Miracle-dz/UniFAR-FTUs huggingface dataset:
Meat Processing and Colon Carcinogenesis: Cooked, Nitrite-Treated, and Oxidized High-Heme Cured Meat Promotes Mucin-Depleted Foci in Rats

Processed meat intake is associated with colorectal cancer risk, but no experimental study supports the epidemiologic evidence. To study the effect of meat processing on carcinogenesis promotion, we first did a 14-day study with 16 models of cured meat. Studied factors, in a 2 × 2 × 2 × 2 design, were muscle color (a proxy for heme level), processing temperature, added nitrite, and packaging. Fischer 344 rats were fed these 16 diets, and we evaluated fecal and urinary fat oxidation and cytotoxicity, three biomarkers of heme-induced carcinogenesis promotion. A principal component analysis allowed for selection of four cured meats for inclusion into a promotion study. These selected diets were given for 100 days to rats pretreated with 1,2-dimethylhydrazine. Colons were scored for preneoplastic lesions: aberrant crypt foci (ACF) and mucin-depleted foci (MDF). Cured meat diets significantly increased the number of ACF/colon compared with a no-meat control diet (P = 0.002). Only the cooked nitrite-treated and oxidized high-heme meat significantly increased the fecal level of apparent total N-nitroso compounds (ATNC) and the number of MDF per colon compared with the no-meat control diet (P < 0.05). This nitrite-treated and oxidized cured meat specifically increased the MDF number compared with similar nonnitrite-treated meat (P = 0.03) and with similar nonoxidized meat (P = 0.004). Thus, a model cured meat, similar to ham stored aerobically, increased the number of preneoplastic lesions, which suggests colon carcinogenesis promotion. Nitrite treatment and oxidation increased this promoting effect, which was linked with increased fecal ATNC level. This study could lead to process modifications to make nonpromoting processed meat. Cancer Prev Res; 3(7); 852–64. ©2010 AACR.
Prompting Multi-Modal Image Segmentation with Semantic Grouping

Multi-modal image segmentation is one of the core issues in computer vision. The main challenge lies in integrating common information between modalities while retaining specific patterns for each modality. Existing methods typically perform full fine-tuning on RGB-based pre-trained parameters to inherit the powerful representation of the foundation model. Although effective, such paradigm is not optimal due to weak transferability and scarce downstream data. Inspired by the recent success of prompt learning in language models, we propose the Grouping Prompt Tuning Framework (GoPT), which introduces explicit semantic grouping to learn modal-related prompts, adapting the frozen pre-trained foundation model to various downstream multi-modal segmentation tasks. Specifically, a class-aware uni-modal prompter is designed to balance intra- and inter-modal semantic propagation by grouping modality-specific class tokens, thereby improving the adaptability of spatial information. Furthermore, an alignment-induced cross-modal prompter is introduced to aggregate class-aware representations and share prompt parameters among different modalities to assist in modeling common statistics. Extensive experiments show the superiority of our GoPT, which achieves SOTA performance on various downstream multi-modal image segmentation tasks by training only < 1% model parameters.
Effects of Commensal Bacteria on Intestinal Morphology and Expression of Proinflammatory Cytokines in the Gnotobiotic Pig

A germ-free neonatal pig model was established to determine the effects of bacterial colonization by different species on small intestinal morphology and proinflammatory cytokine gene expression. Two experimental groups of 16 pigs were aseptically delivered by cesarian section and allocated into 4 gnotobiotic isolators. Pigs were either maintained germ-free (GF), or were orally inoculated with either a single strain of nonpathogenic Escherichia coli (EC) or Lactobacillus fermentum (LF) or conventionalized with adult porcine feces (CV). After 13 days tissue samples were collected at 5 regions corresponding to 5%, 25%, 50%, 75%, and 95% of the small intestine (SI) length. In Experiment 2, the GF isolator became contaminated with Staphylococcus epidermidis (SE). In general, intestinal responses to bacterial colonization were similar among GF, LF, and SE pigs, and intestinal responses in EC pigs were more similar to CV pigs. Responses to bacterial colonization were most pronounced in the distal SI regions (50%–95%), suggesting that nonmicrobiai factors may be more important in the proximal SI. Relative to CV pigs, the distal intestines of GF, LF, and SE pigs were characterized by long villi, shallow crypts, Increased relative intestinal mass, and decreased lamina propria cellularity, whereas SI morphology was intermediate in EC pigs. Relative expression of proinflammatory cytokines interleukin-1β (IL-1β) and IL-6 generally increased distally in the SI and was highest in EC and CV pigs. We observed regional variation in SI morphology and proinflammatory cytokine expression, which differed with bacterial species. This study demonstrates that bacterial species differentially affect intestinal morphology and expression of proinflammatory cytokines and suggests that neonatal bacterial colonization patterns may have long-term effects on intestinal health and development
Omni-Kernel Network for Image Restoration

