactive changes to the promise of serving as building blocks of quantitative descriptions of the electronic structure of complex molecules and materials. However, traditionally, two-electron wavefunctions (geminals) have not enjoyed the popularity and widespread use of the more standard single-particle methods. This has changed recently, with a renewed interest in the development of geminal wavefunctions as an alternative to describing strongly correlated phenomena. Hence, there is a need to find geminal methods that are accurate, computationally tractable, and do not demand significant input from the user (particularly via cumbersome and often ill-behaved orbital optimization steps). Here, we propose new families of geminal wavefunctions inspired by the pair coupled cluster doubles ansatz. We present a new hierarchy of two-electron wavefunctions that extends the one-reference orbital idea to other geminals. Moreover, we show how to incorporate single-like excitations in this framework without leaving the quasiparticle picture. We explore the role of imposing seniority restrictions on these wavefunctions and benchmark these new methods on model strongly correlated systems.

Fanpy: A python library for prototyping multideterminant methods in ab initio quantum chemistry.

Fanpy is a free and open-source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to convert the mathematical formulation of a new wavefunction ansätze to a working implementation. Fanpy is designed based on our recently introduced Flexible Ansatz for N-electron Configuration Interaction (FANCI) framework, where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin-orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system's Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly explore new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for various operating systems. In addition, it adheres to principles of modern software development, including comprehensive documentation, extensive testing, quality assurance, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library.

Significant and variable linear polarization during the prompt optical flash of GRB 160625B.

Newly formed black holes of stellar mass launch collimated outflows (jets) of ionized matter that approach the speed of light. These outflows power prompt, brief and intense flashes of γ-rays known as γ-ray bursts (GRBs), followed by longer-lived afterglow radiation that is detected across the electromagnetic spectrum. Measuring the polarization of the observed GRB radiation provides a direct probe of the magnetic fields in the collimated jets. Rapid-response polarimetric observations of newly discovered bursts have probed the initial afterglow phase, and show that, minutes after the prompt emission has ended, the degree of linear polarization can be as high as 30 per cent-consistent with the idea that a stable, globally ordered magnetic field permeates the jet at large distances from the central source. By contrast, optical and γ-ray observations during the prompt phase have led to discordant and often controversial results, and no definitive conclusions have been reached regarding the origin of the prompt radiation or the configuration of the magnetic field. Here we report the detection of substantial (8.3 ± 0.8 per cent from our most conservative simulation), variable linear polarization of a prompt optical flash that accompanied the extremely energetic and long-lived prompt γ-ray emission from GRB 160625B. Our measurements probe the structure of the magnetic field at an early stage of the jet, closer to its central black hole, and show that the prompt phase is produced via fast-cooling synchrotron radiation in a large-scale magnetic field that is advected from the black hole and distorted by dissipation processes within the jet.

A machine learning analysis of a "normal-like" IDH-WT diffuse glioma transcriptomic subgroup associated with prolonged survival reveals novel immune and neurotransmitter-related actionable targets.

BACKGROUND: Classification of primary central nervous system tumors according to the World Health Organization guidelines follows the integration of histologic interpretation with molecular information and aims at providing the most precise prognosis and optimal patient management. According to the cIMPACT-NOW update 3, diffuse isocitrate dehydrogenase-wild type (IDH-WT) gliomas should be graded as grade IV glioblastomas (GBM) if they possess one or more of the following molecular markers that predict aggressive clinical course: EGFR amplification, TERT promoter mutation, and whole-chromosome 7 gain combined with chromosome 10 loss. METHODS: The Cancer Genome Atlas (TCGA) glioma expression datasets were reanalyzed in order to identify novel tumor subcategories which would be considered as GBM-equivalents with the current diagnostic algorithm. Unsupervised clustering allowed the identification of previously unrecognized transcriptomic subcategories. A supervised machine learning algorithm (k-nearest neighbor model) was also used to identify gene signatures specific to some of these subcategories. RESULTS: We identified 14 IDH-WT infiltrating gliomas displaying a "normal-like" (NL) transcriptomic profile associated with a longer survival. Genes such as C5AR1 (complement receptor), SLC32A1 (vesicular gamma-aminobutyric acid transporter), MSR1 (or CD204, scavenger receptor A), and SYT5 (synaptotagmin 5) were differentially expressed and comprised in gene signatures specific to NL IDH-WT gliomas which were validated further using the Chinese Glioma Genome Atlas datasets. These gene signatures showed high discriminative power and correlation with survival. CONCLUSION: NL IDH-WT gliomas represent an infiltrating glioma subcategory with a superior prognosis which can only be detected using genome-wide analysis. Differential expression of genes potentially involved in immune checkpoint and amino acid signaling pathways is providing insight into mechanisms of gliomagenesis and could pave the way to novel treatment targets for infiltrating gliomas.

