Miracle-dz/UniFAR-FTUs huggingface dataset:
Timing of HPV vaccination as adjuvant treatment of CIN2+ recurrence in women undergoing surgical excision: a meta-analysis and meta-regression

Objective The main aim was to determine the overall vaccine effectiveness (VE) against recurrent cervical intraepithelial neoplasia grade 2 or worse (CIN2+) including specific VE associated with timing of human papillomavirus (HPV) vaccination using data from published studies. Design Meta-analysis and meta-regression. Data sources A computerised literature search was undertaken using the MEDLINE, EMBASE, International Pharmaceutical Abstracts, Derwent Drug File, ProQuest Science and Technology, Cochrane and MedRxiv databases. To be eligible, the studies, with no language restrictions, had to be published between 1 January 2001 and 25 May 2023. Review methods Included were studies with an unvaccinated reference group that assessed CIN2+ recurrence irrespective of the HPV genotype in women undergoing conisation provided. The present study was carried out in compliance with the Preferred Reporting Items for Systematic Review and Meta-Analyses and Meta-analysis Of Observational Studies in Epidemiology guidelines. The risk of study bias was assessed using the Newcastle–Ottawa Quality Assessment Scale. The Grading of Recommendations Assessment, Development, and Evaluation guidelines were used to assess the strength of evidence for the primary outcome. Data synthesis was conducted using meta-analysis and meta-regression. Results Out of a total of 14 322 publications, 20 studies with a total of 21 estimates were included. The overall VE against recurrent CIN2+ irrespective of the HPV genotype achieved 69.5% (95% CI: 54.7% to 79.5%). While the HPV vaccine valency, follow-up duration, type of study including its risk of bias had no effect on VE, the highest VE of 78.1% (95% CI: 68.7% to 84.7%) was reported for women receiving their first dose not earlier than the day of excision. This outcome was supported by additional analyses and a VE prediction interval ranging from 67.1% to 85.4%. Conclusions The outcome of this meta-analysis and meta-regression convincingly showed the beneficial effect of post-excisional HPV vaccination against CIN2+ recurrence. Studies published to date have been unable to determine whether or not vaccination, completed or initiated before conisation, would be associated with more favourable results. PROSPERO registration number CRD42022353530.
SapiPin: Observations on PIN-code typing dynamics

Abstract In this paper, we report on PIN-code typing behaviour on touchscreen devices of 112 subjects. Detailed statistical analysis revealed that the major di erence between subjects is in inter-key latency. Key-press duration variations are insignificant compared to inter-key latency variations. Subjects were grouped into meaningful clusters using clustering. The resulting clusters were of slow, medium, and fast typists. The dataset was split randomly into two equal size subsets. The first subset was used to train different synthetic data generators, while the second subset was used to evaluate an authentication attack using the generated synthetic data. The evaluation showed that slow typists were the hardest to attack. Both the dataset and the software are publicly available at https://github.com/margitantal68/sapipin_paper.
Predicting brain activity using Transformers

The Algonauts challenge [Gifford et al., 2023] called on the community to provide novel solutions for predicting brain activity of humans viewing natural scenes. This report provides an overview and technical details of our submitted solution. We use a general transformer encoder-decoder model to map images to fMRI responses. The encoder model is a vision transformer trained using self-supervised methods (DINOv2). The decoder uses queries corresponding to different brain regions of interests (ROI) in different hemispheres to gather relevant information from the encoder output for predicting neural activity in each ROI. The output tokens from the decoder are then linearly mapped to the fMRI activity. The predictive success (challenge score: 63.5229, rank 2) suggests that features from self-supervised transformers may deserve consideration as models of human visual brain representations and shows the effectiveness of transformer mechanisms (self and cross-attention) to learn the mapping from features to brain responses. Code is available in this github repository.
Cross-pollination is more important than gibberellin application in the germination of the everlasting flowers of Janeirona carrasqueira (morphotype of Comanthera bisulcata)

