A framework for auralization of boundary element method simulations including source and receiver directivity.

The Boundary Element Method (BEM) is a proven numerical prediction tool for computation of room acoustic transfer functions, as are required for auralization of a virtual space. In this paper, it is validated against case studies drawn from the "Ground Truth for Room Acoustical Simulation" database within a framework that includes source and receiver directivity. These aspects are often neglected but are respectively important to include for auralisation applications because source directivity is known to affect how a room is excited and because the human auditory system is sensitive to directional cues. The framework uses weighted-sums of spherical harmonic functions to represent both the source directivity to be simulated and the pressure field predicted in the vicinity of the receiver location, the coefficients of the former being fitted to measured directivity and those of the latter computed directly from the boundary data by evaluating a boundary integral. Three validation cases are presented, one of which includes a binaural receiver. The computed results match measurements closely for the two cases conducted in anechoic conditions but show some significant differences for the third room scenario; here, it is likely that uncertainty in boundary material data limited modelling accuracy.

Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2'-F-c-di-GMP.

Cyclic-di-GMP (c-di-GMP) is a central regulator of bacterial behavior. Various studies have implicated c-di-GMP in biofilm formation and virulence factor production in multitudes of bacteria. Hence it is expected that the disruption of c-di-GMP signaling could provide an effective means to disrupt biofilm and/or virulence factor formation in several bacteria of clinical relevance. C-di-GMP achieves the regulation of bacterial phenotype via binding to several effector molecules including transcription factors, enzymes and riboswitches. Crystal structure analyses of c-di-GMP effector molecules, in complex with the ligand, reveal that various classes of c-di-GMP receptors recognize this dinucleotide using different sets of recognition elements. Therefore, it is plausible that different analogues of c-di-GMP could be used to selectively modulate a specific class of c-di-GMP binding receptors, and hence modulate the bacterial phenotype. Thus far only a detailed study of the differential binding of c-di-GMP analogues to riboswitches, but not proteins, has been reported. In this report, we prepared various 2'-modified analogues of c-di-GMP and studied both polymorphisms of these analogues using DOSY NMR and the binding to several effector proteins, such as PilZ-containing proteins, diguanylate cyclases (DGC) containing I-sites, and phoshphodiesterases (PDE). 2'-Modification of c-di-GMP did not adversely affect the propensity to form higher aggregates, such as octameric forms, in the presence of potassium salts. Interestingly, we find that the selective binding to different classes of c-di-GMP binding proteins could be achieved with the 2'-modified analogues and that 2'-F analogue of c-di-GMP binds to the I-site of DGCs better (four times) than the native dinucleotide, c-di-GMP, whereas c-di-GMP binds to PDEs better (10 times) than 2'-F-c-di-GMP. 2'-F-c-di-GMP potently inhibits c-di-GMP synthesis by DGCs and hence raises the potential that cell permeable analogues of 2'-F-c-di-GMP could be used to disrupt c-di-GMP signaling in bacteria.

Prostate health index can stratify patients with Prostate Imaging Reporting and Data System score 3 lesions on magnetic resonance imaging to reduce prostate biopsies.

We aim to evaluate prostate health index as an additional risk-stratification tool in patients with Prostate Imaging Reporting and Data System score 3 lesions on multiparametric magnetic resonance imaging. Men with biochemical or clinical suspicion of having prostate cancer who underwent multiparametric magnetic resonance imaging in two tertiary centers (Queen Mary Hospital and Princess Margaret Hospital, Hong Kong, China) between January 2017 and June 2022 were included. Ultrasound-magnetic resonance imaging fusion biopsies were performed after prostate health index testing. Those who only had Prostate Imaging Reporting and Data System score 3 lesions were further stratified into four prostate health index risk groups and the cancer detection rates were analyzed. Out of the 747 patients, 47.3% had Prostate Imaging Reporting and Data System score 3 lesions only. The detection rate of clinically significant prostate cancer in this group was 15.0%. The cancer detection rates of clinically significant prostate cancer had statistically significant differences: 5.3% in prostate health index <25.0, 7.4% in prostate health index 25.0-34.9, 17.9% in prostate health index 35.0-54.9, and 52.6% in prostate health index ≥55.0 (P < 0.01). Among the patients, 26.9% could have avoided a biopsy with a prostate health index <25.0, at the expense of a 5.3% risk of missing clinically significant prostate cancer. Prostate health index could be used as an additional risk stratification tool for patients with Prostate Imaging Reporting and Data System score 3 lesions. Biopsies could be avoided in patients with low prostate health index, with a small risk of missing clinically significant prostate cancer.