Advances in the Direct Study of Carbon Burning in Massive Stars.

The ^{12}C+^{12}C fusion reaction plays a critical role in the evolution of massive stars and also strongly impacts various explosive astrophysical scenarios. The presence of resonances in this reaction at energies around and below the Coulomb barrier makes it impossible to carry out a simple extrapolation down to the Gamow window-the energy regime relevant to carbon burning in massive stars. The ^{12}C+^{12}C system forms a unique laboratory for challenging the contemporary picture of deep sub-barrier fusion (possible sub-barrier hindrance) and its interplay with nuclear structure (sub-barrier resonances). Here, we show that direct measurements of the ^{12}C+^{12}C fusion cross section may be made into the Gamow window using an advanced particle-gamma coincidence technique. The sensitivity of this technique effectively removes ambiguities in existing measurements made with gamma ray or charged-particle detection alone. The present cross-section data span over 8 orders of magnitude and support the fusion-hindrance model at deep sub-barrier energies.

Caffeine metabolism in cystic fibrosis: enhanced xanthine oxidase activity.

STUDY OBJECTIVE: To characterize the activities of the P450 mixed-function oxidase CYP1A2 as well as the cytosolic enzymes N-acetyltransferase and xanthine oxidase using caffeine as a probe in children with cystic fibrosis compared to age-matched healthy control subjects. METHODS: After administration of caffeine (cola beverage) to 12 children with cystic fibrosis (age range, 5 to 11 years) and 12 healthy control subjects (age range, 5 to 12 years), urine was collected for 4 hours. Caffeine metabolites were determined by HPLC, and urinary caffeine metabolite ratios were computed to determine liver enzyme activities. In addition, a blood sample was used to detect cystic fibrosis mutant alleles by polymerase chain reaction. RESULTS: The indexes for CYP1A2, N-acetyltransferase, and 8-hydroxylation were similar in both groups of subjects. In contrast, there was a significant difference in the frequency distribution of the xanthine oxidase activity between the two groups. Nine of 12 patients with cystic fibrosis but only one of 12 healthy volunteers had xanthine oxidase activities above 0.42 (Kolmogorov-Smirnov two-sample test, p < 0.01). CONCLUSIONS: Differences in xanthine oxidase may have clinical implications with regard to interindividual variation in xenobiotic biotransformation and the exposure to lung tissue-damaging oxygen radicals. Hepatic enzyme activities appear to be selectively altered in patients with cystic fibrosis.

Structure-function studies of peptides inhibiting the ribonucleotide reductase activity of herpes simplex virus type I.

