Full Sequence Research Articles

Abstract 3233: A novel triple humanized B-hPD-1/hPD-L1/hCCR8 mouse model to evaluate in vivo efficacy of combination therapies

Abstract Regulatory T cells (Tregs) play an immunosuppressive role in the tumor microenvironment (TME), such that altering or depleting Treg function has emerged as an important anti-tumor strategy. Targeting CCR8, which is highly expressed in tumor-infiltrating Tregs, has shown its potency in reducing tumor burden and increasing responsiveness to immune-checkpoint blockade therapy. Collectively, this suggests a need for preclinical models that support Treg-targeted therapies. To address this, Biocytogen developed a triple humanized (B-hPD-1/hPD-L1/hCCR8) mouse model to evaluate in vivo efficacy of combination therapies. In this model, the full coding sequence of murine Ccr8 was replaced by the full coding sequence of human CCR8, while murine Pd-1 and Pd-l1 IgV domains were replaced by their human counterpart gene sequences. Human PD-1 and PD-L1 protein expression was confirmed in B-hPD-1/hPD-L1/hCCR8 mice by flow cytometry, and human CCR8 protein expression was observed in MC38 tumors harvested from B-hPD-1/hPD-L1/hCCR8 mice. Finally, combination therapy using anti-human PD-1 and anti-human CCR8 antibodies were effective in controlling B-hPD-L1 MC38 tumor growth in B-hPD-1/hPD-L1/hCCR8 mice. Altogether, this line provides a powerful preclinical model for in vivo evaluation of therapeutic antibodies. Citation Format: Linlin Wang, Xiao Liu, James Jin, Yuxiang Yu. A novel triple humanized B-hPD-1/hPD-L1/hCCR8 mouse model to evaluate in vivo efficacy of combination therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3233.

Abstract 5208: Development of immunodeficient mice expressing human IL3, GM-CSF, CSF1 and THPO for improved human myeloid and lymphoid cell reconstitution

Abstract Mice reconstituted with human immune cells are essential tools to study human immune reactions in vivo, including those involving cancer immunotherapies. A major limitation of these models is the poor development of human myeloid cells to mediate effective human immune cell-tumor interactions. This is because hematopoietic cells are highly dependent on several human cytokines for efficient differentiation, maturation, and survival. THPO (thrombopoietin) can enhance the maintenance of functional human hematopoietic stem cells, and stimulates the production and differentiation of megakaryocytes, which produce large numbers of platelets in the bone marrow. IL3 (interleukin 3), GM-CSF (granulocyte-macrophage colony-stimulating factor, CSF2) and CSF1 (macrophage colony-stimulating factor, M-CSF) are cytokines that promote the proliferation and differentiation of a variety of myeloid cells, including monocytes, macrophages, granulocytes, dendritic cells, and platelets. Because these cytokines lack sufficient cross-reactivity between human and mice, it is difficult to reconstitute human immune cells of these lineages in immunodeficient mice. Therefore, we predict that genetic humanization of these four cytokines will improve the reconstitution of human myeloid cells in immunodeficient mice. We engineered an M-CSF, GM-CSF, THPO, and IL3 humanized strain in the background of B-NDG mice (NOD.CB17-PrkdcscidIl2rgtm1/Bcgen), termed B-NDG MGMT3 mice. The full sequences of mouse Il3, Csf2, Csf1 and Thpo genes (except the UTRs) were respectively replaced with the coding sequences (CDS) of human IL3, CSF2, CSF1 and THPO genes. Human GM-CSF, CSF1 and THPO proteins were confirmed to be expressed by ELISA in B-NDG MGMT3 mice. Human CD34+ HSCs (3E4) were intravenously engrafted into wild-type B-NDG mice and homozygous B-NDG MGMT3 male and female newborn mice via the temporal vein. B-NDG mice were treated with 1.0 Gy irradiation, while B-NDG MGMT3 mice were not irradiated. The survival rate of B-NDG MGMT3 mice was similar to B-NDG mice until 16 weeks post-CD34+ engraftment. However, the body weight of B-NDG MGMT3 mice was significantly higher than that of B-NDG mice. Analysis of peripheral blood lymphocytes showed that the proportion of hCD45+ cells in B-NDG MGMT3 mice reached 25% starting from 12 weeks after engraftment and continued to rise; levels were significantly higher than that observed in B-NDG mice. The proportions and cell number of T cells, NK cells, monocytes, MDSCs, DCs and Tregs engrafted in B-NDG MGMT3 mice were higher than B-NDG mice. The results indicate that B-NDG MGMT3 mice are a novel humanized model for human myeloid and lymphocytic cell reconstitution that does not require preconditioning. Citation Format: Ruili Lv, Yanhui Nie, Jing Zhang, Jenna Frame, Qiang Liu, James Jin. Development of immunodeficient mice expressing human IL3, GM-CSF, CSF1 and THPO for improved human myeloid and lymphoid cell reconstitution. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5208.