Surprising acid/base and ion-sequestration chemistry of Sn9(4-): HSn9(3-), Ni@HSn9(3-), and the Sn9(3-) ion revisited.

K(4)Sn(9) dissolves in ethylenediamine (en) to give equilibrium mixtures of the diamagnetic HSn(9)(3-) ion along with K(x)Sn(9)((4-x)-) ion pairs, where x = 0, 1, 2, 3. The HSn(9)(3-) cluster is formed from the deprotonation of the en solvent and is the conjugate acid of Sn(9)(4-). DFT studies show that the structure is quite similar to the known isoelectronic RSn(9)(3-) ions (e.g., R = i-Pr). The hydrogen atom of HSn(9)(3-) (δ = 6.18 ppm) rapidly migrates among all nine Sn atoms in an intramolecular fashion; the Sn(9) core is also highly dynamic on the NMR time scale. The HSn(9)(3-) cluster reacts with Ni(cod)(2) to give the Ni@HSn(9)(3-) ion containing a hydridic hydrogen (δ = -28.3 ppm) that also scrambles across the Sn(9) cluster. The Sn(9)(4-) ion competes effectively with 2,2,2-crypt for binding K(+) in en solutions, and the pK(a) of HSn(9)(3-) is similar to that of en (i.e., Sn(9)(4-) is a very strong Brønsted base with a pK(b) comparable to that of the NH(2)CH(2)CH(2)NH(-) anion). Competition studies show that the HSn(9)(3-) ⇄ Sn(9)(4-) + H(+) equilibrium is fully reversible. The HSn(9)(3-) anion is present in significant concentrations in en solutions containing 2,2,2-crypt, yet it has gone undetected for over 30 years.

Source implementation to eliminate low-frequency artifacts in finite difference time domain room acoustic simulation.

The finite difference time domain (FDTD) method is a numerical technique that is straight forward to implement for the simulation of acoustic propagation. For room acoustics applications, the implementation of efficient source excitation and frequency dependent boundary conditions on arbitrary geometry can be seen as two of the most significant problems. This paper deals with the source implementation problem. Among existing source implementation methods, the hard source implementation is the simplest and computationally most efficient. Unfortunately, it generates a large low-frequency modulation in the measured time response. This paper presents a detailed investigation into these side effects. Surprisingly, some of these side effects are found to exist even if a transparent source implementation is used. By combing a time limited approach with a class of more natural source pulse function, this paper develops a source implementation method in FDTD that is as simple and computationally as efficient as a hard source implementation and yet capable of producing results that are virtually the same as a true transparent source. It is believed that the source implementation method developed in this paper will provide an improvement to the practical usability of the FDTD method for room acoustic simulation.

Conservative change to the phosphate moiety of cyclic diguanylic monophosphate remarkably affects its polymorphism and ability to bind DGC, PDE, and PilZ proteins.