Image restoration aims to reconstruct a high-quality image from a degraded low-quality observation. Recently, Transformer models have achieved promising performance on image restoration tasks due to their powerful ability to model long-range dependencies. However, the quadratically growing complexity with respect to the input size makes them inapplicable to practical applications. In this paper, we develop an efficient convolutional network for image restoration by enhancing multi-scale representation learning. To this end, we propose an omni-kernel module that consists of three branches, i.e., global, large, and local branches, to learn global-to-local feature representations efficiently. Specifically, the global branch achieves a global perceptive field via the dual-domain channel attention and frequency-gated mechanism. Furthermore, to provide multi-grained receptive fields, the large branch is formulated via different shapes of depth-wise convolutions with unusually large kernel sizes. Moreover, we complement local information using a point-wise depth-wise convolution. Finally, the proposed network, dubbed OKNet, is established by inserting the omni-kernel module into the bottleneck position for efficiency. Extensive experiments demonstrate that our network achieves state-of-the-art performance on 11 benchmark datasets for three representative image restoration tasks, including image dehazing, image desnowing, and image defocus deblurring. The code is available at https://github.com/c-yn/OKNet.
High School Human Capital Portfolio and College Outcomes

This paper assesses the relationship between courses taken in high school and college major choice. It considers individuals as holding a portfolio of relative human capital rates that may be either similar to those in their major—specialized—or different from those in their major—diversified. Using High School and Beyond survey data, I find a U-shaped relationship between the diversification of the high school courses portfolio and college performance. Policy experiments, using a structural model, suggest that taking an additional quantitative course in high school increases the probability that a college student chooses a STEM major by 4 percentage points.
Time trends in dietary fat intake in a sample of German children and adolescents between 2000 and 2010: not quantity, but quality is the issue

Dietary fat intake in childhood may influence the risk for developing chronic diseases. The objective of the present study was to examine secular trends in the parameters of fat intake between 2000 and 2010 in a sample of German children and adolescents (n 808) participating in the Dortmund Nutritional and Anthropometric Longitudinally Designed (DONALD) Study. Dietary data from 4380 3 d weighed dietary records were analysed using repeated-measures regression to determine time trends in fat quantity, i.e. the intake of total fat, and in fat quality, i.e. the ratios of SFA, MUFA and PUFA. In young children (2–3 years) and in adolescents (13–18 years), total fat intake remained stable over time, but decreased by 0·08 % of total energy (%E) per year in 4–12-year-old children. In 2010, median fat intake was at the upper end of the recommendations. SFA intake decreased slightly in 2–3- and 4–12-year-old children by 0·09 and 0·05 %E per year, respectively. MUFA and PUFA intakes remained stable in all the age groups except in adolescents. Here, PUFA intake decreased initially, but increased between 2005 and 2010. In 2010, only between 3 and 18 % of the respective age groups had an intake of SFA or PUFA within the recommendations. In conclusion, fat quantity and quality did not change substantially between 2000 and 2010. Fat quality, in particular, needs to be improved, since a large percentage of our sample did not meet the recommended intakes for SFA and PUFA.
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses

In this article, we undertake a study of the evolution of human papillomaviruses (HPV), whose potential to cause cervical cancer is well known. First, we found that the existing HPV groups are monophyletic and that the high risk of carcinogenicity taxa are usually clustered together. Then, we present a new algorithm for analyzing the information content of multiple sequence alignments in relation to epidemiologic carcinogenicity data to identify regions that would warrant additional experimental analyses. The new algorithm is based on a sliding window procedure and a p-value computation to identify genomic regions that are specific to HPVs causing disease. Examination of the genomes of 83 HPVs allowed us to identify specific regions that might be influenced by insertions, by deletions, or simply by mutations, and that may be of interest for further analyses. Supplementary Material is provided (see online Supplementary Material at www.libertonline.com ).
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

Transcription Factor (TF) databases contain multitudes of motifs from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq peaks) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant collections of motifs. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools and highlights biologically relevant variations of similar motifs. By clustering 24 entire databases (>7,500 motifs), we show that matrix-clustering correctly groups motifs belonging to the same TF families, and can drastically reduce motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines.
Randomised controlled study of clinical outcome following trophic feeding