The “sempre-vivas” are plants known as “everlasting flowers” because they have inflorescences that retain the appearance of living structures even after being harvested and dried. Given their ornamental potential, some species are widely exploited commercially, and their production occurs almost exclusively through extractivism. However, data on their pollination, reproduction, and germination are limited. Extractivism is an activity of great importance for the residents of the Espinhaço Meridional municipalities, and research is essential for establishing plans and proposals for the management of these native species. Given this scenario, we studied the pollinators and the importance of cross- and autogamy for reproductive success of Janeirona carrasqueira (morphotype of Comanthera bisulcata (Körn) L.R. Parra & Giul), commercially collected in Diamantina, Minas Gerais. We also evaluated germination and the influence of the exogenous application of gibberellin (GA3) on seeds. Pollinators were observed during the flowering period in beds cultivated with this species in the native Campo Rupestre area of Diamantina, Minas Gerais. The inflorescences of the species were collected from two different environments: one isolated from pollinating insects (inside the greenhouse), and the other open in the presence of pollinators. The seeds were removed from the flower heads and subjected to exogenous application of gibberellin (0–control and 500 ppm). The flowers showed a generalist pollination strategy, including visitors who collected pollen and nectar as well as those who exclusively collected nectar. For germination, the most influential factor was cross-pollination and not gibberellin application. We conclude that the pollination system represents a determining mechanism and is a very important factor to be considered in management plans aimed at species conservation. Highlights – Comanthera bisulcata employs a generalist pollination strategy. – The pollination system is a crucial mechanism for germination. – Cross-pollination is more important than gibberellin application – Reproduction is a crucial aspect to be taken into account in the management plans of the species.
A simulated study exploring and testing Fuzzy Logic AI and IoT-enabled hydroponic dosing systems aimed at rural subsistence farmers in South Africa

This paper analyses the suitability of a Fuzzy Logic (FL) AI-trained machine learning model to assist IoT-based smart hydroponics for deployment with South African rural subsistence farmers. To answer these questions, a fuzzy logic model was developed to accurately determine and adjust outputs, based on inputs received from IoT sensors monitoring the nutrient solution and environment conditions in the hydroponics system. We conducted an initial evaluation of the FL-AI, followed by a real-world test based on an existing data set and finally conducted testing on simulated data to ensure that the AI can accurately determine crisp values to pass to a cloud based IoT platform accessed by a micro-controller which adjusts the environment variables of the hydroponics system. This approach was followed to ensure that we respect the time and availability of our research participants. We found that the system was able to accurately determine the necessary crisp values needed by the microcontroller. We further report on the suitability of FL-AI for rural subsistence farmers as the AI is less complex, reduces energy consumption, and resource waste, and the burden of manually monitoring and adjusting hydroponics systems, and is easy to use for first-time growers. We further discuss crucial lessons learned particularly in the South African and other Low to Middle Income Countries (LMIC) context, such as the necessity of solar power-enabled systems and local wifi networks rather than cloud-based IoT platforms.
Extensive rewiring of the gene regulatory interactions between in vitro–produced conceptuses and endometrium during attachment

