Early mandated social distancing is a strong predictor of reduction in peak daily new COVID-19 cases.

OBJECTIVES: Mandated social distancing has been applied globally to reduce the spread of coronavirus disease 2019 (COVID-19). However, the beneficial effects of this community-based intervention have not been proven or quantified for the COVID-19 pandemic. STUDY DESIGN: This is a regional population-level observational study. METHODS: Using publicly available data, we examined the effect of timing of mandated social distancing on the rate of COVID-19 cases in 119 geographic regions, derived from 41 states within the United States and 78 other countries. The highest number of new COVID-19 cases per day recorded within a geographic unit was the primary outcome. The total number of COVID-19 cases in regions where case numbers had reached the tail end of the outbreak was an exploratory outcome. RESULTS: We found that the highest number of new COVID-19 cases per day per million persons was significantly associated with the total number of COVID-19 cases per million persons on the day before mandated social distancing (ß = 0.66, P < 0.0001). These findings suggest that if mandated social distancing is not initiated until the number of existing COVID-19 cases has doubled, the eventual peak would result in 58% more COVID-19 cases per day. Subgroup analysis on those regions where the highest number of new COVID-19 cases per day has peaked showed increase in ß values to 0.85 (P < 0.0001). The total number of cases during the outbreak in a region was strongly predicted by the total number of COVID-19 cases on the day before mandated social distancing (ß = 0.97, P < 0.0001). CONCLUSIONS: Initiating mandated social distancing when the numbers of COVID-19 cases are low within a region significantly reduces the number of new daily COVID-19 cases and perhaps also reduces the total number of cases in the region.

Investigation of the extraction complexes of palladium(II) with novel thiodiglycolamide and dithiodiglycolamide ligands by EXAFS and computational methods.

The structure of the extraction complexes of palladium(II) with novel ligands, namely, N,N,N',N'-tetra-(2-ethylhexyl) thiodiglycolamide (T(2EH)TDGA) and N,N,N',N'-tetra-(2-ethylhexyl) dithiodiglycolamide (DTDGA), have been determined by extended X-ray absorption fine structure spectroscopy (EXAFS). The interpretation of the EXAFS data is well supported by theoretical calculations of the complex geometry based on density functional theory (DFT). T(2EH)TDGA, having one thioetheric 'S' atom, forms a square planar complex with the Pd(II) ion, exhibiting 2: 1stoichiometry with one sulphur atom and one carbonyl oxygen atom from each T(2EH)TDGA molecule interacting with Pd(II) at distances of 2.24 and 2.04 Å, respectively. On the other hand, DTDGA, having two 'S' atoms in addition to two carbonyl groups, forms a square planar complex with Pd(II), exhibiting 1: 1stoichiometry, wherein both the sulphur atoms and the carbonyl oxygen of DTDGA interact with Pd(II) at distances of 2.29 and 2.05 Å, respectively. The slight distortion from the perfect square planar geometry could be attributed to the steric hindrance imposed by the bulky alkyl group of the amidic moieties. DFT calculations for the Pd-ligand complexes show that the Pd(II)-DTDGA complex with 1: 1stoichiometry is energetically more stable than the Pd(II)-T(2EH)TDGA complex with 1: 2stoichiometry. Among the two possible Pd(II)-T(2EH)TDGA complex geometries, the cis configuration appears more favorable. The methodology of fitting the EXAFS data has been validated by fitting the EXAFS data of a Pd(II)-aquo complex which showed square planar geometry with two axial water molecules constituting the secondary hydration sphere.

Facilitated transport of Pd(II) through a supported liquid membrane (SLM) containing N,N,N',N'-tetra-(2-ethylhexyl) thiodiglycolamide T(2EH)TDGA: a novel carrier.