Ac-Tyr298-Ala299-Gly300-Thr301-Val302-I le303-Asn304-Asp305-Leu306-OH (Ac-VZV R2-(298-306)) represents the acetylated form of the C-terminus of varicella-zoster virus (VZV) ribonucleotide reductase subunit 2 (R2). This peptide possesses a high degree of homology with the C-terminus nonapeptide of the herpes simplex virus (HSV) type I and II ribonucleotide reductase R2 protein and is 15 times more potent than the latter in its in vitro inhibition of HSV-1 reductase activity. Accordingly, a new series of analogues based on this structure was studied in vitro. The replacement of Asp305 by Asn, Glu, Gln, Ser, or Cys; of Asn304 by Gln or Ser; of Ile303 and Val302 by D-Val; and of Tyr298 by Cha induced an important loss of inhibitory potency. The substitution of Asn304 by Asp; of Thr301 by Cys, Ser, or Val; of Gly300 by Ala or Val; of Ala299 by Val; or of Tyr298 by homoPhe, 4'-fluoro-Phe, 4'-chloro-Phe, 3'-iodo-Tyr, Me-Tyr, or For-Trp led to a moderate decrease of the Ac-VZV R2-(298-306) potency. The replacement of Val302 by Ile; Ala299 by Cys, Ser, or Thr; or the insertion of a six- or eight-carbon chain between Tyr298 and the NH2 terminus either preserved or slightly increased the inhibitory potency of Ac-VZV R2-(298-306). Finally, the substitution of Tyr298 by Trp or the addition of 4'-nitro-Phe at the amino terminus resulted in a 3-fold increase of potency. Altogether, these results stress the importance of the structural integrity of the minimum active core 302-306 in preserving the inhibitory potency and suggest that further studies on monosubstitutions could be directed at the portion 298-301 of the peptide.

Hypoxia, arterial pH and theophylline disposition.

Theophylline is a bronchodilator used extensively in the management of obstructive pulmonary disease. Factors implicated in altered theophylline clearance include smoking, age, concomitant drug intake, liver disease and left ventricular heart failure. However, evidence now suggests that theophylline clearance may be altered by changes in severity of the pulmonary obstruction, hypoxia and variation in arterial pH. The in vitro disposition of theophylline has been evaluated in isolated rat livers and mouse hepatocytes. In vivo studies have assessed the metabolism of theophylline under hypoxia in rats, rabbits and dogs. In isolated mouse hepatocytes and rat livers, low oxygen concentrations resulted in higher theophylline concentrations, a longer elimination half-life and a decrease in the production of the metabolite 1,3-dimethyl uric acid, suggesting impaired metabolism of theophylline. In rabbits, hypoxia, hypercapnia and respiratory acidosis decreased total body clearance and increased plasma theophylline concentrations. On the other hand, experiments involving dogs showed no significant changes in theophylline concentrations or pharmacokinetic parameters with hypoxia. At present, animal studies remain inconclusive. This can be attributed to the use of different animal models and variations in study methodology, including the extent and duration of hypoxia and acidaemia, concurrent acid-base disorders such as hypercapnia, as well as the severity of pulmonary obstruction. Human studies assessing alterations in theophylline disposition secondary to the hypoxia present in pulmonary disease are few and include mostly case reports and observational studies. There is evidence suggesting decreased theophylline clearance and protein binding during acute illness and some consensus can be achieved using case reports and controlled studies. There is additional evidence that drug clearance decreases with age and that elderly patients may have a decreased theophylline clearance at baseline. However, the most obvious markers appear to be the severity of pulmonary disease and the rate of change in the patient's condition. Caution should be exercised when administering theophylline to elderly patients with chronic obstructive pulmonary disease presenting with acute exacerbations of a concomitant respiratory illness, as these patients appear to be most likely to exhibit altered theophylline metabolism. Therefore, they would be at increased risk for toxicity should conventional dosages be used during an acute respiratory event.

Resurgence of sleeping sickness in Tambura County, Sudan.

Endemic foci of human African trypanosomiasis are present in southern Sudan. In 1996 and 1997, trypanosomiasis increased sharply in Tambura County. To define the magnitude and geographic distribution of the outbreak, we conducted a prevalence survey using population-based cluster sampling in 16 villages: 1,358 participants answered questions about routine activities and tsetse fly contact and received serologic testing. Seroprevalence in the surveyed area was 19.4% (95% confidence interval = 16.9%, 21.8%). We confirmed infection in 66% of seropositive persons who received one parasitologic examination and in 95% of those who had serial examinations of lymph node fluid and blood. Activities related to the civil war, such as temporary migration, were not associated with seropositive status. Since the previous population screening in 1988, the trypanosomiasis prevalence increased two orders of magnitude, and the proportion of villages affected increased from 54% to 100%. Our results suggest that there may be 5,000 cases in Tambura County. The absence of trypanosomiasis control for nearly a decade is a factor in the resurgence of the disease.

