Miracle-dz/UniFAR-FTUs huggingface dataset:
Coloring the Blank Slate: Pre-training Imparts a Hierarchical Inductive Bias to Sequence-to-sequence Models

Relations between words are governed by hierarchical structure rather than linear ordering. Sequence-to-sequence (seq2seq) models, despite their success in downstream NLP applications, often fail to generalize in a hierarchy-sensitive manner when performing syntactic transformations—for example, transforming declarative sentences into questions. However, syntactic evaluations of seq2seq models have only observed models that were not pre-trained on natural language data before being trained to perform syntactic transformations, in spite of the fact that pre-training has been found to induce hierarchical linguistic generalizations in language models; in other words, the syntactic capabilities of seq2seq models may have been greatly understated. We address this gap using the pre-trained seq2seq models T5 and BART, as well as their multilingual variants mT5 and mBART. We evaluate whether they generalize hierarchically on two transformations in two languages: question formation and passivization in English and German. We find that pre-trained seq2seq models generalize hierarchically when performing syntactic transformations, whereas models trained from scratch on syntactic transformations do not. This result presents evidence for the learnability of hierarchical syntactic information from non-annotated natural language text while also demonstrating that seq2seq models are capable of syntactic generalization, though only after exposure to much more language data than human learners receive.
ToxiGen: A Large-Scale Machine-Generated Dataset for Adversarial and Implicit Hate Speech Detection

Toxic language detection systems often falsely flag text that contains minority group mentions as toxic, as those groups are often the targets of online hate. Such over-reliance on spurious correlations also causes systems to struggle with detecting implicitly toxic language.To help mitigate these issues, we create ToxiGen, a new large-scale and machine-generated dataset of 274k toxic and benign statements about 13 minority groups. We develop a demonstration-based prompting framework and an adversarial classifier-in-the-loop decoding method to generate subtly toxic and benign text with a massive pretrained language model. Controlling machine generation in this way allows ToxiGen to cover implicitly toxic text at a larger scale, and about more demographic groups, than previous resources of human-written text. We conduct a human evaluation on a challenging subset of ToxiGen and find that annotators struggle to distinguish machine-generated text from human-written language. We also find that 94.5% of toxic examples are labeled as hate speech by human annotators. Using three publicly-available datasets, we show that finetuning a toxicity classifier on our data improves its performance on human-written data substantially. We also demonstrate that ToxiGen can be used to fight machine-generated toxicity as finetuning improves the classifier significantly on our evaluation subset.
Premise-based Multimodal Reasoning: Conditional Inference on Joint Textual and Visual Clues

It is a common practice for recent works in vision language cross-modal reasoning to adopt a binary or multi-choice classification formulation taking as input a set of source image(s) and textual query. In this work, we take a sober look at such an “unconditional” formulation in the sense that no prior knowledge is specified with respect to the source image(s). Inspired by the designs of both visual commonsense reasoning and natural language inference tasks, we propose a new task termed “Premise-based Multi-modal Reasoning” (PMR) where a textual premise is the background presumption on each source image.The PMR dataset contains 15,360 manually annotated samples which are created by a multi-phase crowd-sourcing process. With selected high-quality movie screenshots and human-curated premise templates from 6 pre-defined categories, we ask crowd-source workers to write one true hypothesis and three distractors (4 choices) given the premise and image through a cross-check procedure.
Electronically Reconfigurable Circuits for Millimeter-Wave and Beyond

Millimeter-wave (mm-Wave) wireless communication systems often employ phased array architecture to overcome the high path loss and to provide spatial selectivity. As the number of elements in the array increases, the complexity as well as physical area required for the circuitry also increase. This calls for circuit blocks that are multifunctional and can be electronically reconfigured. This dissertation presents the analyses, designs and implementations of electronically reconfigurable circuit blocks that operate bidirectionally and at multiple frequency bands.The first part of the dissertation discusses three mm-Wave reconfigurable circuit blocks realized using the constructive wave amplification technique (CCWA) in both SiGe BiCMOS and CMOS SOI processes. First, a power amplifier is designed at 60 GHz in a 0.12-μm SiGe BiCMOS process that incorporates a CMOS-bipolar cascode (BiFET) feedback circuit topology. Second, a dual Q- and W- band, bidirectional amplifier is demonstrated in a 45-nm CMOS SOI process where operations at different bands and directions are realized by electronically config- uring the feedback “field of FETs”. The bidirectional concept is then extended to the design of a three-port V-band reconfigurable active circulator that directs traveling waves between different pairs of ports while providing isolation from the remaining ports.Secondly, a switchless bidirectional front-end architecture is demonstrated in a 90-nm SiGe BiCMOS process. The proposed architecture enables a time-division duplexed (TDD) operation without the use of high-speed transmit and receive (T/R) switch. A passive transmission line matching network is used to isolate the power amplifier and low-noise amplifier and a bidirectional passive mixer is used for up- and down-conversion of the signal. The front-end is incorporated to a two-element linear coupled oscillator array to form a local oscillator beamforming transceiver.Finally, a high-speed track-and-hold amplifier (THA) is demonstrated in a 90-nm SiGe BiCMOS process. This work demonstrates the competitiveness of advance integrated silicon processes when being benchmarked against high performance III-V processes. The continuous improvement of silicon-based transistors will allow integrated systems to operate at higher frequencies. All the circuits techniques present in this dissertation are applicable to the design at mm-Wave and beyond.
Screen printed feature size capabilities