Pregnancy loss is a significant problem when embryos produced in vitro are transferred to a synchronized uterus. Currently, mechanisms that underlie losses of in vitro-produced embryos during implantation are largely unknown. We investigated this problem using cattle as a model of conceptus attachment by analyzing transcriptome data of paired extraembryonic membrane and endometrial samples collected on gestation days 18 and 25, which spans the attachment window in cattle. We identified that the transfer of an in vitro-produced embryo caused a significant alteration in transcript abundance of hundreds of genes in extraembryonic and endometrial tissues on gestation days 18 and 25, when compared to pregnancies initiated by artificial insemination. Many of the genes with altered transcript abundance are associated with biological processes that are relevant to the establishment of pregnancy. An integrative analysis of transcriptome data from the conceptus and endometrium identified hundreds of putative ligand-receptor pairs. There was a limited variation of ligand-receptor pairs in pregnancies initiated by in vitro-produced embryos on gestation day 18, and no alteration was observed on gestation day 25. In parallel, we identified that in vitro production of embryos caused an extensive alteration in the co-expression of genes expressed in the extraembryonic membranes and the corresponding endometrium on both gestation days. Both the transcriptional dysregulation that exists in the conceptus or endometrium independently, and the rewiring of gene transcription between the conceptus and endometrium are a potential component of the mechanisms that contribute to pregnancy losses caused by in vitro production of embryos. SIGNIFICANCE STATEMENT The successful establishment of pregnancies following the transfer of an in vitro produced embryo is essential for cattle production and assisted human reproduction. Most of the pregnancies initiated by the transfer of an in vitro produced embryo fail, in part because of dysfunctional interaction between the embryo and endometrium during pregnancy establishment. Our study identified that conceptuses produced in vitro and their corresponding endometrium have massive dysregulation in gene activity during the peri-implantation window, which affects crucial biological functions necessary for pregnancy. These gene expression alterations are a major contributor to the high rates of pregnancy loss following the transfer of an in vitro produced embryo. Our findings have implications for improving assisted reproduction in both agriculture and biomedicine.
Direct photoreception of a pituitary endocrine cell, melanotroph, induces a hormone release

In addition to canonical photoreception by the eye, many other organs express non-visual photoreceptors although their biological significance is mostly unknown. Here, we discovered a novel phenomenon in which the pituitary of medaka directly receives light, which induces hormone release. Ca2+ imaging analysis revealed that a melanotroph, a pituitary endocrine cell secreting melanocyte-stimulating hormone (MSH), robustly increases [Ca2+]i during short-wavelength light irradiation. Moreover, we identified Opn5m as the key molecule of this mechanism. The significance of this phenomenon was suggested to be involved in UV protection because knockout of opn5m significantly reduced the expression of tyrosinase, the rate-limiting enzyme for melanogenesis, in the skin. These results suggest a novel mechanism in which direct reception of short-wavelength light by pituitary endocrine cells triggers the pathway to enhance UV protection. One-Sentence Summary An endocrine cell of the pituitary was proven to be a photoreceptive cell that enables autonomous hormone release.
Enterovirus-A71 exploits Rab11 to recruit chaperones for virus morphogenesis

Enterovirus 71 (EV-A71) causes Hand, Foot and Mouth Disease (HFMD) in children and has been associated with neurological complications. A siRNA screen in EV-A71 infected-motor neurons identified small GTPase Rab11a as a pro-viral host factor. Rab11a and Rab11b isoforms were interchangeably exploited by strains from major EV-A71 genogroups and Coxsackievirus 16, another major causative agent of HFMD. We showed that Rab11 did not play a role in viral entry, IRES-mediated protein translation, or viral genome replication, although it co-localized with replication organelles. GTPase-defective Rab11 mutants had no effect on EV-A71 replication, ruling out Rab11 involvement in intracellular trafficking of viral or host components. Instead, reduced VP2:VP0 ratio in siRab11-treated cells supported a role in provirion maturation. Co-immunoprecipitation and mass spectrometry revealed chaperones as Rab11 top interacting partners during infection. Among which, CCT8 subunit of the chaperone complex TRiC/CCT was found to interact with viral structural proteins specifically. Together, this study describes a novel, unconventional role for Rab11 during viral infection, where it participates in the complex process of virus morphogenesis by recruiting essential chaperone proteins.
Social attention across development in common ravens and carrion crows