Evaluation of the role of neurolinins and urecholine hypersensitivity in an animal model of infravesical outflow obstruction.

OBJECTIVES: To determine whether detrusor muscle strips from a male rat with infravesical outflow obstruction model demonstrate supersensitivity to parasympathomimetic and neurokinin NK-1 and NK-2 selective agonists. METHODS: Bladder instability developed after 6 weeks of partial urethral obstruction. The micturition frequency and voided volume were determined in unanesthetized animals. Detrusor hypertrophy was confirmed by evaluation of bladder weight. In vitro organ bath was used to compare the affinity and maximal activity of bethanechol and neurokinin NK-1 and NK-2 selective agonists on strips from the detrusor muscle of sham and obstructed rats. Bethanechol, N-Ac[Arg6, Sar9, Met(O2)]-SP(6-11), and [beta-Ala8]-NKA(4-10) were used to characterize cholinergic muscarinic, neurokinin NK-1 and NK-2 receptors. Results. No significant differences in affinities and maximal responses were found using 10-mg detrusor muscle strips with each of the three agonists. CONCLUSIONS: Bladder instability produced by outlet obstruction does not involve changes in the affinity or maximal activity of cholinergic muscarinic, neurokinin NK-1 and NK-2 receptors. Furthermore, detrusor supersensitivity to neurokinins or bethanechol was not seen. This suggests that bladder instability is not due to an increased affinity or maximal response to neurokinins or parasympathomimetics.

Silver-Russell syndrome. A family with symmetric and asymmetric siblings.

Two siblings with Silver-Russell syndrome (SRS) were studied. Only one child had asymmetry. To our knowledge, this is the first report of the existence of both the "Silver" and "Russell" variants in a nuclear family, and provides additional evidence for considering SRS to be a single syndrome with a wide spectrum of clinical manifestations.

A comparison of functional indexes, derived from screening tests, of chronic alcoholic neurotoxicity in the cerebral cortex, retina and peripheral nervous system.

Thirty abstinent alcoholics and 30 age-, education- and occupation-matched normal control subjects were tested with the Category test, the Lanthony-15 test of color discrimination and the Biothesiometer test of vibration detection threshold. Multivariate analysis of covariance revealed significant impairment of the alcoholics on these tasks (p < .007), but univariate analysis revealed that only the Category test yielded a significant difference (p < .001). Canonical correlation analysis, with age and education partialed out, was calculated on the alcoholics' data to determine whether duration, mean and maximum alcohol consumption, age of onset of alcoholism and duration of abstinence predicted performance on the tasks. The prediction was significant (p < .001). Multiple regression analysis revealed that vibration threshold, color preception and Category test performance were decreasingly predicted by the alcohol-related variables (p < .001, .006, .051, respectively). There was no higher incidence of hereditary dyschromatopsia in the alcoholic group than the control group. It was therefore concluded that all three functions (Category test performance, color discrimination, vibrotactile sensitivity) were impaired as a result of alcohol consumption.

Nodding syndrome in Mundri county, South Sudan: environmental, nutritional and infectious factors.

BACKGROUND: Nodding Syndrome is a seizure disorder of children in Mundri County, Western Equatoria, South Sudan. The disorder is reported to be spreading in South Sudan and northern Uganda. OBJECTIVE: To describe environmental, nutritional, infectious, and other factors that existed before and during the de novo 1991 appearance and subsequent increase in cases through 2001. METHODS: Household surveys, informant interviews, and case-control studies conducted in Lui town and Amadi village in 2001-2002 were supplemented in 2012 by informant interviews in Lui and Juba, South Sudan. RESULTS: Nodding Syndrome was associated with Onchocerca volvulus and Mansonella perstans infections, with food use of a variety of sorghum (serena) introduced as part of an emergency relief program, and was inversely associated with a history of measles infection. There was no evidence to suggest exposure to a manmade neurotoxic pollutant or chemical agent, other than chemically dressed seed intended for planting but used for food. Food use of cyanogenic plants was documented, and exposure to fungal contaminants could not be excluded. CONCLUSION: Nodding Syndrome in South Sudan has an unknown etiology. Further research is recommended on the association of Nodding Syndrome with onchocerciasis/mansonelliasis and neurotoxins in plant materials used for food.

