Chromosomal evolution in Brassicacae: Allopolyploidy, aneuploidy and transgene transmission [abstract]

Abstract only availablePolyploidy is a eukaryotic phenomenon common to plants that serves as an evolutionary mechanism for speciation. Diploid species undergo polyploidization through single genome duplication (autopolyploidy) or by the hybridization of genomes from two or more distinct progenitor species (allopolyploidy). Aneuploidy can arise where offspring possess extra or fewer chromosomes than their progenitors. Over successive generations, changes in chromosomal number and rearrangement can lead to speciation or differentiation of ecotypes within a species. Using advanced molecular cytogenetics and fluorescent in situ hybridization (FISH), we can distinguish chromosomes and genomic markers among different ecotypes and species. In the agricultural industry where genetically modified organisms (GMOs) are used, aneuploidy and homoeologous recombination of transgenic elements presents a potential mechanism of moving transgenes from GMO crops into the genomes of wild diploids. These wild diploids then have the potential to become "superweeds" that can disrupt ecological systems. The goal of this study was to investigate the movement of a transgene from an allopolyploid to a diploid in controlled greenhouse crosses. Transgenic Brassica napus allopolyploid plants (AACC) were backcrossed to natural Brassica rapa (AA) recurrently over three generations. We examined each of the three backcross generations for chromosome number and gene transmission. Molecular cytogenetic analysis was performed on flower buds from each backcross, chromosome numbers were recorded and gene transmission was analyzed by PCR. As expected, we found aneuploidy in Brassica napus x Brassica rapa hybrids suggesting potential for homoeologous recombination of transgenes into non-transgenic diploid species. Surprisingly, despite aneuploidy, we also found a high rate of both germination and transmission of the transgene into wild Brassica rapa, suggesting the need to find safe sites in Brassica napus to insert transgenes

Loss to Follow-Up from HIV Screening to ART Initiation in Rural China.

BackgroundPatients who are newly screened HIV positive by EIA are lost to follow-up due to complicated HIV testing procedures. Because this is the first step in care, it affects the entire continuum of care. This is a particular concern in rural China.Objective(s)To assess the routine HIV testing completeness and treatment initiation rates at 18 county-level general hospitals in rural Guangxi.MethodsWe reviewed original hospital HIV screening records. Investigators also engaged with hospital leaders and key personnel involved in HIV prevention activities to characterize in detail the routine care practices in place at each county.Results699 newly screened HIV-positive patients between January 1 and June 30, 2013 across the 18 hospitals were included in the study. The proportion of confirmatory testing across the 18 hospitals ranged from 14% to 87% (mean of 43%), and the proportion of newly diagnosed individuals successfully initiated antiretroviral treatment across the hospitals ranged from 3% to 67% (mean of 23%). The average interval within hospitals for individuals to receive the Western Blot (WB) and CD4 test results from HIV positive screening (i.e. achieving testing completion) ranged from 14-116 days (mean of 41.7 days) across the hospitals. The shortest interval from receiving a positive EIA screening test result to receiving WB and CD4 testing and counseling was 0 day and the longest was 260 days.ConclusionThe proportion of patients newly screened HIV positive that completed the necessary testing procedures for HIV confirmation and received ART was very low. Interventions are urgently needed to remove barriers so that HIV patients can have timely access to HIV/AIDS treatment and care in rural China

hSef potentiates EGF-mediated MAPK signaling through affecting EGFR trafficking and degradation

Sef (similar expression to fgf genes) was identified as an effective antagonist of fibroblast growth factor (FGF) in vertebrates. Previous reports have demonstrated that Sef interacts with FGF receptors (FGFRs) and inhibits FGF signaling, however, its role in regulating epidermal growth factor receptor (EGFR) signaling remains unclear. In this report, we found that hSef localizes to the plasma membrane (PM) and is subjected to rapid internalization and well localizes in early/recycling endosomes while poorly in late endosomes/lysosomes. We observed that hSef interacts and functionally colocalizes with EGFR in early endosomes in response to EGF stimulation. Importantly, we demonstrated that overexpression of hSef attenuates EGFR degradation and potentiates EGF-mediated mitogen-activated protein kinase (MAPK) signaling by interfering EGFR trafficking. Finally, our data showed that, with overexpression of hSef, elevated levels of Erk phosphorylation and differentiation of rat pheochromocytoma (PC12) cells occur in response to EGF stimulation. Taken together, these data suggest that hSef plays a positive role in the EGFR-mediated MAPK signaling pathway. This report, for the first time, reveals opposite roles for Sef in EGF and FGF signalings

