Clustering swap prediction for image-text pre-training.

It is essential to delve into the strategy of multimodal model pre-training, which is an obvious impact on downstream tasks. Currently, clustering learning has achieved noteworthy benefits in multiple methods. However, due to the availability of open image-text pairs, it is challenging for multimodal with clustering learning. In this paper, we propose an approach that utilizes clustering swap prediction strategy to learn image-text clustering embedding space by interaction prediction between image and text features. Unlike existing models with clustering learning, our method (Clus) allows for an open number of clusters for web-scale alt-text data. Furthermore, in order to train the image and text encoders efficiently, we introduce distillation learning approach and evaluate the performance of the image-encoder in downstream visual tasks. In addition, Clus is pre-trained end-to-end by using large-scale image-text pairs. Specifically, both text and image serve as ground truth for swap prediction, enabling effective representation learning. Concurrently, extensive experiments demonstrate that Clus achieves state-of-the-art performance on multiple downstream fine-tuning and zero-shot tasks (i.e., Image-Text Retrieval, VQA, NLVR2, Image Captioning, Object Detection, and Semantic Segmentation).

Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology.

Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35-100.00%); 100.00% sensitivity for T18 (71.51-100.00%); and 100.00% sensitivity for T13 analyses (66.37-100.00%). The specificities were >99% for each trisomy (99.7% (99.01-99.97%) for T21; 99.5% (98.62-99.85%) for T18; 99.7% (99.03-99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.

Non-anesthetist-administered moderate sedation with midazolam and fentanyl for outpatient MRI-aided hybrid intracavitary and interstitial brachytherapy in cervix cancer: a single-institution experience.

PURPOSE: The aim of the study was to determine the feasibility of interstitial brachytherapy under non-anesthetist-administered moderate sedation, to identify factors influencing the insertion, and the total procedural time. MATERIAL AND METHODS: A total of 47 insertions with hybrid intracavitary and interstitial applicators were performed in 23 patients from March 2017 to March 2020. Moderate sedation was achieved with intravenous midazolam and fentanyl administered by non-anesthetist. Insertion time and procedural time was recorded. Univariate and multivariate analysis were performed to evaluate the impact of different factors on insertion and procedural time. RESULTS: A total of 238 needles (range, 2-8 per insertion) were implanted, with an average insertion depth of 30 mm (range, 20-40 mm). The mean doses for midazolam and fentanyl were 3 mg (standard deviation [SD] = 1) and 53.3 mcg (SD = 23.9) per insertion, respectively. The median insertion time was 30 minutes (interquartile range [IQR] = 22-40), and the median total procedural time was 4.3 hours (IQR = 3.6-5.2). First time insertion, insertions performed before 2019, and higher midazolam dose were associated with significantly longer insertion time, whereas longer insertion time, MRI-based planning, and insertions performed before 2019 were associated with significantly longer total procedural time. CONCLUSIONS: Outpatient interstitial brachytherapy with non-anesthetist-administered sedation is achievable and well-tolerated. This method may significantly lessen the burden on hospital resources and has the potential to be cost-effective.

In vitro modeling of glioblastoma initiation using PDGF-AA and p53-null neural progenitors.

BACKGROUND: Imagining ways to prevent or treat glioblastoma (GBM) has been hindered by a lack of understanding of its pathogenesis. Although overexpression of platelet derived growth factor with two A-chains (PDGF-AA) may be an early event, critical details of the core biology of GBM are lacking. For example, existing PDGF-driven models replicate its microscopic appearance, but not its genomic architecture. Here we report a model that overcomes this barrier to authenticity. METHODS: Using a method developed to establish neural stem cell cultures, we investigated the effects of PDGF-AA on subventricular zone (SVZ) cells, one of the putative cells of origin of GBM. We microdissected SVZ tissue from p53-null and wild-type adult mice, cultured cells in media supplemented with PDGF-AA, and assessed cell viability, proliferation, genome stability, and tumorigenicity. RESULTS: Counterintuitive to its canonical role as a growth factor, we observed abrupt and massive cell death in PDGF-AA: wild-type cells did not survive, whereas a small fraction of null cells evaded apoptosis. Surviving null cells displayed attenuated proliferation accompanied by whole chromosome gains and losses. After approximately 100 days in PDGF-AA, cells suddenly proliferated rapidly, acquired growth factor independence, and became tumorigenic in immune-competent mice. Transformed cells had an oligodendrocyte precursor-like lineage marker profile, were resistant to platelet derived growth factor receptor alpha inhibition, and harbored highly abnormal karyotypes similar to human GBM. CONCLUSION: This model associates genome instability in neural progenitor cells with chronic exposure to PDGF-AA and is the first to approximate the genomic landscape of human GBM and the first in which the earliest phases of the disease can be studied directly.

Assessing dose contribution to pelvic lymph nodes in intracavitary brachytherapy for cervical cancer.