Clinical and epidemiologic characteristics of nodding syndrome in Mundri County, southern Sudan.

BACKGROUND: Nodding syndrome (repetitive nodding and progressive generalized seizures) is assuming epidemic proportions in South Sudan, Tanzania and Uganda. OBJECTIVE: To describe clinical and epidemiological features of nodding syndrome in southern Sudan based on preliminary investigations conducted in 2001 and 2002. METHOD: Household surveys, clinical, electrophysiological (EEG) assessments, informant interviews and case-control studies were conducted in the town of Lui and the village of Amadi in southern Sudan. RESULTS: Nodding syndrome is characterized by involuntary repetitive nodding of the head, progressing to generalized seizures; mental and physical deterioration. The EEGs were consistent with progressive epileptic encephalopathy. Prevalence of Nodding syndrome in Lui and Amadi was 2.3% and 6.7% respectively. All case control studies showed a positive association between cases and Onchocerca volvulus. A history of measles was negatively associated with being a case: 2/13 of cases and 11/19 of controls had had measles: odds ratio 0.13 (95% CI 0.02, 0.76). Environmental assessment did not reveal any naturally occurring or manmade neurotoxic factors to explain Nodding Syndrome, although fungal contamination of food could not be ruled out. CONCLUSION: Nodding Syndrome was strongly associated with Onchocerca volvulus. There was no evidence to suggest an environmental pollutant, chemical agent, or other toxic factor.

Fatal hepatotoxicity following oral administration of amiodarone.

OBJECTIVE: To report a case of fatal hepatotoxicity associated with the chronic use of oral amiodarone. CASE SUMMARY: Long-term administration of amiodarone for the control of intractable ventricular tachycardia was associated with fatal hepatotoxicity in a patient receiving amiodarone for 14 months. DISCUSSION: Although most hepatic adverse effects associated with amiodarone are transient and reversible with time, deaths resulting from amiodarone-induced hepatotoxicity have been reported. The relation of hepatotoxicity to cumulative dose and duration of therapy is debated. The histopathologic features of amiodarone-induced hepatotoxicity include Mallory bodies, steatosis, intralobular inflammatory infiltrates, fibrosis, and phospholipidosis. CONCLUSIONS: Evidence pertaining to both mild and severe amiodarone toxicity indicates that cumulative dose may correlate with overall toxicity and, therefore, maintenance doses should be kept as low as possible. Patients should be followed with monitoring of liver function test results every 3-6 months.

Re-emergence of epidemic sleeping sickness in southern Sudan.

A resurgence of sleeping sickness developed in southern Sudan during the past decade. Prevalence of confirmed Trypanosoma brucei gambiense infection in humans now exceeds 5% in several foci. From 1997 to 1999, trypanosomiasis control programmes in three counties of Western Equatoria Province detected 3785 new cases among 67 181 persons screened. A major contributing factor in the re-emergence of epidemic sleeping sickness was the lack of active case-finding throughout the 1990s. Although the situation is improving in sites where trypanosomiasis programmes have been recently implemented, co-ordination and additional international assistance are needed to bring sleeping sickness under control in Sudan.

Understanding beliefs and meanings in the experience of cancer: a concept analysis.

Although the concepts of belief and meaning are commonly used in the cancer literature, there is often an overlap in the use of the terms. Some consider the two terms as synonyms while others link them as successive elements in adjustment. Using an adaptation of the methods of concept analysis, this article differentiates belief and meaning, and also suggests that meaning exists at two levels. The defining attributes and antecedents of these closely related concepts are identified and a model case illustrating each is presented. Clarity in the conceptual definitions of beliefs and meanings can help researchers select measures that accurately reflect the phenomenon of interest. Similarly, differentiation between the concepts can help practitioners in planning focused interventions that explore clients' existing beliefs and situational and existential meanings.