AIMS To determine the effect of trophic feeding on clinical outcome in ill preterm infants. METHODS A randomised, controlled, prospective study of 100 preterm infants, weighing less than 1750 g at birth and requiring ventilatory support and parenteral nutrition, was performed. Group TF (48 infants) received trophic feeding from day 3 (0.5–1 ml/h) along with parenteral nutrition until ventilatory support finished. Group C (52 infants) received parenteral nutrition alone. “Nutritive” milk feeding was then introduced to both groups. Clinical outcomes measured included total energy intake and growth over the first six postnatal weeks, sepsis incidence, liver function, milk tolerance, duration of respiratory support, duration of hospital stay and complication incidence. RESULTS Groups were well matched for birthweight, gestation and CRIB scores. Infants in group TF had significantly greater energy intake, mean difference 41.4 (95% confidence interval 9, 73.7) kcal/kg p=0.02; weight gain, 130 (CI 1, 250) g p = 0.02; head circumference gain, mean difference 0.7 (CI 0.1, 1.3) cm, p = 0.04; fewer episodes of culture confirmed sepsis, mean difference −0.7 (−1.3, −0.2) episodes, p = 0.04; less parenteral nutrition, mean difference −11.5 (CI −20, −3) days, p = 0.03; tolerated full milk feeds (165 ml/kg/day) earlier, mean difference −11.2 (CI −19, −3) days, p = 0.03; reduced requirement for supplemental oxygen, mean difference −22.4 (CI−41.5, −3.3) days, p = 0.02; and were discharged home earlier, mean difference −22.1 (CI −42.1, −2.2) days, p = 0.04. There was no significant difference in the relative risk of any complication. CONCLUSIONS Trophic feeding improves clinical outcome in ill preterm infants requiring parenteral nutrition. Key messages Timing of the introduction of milk feeds in sick low birthweight infants is controversial. Almost all infants with non-surgical illness can tolerate at least some milk as trophic feeds. Trophic feeding leads to improved energy intake, weight gain, milk tolerance, less sepsis and earlier hospital discharge. No increase in major complication rate is seen following trophic feeding.
Slow sleep spindle activity, declarative memory, and general cognitive abilities in children.

STUDY OBJECTIVES Functional interactions between sleep spindle activity, declarative memory consolidation, and general cognitive abilities in school-aged children. DESIGN Healthy, prepubertal children (n = 63; mean age 9.56 ± 0.76 y); ambulatory all-night polysomnography (2 nights); investigating the effect of prior learning (word pair association task; experimental night) versus nonlearning (baseline night) on sleep spindle activity; general cognitive abilities assessed using the Wechsler Intelligence Scale for Children-IV (WISC-IV). MEASUREMENTS AND RESULTS Analysis of spindle activity during nonrapid eye movement sleep (N2 and N3) evidenced predominant peaks in the slow (11-13 Hz) but not in the fast (13-15 Hz) sleep spindle frequency range (baseline and experimental night). Analyses were restricted to slow sleep spindles. Changes in spindle activity from the baseline to the experimental night were not associated with the overnight change in the number of recalled words reflecting declarative memory consolidation. Children with higher sleep spindle activity as measured at frontal, central, parietal, and occipital sites during both baseline and experimental nights exhibited higher general cognitive abilities (WISC-IV) and declarative learning efficiency (i.e., number of recalled words before and after sleep). CONCLUSIONS Slow sleep spindles (11-13 Hz) in children age 8-11 y are associated with inter-individual differences in general cognitive abilities and learning efficiency.
Putting Frames in Perspective

This paper attempts to bridge the gap between FrameNet frames and inference. We describe a computational formalism that captures structural relationships among participants in a dynamic scenario. This representation is used to describe the internal structure of FrameNet frames in terms of parameters for event simulations. We apply our formalism to the commerce domain and show how it provides a flexible means of accounting for linguistic perspective and other inferential effects.
Analog Placement with Symmetry and Other Placement Constraints

In order to handle device matching in analog circuits, some pairs of modules are required to be placed symmetrically. This paper addresses this device-level placement problem for analog circuits and our approach can handle symmetry constraint and other placement constraints simultaneously. The problem of placing devices with symmetry constraint has been extensively studied but none of the previous works has considered symmetry constraint with other placement constraints simultaneously. Instead of handling the constraints by having a penalty term in the cost function to penalize violations, a unified method is proposed that, by adjusting the edge weights in a pair of constraint graphs, can try to satisfy all the placement and symmetry constraints simultaneously in a candidate floorplan solution. The maximum distance of the modules in a symmetry group from the corresponding symmetry axis will be minimized in this weight adjusting step, in order to minimize the total packing area. We have compared our method with the most updated results on this problem (Balasa et al., 2004) when there are only symmetry constraints and results show that our approach can give solutions of better quality, in an acceptable amount of run time. We will also demonstrate the effectiveness of our approach in handling different types of constraints simultaneously by testing on data sets with both symmetry and other placement constraints, and the results are very promising
Excessive pressure in multichambered cuffs used for sequential compression therapy.