The cyclic dinucleotide c-di-GMP is a master regulator of bacterial virulence and biofilm formation. The activations of c-di-GMP metabolism proteins, diguanylate cyclases (DGCs) and phosophodiesterases (PDEs), usually lead to diametrically opposite phenotypes in bacteria. Analogues of c-di-GMP, which can selectively modulate the activities of c-di-GMP processing proteins, will be useful chemical tools for studying and altering bacterial behavior. Herein we report that a conservative modification of one of the phosphate groups in c-di-GMP with a bridging sulfur in the phosphodiester linkage affords an analogue called endo-S-c-di-GMP. Computational, NMR (including DOSY), and CD experiments all reveal that, unlike c-di-GMP, endo-S-c-di-GMP does not readily form higher aggregates. The lower propensity of endo-S-c-di-GMP to form aggregates (as compared to that of c-di-GMP) is probably due to a higher activation barrier to convert from the "open" conformer (where the two guanines are on opposite faces) to the "closed" conformer (where the two guanines are on the same face). Consequently, endo-S-c-di-GMP has selectivity for proteins that bind monomeric but not dimeric c-di-GMP, which form from the "closed" conformer. For example, endo-S-c-di-GMP can inhibit the hydrolysis of c-di-GMP by RocR (a PDE enzyme that binds monomeric c-di-GMP) but did not bind to Alg44 (a PilZ protein) or regulate WspR (a DGC enzyme that has been shown to bind to dimeric c-di-GMP). This work demonstrates that selective binding to different classes of c-di-GMP binding proteins could be achieved by altering analogue conformer populations (conformational steering). We provide important design principles for the preparation of selective PDE inhibitors and reveal the role played by the c-di-GMP backbone in c-di-GMP polymorphism and binding to processing proteins.

Iliac artery dissection - A rare complication of renal transplantation: A case report and literature review.

External iliac artery dissection is a rare and under-reported vascular complication after renal transplantation. The etiology is yet to be fully understood. The presentation, investigation and management of this condition are highly variable. Here we report a 52-year-old man successfully treated by endovascular stenting with nitinol stents for an external iliac artery dissection proximal to the anastomosis.

Prefluorescent nitroxide probe for the highly sensitive determination of peroxyl and other radical oxidants.

Fluorescamine derivatized 3-amino-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (I) is shown to undergo an irreversible reaction with peroxyl radicals and other radical oxidants to generate a more highly fluorescent diamagnetic product (II) and thus can be used as a highly sensitive and versatile probe to determine oxidant production optically, either by monitoring the changes in fluorescence intensity, by HPLC analysis with fluorescence detection, or by a combination of both approaches. By changing the [O2]/[I] ratio, we show that peroxyl radicals can be detected and quantified preferentially in the presence of other radical oxidants. Detection of photochemically produced peroxyl radicals is achieved by employing 3-amino-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (3-ap) alone, followed by derivatization with fluorescamine. With employment of HPLC analysis, the detection limit of II at a S/N of 2 is approximately 3 nM for a 125 microL injection. Preliminary applications include the detection of peroxyl radicals generated thermally in soybean phosphatidylcholine liposomes and produced photochemically in tap water.

Substituent-dependent exchange mechanisms in highly fluxional RSn9(3-) anions.

119Sn NMR studies show that the RSn9(3-) ions (R=i-Pr, Sn(C6H11)3) are highly fluxional in solution, where the exchange mechanisms involve rapid migration of the R group in the latter but not in the former.

An analytical model for turbulence scattered rays in the shadow zone for outdoor sound propagation calculation.

In outdoor sound propagation, an inherent problem of the ray tracing method is its inability to determine the sound pressure level in the shadow zone, where geometrical rays do not penetrate. This is a serious problem in a turbulent atmosphere where significant sound energy will be scattered into the shadow. Empirical corrections that are determined from measurements or numerical simulations are limited to situations within the bounds of the empirical corrections. This paper describes a different approach where the ray tracing model is modified analytically into a scattered ray model. Rays are first diffracted from the shadow boundary, which is determined by the geometrical ray paths. The diffracted rays are then scattered by turbulence in their way to the receiver. The amount of scatter is determined from turbulence statistics that are determined from a Gaussian turbulence model. Most of the statistics are determined analytically except one element, which is determined empirically from numerical simulations. This turbulence scattered ray model is shown to have good accuracy against calculations based on the parabolic equation, and against previously published measurement data. It was found that the agreement is good both with and without turbulence, at distance up to 2 km from the shadow boundary.

Ketal Sugar Conversion Into Green Hydrocarbons by Faujasite Zeolite in a Typical Catalytic Cracking Process.