PURPOSE: In radical radiotherapy for cervical cancer, high-dose-rate (HDR) brachytherapy is commonly used after external beam radiation therapy (EBRT) to deliver a cumulative EQD2 of 80 to 90 Gy to the primary tumor. However, there is less certainty regarding brachytherapy dose contribution to the pelvic lymph nodes. This poses a challenge as to how high a preceding EBRT dose should be prescribed to gross nodal disease, in order to achieve a cumulative tumoricidal effect. Hence, this study aims to quantify brachytherapy dose contribution to individual pelvic nodal groups, using computed tomography (CT) planning with the Manchester system. MATERIAL AND METHODS: This is a single institution retrospective dosimetric study. CT planning datasets from 40 patients who received EBRT followed by intracavitary HDR brachytherapy (5 or 6 Gy fractions) were retrieved. The external iliac (EI), internal iliac (II), and obturator (OB) lymph node groups were contoured on each CT dataset. Applying the initial brachytherapy plan, mean doses to each nodal group were calculated for every patient, and averaged across the respective (5 or 6 Gy) study populations. RESULTS: With a brachytherapy dose of 5 Gy to Manchester point A, the mean absolute doses received by the EI, II, and OB groups were 0.79, 1.12, and 1.34 Gy respectively, corresponding to EQD2s (α/ß = 10) of 0.71, 1.04, and 1.27 Gy respectively. With a brachytherapy dose of 6 Gy, the mean absolute doses received by the EI, II, and OB groups were 1.16, 1.56, and 1.80 Gy respectively, corresponding to EQD2s of 1.08, 1.49, and 1.77 Gy, respectively. CONCLUSIONS: Our study demonstrates that pelvic lymph nodes receive substantial dose contributions from HDR brachytherapy in cervical cancer. This should be taken into account by the radiation oncologist during EBRT planning, and adequate external beam boost doses calculated to achieve cumulative tumoricidal doses to pelvic nodal disease.

Global Genomic Diversity of Human Papillomavirus 11 Based on 433 Isolates and 78 Complete Genome Sequences.

UNLABELLED: Human papillomavirus 11 (HPV11) is an etiological agent of anogenital warts and laryngeal papillomas and is included in the 4-valent and 9-valent prophylactic HPV vaccines. We established the largest collection of globally circulating HPV11 isolates to date and examined the genomic diversity of 433 isolates and 78 complete genomes (CGs) from six continents. The genomic variation within the 2,800-bp E5a-E5b-L1-upstream regulatory region was initially studied in 181/207 (87.4%) HPV11 isolates collected for this study. Of these, the CGs of 30 HPV11 variants containing unique single nucleotide polymorphisms (SNPs), indels (insertions or deletions), or amino acid changes were fully sequenced. A maximum likelihood tree based on the global alignment of 78 HPV11 CGs (30 CGs from our study and 48 CGs from GenBank) revealed two HPV11 lineages (lineages A and B) and four sublineages (sublineages A1, A2, A3, and A4). HPV11 (sub)lineage-specific SNPs within the CG were identified, as well as the 208-bp representative region for CG-based phylogenetic clustering within the partial E2 open reading frame and noncoding region 2. Globally, sublineage A2 was the most prevalent, followed by sublineages A1, A3, and A4 and lineage B. IMPORTANCE: This collaborative international study defined the global heterogeneity of HPV11 and established the largest collection of globally circulating HPV11 genomic variants to date. Thirty novel complete HPV11 genomes were determined and submitted to the available sequence repositories. Global phylogenetic analysis revealed two HPV11 variant lineages and four sublineages. The HPV11 (sub)lineage-specific SNPs and the representative region identified within the partial genomic region E2/noncoding region 2 (NCR2) will enable the simpler identification and comparison of HPV11 variants worldwide. This study provides an important knowledge base for HPV11 for future studies in HPV epidemiology, evolution, pathogenicity, prevention, and molecular assay development.

Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences.