Novel SVPWM for Open Winding PMSM Drives With Simultaneous Common Mode Voltage Control and Full Frequency Zero Sequence Current Suppression

Zero sequence voltage (ZSV) can cause zero sequence current (ZSC), while variation of common mode voltage (CMV) can cause bearing current in an open winding (OW) permanent magnet synchronous machine (PMSM) fed by common dc -bus dual two-level inverters. This article proposes a novel space vector pulsewidth modulation (SVPWM) strategy for simultaneously eliminating CMV variation and suppressing full frequency ZSC harmonics in either linear or over modulation region by optimal selection of switching combinations. The proposed SVPWM can reduce large ZSV ripples and number of switching actions in the conventional CMV control method for the common dc -bus OW drive. Thus, high-frequency ZSC harmonics and switching frequency can be significantly reduced in both linear and over modulation regions. Moreover, the proposed SVPWM can suppress large low-frequency ZSC harmonics induced by the conventional method in over modulation region. The superior performances of CMV variation elimination and full frequency ZSC suppression in the proposed SVPWM are verified by experiments.

The evolution of fast turbulent deflagrations to detonations

We use advanced experimental techniques to explore turbulence-induced deflagration-to-detonation transition (tDDT) in hydrogen–air mixtures. We analyze the full sequence of turbulent flame evolution from fast deflagration-to-detonation using simultaneous direct measurements of pressure, turbulence, and flame, shock, and flow velocities. We show that fast turbulent flames that accelerate and develop shocks are characterized by turbulent flame speeds that exceed the Chapman–Jouguet deflagration speed in agreement with the tDDT theory and direct numerical simulation (DNS) results. Velocity and pressure evolutions are provided to detail the governing mechanisms that drive turbulent flame acceleration. Turbulent flame speeds and fluctuations are examined to reveal flow field characteristics of the tDDT process. This work contributes to the understanding of fundamental mechanisms responsible for spontaneous initiation of detonations by fast turbulent flames.

Validation of a shortened MR imaging protocol for pediatric spinal pathology.

Conventional pediatric spine MRI protocols have multiple sequences resulting in long acquisition times. Sedation is consequently required. This study evaluates the diagnostic capability of a limited MRI spine protocol for selected common pediatric indications. Spine MRIs at CHEO between 2017 and 2020 were reviewed across pediatric patients younger than four years old. Two blinded neuroradiologists reviewed limited scan sequences, and results were independently compared to previously reported findings from the complete imaging series. T2 sagittal sequences from the craniocervical junction to sacrum and T1 axial sequence of the lumbar spine constitute the short protocol, with the outcomes of interest being cerebellar ectopia, syrinx, level of conus, filum < 2mm, fatty filum, and spinal dysraphism. A total of 105 studies were evaluated in 54 male and 51 female patients (mean age 19.2months). The average combined scan time of the limited sequences was 15min compared to 35min for conventional protocols (delta = 20min). The average percent agreement between full and limited sequences was > 95% in all but identifying a filum < 2mm, where the percent agreement was 87%. Using limited MR sequences had high sensitivity (> 0.91) and specificity (> 0.99) for the detection of cerebellar ectopia, syrinx, fatty filum, and spinal dysraphism. This study demonstrates that selected spinal imaging sequences allow for consistent and accurate diagnosis of specific clinical conditions. A limited spine imaging protocol has potential as a screening test to reduce the need for full-sequence MRI scans. Further work is needed to determine utility of selected imaging for other clinical indications.

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype.

The genome sequence of the diploid and highly homozygous V. vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from nine selfings of cv. 'Helfensteiner' (cross of cv. 'Pinot noir' and 'Schiava grossa') instead of a single 'Pinot noir'. These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing towards the eventual elaboration of the grapevine pangenome.