A novel carrier, N,N,N',N'-tetra-(2-ethylhexyl) thiodiglycolamide, T(2EH)TDGA has been studied for transport of Pd(II) from nitric acid medium across a supported liquid membrane (SLM). Pd(II) was found to be almost quantitatively transported (≈ 99.9%) within 2h from 3.0M HNO(3) medium using 0.05 M T(2EH)TDGA in n-dodecane as carrier and 0.01 M thiourea in 0.2M HNO(3) as strippant. Pd(II) transport was also studied against various parameters like feed acidity, carrier concentration, membrane pore size, etc. Palladium transport was found to be diffusion controlled and the diffusion co-efficient value was found to be 3.56 × 10(-5)cm(2)/s. Selectivity of T(2EH)TDGA for palladium over other fission products was found to be quite high, with the separation factors for Pd, with respect to different fission products being >10(3). With respect to leaching out of carrier from the membrane support, the membrane was found to be stable for six consecutive cycles. Thus, T(2EH)TDGA can be used as an efficient carrier of Pd(II) from nitric acid medium.

Extractive spectrophotometric determination of palladium with N,N,N',N'-tetra(2-ethylhexyl)-thiodiglycolamide T(2EH)TDGA.

A precise, sensitive and selective method for the spectrophotometric determination of palladium (II) using N,N,N',N'-tetra(2-ethylhexyl) thiodiglycolamide T(2EH)TDGA as an extractant is described. Palladium (II) forms yellow colored complex with T(2EH)TDGA which exhibits an absorption maximum at ∼ 300 nm. The colored complex obeys Beer's law in the concentration range 1.0-15.0 µg ml(-1) of palladium with a molar absorptivity of 1.29 × 10(5)M(-1)cm(-1). The effects of various experimental parameters have been studied to establish the optimum conditions for the extraction and determination of palladium. The precision of the method has been evaluated and the relative standard deviation has been found to be less than 0.5%. The method has been successfully applied to the determination of palladium in simulated high level liquid waste (SHLW) solution.

Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics.

Through the use of in vitro selection techniques, a number of RNA aptamers have been selected for their ability to bind ligands with high affinity and specificity. The three-dimensional solution structures of a number of these complexes have been solved within the last 4 years. This review focuses on the structural characterization of the RNA aptamers bound to the cofactors FMN and AMP, the amino acids arginine and citrulline, the drug theophylline and the aminoglycoside antibiotic tobramycin in solution. Analysis of the structural features of these complexes allows the identification of molecular themes in RNA aptamer structure, recognition and discrimination.

Solution conformation of the (+)-trans-anti-benzo[g]chrysene-dA adduct opposite dT in a DNA duplex.

The solution structure of the adduct derived from the covalent bonding of the fjord region (+)-(11S, 12R, 13R, 14S) stereoisomer of anti -11,12-dihydroxy-13,14-epoxy-11,12,13, 14-tetrahydrobenzo[g]chrysene, (+)- anti -B[g]CDE, to the exocyclic N(6)amino group of the adenine residue dA6, (designated (+)- trans-anti -(B[g]C)dA6), positioned opposite a thymine residue dT17 in the DNA sequence context d(C1-T2-C3-T4-C5-(B[g]C)A6-C7-T8-T9-C10-C11). d(G12-G13-A14-A15-G16-T17-G18-A19-G20++ +-A21-G22) (designated (B[g]C)dA. dT 11-mer duplex), has been studied using structural information derived from NMR data in combination with molecular dynamics (MD) calculations. The solution structure of the (+)- trans-anti -(B[g]C)dA.dT 11-mer duplex has been determined using an MD protocol where both interproton distance and dihedral angle restraints deduced from NOESY and COSY spectra are used during the refinement process, followed by additional relaxation matrix refinement to the observed NOESY intensities to account for spin diffusion effects. The results established that the covalently attached benzo[g]chrysene ring intercalates into the DNA helix directed towards the 5'-side of the modified strand and stacks predominantly with dT17 when intercalated between dC5.dG18 and (B[g]C)dA6.dT17 base-pairs. All base-pairs, including the modified (B[g]C)dA6.dT17 base-pair, are aligned through Watson-Crick pairing as in normal B -DNA. In addition, the potential strain associated with the highly sterically hindered fjord region of the aromatic portion of the benzo[g]chrysenyl ring is relieved through the adoption of a non-planar, propeller-like geometry within the chrysenyl ring system. This conformation shares common structural features with the related (+)- trans-anti -(B[c]Ph)dA adduct in the identical base sequence context, derived from the fjord region (+)-(1S,2R,3R,4S)-3, 4-dihydroxy-1,2-epoxy-1,2,3,4-tetrahydrobenzo[c]phenanthrene stereoisomer, in which intercalation is also observed towards the 5'-side of the modified dA6.dT17 base-pair.

