Microscopic origin of tunable assembly forces in chiral active environments.

Across a variety of spatial scales, from nanoscale biological systems to micron-scale colloidal systems, equilibrium self-assembly is entirely dictated by-and therefore limited by-the thermodynamic properties of the constituent materials. In contrast, nonequilibrium materials, such as self-propelled active matter, expand the possibilities for driving the assemblies that are inaccessible in equilibrium conditions. Recently, a number of works have suggested that active matter drives or accelerates self-organization, but the emergent interactions that arise between solutes immersed in actively driven environments are complex and poorly understood. Here, we analyze and resolve two crucial questions concerning actively driven self-assembly: (i) how, mechanistically, do active environments drive self-assembly of passive solutes? (ii) Under which conditions is this assembly robust? We employ the framework of odd hydrodynamics to theoretically explain numerical and experimental observations that chiral active matter, i.e., particles driven with a directional torque, produces robust and long-ranged assembly forces. Together, these developments constitute an important step towards a comprehensive theoretical framework for controlling self-assembly in nonequilibrium environments.

The effect of cycles of genomic selection on the wheat (T. aestivum) genome.

KEY MESSAGE: We documented changes in the wheat genome attributed to genomic selection including loss of diversity, and changes in population structure and linkage disequilibrium patterns. We conclude that training and prediction populations need to co-evolve instead of the use of a static training population. Genomic selection (GS) is widely used in plant breeding to shorten breeding cycles. Our objective was to assess the impact of rapid cycling GS on the wheat genome. We used 3927 markers to genotype a training population (YTP) and individuals from five cycles (YC1-YC5) of GS for grain yield. We assessed changes of allele frequency, genetic distance, population structure, and linkage disequilibrium (LD). We found 27.3% of all markers had a significant allele frequency change by YC5, 18% experienced a significant change attributed to selection, and 9.3% had a significant change due to either drift or selection. A total of 725 of 3927 markers were fixed by YC5 with selection fixing 7.3% of the 725 markers. The genetic distance between cycles increased over time. The Fst value of 0.224 between YTP and YC5 indicates their relationship was low. The number LD blocks decreased over time and the correlation between LD matrices also decreased over time. Overall, we found a reduction in genetic diversity, increased genetic differentiation of cycles from the training population, and restructuring of the LD patterns over cycles. The accuracy of GS depends on the genomic similarity of the training population and the prediction populations. Our results show that the similarity can decline rapidly over cycles of GS and compromise the predictive ability of the YTP-based model. Our results support implementing a GS scheme where the training and prediction populations co-evolve instead of the use of a static training population.

Supervised learning and the finite-temperature string method for computing committor functions and reaction rates.

A central object in the computational studies of rare events is the committor function. Though costly to compute, the committor function encodes complete mechanistic information of the processes involving rare events, including reaction rates and transition-state ensembles. Under the framework of transition path theory, Rotskoff et al. [Proceedings of the 2nd Mathematical and Scientific Machine Learning Conference, Proceedings of Machine Learning Research (PLMR, 2022), Vol. 145, pp. 757-780] proposes an algorithm where a feedback loop couples a neural network that models the committor function with importance sampling, mainly umbrella sampling, which collects data needed for adaptive training. In this work, we show additional modifications are needed to improve the accuracy of the algorithm. The first modification adds elements of supervised learning, which allows the neural network to improve its prediction by fitting to sample-mean estimates of committor values obtained from short molecular dynamics trajectories. The second modification replaces the committor-based umbrella sampling with the finite-temperature string (FTS) method, which enables homogeneous sampling in regions where transition pathways are located. We test our modifications on low-dimensional systems with non-convex potential energy where reference solutions can be found via analytical or finite element methods, and show how combining supervised learning and the FTS method yields accurate computation of committor functions and reaction rates. We also provide an error analysis for algorithms that use the FTS method, using which reaction rates can be accurately estimated during training with a small number of samples. The methods are then applied to a molecular system in which no reference solution is known, where accurate computations of committor functions and reaction rates can still be obtained.

Genome-Wide Association Study Reveals Novel Genetic Loci for Quantitative Resistance to Septoria Tritici Blotch in Wheat (Triticum aestivum L.).