Two fragments of HBV DNA integrated into chrX: 11009033 and its genetic regulation in HepG2.2.15.

Hepatitis B virus (HBV) integration into human genome causes hepatocellular carcinoma (HCC). The present study used inverse nested PCR; the full sequence of HBV DNA fragments of the chrX: 111009033 integration site was detected (987bp), containing two fragments of double‑stranded linear DNA with the same orientation (1,744‑1,094 and 1,565‑1,228nt). By reverse transcription‑quantitative PCR, HBV‑cell fusion transcript was observed in HepG2.2.15 cells. The mean copy number of this site in cells with H2O2 treatment (8.73x10‑2±1.65x10‑2 copies/cell) was significantly higher than that in the cells without H2O2 treatment (3.02x10‑2±2.33x10‑2 copies/cell; P<0.0001). The mean levels of P21‑activated kinase3 (PAK3) were 15.67±5.65 copies/cell in HepG2.2.15 cells with H2O2 treatment, significantly higher than in the cells without H2O2 treatment (11.34±4.58 copies/cell, P=0.0076) and in HepG2 cells (5.92±1.54 copies/cell, P<0.0001). Significant difference of PAK3 levels was also found between HepG2.2.15 cells without H2O2 treatment and HepG2 cells (11.34±4.58 vs. 5.92±1.54 copies/cell, P<0.0001). The average copy numbers of the integration site chrX: 111009033 were positively correlated with the average levels of PAK3 (P=0.0013). The overall trend of PAK3 expression was significantly increased in HepG2.2.15 cells with H2O2 treatment compared with that in HepG2.2.15 cells without H2O2 treatment (37.63±8.16 and 31.38±7.94, P=0.008) and HepG2 cells (21.67±7.88, P<0.0001). In summary, the chrX: 11009033 integration site may originate from primary human hepatocytes, occurrence and clonal expansion of which may upregulate PAK3 expression, which may contribute to hepatocarcinogenesis.

Selection and truncation of aptamers as fluorescence sensing platforms for selective and sensitive detection of nitrofurazone

Nitrofurazone (NFZ) is an antibiotic banned in many countries, as its residue seriously harms the human body. Herein, anti-NFZ aptamers were selected and identified based on the magnetic bead SELEX technique using a ssDNA library with a full length of 90 nucleotides (nt). Five full sequence candidate aptamers (NFZ8, NFZ24, NFZ28, NFZ34, and NFZ70) were obtained by secondary structure analysis. We optimized the entire sequence to obtain a truncated aptamer, a 16 nt sequence (NFZ8-1:5′-GTTCTATTGAAAAAAC-3′) that showed the highest affinity for NFZ (Kd = 76.11 nM). The binding site of NFZ and aptamer NFZ8-1 was found to be "GAA" by molecular docking. In addition, utilizing the most special truncated aptamer NFZ8-1 as the identification probe, a graphene oxide fluorescent aptasensor is an innovative for the detection of NFZ residue that showed a wide linear reach from 1.25 to 160 ng/mL and a low limit of detection of 1.13 ng/mL. In the actual water environment sample detection, the recovery rate ranged from 95.21 to 113.66%, and the coefficient of variation ranged from 3.53 to 11.24%. These results demonstrate that the NFZ-truncated aptamer applied to the aptasensor provides a novel methodology for recognizing NFZ residues.