Structure, recognition and adaptive binding in RNA aptamer complexes.

Novel features of RNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of RNA aptamers that bind cofactors, aminoglycoside antibiotics, amino acids and peptides with high affinity and specificity. This review presents the solution structures of RNA aptamer complexes with adenosine monophosphate, flavin mononucleotide, arginine/citrulline and tobramycin together with an example of hydrogen exchange measurements of the base-pair kinetics for the AMP-RNA aptamer complex. A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.

Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex.

BACKGROUND: Aminoglycoside antibiotics are known to target ribosomal, retroviral and catalytic RNAs with high affinity and specificity. Recently, in vitro selection experiments have identified RNA aptamers that bind to aminoglycoside antibiotics with nanomolar affinity and stringent specificity, allowing discrimination between closely related family members. There has, to date, been limited structural information on the molecular basis of such saccharide-RNA recognition. RESULTS: We describe a solution-structure determination of the tobramycin-RNA aptamer complex, obtained using NMR and molecular dynamics. The structure gives insight into the molecular features associated with saccharide-RNA recognition. Tobramycin adopts a defined alignment and binds to the RNA major groove centered about a stem-loop junction site. A portion of the bound tobramycin is encapsulated between the floor of the major groove and a looped-out cytosine residue that forms a flap over the binding site in the complex. CONCLUSIONS: The emergence of antibiotic-resistant pathogens and their impact on human health continues to be a major concern in the medical community. Rational modification of existing antibiotics aimed at improving their efficacy requires a molecular view of their receptor-binding sites. We have provided such a molecular view for a member of the aminoglycoside antibiotic family that targets RNA.

Molecular recognition in the FMN-RNA aptamer complex.

We report on a combined NMR-molecular dynamics calculation approach that has solved the solution structure of the complex of flavin mononucleotide (FMN) bound to the conserved internal loop segment of a 35 nucleotide RNA aptamer identified through in vitro selection. The FMN-RNA aptamer complex exhibits exceptionally well-resolved NMR spectra that have been assigned following application of two, three and four-dimensional heteronuclear NMR techniques on samples containing uniformly 13C, 15N-labeled RNA aptamer in the complex. The assignments were aided by a new through-bond NMR technique for assignment of guanine imino and adenine amino protons in RNA loop segments. The conserved internal loop zippers up through the formation of base-pair mismatches and a base-triple on complex formation with the isoalloxazine ring of FMN intercalating into the helix between a G.G mismatch and a G.U.A base-triple. The recognition specificity is associated with hydrogen bonding of the uracil like edge of the isoalloxazine ring of FMN to the Hoogsteen edge of an adenine at the intercalation site. There is significant overlap between the intercalated isoalloxazine ring and its adjacent base-triple platform in the complex. The remaining conserved residues in the internal loop participate in two G.A mismatches in the complex. The zippered-up internal loop and flanking stem regions form a continuous helix with a regular sugar-phosphate backbone except at a non-conserved adenine, which loops out of the helix to facilitate base-triple formation. Our solution structure of the FMN-RNA aptamer complex is to our knowledge the first structure of an RNA aptamer complex and outlines folding principles that are common to other RNA internal and hairpin loops, and molecular recognition principles common to model self-replication systems in chemical biology.

A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times.

Long-mixing-time data (tau m > 200 ms) from NOE spectra have largely been ignored as a source of protein structural information due to the effects of spin diffusion on calculated interproton distances when using the two-spin approximation. An effective approach for incorporating spin-diffusion effects in an average way into refinements is to choose distance bounds based on distributions of distances observed in NOE back calculations on homologous proteins from a protein structure database. We have determined distributions of interproton distances characteristic of newly observed NOE cross peaks for the proteins crambin, PTI, and echistatin at long mixing times. A relaxation-matrix analysis was used to model the effects of spin diffusion. Constraint ranges were constructed from the interproton distance distributions which can be used in standard protein-refinement programs based on the two-spin approximation. Back calculations are also used to analyze constraint ranges typically used for protein structure determinations based on NOE spectra at shorter mixing times.