Fluidized catalytic cracking (FCC) converts hydrocarbons in the presence of a catalyst based on faujasite zeolite (USY and REY). While hydrocarbon is poorly reactive, biomass and its derived compounds are highly functionalized and not suitable to a typical FCC process. To overcome this limitation biomass was first converted into a dense and stable bio-crude composed mainly of ketal-sugar derivatives by using acetone in diluted acid. Here, a representative compound of this bio-crude, 1,2:3,5-di-O-isopropylidene-α-D-xylofuranose (DX) in n-hexane, was converted by USY and a commercial FCC catalyst containing USY, at 500°C, in a fixed bed and fluidized bed reactors, respectively. Faujasite Y is very efficient in converting DX. More than 95% conversion was observed in all tests. Over 60 wt.% was liquid products, followed by gas products and only around 10% or less in coke. The higher the catalyst activity the greater the aromatics in the liquid products and yet higher coke yields were observed. In particular, simulating more practical application conditions: using deactivated catalyst in a fluidized bed reactor, improved green hydrocarbons production (mono-aromatic up to 10 carbons and light hydrocarbon up to eight carbons) and unprecedented lower coke yield (≈5 wt.%) for bio-feeds. The present results further suggest that catalyst will play a primary role to convert the bio-crude into target hydrocarbons and overcome the transition of a non-renewable to a renewable refinery feed.

BioTarget: A Computational Framework Identifying Cancer Type Specific Transcriptional Targets of Immune Response Pathways.

Transcriptome data can provide information on signaling pathways active in cancers, but new computational tools are needed to more accurately quantify pathway activity and identify tissue-specific pathway features. We developed a computational method called "BioTarget" that incorporates ChIP-seq data into cellular pathway analysis. This tool relates the expression of transcription factor TF target genes (based on ChIP-seq data) with the status of upstream signaling components for an accurate quantification of pathway activity. This analysis also reveals TF targets expressed in specific contexts/tissues. We applied BioTarget to assess the activity of TBX21 and GATA3 pathways in cancers. TBX21 and GATA3 are TF regulators that control the differentiation of T cells into Th1 and Th2 helper cells that mediate cell-based and humoral immune responses, respectively. Since tumor immune responses can impact cancer progression, the significance of our pathway scores should be revealed by effective patient stratification. We found that low Th1/Th2 activity ratios were associated with a significantly poorer survival of stomach and breast cancer patients, whereas an unbalanced Th1/Th2 response was correlated with poorer survival of colon cancer patients. Lung adenocarcinoma and lung squamous cell carcinoma patients had the lowest survival rates when both Th1 and Th2 responses were high. Our method also identified context-specific target genes for TBX21 and GATA3. Applying the BioTarget tool to BCL6, a TF associated with germinal center lymphocytes, we observed that patients with an active BCL6 pathway had significantly improved survival for breast, colon, and stomach cancer. Our findings support the effectiveness of the BioTarget tool for transcriptome analysis and point to interesting associations between some immune-response pathways and cancer progression.

Gasoline from biomass through refinery-friendly carbohydrate-based bio-oil produced by ketalization.

The introduction of biomass-derived compounds as an alternative feed into the refinery structure that already exists can potentially converge energy uses with ecological sustainability. Herein, we present an approach to produce a bio-oil based on carbohydrate-derived isopropylidene ketals obtained by reaction with acetone under acidic conditions directly from second-generation biomass. The obtained bio-oil showed a greater chemical inertness and miscibility with gasoil than typical bio-oil from fast pyrolysis. Catalytic upgrading of the bio-oil over zeolites (USY and Beta) yielded gasoline with a high octane number. Moreover, the co-processing of gasoil and bio-oil improved the gasoline yield and quality compared to pure gasoil and also reduced the amount of oxygenated compounds and coke compared with pure bio-oil, which demonstrates a synergistic effect.

Trapping a labile adduct formed between an ortho-quinone methide and 2'-deoxycytidine.

Selective oxidation by bis[(trifluoroacetoxy)iodo]benzene (BTI) provides an effective trap for quenching adducts formed reversibly between dC and an ortho-quinone methide (QM) under physiological conditions. A model adduct generated by 4-methyl-o-QM and 2'-deoxycytidine is rapidly converted by intramolecular cyclization and loss of aromaticity to a characteristic product for quantifying QM alkylation. However, BTI induces a surprising rearrangement driven by overoxidation of a derivative lacking an alkyl substituent at the 4-position of the QM.

Solution dynamics and gas-phase chemistry of Pd2@Sn18 4-.