Benchmarking Retrieval-Augmented Generation for Medicine

While large language models (LLMs) have achieved state-of-the-art performance on a wide range of medical question answering (QA) tasks, they still face challenges with hallucinations and outdated knowledge. Retrieval-augmented generation (RAG) is a promising solution and has been widely adopted. However, a RAG system can involve multiple flexible components, and there is a lack of best practices regarding the optimal RAG setting for various medical purposes. To systematically evaluate such systems, we propose the Medical Information Retrieval-Augmented Generation Evaluation (MIRAGE), a first-of-its-kind benchmark including 7,663 questions from five medical QA datasets. Using MIRAGE, we conducted large-scale experiments with over 1.8 trillion prompt tokens on 41 combinations of different corpora, retrievers, and backbone LLMs through the MedRAG toolkit introduced in this work. Overall, MedRAG improves the accuracy of six different LLMs by up to 18% over chain-of-thought prompting, elevating the performance of GPT-3.5 and Mixtral to GPT-4-level. Our results show that the combination of various medical corpora and retrievers achieves the best performance. In addition, we discovered a log-linear scaling property and the "lost-in-the-middle" effects in medical RAG. We believe our comprehensive evaluations can serve as practical guidelines for implementing RAG systems for medicine.Comment: Homepage: https://teddy-xionggz.github.io/benchmark-medical-rag

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

Background: Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings: Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of similar to 7.9 million base pairs (Mb), representing a similar to 300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained similar to 24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Conclusions: Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.Peer reviewe

Urethral orifice hyaluronic acid injections: a novel animal model of bladder outlet obstruction

BACKGROUND: We produced a novel model of bladder outlet obstruction (BOO) by periurethral injection of hyaluronic acid and compared the cystometric features, postoperative complications, and histopathological changes of that model with that of traditional open surgery. METHODS: Forty female Sprague-Dawley rats were divided into three groups. Fifteen rats were subcutaneously injected with 0.2 ml hyaluronic acid at 5, 7, and 12 o’clock around the urethral orifice. Another fifteen rats underwent traditional open partial proximal urethral obstruction surgery, and 10 normal rats used as controls. After 4 weeks, filling cystometry, postoperative complications, and histopathological features were evaluated in each group. Three rats were also observed for 12 weeks after hyaluronic acid injection to evaluate the long-term effect. RESULTS: Hyaluronic acid periurethral injection caused increased maximum cystometric capacity, maximum bladder pressure, micturition interval, and post-void residual urine volume compared with control (p < 0.01). The injection group had significantly shorter operative time, less incidence of incision infection and bladder stone formation compared with the surgery group (p < 0.01). Hematoxylin and eosin (HE) staining showed suburothelial and interstitial hyperemia edema and smooth muscle hypertrophy in both injection and surgery bladders; these were not observed in the control group. Bladder weight and thickness of smooth muscle in the injection and surgery groups were significantly greater than those in the control group (p < 0.01). Urethral epithelial hyperplasia and lamina propria inflammation were observed in the surgery group but not in the injection or control groups. Rats periurethrally injected hyaluronic acid were stable the compound was not fully absorbed in any rat after 12 weeks. CONCLUSIONS: Hyaluronic acid periurethral injection generates a simple, effective, and persistent animal model of BOO with lower complications, compared with traditional surgery

Seeing is Believing: Detecting Sybil Attack in FANET by Matching Visual and Auditory Domains

The flying ad hoc network (FANET) will play a crucial role in the B5G/6G era since it provides wide coverage and on-demand deployment services in a distributed manner. The detection of Sybil attacks is essential to ensure trusted communication in FANET. Nevertheless, the conventional methods only utilize the untrusted information that UAV nodes passively ``heard'' from the ``auditory" domain (AD), resulting in severe communication disruptions and even collision accidents. In this paper, we present a novel VA-matching solution that matches the neighbors observed from both the AD and the ``visual'' domain (VD), which is the first solution that enables UAVs to accurately correlate what they ``see'' from VD and ``hear'' from AD to detect the Sybil attacks. Relative entropy is utilized to describe the similarity of observed characteristics from dual domains. The dynamic weight algorithm is proposed to distinguish neighbors according to the characteristics' popularity. The matching model of neighbors observed from AD and VD is established and solved by the vampire bat optimizer. Experiment results show that the proposed VA-matching solution removes the unreliability of individual characteristics and single domains. It significantly outperforms the conventional RSSI-based method in detecting Sybil attacks. Furthermore, it has strong robustness and achieves high precision and recall rates.Comment: 7 pages, 9 figures, 1 tabl

Communication-Assisted Sensing in 6G Networks

The exploration of coordination gain achieved through the synergy of sensing and communication (S&C) functions plays a vital role in improving the performance of integrated sensing and communication systems. This paper focuses on the optimal waveform design for communication-assisted sensing (CAS) systems within the context of 6G perceptive networks. In the CAS process, the base station actively senses the targets through device-free wireless sensing and simultaneously transmits the pertinent information to end-users. In our research, we establish a CAS framework grounded in the principles of rate-distortion theory and the source-channel separation theorem (SCT) in lossy data transmission. This framework provides a comprehensive understanding of the interplay between distortion, coding rate, and channel capacity. The purpose of waveform design is to minimize the sensing distortion at the user end while adhering to the SCT and power budget constraints. In the context of target response matrix estimation, we propose two distinct waveform strategies: the separated S&C and dual-functional waveform schemes. In the former strategy, we develop a simple one-dimensional search algorithm, shedding light on a notable power allocation tradeoff between the S&C waveform. In the latter scheme, we conceive a heuristic mutual information optimization algorithm for the general case, alongside a modified gradient projection algorithm tailored for the scenarios with independent sensing sub-channels. Additionally, we identify the presence of both subspace tradeoff and water-filling tradeoff. Finally, we validate the effectiveness of the proposed algorithms through numerical simulations