Three-dimensional structure of echistatin and dynamics of the active site.

The snake venom protein echistatin contains the cell recognition sequence Arg-Gly-Asp and is a potent inhibitor of platelet aggregation. The three-dimensional structure of echistatin and the dynamics of the active RGD site are presented. A set of structures was determined using the Distance Geometry method and subsequently refined by Molecular Dynamics and energy minimization. Disulfide pairings are suggested, based on violations of experimental constraints. The structures satisfy 230 interresidue distance constraints, derived from nuclear Overhauser effect measurements, five hydrogen-bonding constraints, and 21 torsional constraints from vicinal spin-spin coupling constants. The segment from Gly5 to Cys20 and from Asp30 to Asn42 has a well-defined conformation and the Arg-Gly-Asp sequence, which adopts a turn-like structure, is located at the apex of a nine-residue loop connecting the two strands of a distorted beta-sheet. The mobility of the Arg-Gly-Asp site has been quantitatively characterized by 15N relaxation measurements. The overall correlation time of echistatin was determined from fluorescence measurements, and was used in a model-free analysis to determine internal motional parameters. The active site has order parameters of 0.3-0.5, i.e., among the smallest values ever observed at the active site of a protein. Correlation of the flexible region of the protein as characterized by relaxation experiments and the NMR solution structures was made by calculating generalized order parameters from the ensemble of three-dimensional structures. The motion of the RGD site detected experimentally is more extensive than a simple RGD loop 'wagging' motional model, suggested by an examination of superposed solution structures.

Cloning and characterization of the gene coding for the human acrosomal protein SP-10.

SP-10 is a human intra-acrosomal protein that is first detected in the developing acrosome of round spermatids and is observed associated with the acrosomal membranes and matrix of mature sperm. Recombinant SP-10 is currently being tested as a contraceptive vaccine immunogen on the basis of its tissue specificity as well as functional assays indicating that anti-SP-10 antisera inhibit sperm-egg interactions. In the present study, structural characterization of the human SP-10 gene was undertaken to investigate the expression of the gene and to identify possible functions of the SP-10 protein within the acrosome. Genomic blots indicate that SP-10 is encoded by a single-copy gene. Mapping and sequencing of the 8-kb SP-10 gene show that the SP-10 mRNA consists of exons of 119, 487, 113, and 390 bp with each exon coding for a distinct structural domain within the SP-10 protein. An in-frame alternatively spliced form of the SP-10 mRNA, identified during SP-10 cDNA characterization, employs the same 3' splice site as the 487-bp exon and a unique 5' splice site within the 487-bp exon. Previous comparisons of human, baboon, and macaque SP-10 cDNA sequences indicated that the baboon and macaque cDNAs contained 60 bp (20 aa) not present in the human SP-10 cDNA. Analysis of the human SP-10 genomic sequence suggests that a 60-bp deletion may have occurred during the evolution of the human SP-10 gene by homologous recombination.(ABSTRACT TRUNCATED AT 250 WORDS)

Theoretical predictions of DNA hairpin loop conformations: correlations with thermodynamic and spectroscopic data.