UNLABELLED: Human papillomavirus type 6 (HPV6) is the major etiological agent of anogenital warts and laryngeal papillomas and has been included in both the quadrivalent and nonavalent prophylactic HPV vaccines. This study investigated the global genomic diversity of HPV6, using 724 isolates and 190 complete genomes from six continents, and the association of HPV6 genomic variants with geographical location, anatomical site of infection/disease, and gender. Initially, a 2,800-bp E5a-E5b-L1-LCR fragment was sequenced from 492/530 (92.8%) HPV6-positive samples collected for this study. Among them, 130 exhibited at least one single nucleotide polymorphism (SNP), indel, or amino acid change in the E5a-E5b-L1-LCR fragment and were sequenced in full. A global alignment and maximum likelihood tree of 190 complete HPV6 genomes (130 fully sequenced in this study and 60 obtained from sequence repositories) revealed two variant lineages, A and B, and five B sublineages: B1, B2, B3, B4, and B5. HPV6 (sub)lineage-specific SNPs and a 960-bp representative region for whole-genome-based phylogenetic clustering within the L2 open reading frame were identified. Multivariate logistic regression analysis revealed that lineage B predominated globally. Sublineage B3 was more common in Africa and North and South America, and lineage A was more common in Asia. Sublineages B1 and B3 were associated with anogenital infections, indicating a potential lesion-specific predilection of some HPV6 sublineages. Females had higher odds for infection with sublineage B3 than males. In conclusion, a global HPV6 phylogenetic analysis revealed the existence of two variant lineages and five sublineages, showing some degree of ethnogeographic, gender, and/or disease predilection in their distribution. IMPORTANCE: This study established the largest database of globally circulating HPV6 genomic variants and contributed a total of 130 new, complete HPV6 genome sequences to available sequence repositories. Two HPV6 variant lineages and five sublineages were identified and showed some degree of association with geographical location, anatomical site of infection/disease, and/or gender. We additionally identified several HPV6 lineage- and sublineage-specific SNPs to facilitate the identification of HPV6 variants and determined a representative region within the L2 gene that is suitable for HPV6 whole-genome-based phylogenetic analysis. This study complements and significantly expands the current knowledge of HPV6 genetic diversity and forms a comprehensive basis for future epidemiological, evolutionary, functional, pathogenicity, vaccination, and molecular assay development studies.

Short DNA sequences inserted for gene targeting can accidentally interfere with off-target gene expression.

Targeting of genes in mice, a key approach to study development and disease, often leaves a neo cassette, loxP, or FRT sites inserted in the mouse genome. Insertion of neo can influence the expression of neighboring genes, but similar effects have not been reported for loxP sites. We therefore performed microarray analyses of mice in which the Ncam or the Tnr gene were targeted either by insertion of neo or loxP/FRT sites. In the case of Ncam, neo, but not loxP/FRT insertion, led to a 2-fold reduction in mRNA levels of 3 genes located at distances between 0.2 and 3.1 Mb from the target. In contrast, after introduction of loxP/FRT sites into introns of Tnr, we observed a 2.5- to 4-fold reduction in the transcript level of the Gas5 gene, 1.1 Mb away from Tnr, most probably due to disruption of a conserved regulatory element in Tnr. Insertion of short DNA sequences such as loxP/FRT can thus influence off-target mRNA levels if these sites are accidentally placed into regulatory elements. Our results imply that conditional knockout mice should be analyzed for genomic positional side effects that may influence the animals' phenotypes.

Gene expression analysis of nuclear factor I-A deficient mice indicates delayed brain maturation.

BACKGROUND: Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies have shown that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. RESULTS: To identify potential NFI-A target genes involved in the observed tissue malformations, we analyzed gene expression in brains from Nfia-/- and Nfia+/+ littermate mice at the mRNA level using oligonucleotide microarrays. In young postnatal animals (postnatal day 16), 356 genes were identified as being differentially regulated, whereas at the late embryonic stage (embryonic day 18) only five dysregulated genes were found. An in silico analysis identified phylogenetically conserved NFI binding sites in at least 70 of the differentially regulated genes. Moreover, assignment of gene function showed that marker genes for immature neural cells and neural precursors were expressed at elevated levels in young postnatal Nfia-/- mice. In contrast, marker genes for differentiated neural cells were downregulated at this stage. In particular, genes relevant for oligodendrocyte differentiation were affected. CONCLUSION: Our findings suggest that brain development, especially oligodendrocyte maturation, is delayed in Nfia-/- mice during the early postnatal period, which at least partly accounts for their phenotype. The identification of potential NFI-A target genes in our study should help to elucidate NFI-A dependent transcriptional pathways and contribute to enhanced understanding of this period of brain formation, especially with regard to the function of NFI-A.

A role for nuclear factor I in the intrinsic control of cerebellar granule neuron gene expression.

Nervous system formation requires the elaboration of a complex series of differentiation events in both a spatially and maturation-regulated manner. A fundamental question is how neuronal subtype specification and developmental gene expression are controlled within maturing neurons. The alpha6 subunit of the gamma-aminobutyric acid type A (GABA(A)) receptor (GABRA6) is preferentially expressed in cerebellar granule neurons and is part of an intrinsic program directing their differentiation. We have employed a lentiviral approach to examine the transcriptional mechanisms controlling neuronal subtype-selective expression of this gene. These studies demonstrated that nuclear factor I (NFI) proteins are required for both transgenic GABRA6 promoter activity as well as endogenous expression of this gene in cerebellar granule neurons. Chromatin immunoprecipitation also showed that NFI proteins are bound to the GABRA6 promoter in these cells in vivo. Furthermore, analyses of gene knockout mice revealed that Nfia is specifically required for normal expression of the GABRA6 gene in cerebellar granule neurons. NFI expression and DNA binding activity are highly enriched in granule neurons, implicating this transcription factor family in the neuronal subtype-selective expression of the GABRA6 gene. These studies define a new role for NFI proteins as neuronal subtype-enriched transcriptional regulators that participate in an intrinsic transcriptional program directing the differentiation of cerebellar granule neurons.