Septoria tritici blotch, caused by the fungus Zymoseptoria titici, poses serious and persistent challenges to wheat cultivation in Ethiopia and worldwide. Deploying resistant cultivars is a major component of controlling septoria tritici blotch (STB). Thus, the objective of this study was to elucidate the genomic architecture of STB resistance in an association panel of 178 bread wheat genotypes. The association panel was phenotyped for STB resistance, phenology, yield, and yield-related traits in three locations for 2 years. The panel was also genotyped for single nucleotide polymorphism (SNP) markers using the genotyping-by-sequencing (GBS) method, and a total of 7,776 polymorphic SNPs were used in the subsequent analyses. Marker-trait associations were also computed using a genome association and prediction integrated tool (GAPIT). The study then found that the broad-sense heritability for STB resistance ranged from 0.58 to 0.97 and 0.72 to 0.81 at the individual and across-environment levels, respectively, indicating the presence of STB resistance alleles in the association panel. Population structure and principal component analyses detected two sub-groups with greater degrees of admixture. A linkage disequilibrium (LD) analysis in 338,125 marker pairs also detected the existence of significant (p ≤ 0.01) linkage in 27.6% of the marker pairs. Specifically, in all chromosomes, the LD between SNPs declined within 2.26-105.62 Mbp, with an overall mean of 31.44 Mbp. Furthermore, the association analysis identified 53 loci that were significantly (false discovery rate, FDR, <0.05) associated with STB resistance, further pointing to 33 putative quantitative trait loci (QTLs). Most of these shared similar chromosomes with already published Septoria resistance genes, which were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A,3 B, 3D, 4A, 5A, 5B, 6A, 7A, 7B, and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D, and 6B appeared to be novel. Dissecting the detected loci on IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions that are involved in plant defense responses. These putative QTLs explained 2.7-13.2% of the total phenotypic variation. Seven of the QTLs (R 2 = 2.7-10.8%) for STB resistance also co-localized with marker-trait associations (MTAs) for agronomic traits. Overall, this analysis reported on putative QTLs for adult plant resistance to STB and some important agronomic traits. The reported and novel QTLs have been identified previously, indicating the potential to improve STB resistance by pyramiding QTLs by marker-assisted selection.

The clot thickens: role of mechanical thrombectomy in intermediate to high-risk pulmonary embolism in the peri-operative setting-a case report.

BACKGROUND: European Society of Cardiology (ESC) recommends catheter-directed thrombectomy for management of high-risk pulmonary embolism (PE) with contraindications to thrombolytics or in patients that have failed thrombolytic therapy, as well as intermediate-risk PE with haemodynamic deterioration. In this case report, the role of catheter-directed mechanical thrombectomy is highlighted in the urgent peri-operative setting. CASE SUMMARY: A 71-year-old female presented with 10 days of progressive lower extremity weakness and was found to have malignant cord compression along with incidental saddle, intermediate-high-risk PE that extended to all lobes on chest computed tomography. Given the intermediate to high-risk PE with acute cor pulmonale, urgent need for surgery, and risk of haemodynamic collapse upon induction of general anaesthesia, the decision was made to proceed with urgent percutaneous treatment of the PE. Percutaneous catheter-directed thrombectomy was successfully performed. The patient returned to the intensive care unit in stable condition and was able to then receive urgent cord decompression and further treatment for malignancy with no complication. DISCUSSION: In this case, single-session thrombectomy resulted in rapid reduction of pre-operative cardiopulmonary risk by alleviating the right ventricular strain, allowing urgent cord decompression surgery to proceed with optimized haemodynamics, no bleeding events, and no further oxygen requirements. While peri-operative risk stratification for cardiovascular outcomes is well established in current guidelines, there are no clear guidelines for peri-operative risk stratification in the setting of pulmonary embolism. The importance of the multidisciplinary PE Response Team is thus emphasized, as well as the importance of continuous evaluation of clinical decompensation in PE.

Catheter-Directed Thrombectomy for Pulmonary Embolism in the Setting of Acute Stroke.