Corrections to the Library of America Edition of Stevens’s Poetry

Corrections to the Library of America Edition of Stevens’s Poetry John N. Serio WALLACE STEVENS was lucky to have Alfred A. Knopf as his publisher. Despite the limited sales of Harmonium in 1923 and the early reviews labeling Stevens as an aesthete and a dandy, Knopf reissued Harmonium in a slightly expanded edition in 1931.1 Then, starting with Ideas of Order in 1936, book after book followed in fairly short order: The Man with the Blue Guitar & Other Poems (1937); Parts of a World (1942); Transport to Summer (1947); The Auroras of Autumn (1950); and The Necessary Angel: Essays on Reality and the Imagination (1951). Between 1950 and 1953, Knopf reissued all of the previously published poetry volumes and in 1954 published The Collected Poems of Wallace Stevens. But Knopf did not stop there. Soon after Stevens’s death in 1955, the firm published Opus Posthumous (1957) and, under various imprints, continued to keep Stevens in the public eye: Letters of Wallace Stevens (1966); The Palm at the End of the Mind: Selected Poems and a Play (1971); Souvenirs and Prophecies: The Young Wallace Stevens (1977); Parts of a World: Wallace Stevens Remembered; An Oral Biography (1977); Opus Posthumous: Revised, Enlarged, and Corrected Edition (1989); Wallace Stevens: Selected Poems (2009); and The Collected Poems of Wallace Stevens: Corrected Edition (2015). It goes without saying that Knopf contributed significantly to Stevens’s reputation as one of America’s greatest twentieth-century poets. Yet, as the two above-cited “corrected” editions indicate, Stevens was not always well served by his publisher. Milton J. Bates expanded considerably Opus Posthumous by adding uncollected pieces, full sequences, and the more recently discovered typescript of “From the Journal of Crispin.” But he also silently corrected misspellings and errors (OP 1989 v-vii). In Chris Beyers and my own corrected edition of The Collected Poems, we rectified well over a hundred mistakes, which had been the result of rushing the book into print to meet the October 2, 1954, deadline that marked the occasion of Stevens’s seventy-fifth birthday.2 For the texts of The Collected Poems, Knopf relied on the previously published individual volumes, and thus errors in those books persisted in The Collected Poems. Although the [End Page 1] first publication of “Le Monocle de Mon Oncle” in Harmonium (1923) had the correct line order in section VIII, The Collected Poems used the revised 1931 edition, which had transposed lines 7 and 9. Slight mistakes in typing led to the errors of “Pack the heart” instead of “Peck the heart” in “The Man on the Dump” in Parts of a World (PW 24; CP 203), a comma instead of a period after “absolute” in line 13 of “Crude Foyer” (TS 27; CP 305), and “hollowed out of hollow-bright” instead of “hallowed out of hollow-bright” in “Description Without Place” in Transport to Summer (TS 76; CP 345). Whole lines were dropped in “Autumn Refrain” and “Anything Is Beautiful If You Say It Is,” as they were skipped in Ideas of Order and Parts of a World, respectively. Typographical errors not found in the original books crept into the collected volume as well. In “The Paltry Nude Starts on a Spring Voyage,” “scrurry” appears instead of “scurry” (CP 6); in “The Comedian as the Letter C,” “if,” in the line “Which was, and if, chief motive” (CP 34), occurs instead of “is”; in “The Emperor of Ice-Cream,” the incomplete sentence of “Take from the dresser of deal” (CP 64) ends with a period instead of a comma; and in “Stars at Tallapoosa,” the line “There is no moon, on single, silvered leaf” (CP 71) should have been “There is no moon, no single, silvered leaf.” All were correct in Harmonium (18; 55; 95; 106). In “Farewell to Florida,” the line “The trees likes bones” (CP 118) should have been “The trees like bones,” as it was in Ideas of Order (4). In “The Good Man Has No Shape,” “Sour wine to warn him” (CP 364) should have been “Sour wine to warm him,” as in Transport to Summer (96). In “The Auroras of Autumn,” a comma appears instead of a...

The p-Arms of Human Acrocentric Chromosomes Play by a Different Set of Rules.

The p-arms of the five human acrocentric chromosomes bear nucleolar organizer regions (NORs) comprising ribosomal gene (rDNA) repeats that are organized in a homogeneous tandem array and transcribed in a telomere-to-centromere direction. Precursor ribosomal RNA transcripts are processed and assembled into ribosomal subunits, the nucleolus being the physical manifestation of this process. I review current understanding of nucleolar chromosome biology and describe current exploration into a role for the NOR chromosomal context. Full DNA sequences for acrocentric p-arms are now emerging, aided by the current revolution in long-read sequencing and genome assembly. Acrocentric p-arms vary from 10.1 to 16.7 Mb, accounting for ∼2.2% of the genome. Bordering rDNA arrays, distal junctions, and proximal junctions are shared among the p-arms, with distal junctions showing evidence of functionality. The remaining p-arm sequences comprise multiple satellite DNA classes and segmental duplications that facilitate recombination between heterologous chromosomes, which is likely also involved in Robertsonian translocations. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 24 is August 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A double-strain TM (gp45) polypeptide antigen and its application in the serodiagnosis of equine infectious anemia