A computational procedure for generating conformations of DNA hairpin loop structures from a broad range of low-energy starting states is described. The starting point of the modeling is the distribution of oligonucleotide chain conformations obtained from Monte Carlo simulations of feasible dinucleotide steps. Structures which meet the spatial criteria for hairpin loop formation are selected from the distributions and subsequently minimized using all-atom molecular mechanics. Both d(CTnG) and d(CAnG) oligomers, where n = 3, 4, or 5, are modeled. These sequences are chosen because of the large number of published NMR and thermodynamic studies on DNA hairpins containing thymine or adenine residues. The minimized three-dimensional hairpin loop structures are compared with one another as well as analyzed in terms of available experimental data. The computational approach provides the first detailed analysis of DNA hairpin loop structure in terms of a multistate conformational model. Investigation of the minimized conformations reveals several interesting structural features. First, hairpin loops of the same sequence adopt several distinctly different conformations, as opposed to minor variants of the same equilibrium structure, that could potentially interconvert in solution. Second, in contrast to double-helical nucleic acids, the hairpin loop models exhibit hydrophobic and hydrophilic surfaces. The different disposition of hydrophobic groups in loops versus duplexes could modulate both protein-nucleic acid interactions and nucleic acid self-associations. Third, perpendicular aromatic interactions of loop residues are observed in many of the computed hairpins. This sort of interaction might be important in the stabilization of non-hydrogen-bonded nucleic acid secondary and tertiary structures. The predicted structural features in the models help, in addition, to account for the unusual thermodynamic properties of DNA hairpin loops. Comparison of the theoretically-generated NOEs in different structures further reveals that very different molecular structures and interactions can, in principle, produce the same NOEs. The multistate description suggested by this observation differs from the conventional interpretation of DNA solution structure in terms of the fluctuations about a single preferred chain conformation. There is not necessarily only one set of closely related structures consistent with the observed data.

Vaccines for control of fertility.

PIP: Major developments in birth control vaccines are on the horizon. The human chorionic gonadotropin (hCG) vaccine has entered phase II clinical trials after successful completion of phase I studies at 5 centers in India and 4 centers abroad. It is the most advanced vaccine of its type in the world. The trials are being conducted on women of proven fertility who are sexually active. The available results indicate the efficiency of the vaccine to prevent pregnancy in women at or above titres of 50 ng/ml. A vaccine inducing antibodies against gonadotropin releasing hormone (GnRH) has been approved in India for trials in postpartum women, to determine whether immunization can help prolong lactational amenorrhea. The GnRH vaccine is also in clinical trial in prostate cancer patients at 2 centers in India and in Austria and the Dominican Republic. The follicle stimulating hormone (FSH) vaccine is about to enter phase I clinical trial after completing experimental and toxicological studies. A vaccine against FSH has been developed for human males employing ovine FSH (oFSH) as an immunogen. oFSH adsorbed on alum induces antibodies reactive with human FSH in bonnet monkeys. Immunization leads to oligospermia with resultant impairment of fertilization potential. No reduction in testosterone levels has been reported. Research is in progress to identify antigens on spermatozoa, which could serve as vaccine candidates. PH-20, a protein located on the inner acrosomal membrane of capacitated sperms, has been reported to have 100% contraceptive efficacy in both sexes of guinea pigs in active immunization studies. cDNA probes of PH-20 cross-react with genomic DNAs of mouse, rat, hamster, and human. The sperm antigen, lactate dehydrogenase C4 (LDH-C4), is a glycolytic enzyme. Active immunization with LDH-C4 suppressed fertility in mice, rabbits, and baboons. SP-10, which is a testis-specific human sperm protein, is also a promising candidate.^ieng

Effect of infection of the genital tract on the concentration of IgG and albumin in bull serum and semen.

Bovine IgG and albumin concentrations were determined from serum and semen of 59 bulls that were divided into 4 groups: 35 non-infected bulls (Group 1); 10 with vesiculitis due to Corynebacterium pyogenes (Group 2); 10 bulls with orchitis due to Chlamydia psittaci (Group 3); and 4 bulls with infectious vesiculitis (Group 4) sampled both before and after antibiotic treatment. Serum IgG concentrations (25 mg/ml approximately) were similar in non-infected (Gp 1) and infected bulls (Gp 2,3,4) whereas serum albumin concentrations were greater in infected than in non-infected bulls (51 mg/ml vs.41 mg/ml; p less than 0.01). By contrast, both semen IgG and albumin concentrations in infected bulls (0.47 and 0.54 mg/ml respectively) were significantly different from those of non-infected bulls (0.14 and 0.32 mg/ml; p less than 0.01). In addition, bulls with chlamydial orchitis had both semen (but not serum) IgG and albumin levels higher than those suffering from vesiculitis (p less than 0.01). Antibiotic therapy led to recovery and simultaneously to decreased concentrations of semen IgG and albumin. These results strongly suggest a local IgG synthesis or selective diffusion after such genital infections and further indicate that semen IgG and albumin assays could be a new and valuable tool for diagnosis and evaluation of genital infections.