A 79-year-old male presented with an acute stroke and was treated with tissue plasminogen activator (tPA). His neurological symptoms improved, but he subsequently developed hemodynamic instability requiring intubation and vasopressors. Imaging studies revealed a massive pulmonary embolism as the cause of his worsening clinical picture. Mechanical thrombectomy using traditional devices was deemed too risky as the patient could not safely tolerate the usual anticoagulation dosage these devices require. The Penumbra Indigo® system (Alameda, CA, USA) was thus chosen for its ability to achieve thrombus aspiration within a lower therapeutic heparin range. Pulmonary artery aspiration thrombectomy was done using the device, and three days after the procedure, he was extubated and weaned completely off vasopressors. The therapy's efficacy despite the patient's unique life-threatening conditions demonstrates a novel application of the state-of-the-art pulmonary embolism treatment currently in research.

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia.

Grain yield is a trait of paramount importance in the breeding of all cereals. In wheat (Triticum aestivum L.), yield has steadily increased since the Green Revolution, though the current rate of increase is not forecasted to keep pace with demand due to growing world population and increasing affluence. While several genome-wide association studies (GWAS) on yield and related component traits have been performed in wheat, the previous lack of a reference genome has made comparisons between studies difficult. In this study, a GWAS for yield and yield-related traits was carried out on a population of 322 soft red winter wheat lines across a total of four rain-fed environments in the state of Virginia using single-nucleotide polymorphism (SNP) marker data generated by a genotyping-by-sequencing (GBS) protocol. Two separate mixed linear models were used to identify significant marker-trait associations (MTAs). The first was a single-locus model utilizing a leave-one-chromosome-out approach to estimating kinship. The second was a sub-setting kinship estimation multi-locus method (FarmCPU). The single-locus model identified nine significant MTAs for various yield-related traits, while the FarmCPU model identified 74 significant MTAs. The availability of the wheat reference genome allowed for the description of MTAs in terms of both genetic and physical positions, and enabled more extensive post-GWAS characterization of significant MTAs. The results indicate a number of promising candidate genes contributing to grain yield, including an ortholog of the rice aberrant panicle organization (APO1) protein and a gibberellin oxidase protein (GA2ox-A1) affecting the trait grains per square meter, an ortholog of the Arabidopsis thaliana mother of flowering time and terminal flowering 1 (MFT) gene affecting the trait seeds per square meter, and a B2 heat stress response protein affecting the trait seeds per head.

Outcomes following radiation for cutaneous squamous cell carcinoma of the head and neck: Associations between immune suppression and recurrence.

BACKGROUND: Data evaluating outcomes and patterns of recurrence following radiation therapy (RT) for cutaneous squamous cell carcinoma (cSCC) of the head and neck are limited. METHODS: We performed a retrospective analysis of 111 head and neck cSCC patients treated with RT at 4 affiliated institutions. RESULTS: With median follow-up of 7 months, there were 29 (26%) recurrences, 73% of which were nodal (n = 21). Immunosuppression (IS) was the only factor associated with recurrence (47% in IS, 22% in non-IS, P = .04), and also with time to recurrence in multivariate analysis (HR 5.5; P = .03). No factors were associated with recurrence among patients who received definitive RT. The majority of patients who recurred were salvaged with surgery (n = 20, 69%). CONCLUSION: In a cohort of cSCC treated with radiotherapy, there was an association between IS and increased failure risk. The majority of failures were salvaged surgically.

The impact of global warming on germination and seedling emergence in Alliaria petiolata, a woodland species with dormancy loss dependent on low temperature.

The impact of global warming on seed dormancy loss and germination was investigated in Alliaria petiolata (garlic mustard), a common woodland/hedgerow plant in Eurasia, considered invasive in North America. Increased temperature may have serious implications, since seeds of this species germinate and emerge at low temperatures early in spring to establish and grow before canopy development of competing species. Dormancy was evaluated in seeds buried in field soils. Seedling emergence was also investigated in the field, and in a thermogradient tunnel under global warming scenarios representing predicted UK air temperatures through to 2080. Dormancy was simple, and its relief required the accumulation of low temperature chilling time. Under a global warming scenario, dormancy relief and seedling emergence declined and seed mortality increased as soil temperature increased along a thermal gradient. Seedling emergence advanced with soil temperature, peaking 8 days earlier under 2080 conditions. The results indicate that as mean temperature increases due to global warming, the chilling requirement for dormancy relief may not be fully satisfied, but seedling emergence will continue from low dormancy seeds in the population. Adaptation resulting from selection of this low dormancy proportion is likely to reduce the overall population chilling requirement. Seedling emergence is also likely to keep pace with the advancement of biological spring, enabling A. petiolata to maintain its strategy of establishment before the woodland canopy closes. However, this potential for adaptation may be countered by increased seed mortality in the seed bank as soils warm.