Sn9(4-) reacts with Pd(PPh3)4 in ethylenediamine/toluene solvent mixtures in the presence of 2,2,2-cryptand to give the Pd2@Sn18(4-) cluster as the K(2,2,2,-crypt)+ salt. The cluster is isostructural with Pd2@Ge18(4-) and has a nuclearity different from that of the Pt and Ni analogues, Ni2@Sn17(4-) and Pt2@Sn17(4-). The Pd2@Sn18(4-) ion has a deltahedral capsulelike structure with 40 cluster bonding electrons and is the largest free-standing polystannide characterized to date. Like Pt2@Sn17(4-), the Pd2@Sn18(4-) complex is highly dynamic in solution, showing a single (119)Sn NMR resonance indicative of an intramolecular liquidlike dynamic exchange. LDI-MS studies of the crystalline sample show extensive fragmentation and the formation of five gas-phase cluster series: Sn(x)- (1 < x < 12), PdSn(x-1) - (4 < x < 18), Pd 2Sn(x-2) - (6 < x < 21), Pd3Sn(x-3) - (8 < x < 21), and Pd 4Sn(x-4) - (13 < x < 21). The most abundant ion in the gas phase is the PdSn(10) - cluster, which presumably has an Sn(10) bicapped-square-antiprismatic structure with an endohedral Pd (e.g., Ni@Pb(10)(2-)).

Refolding foldamers: triazene-arylene oligomers that change shape with chemical stimuli.

We describe the preparation of five triazene-arylene oligomers (3, 4, 7, 8, and 11) and investigations of their folding properties in aqueous solution. These oligomers contain four 2-fold rotors and populate a conformational ensemble comprising at least 10 states. Extensive 1D and 2D NMR studies as well as X-ray crystallography establish that the presence of three members of the cucurbit[n]uril family (CB[n]), CB[10], CB[7], and CB[8], results in the selective population of the (a,a,a,a)-, (a,s,s,a)-, and (a,a,a,s)-conformers. As a result of the high affinity and highly selective binding properties of the CB[n] family, it is possible to fold a single foldamer strand (3) into the CB[8].(a,a,a,s)-3 conformer by the addition of CB[8], then unfold and refold it into the CB[7].(a,s,s,a)-3.CB[7] conformer by addition of CB[7] and 3,5-dimethylaminoadamantane (17), then unfold and refold it again into the CB[10].(a,a,a,a)-3 conformer by addition of CB[10].CB[5] and aminoadamantane (18). The transformation of CB[8].(a,a,a,s)-3 into CB[7].(a,s,s,a)-3.CB[7] proceeds through the intermediacy of CB [8].(a,a,s,a)-3.CB[7], which enhances the rate of dissociation of strand 3 from CB[8].

Cluster growth and fragmentation in the highly fluxional platinum derivatives of Sn9 4-: synthesis, characterization, and solution dynamics of Pt2@Sn17 4- and Pt@Sn9H 3-.

Sn94- reacts with Pt(PPh3)4 in ethylenediamine/toluene solvent mixtures in the presence of 2,2,2-cryptand to give four different complexes: "Rudolph's complex" of proposed formula [Sn9Pt(PPh3)x]4- (2), the previously reported [Pt@Sn9Pt(PPh3)]2- ion (3), and the title complexes Pt2@Sn174- (4) and Pt@Sn9H3- (5). The use of Pt(norbornene)3 instead of Pt(PPh3)4 gives complex 4 exclusively. The structure of 4 contains two Pt atoms centered in a capsule-shaped Sn17 cage. The complex is highly dynamic in solution showing single, mutually coupled 119Sn and 195Pt NMR resonances indicative of an intramolecular liquidlike dynamic exchange process. Complex 5 has been characterized by selectively decoupled 1H, 119Sn, and 195Pt NMR experiments and shows similar liquidlike fluxionality. In addition, the H atom scrambles across the cage showing small couplings to both Sn and Pt atoms. Neither 3 nor 4 obeys Wades rules; they adopt structures more akin to the subunits in alloys such as PtSn4. The structural and chemical relevance to supported PtSn4 heterogeneous catalysts is discussed.