Underlying social learning and other important aspects of successful adaptation to social life is social awareness, where individuals are required to pay attention and respond flexibly to others in their environment. We tested the influence of social context (alone, affiliate, non-affiliate, heterospecific) on behavioural interactions (manipulation, caching, head & body out of sight i.e. barrier use) with food and objects during development at fledging (1-2 months), juvenile (3-8 months) and sub-adult (14-18 months old) in 10 carrion crows (Corvus corone; C. cornix) and nine common ravens (C. corax). These species are closely related, generalist corvids and subjects were all hand-reared and housed in highly comparable conditions. Both species will routinely cache, i.e. hide food and other items for later recovery, and engage in cache-pilfering (stealing) strategies. They will interact and ‘play’ with objects, potentially as part of developing social bonding and/or physical skills. We found that corvid behaviour was influenced by social context, with birds showing higher frequency of ‘head & body out of sight’ behaviour while others were observing than when alone, suggesting they have an awareness of other’s presence and respond by using barriers when interacting with items. There were no differences based on observer identity, supporting an interpretation of item interaction and play potentially driving development of physical skills in this setting. There were developmental effects, including increased manipulation and use of barriers as juveniles as well as increased caching with age. Ravens generally cached more than crows. Objects were manipulated more frequently than food, while barriers were used more with food, indicating that food was more likely to be actively hidden while objects may promote open play. We discuss our findings in relation to other social and developmental influences on behaviour and the wider ramifications for identifying the drivers of play in animals.
TIM3 is a context-dependent co-regulator of cytotoxic T cell function

TIM3 is a co-regulatory receptor that is highly expressed on multiple immune cell types, including on T cells after prolonged exposure to antigen. It marks functionally suppressed cytotoxic T lymphocytes (CTL) in the tumor microenvironment. However, it is unresolved whether TIM3 acts directly on suppressed CTL. Moreover, the nature of TIM3 ligands remains controversial. Paradoxically, TIM3 combines inhibitory function in vivo with costimulatory signaling capability in vitro. Here we have investigated TIM3 in the direct interaction of suppressed murine and human CTL with tumor target cell using spheroids. TIM3 directly inhibited the function of such CTL. TIM3 regulated the ability of suppressed CTL to polarize their cytoskeleton as a required step in cytolysis. Expression of CEACAM1 in cis, on the CTL, blocked TIM3 function, expression of CEACAM1 and galectin9 in trans, on the tumor target cells, enhanced TIM3 function. TIM3 only functioned as an inhibitory receptor on the spheroid-suppressed CTL, not on active CTL in a two-dimensional tissue culture model. These data suggest that TIM3 amplifies T cell function, serving as a co-inhibitory or co-stimulatory receptor depending on the functional context of the T cell it is expressed on.
FLN-2 functions in parallel to LINC complexes and Cdc42/actin pathways during P-cell nuclear migration through constricted spaces in Caenorhabditis elegans

Nuclear migration through narrow constrictions is important for development, metastasis, and pro-inflammatory responses. Studies performed in tissue culture cells have implicated LINC (linker of nucleoskeleton and cytoskeleton) complexes, microtubule motors, the actin cytoskeleton, and nuclear envelope repair machinery as important mediators of nuclear movements through constricted spaces. However, little is understood about how these mechanisms operate to move nuclei in vivo. In C. elegans larvae, 6 pairs of hypodermal P cells migrate from lateral to ventral positions through a constricted space between the body wall muscles and the cuticle. P-cell nuclear migration is mediated in part by LINC complexes using a microtubule-based pathway and by an independent CDC-42/actin-based pathway. However, when both LINC complex and actin-based pathways are knocked out, many nuclei still migrate, suggesting the existence of additional pathways. Here we show that FLN-2 functions in a third pathway to mediate P-cell nuclear migration. The predicted N-terminal actin binding domain in FLN-2 that is found in canonical filamins is dispensable for FLN-2 function, this and structural predictions suggest that FLN-2 is not a divergent filamin. The immunoglobulin (Ig)-like repeats 4-8 of FLN-2 were necessary for P-cell nuclear migration. Furthermore, in the absence of the LINC complex component unc-84, fln-2 mutants had an increase in P-cell nuclear rupture. We conclude that FLN-2 functions to maintain the integrity of the nuclear envelope in parallel with the LINC complex and CDC-42/actin-based pathways to move P-cell nuclei through constricted spaces.
Query Processing in Sensor Networks