Problems and Progress regarding Sex Bias and Omission in Neuroscience Research.

Neuroscience research has historically ignored female animals. This neglect comes in two general forms. The first is sex bias, defined as favoring one sex over another; in this case, male over female. The second is sex omission, which is the lack of reporting sex. The recognition of this phenomenon has generated fierce debate across the sciences. Here we test whether sex bias and omission are still present in the neuroscience literature, whether studies employing both males and females neglect sex as an experimental variable, and whether sex bias and omission differs between animal models and journals. To accomplish this, we analyzed the largest-ever number of neuroscience articles for sex bias and omission: 6636 articles using mice or rats in 6 journals published from 2010 to 2014. Sex omission is declining, as increasing numbers of articles report sex. Sex bias remains present, as increasing numbers of articles report the sole use of males. Articles using both males and females are also increasing, but few report assessing sex as an experimental variable. Sex bias and omission varies substantially by animal model and journal. These findings are essential for understanding the complex status of sex bias and omission in neuroscience research and may inform effective decisions regarding policy action.

Synthesis and Photoisomerization of Substituted Dibenzofulvene Molecular Rotors.

The synthesis, spectral and structural characterization, and photoisomerization of a family of 2-substituted dibenzofulvene molecular actuators based on (2,2,2-triphenylethylidene)fluorene (TEF) are reported. The 2-substituted species investigated are nitro (NTEF), cyano (CTEF), and iodo (ITEF). X-ray structures of these three compounds and three intermediates were determined to assign alkene configuration and investigate the effects of the 2-substituents on steric gearing. The addition-elimination reaction of Z-9 with trityl anion to form Z-10 proceeded with complete retention of configuration. Rates of photoisomerization were measured at irradiation wavelengths between 266-355 nm in acetonitrile/dioxane solutions at room temperature. Photoisomerization quantum yields (φ) were calculated by means of a mathematical model that accounts for a certain degree of photodecomposition in the cases of CTEF and ITEF. Quantum yields vary significantly with substituent, having maximum values of φ=0.26 for NTEF, 0.39 for CTEF, and 0.50 for ITEF. NTEF is photochemically robust and has a large quantum yield for photoisomerization in the near-UV, making it a particularly promising drive rotor moiety for light-powered molecular devices.

Joint linkage QTL analyses for partial resistance to Phytophthora sojae in soybean using six nested inbred populations with heterogeneous conditions.

Partial resistance to Phytophthora sojae in soybean is controlled by multiple quantitative trait loci (QTL). With traditional QTL mapping approaches, power to detect such QTL, frequently of small effect, can be limited by population size. Joint linkage QTL analysis of nested recombinant inbred line (RIL) populations provides improved power to detect QTL through increased population size, recombination, and allelic diversity. However, uniform development and phenotyping of multiple RIL populations can prove difficult. In this study, the effectiveness of joint linkage QTL analysis was evaluated on combinations of two to six nested RIL populations differing in inbreeding generation, phenotypic assay method, and/or marker set used in genotyping. In comparison to linkage analysis in a single population, identification of QTL by joint linkage analysis was only minimally affected by different phenotypic methods used among populations once phenotypic data were standardized. In contrast, genotyping of populations with only partially overlapping sets of markers had a marked negative effect on QTL detection by joint linkage analysis. In total, 16 genetic regions with QTL for partial resistance against P. sojae were identified, including four novel QTL on chromosomes 4, 9, 12, and 16, as well as significant genotype-by-isolate interactions. Resistance alleles from PI 427106 or PI 427105B contributed to a major QTL on chromosome 18, explaining 10-45% of the phenotypic variance. This case study provides guidance on the application of joint linkage QTL analysis of data collected from populations with heterogeneous assay conditions and a genetic framework for partial resistance to P. sojae.