Lentiviruses, including equine infectious anemia virus (EIAV), are considered viral quasispecies because of their intrinsic genetic, structural and phenotypic variability. Immunoenzymatic tests (ELISA) for EIAV reported in the literature were obtained mainly by using the capsid protein p26, which is derived almost exclusively from a single strain (Wyoming), and do not reflect the great potential epitopic variability of the EIAV quasispecies. In this investigation, the GenBank database was exploited in a systematic approach to design a set of representative protein antigens useful for EIAV serodiagnosis. The main bioinformatic tools used were clustering, molecular modelling, epitope predictions and aggregative/ solubility predictions. This approach led to the design of two antigenic proteins, i.e. a full sequence p26 capsid protein and a doublestrain polypeptide derived from the gp45 transmembrane protein fused to Maltose Binding Protein (MBP) that were expressed by recombinant DNA technology starting from synthetic genes, and analyzed by circular dichroism (CD) spectroscopy. Both proteins were used in an indirect ELISA test that can address some of the high variability of EIAV. The novel addition of the gp45 double-strain antigen contributed to enhance the diagnostic sensitivity and could be also useful for immunoblotting application.

Nuclease P1 Digestion for Bottom-Up RNA Sequencing of Modified siRNA Therapeutics.

siRNA therapeutics provide a selective and powerful approach to reduce the expression of disease-causing genes. For regulatory approval, these modalities require sequence confirmation which is typically achieved by intact tandem mass spectrometry sequencing. However, this process produces highly complex spectra which are difficult to interpret and typically results in less than full sequence coverage. We sought to develop a bottom-up siRNA sequencing platform to ease sequencing data analysis and provide full sequence coverage. Analogous to bottom-up proteomics, this process requires chemical or enzymatic digestion to reduce the oligonucleotide length down to analyzable lengths, but siRNAs commonly contain modifications that inhibit the degradation process. We tested six digestion schemes for their feasibility to digest the 2' modified siRNAs and identified that nuclease P1 provides an effective digestion workflow. Using a partial digestion, nuclease P1 provides high 5' and 3' end sequence coverage with multiple overlapping digestion products. Additionally, this enzyme provides high-quality and highly reproducible RNA sequencing no matter the RNA phosphorothioate content, 2'-fluorination status, sequence, or length. Overall, we developed a robust enzymatic digestion scheme for bottom-up siRNA sequencing using nuclease P1, which can be implemented into existing sequence confirmation workflows.

Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments.We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species.We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained.We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.

Characteristics of staphylococcal cassette chromosome mec and lugdunin operon genes in the complete genome of Staphylococcus lugdunensis.

Characteristics of staphylococcal cassette chromosome mec and lugdunin operon genes in the complete genome of Staphylococcus lugdunensis.

Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders

Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers’ conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F Kd = 12.5 ± 1.7 nM; MLT-A-4F Kd = 11.2 ± 1.6 nM; MLT-A-2F Kd = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.

Tightness of discrete Gibbsian line ensembles

A discrete Gibbsian line ensemble L=(L1,…,LN) consists of N independent random walks on the integers conditioned not to cross one another, i.e., L1≥⋯≥LN. In this paper we provide sufficient conditions for convergence of a sequence of suitably scaled discrete Gibbsian line ensembles fN=(f1N,…,fNN) as the number of curves N tends to infinity. Assuming log-concavity and a KMT-type coupling for the random walk jump distribution, we prove that under mild control of the one-point marginals of the top curves with a global parabolic shift, the full sequence (fN) is tight in the topology of uniform convergence over compact sets, and moreover any weak subsequential limit possesses the Brownian Gibbs property. If in addition the top curves converge in finite-dimensional distributions to the parabolic Airy2 process, then a result of Dimitrov (2021) implies that (fN) converges to the parabolically shifted Airy line ensemble. These results apply to a broad class of discrete jump distributions, including geometric as well as any log-concave distribution whose support forms a compact integer interval.