BACKGROUND AND PURPOSE Pneumatic compression devices, used as part of the therapeutic strategy for lymphatic drainage, often have cuffs with multiple chambers that are inflated sequentially. The purpose of this study was to investigate (1) the relationship between cuff chamber pressure (P(chamber)) and the pressure on the cuff-skin interface (P(interface)) and (2) the mechanical interaction of cuff chambers and consequences for device control. SUBJECTS AND METHODS In this study, we used 3 cylindrical (60-, 80-, and 100-mm-diameter) model limbs and 1 ellipsoidal model of the arm to test a commercially available pressure controller using "target pressures," indicated by the controller, of 30, 60, 80, and 100 mm Hg. We studied the time course of P(chamber) and P(interface) during the inflation sequence and the effect of local curvature on P(interface). RESULTS Our data indicated that, overall, P(interface) is of the same order of magnitude as P(chamber). There was some effect of model diameter and shape, with the smaller curvatures yielding the highest P(interface). Cuff chamber interaction led to P(chamber) and P(interface) values in the most distal (first inflated) chamber that were up to 80% higher than the target pressure. For the 80-mm cylindrical model, for instance, pressure in this chamber reached 54, 98, 121, and 141 mm Hg, respectively, instead of the 30, 60, 80, and 100 mm Hg indicated by the controller. DISCUSSION AND CONCLUSION The discrepancy between the target pressure, indicated by the controller, and the pressure measured inside the cuff chambers undermines the therapeutic control and efficacy of the pneumatic compression devices. Because the measured pressures were far beyond the pressure level indicated by the controller, it is recommended that pneumatic compression devices be used at much lower target pressures (<30 mm Hg) than those applied in clinical practice.
Dynamic searchable symmetric encryption

Searchable symmetric encryption (SSE) allows a client to encrypt its data in such a way that this data can still be searched. The most immediate application of SSE is to cloud storage, where it enables a client to securely outsource its data to an untrusted cloud provider without sacrificing the ability to search over it. SSE has been the focus of active research and a multitude of schemes that achieve various levels of security and efficiency have been proposed. Any practical SSE scheme, however, should (at a minimum) satisfy the following properties: sublinear search time, security against adaptive chosen-keyword attacks, compact indexes and the ability to add and delete files efficiently. Unfortunately, none of the previously-known SSE constructions achieve all these properties at the same time. This severely limits the practical value of SSE and decreases its chance of deployment in real-world cloud storage systems. To address this, we propose the first SSE scheme to satisfy all the properties outlined above. Our construction extends the inverted index approach (Curtmola et al., CCS 2006) in several non-trivial ways and introduces new techniques for the design of SSE. In addition, we implement our scheme and conduct a performance evaluation, showing that our approach is highly efficient and ready for deployment.
Myocardial Insulin-Like Growth Factor-I Gene Expression During Recovery From Heart Failure After Combined Left Ventricular Assist Device and Clenbuterol Therapy

Background—Patients who undergo mechanical support with a left ventricular assist device (LVAD) exhibit reverse remodeling and in some cases recover from heart failure. We have developed a combination therapy using LVAD support combined with pharmacological therapy to maximize reverse remodeling, followed by the β2 adrenergic agonist clenbuterol. We recently found that clenbuterol induces insulin-like growth factor I (IGF-I) in cardiac myocytes in vitro. The purpose of this study is to examine IGF-I expression in recovery patients after combination therapy. Methods and Results—Myocardial mRNA levels were determined by real-time quantitative polymerase chain reaction in 12 recovery patients (at LVAD implantation, explantation, and 1 year after explantation). IGF-I mRNA was elevated at the time of LVAD explantation relative to donors, with 2 groups distinguishable: Those with low IGF-I mRNA at implantation who showed significant increase during recovery and those with high IGF-I mRNA at implantation who remained high. Levels returned to normal by 1 year after explantation. Microarray analysis of implantation and explantation samples of recovery patients further revealed elevated IGF-II and IGF binding proteins IGFBP4 and IGFBP6. IGF-I levels correlated with stromal cell-derived factor mRNA measured both in LVAD patients and in a wider cohort of heart failure patients. Conclusions—The data suggest involvement of elevated myocardial IGF-I mRNA in recovery. IGF-I may act to limit atrophy and apoptosis during reverse remodeling and to promote repair and regeneration in concert with stromal cell derived factor.