Novel quantitative trait loci for partial resistance to Phytophthora sojae in soybean PI 398841.

Phytophthora root and stem rot caused by Phytophthora sojae Kaufmann and Gerdemann is one of the most severe soybean [Glycine max (L.) Merr] diseases in the USA. Partial resistance is as effective in managing this disease as single-gene (Rps gene)-mediated resistance and is more durable. The objective of this study was to identify quantitative trait loci (QTL) associated with partial resistance to P. sojae in PI 398841, which originated from South Korea. A population of 305 F7:8 recombinant inbred lines derived from a cross of OX20-8 × PI 398841 was used to evaluate partial resistance against P. sojae isolate C2S1 using a tray test. Composite interval mapping using a genome-wide logarithm of odd (LOD) threshold detected three QTL on chromosomes 1, 13, and 18, which individually explained 4-16 % of the phenotypic variance. Seven additional QTL, accounting for 2-3 % of phenotypic variance each, were identified using chromosome-wide LOD thresholds. Seven of the ten QTL for resistance to P. sojae were contributed by PI 398841. Seven QTL co-localized with known Rps genes and previously reported QTL for soil-borne root pathogens, isoflavone, and seed oil. Three QTL on chromosomes 3, 13, and 18 co-localized with known Rps genes, but PI 398841 did not exhibit an Rps gene-mediated resistance response following inoculation with 48 different isolates of P. sojae. PI 398841 is potentially a source of novel genes for improving soybean cultivars for partial resistance to P. sojae.

Differential binding between PatS C-terminal peptide fragments and HetR from Anabaena sp. PCC 7120.

Heterocyst differentiation in the filamentous cyanobacterium Anabaena sp. strain PCC 7120 occurs at regular intervals under nitrogen starvation and is regulated by a host of signaling molecules responsive to availability of fixed nitrogen. The heterocyst differentiation inhibitor PatS contains the active pentapeptide RGSGR (PatS-5) at its C-terminus considered the minimum PatS fragment required for normal heterocyst pattern formation. PatS-5 is known to bind HetR, the master regulator of heterocyst differentiation, with a moderate affinity and a submicromolar dissociation constant. Here we characterized the affinity of HetR for several PatS C-terminal fragments by measuring the relative ability of each fragment to knockdown HetR binding to DNA in electrophoretic mobility shift assays and using isothermal titration calorimetry (ITC). HetR bound to PatS-6 (ERGSGR) >30 times tighter (K(d) = 7 nM) than to PatS-5 (K(d) = 227 nM) and >1200 times tighter than to PatS-7 (DERGSGR) (K(d) = 9280 nM). No binding was detected between HetR and PatS-8 (CDERGSGR). Quantitative binding constants obtained from ITC measurements were consistent with qualitative results from the gel shift knockdown assays. CW EPR spectroscopy confirmed that PatS-6 bound to a MTSL spin-labeled HetR L252C mutant at a 10-fold lower concentration compared to PatS-5. Substituting the PatS-6 N-terminal glutamate to aspartate, lysine, or glycine did not alter binding affinity, indicating that neither the charge nor size of the N-terminal residue's side chain played a role in enhanced HetR binding to PatS-6, but rather increased binding affinity resulted from new interactions with the PatS-6 N-terminal residue peptide backbone.

Solution structure of the HIV-1 exon splicing silencer 3.