A taxonomic and phylogenetic contribution to Torula: T. phytolaccae sp. nov. on Phytolacca acinosa from China

Torula species are commonly reported as saprobes in aquatic and terrestrial habitats worldwide. They have been explored as an interesting source of secondary metabolites. As a result of an investigation of Torula species associated with Phytolacca acinosa in Yunnan, China, T. phytolaccae sp. nov. is described and illustrated. The establishment of a new species is justified based on morphological characteristics and multi-locus phylogenetic analyses. The new species has unique terminal and lateral, monoblastic, doliiform to cupulate conidiogenous cells with phragmosporous, catenate, acrogenous, 2–12-septate, predominantly 3–5-septate, pale brown to dark brown conidia which sometimes consisted of subhyaline to pale brown apex. Phylogenetic analyses of the combined LSU, SSU, ITS, tef1-α and rpb2 sequences generated from maximum likelihood, maximum parsimony and Bayesian inference further showed that T. phytolaccae forms a sister branch with T. herbarum (CBS 246.57), T. hollandica and T. pluriseptata. This study contributes an additional species in Torula with a full description, illustration, and DNA sequences for further contribution toward the circumscription of species in Torula and understanding their phylogenetic relationships.

Successor-like representation guides the prediction of future events in human visual cortex and hippocampus.

Human agents build models of their environment, which enable them to anticipate and plan upcoming events. However, little is known about the properties of such predictive models. Recently, it has been proposed that hippocampal representations take the form of a predictive map-like structure, the so-called successor representation (SR). Here, we used human functional magnetic resonance imaging to probe whether activity in the early visual cortex (V1) and hippocampus adhere to the postulated properties of the SR after visual sequence learning. Participants were exposed to an arbitrary spatiotemporal sequence consisting of four items (A-B-C-D). We found that after repeated exposure to the sequence, merely presenting single sequence items (e.g., - B - -) resulted in V1 activation at the successor locations of the full sequence (e.g., C-D), but not at the predecessor locations (e.g., A). This highlights that visual representations are skewed toward future states, in line with the SR. Similar results were also found in the hippocampus. Moreover, the hippocampus developed a coactivation profile that showed sensitivity to the temporal distance in sequence space, with fading representations for sequence events in the more distant past and future. V1, in contrast, showed a coactivation profile that was only sensitive to spatial distance in stimulus space. Taken together, these results provide empirical evidence for the proposition that both visual and hippocampal cortex represent a predictive map of the visual world akin to the SR.

Improved identification of cancer driver mutations using evolutionary patterns of local functional spatial regions on protein structures.

Protein sequences provide rich information for understanding protein functions. An important task is to quantitatively characterize the evolutionary patterns that is directly under the selection pressure biased towards biochemical functions. Here we employ a continuous time Markov model to describe the evolutionary process of protein, and estimate full sequence length and region-specific substitution rates of residues on these surface pockets. Our method is validated by accurate reconstruction of the Jones-Taylor-Thorton Matrix. In addition, our method can accurately identify alpha-amylase that all perform similar biochemical functions through evolutionary analysis of surface pockets on their PDB structure. Furthermore, we show that there are characteristic patterns of evolution on local regions of 242 confirmed cancer driver mutation genes. We also discuss how these evolutionary patterns compare with those derived from full protein sequences. In addition, we show how new scoring matrix based on these local regional evolutionary patterns can improve sensitivity of prediction of cancer driver mutations.

MyoPS-Net: Myocardial pathology segmentation with flexible combination of multi-sequence CMR images.

Myocardial pathology segmentation (MyoPS) can be a prerequisite for the accurate diagnosis and treatment planning of myocardial infarction. However, achieving this segmentation is challenging, mainly due to the inadequate and indistinct information from an image. In this work, we develop an end-to-end deep neural network, referred to as MyoPS-Net, to flexibly combine five-sequence cardiac magnetic resonance (CMR) images for MyoPS. To extract precise and adequate information, we design an effective yet flexible architecture to extract and fuse cross-modal features. This architecture can tackle different numbers of CMR images and complex combinations of modalities, with output branches targeting specific pathologies. To impose anatomical knowledge on the segmentation results, we first propose a module to regularize myocardium consistency and localize the pathologies, and then introduce an inclusiveness loss to utilize relations between myocardial scars and edema. We evaluated the proposed MyoPS-Net on two datasets, i.e., a private one consisting of 50 paired multi-sequence CMR images and a public one from MICCAI2020 MyoPS Challenge. Experimental results showed that MyoPS-Net could achieve state-of-the-art performance in various scenarios. Note that in practical clinics, the subjects may not have full sequences, such as missing LGE CMR or mapping CMR scans. We therefore conducted extensive experiments to investigate the performance of the proposed method in dealing with such complex combinations of different CMR sequences. Results proved the superiority and generalizability of MyoPS-Net, and more importantly, indicated a practical clinical application. The code has been released via https://github.com/QJYBall/MyoPS-Net.