Smart sensors are small wireless computing devices that sense information such as light and humidity at extremely high resolutions. A smart sensor query-processing architecture using database technology can facilitate deployment of sensor networks. Smart-sensor technology enables a broad range of ubiquitous computing applications. Their low cost, small size, and untethered nature lets them sense information at previously unobtainable resolutions. We discuss about query processing in sensor networks.
User View ( uniform at all times ) Actual Observations Made at Various Times time

Real-world data — especially when generated by distributed measurement infrastructures such as sensor networks — tends to be incomplete, imprecise, and erroneous, making it impossible to present it to users or feed it directly into applications. The traditional approach to dealing with this problem is to first process the data using statistical or probabilistic models that can provide more robust interpretations of the data. Current database systems, however, do not provide adequate support for applying models to such data, especially when those models need to be frequently updated as new data arrives in the system. Hence, most scientists and engineers who depend on models for managing their data do not use database systems for archival or querying at all; at best, databases serve as a persistent raw data store. In this paper we define a new abstraction called modelbased views and present the architecture of MauveDB, the system we are building to support such views. Just as traditional database views provide logical data independence, model-based views provide independence from the details of the underlying data generating mechanism and hide the irregularities of the data by using models to present a consistent view to the users. MauveDB supports a declarative language for defining model-based views, allows declarative querying over such views using SQL, and supports several different materialization strategies and techniques to efficiently maintain them in the face of frequent updates. We have implemented a prototype system that currently supports views based on regression and interpolation, using the Apache Derby open source DBMS, and we present results that show the utility and performance benefits that can be obtained by supporting several different types of modelbased views in a database system.
In-depth immunometabolic profiling by measuring single-cell protein translation inhibition via bioorthogonal noncanonical amino acid tagging (SCENITH-BONCAT)

Motivation Seahorse Extracellular Flux (XF) analysis has been influential in immunometabolism research, measuring cellular oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) to determine immune cell metabolic profiles. However, Seahorse XF has several limitations, relying on purified adherent cells, relatively high cell numbers, and specialized equipment and reagents. Recently, a novel flow cytometry-based technique called SCENITH (Single Cell Energetic metabolism by profiling Translation inhibition) was introduced, which measures cellular protein synthesis through puromycin staining as a proxy for metabolic activity in single cells. The current limitation of SCENITH is its reliance on a specific anti-puromycin antibody that is not commercially available. To address this, we propose an alternative approach using biorthogonal noncanonical amino acid tagging (BONCAT) to measure protein synthesis. Summary The field of immunometabolism has revealed that cellular energy metabolism significantly contributes to immune cell function. Disturbances in immune cell metabolism have been associated with various diseases, including obesity, atherosclerosis, and cancer. To further advance immunometabolic research, developing novel methods to study the metabolism of immune cells in complex samples is required. Here, we introduce SCENITH-BONCAT, an adapted version of SCENITH which utilizes click-labeling of homopropargylglycine (HPG), an alkyne-bearing methionine analog, to measure protein synthesis as a proxy of metabolic activity. SCENITH-BONCAT successfully reproduced known metabolic signatures of immune cell activation. Specifically, LPS/IFNγ-induced classical activation increased glycolytic capacity, and IL-4-induced alternative activation enhanced mitochondrial dependence in human macrophages. The assay’s applicability was further explored in peripheral blood mononuclear cells (PBMCs) from healthy volunteers, revealing diverse metabolic rewiring in immune cell subsets upon stimulation with different activators. Cryopreserved PBMCs showed reduced HPG incorporation and mitochondrial dependence compared to freshly isolated cells, warranting attention to cellular mitochondrial health during cryopreservation. Finally, SCENITH-BONCAT was used to analyze murine tissue-resident immune cells from different organs. Principal component analysis (PCA) revealed tissue-specific clustering based on metabolic profiles, likely driven by microenvironmental priming of tissue-resident immune cells. In conclusion, SCENITH-BONCAT offers valuable insights into immune cell metabolic responses and presents a powerful platform for studying immune cell metabolism in complex samples and tissue-resident immune populations in both human and murine studies.