Alternative splicing of the human immunodeficiency virus type 1 (HIV-1) genomic RNA is necessary to produce the complete viral protein complement, and aberrations in the splicing pattern impair HIV-1 replication. Genome splicing in HIV-1 is tightly regulated by the dynamic assembly/disassembly of trans host factors with cis RNA control elements. The host protein, heterogeneous nuclear ribonucleoprotein (hnRNP) A1, regulates splicing at several highly conserved HIV-1 3' splice sites by binding 5'-UAG-3' elements embedded within regions containing RNA structure. The physical determinants of hnRNP A1 splice site recognition remain poorly defined in HIV-1, thus precluding a detailed understanding of the molecular basis of the splicing pattern. Here, the three-dimensional structure of the exon splicing silencer 3 (ESS3) from HIV-1 has been determined using NMR spectroscopy. ESS3 adopts a 27-nucleotide hairpin with a 10-bp A-form stem that contains a pH-sensitive A(+)C wobble pair. The seven-nucleotide hairpin loop contains the high-affinity hnRNP-A1-responsive 5'-UAGU-3' element and a proximal 5'-GAU-3' motif. The NMR structure shows that the heptaloop adopts a well-organized conformation stabilized primarily by base stacking interactions reminiscent of a U-turn. The apex of the loop is quasi-symmetric with UA dinucleotide steps from the 5'-GAU-3' and 5'-UAGU-3' motifs stacking on opposite sides of the hairpin. As a step towards understanding the binding mechanism, we performed calorimetric and NMR titrations of several hnRNP A1 subdomains into ESS3. The data show that the UP1 domain forms a high-affinity (K(d)=37.8±1.1 nM) complex with ESS3 via site-specific interactions with the loop.

Evidence for direct binding between HetR from Anabaena sp. PCC 7120 and PatS-5.

HetR, master regulator of heterocyst differentiation in the filamentous cyanobacterium Anabaena sp. strain PCC 7120, stimulates heterocyst differentiation via transcriptional autoregulation and is negatively regulated by PatS and HetN, both of which contain the active pentapeptide RGSGR. However, the direct targets of PatS and HetN remain uncertain. Here, we report experimental evidence for direct binding between HetR and the C-terminal RGSGR pentapeptide, PatS-5. Strains with a hetR allele coding for conservative substitutions at residues 250-256 had altered patterns of heterocysts and, in some cases, reduced sensitivity to PatS-5. Cysteine scanning mutagenesis coupled with electron paramagnetic resonance (EPR) spectroscopy showed quenching of spin label motion at HetR amino acid 252 upon titration with PatS-5, indicating direct binding of PatS-5 to HetR. Gel shift assays indicated that PatS-5 disrupted binding of HetR to a 29 base pair inverted-repeat-containing DNA sequence upstream from hetP. Double electron-electron resonance EPR experiments confirmed that HetR existed as a dimer in solution and indicated that PatS-5 bound to HetR without disrupting the dimer form of HetR. Isothermal titration calorimetry experiments corroborated direct binding of PatS-5 to HetR with a K(d) of 227 nM and a 1:1 stoichiometry. Taken together, these results indicated that PatS-5 disrupted HetR binding to DNA through a direct HetR/PatS interaction. PatS-5 appeared to either bind in the vicinity of HetR amino acid L252 or, alternately, to bind in a remote site that leads to constrained motion of this amino acid via an allosteric effect or change in tertiary structure.

Polygenic inheritance of canopy wilting in soybean [Glycine max (L.) Merr.].

As water demand for agriculture exceeds water availability, cropping systems need to become more efficient in water usage, such as deployment of cultivars that sustain yield under drought conditions. Soybean cultivars differ in how quickly they wilt during water-deficit stress, and this trait may lead to yield improvement during drought. The objective of this study was to determine the genetic mechanism of canopy wilting in soybean using a mapping population of recombinant inbred lines (RILs) derived from a cross between KS4895 and Jackson. Canopy wilting was rated in three environments using a rating scale of 0 (no wilting) to 100 (severe wilting and plant death). Transgressive segregation was observed for the RIL population with the parents expressing intermediate wilting scores. Using multiple-loci analysis, four quantitative trait loci (QTLs) on molecular linkage groups (MLGs) A2, B2, D2, and F were detected (P

Impact of acquisition geometry, image processing, and patient size on lesion detection in whole-body 18F-FDG PET.

UNLABELLED: The aim of this work was to develop a rigorous evaluation methodology to assess performance of different acquisition and processing methods for variable patient sizes in the context of lesion detection in whole-body (18)F-FDG PET. METHODS: Fifty-nine bed positions were acquired in 32 patients in 2-dimensional (2D) and 3-dimensional (3D) modes 1-4 h after (18)F-FDG injection (740 MBq) using a BGO PET scanner. Three spheres (1.0-, 1.3-, and 1.6-cm diameter) containing (68)Ge were also imaged separately in air, at locations corresponding to possible lesion sites in 2D and 3D (590 targets per condition). Each bed position was acquired for 7 min in 2D and 6 min in 3D and corrected for randoms using delayed window randoms subtraction (DWS) or randoms variance reduction (RVR). Sphere sinograms were attenuated using the 2D or 3D attenuation map derived from the transmission scan of the patient, after scaling 2D and 3D sinograms with identical factors to ensure marginal detectability. Resulting 2D sinograms were reconstructed with filtered backprojection (FBP) and ordered-subsets expectation maximization (OSEM) without any scatter or attenuation correction (FBP-NATS and OSEM-NATS) or corrected for scatter and attenuation and reconstructed using FBP (FBP-ATT) or attenuation-weighted OSEM (AWOSEM). 3D sinograms were processed identically after Fourier rebinning. Next, reconstructed volumes were compared on the basis of performance of a 3-channel Hotelling observer (CHO-SNR [SNR is signal-to-noise ratio]) in detecting the presence of a sphere of unknown size on an anatomic background while modeling observer noise. The noise equivalent count (NEC) rate was computed in 2D and 3D for 3 different phantoms sizes (40, 60, and 95 kg) and compared with lesion detection SNR. RESULTS: 3D imaging yielded better lesion detectability than 2D (P < 0.025, 2-tailed paired t test) in patients of normal size (body mass index [BMI] < or = 31). However, 2D imaging yielded better lesion detectability than 3D in large patients (BMI > 31), as 3D performance deteriorated in large patients (P < 0.05). 2D and 3D yielded similar results for different lesion sizes. CHO-SNR were 40% greater for AWOSEM, FBP-ATT, and FBPNAT than for OSEM (P < 0.05), and AWOSEM yielded significantly better lesion detectability than did FBP. In all patients, RVR yielded a systematic improvement in CHO-SNR over DWS in both 2D and 3D. radicalNEC was characterized by a behavior similar to that of SNR(CHO) for the 3 different phantom sizes considered in this study.

CT and PET: early prognostic indicators of response to imatinib mesylate in patients with gastrointestinal stromal tumor.

OBJECTIVE: We report results from a pilot study aimed at optimizing the use of CT bidimensional measurements and 18F-FDG PET maximum standardized uptake values (SUVs-(max)) for determining response to prolonged imatinib mesylate treatment in patients with advanced gastrointestinal stromal tumors (GISTs). SUBJECTS AND METHODS: Sixty-three patients enrolled in a multicenter trial evaluating imatinib mesylate therapy for advanced GIST underwent FDG PET at baseline and 1 month after initiation of treatment. Of these 63 patients, 58 underwent concomitant CT. Time-to-treatment failure (TTF) was used as the outcome measure. Patients were followed up over a range of 23.7 to 37 months (median, 31.7 months). The predictive power of change in CT bidimensional measurements, change in PET SUVmax, and PET SUVmax at 1 month after initiation of treatment were determined, optimized, and compared. The effectiveness of combining metrics was also evaluated. RESULTS: Both a threshold PET SUVmax value of 2.5 at 1 month (p = 0.04) and the European Organization for Research and Treatment of Cancer (EORTC) criteria for partial response on FDG PET (25% reduction in PET SUVmax) at 1 month (p = 0.004) were predictive of prolonged treatment success. The Southwest Oncology Group (SWOG) criteria for partial response ((3) 50% reduction in CT bidimensional measurements) at 1 month were not predictive (p = 0.55) of TTF. Optimizing metrics improved results performance. An optimized PET SUVmax threshold of 3.4 (p = 0.00002), a reduction in the SUVmax of 40% (p = 0.002), and an optimized CT bidimensional measurement threshold--that is, no growth from baseline to 1 month (p = 0.00005)--outperformed the existing standards (i.e., EORTC and SWOG criteria). Combinations of metrics did not improve performance. CONCLUSION: The two best metrics were the optimized PET SUVmax threshold of 3.4 at 1 month (p = 0.00002) and the optimized CT bidimensional measurement threshold (no growth from baseline to 1 month, p = 0.00005) in this patient group.