As interconnect technology drives the demand on printed thick film feature size smaller, screen and stencil process capabilities develop to keep pace. This paper provides an overview of the screen and stencil products available for screen printing fine feature electronic designs. Screen performance, cost comparison and application are combined with SEM and process photos of printed line and space geometries down to 20 microns. Examples and process results for green tape and alumina ceramic substrates in combination with silver and gold conductor pastes will be evaluated. Stencil options for via fill applications down to 50 microns will also be discussed. In total, a comprehensive look at exploring the limits of screen and stencil capabilities.
Alternative to ZnO to establish balanced intestinal microbiota for weaning piglets

A wide range of phytobiotic feed additives are available on the market claiming to have beneficial effects on the growth of the host animal and to promote the development of a balanced microflora. The present study investigated the effects of the phytobiotic-prebiotic mixture of curcumin, wheat germ, and chicory on the growth performance and on the intestinal microflora composition of weaning piglets. Post weaning diarrhea causes significant losses for the producers, most commonly it is prevented by feeding high doses of zinc oxide (ZnO). The effect of a phytobiotic-prebiotic feed additive (1 kg T-1) was compared to a positive control (3.1 kg T-1 ZnO) and to a negative control (no feed supplement) in an in vivo animal trial. There was no significant difference in the final body weight and average daily gain of the trial and positive control groups, and both groups showed significantly (P<0.05) better results than the negative control. The feed conversion ratio of the phytobiotic-prebiotic supplemented group was significantly improved (P<0.05) compared to both controls. Both phytobiotic-prebiotic mixture and ZnO were able to significantly reduce (P<0.05) the amount of coliforms after weaning, even though ZnO reduced the amount of coliforms more efficiently than the trial feed additive, it also reduced the amount of potentially beneficial bacteria. Metagenomic data also corroborated the above conclusion. In the trial and positive control groups, the relative abundance of Enterobacteriaceae decreased by 85 and 88% between 3 weeks and 6 weeks of age, while in the negative control group a slight increase occurred. Lactobacillaceae were more abundant in the trial group (29.98%) than in the positive (8.67%) or in the negative (22.45%) control groups at 6 weeks of age. In summary, this study demonstrated that a phytobiotic-prebiotic feed additive may be a real alternative to ZnO for the prevention of post weaning diarrhea and promote the development of a balanced gut system.
Association between osteoporosis and periodontal disease among menopausal women: The 2013–2015 Korea National Health and Nutrition Examination Survey

Background This cross-sectional study aimed to investigate the association between osteoporosis and periodontal disease among Korean menopausal women, as well as the association between osteoporosis and periodontal disease according to duration after menopause. Methods Of a total of 22,948 subjects who participated in the Korea National Health and Nutrition Examination Survey, from 2013 to 2015 the final study population was limited to 2,573 subjects with no missing values. The subjects were divided into two groups, normal bone mineral density (BMD) and osteoporosis, according to the T-score obtained from bone densitometry. Scores of ≥ 3 points for the community periodontal index of treatment needs were reclassified as periodontal disease. Moreover, after stratification of the variable ‘duration after menopause’ into 0–4, 5–9, and ≥10 years, binary logistic regression analysis was performed to investigate the association between osteoporosis and periodontal disease according to the duration after menopause. Results There was an association between osteoporosis and periodontal disease. The osteoporosis group had an adjusted odds ratio [OR] of 1.25 (95% confidence interval [CI]: 1.00–1.56) for periodontal disease compared to the normal BMD group. Of note, the osteoporosis group in the menopausal transition stage (0–4 years after menopause) showed an adjusted OR of 2.08 (95% CI: 1.15–3.77) for developing periodontal disease. Conclusions Osteoporosis was associated with periodontal disease and the association was strongest among women in the menopausal transition stage, 0–4 years after menopause. Oral health promotion, including regular oral examination and oral hygiene care, is particularly useful for menopausal transition women with osteoporosis.
Long-term associations between amyloid positron emission tomography, sex, apolipoprotein E and incident dementia and mortality among individuals without dementia: hazard ratios and absolute risk

Abstract Dementia and mortality rates rise inexorably with age and consequently interact. However, because of the major logistical difficulties in accounting for both outcomes in a defined population, very little work has examined how risk factors and biomarkers for incident dementia are influenced by competing mortality. The objective of this study was to examine long-term associations between amyloid PET, APOE ɛ4, sex, education and cardiovascular/metabolic conditions, and hazard and absolute risk of dementia and mortality in individuals without dementia at enrolment. Participants were enrolled in the Mayo Clinic Study of Aging, a population-based study of cognitive ageing in Olmsted County, MN, USA. All were without dementia and were age 55–92 years at enrolment and were followed longitudinally. Predictor variables were amyloid PET, APOE ɛ4 status, sex, education, cardiovascular/metabolic conditions and age. The main outcomes were incident dementia and mortality. Multivariable, multi-state models were used to estimate mortality and incident dementia rates and absolute risk of dementia and mortality by predictor variable group. Of the 4984 participants in the study, 4336 (87%) were cognitively unimpaired and 648 (13%) had mild cognitive impairment at enrolment. The median age at enrolment was 75 years; 2463 (49%) were women. The median follow-up time was 9.4 years (7.5 years after PET). High versus normal amyloid (hazard ratio 2.11, 95% confidence interval 1.43–2.79), APOE ɛ4 (women: hazard ratio 2.24, 95% confidence interval 1.80–2.77; men: hazard ratio 1.37, 95% confidence interval 1.09–1.71), older age and two additional cardiovascular/metabolic conditions (hazard ratio 1.37, 95% confidence interval 1.22–1.53) were associated with the increased hazard of dementia (all P < 0.001). Among APOE ɛ4 carriers with elevated amyloid, remaining lifetime risk of dementia at age 65 years was greater in women [74% (95% confidence interval 65–84%) high and 58% (95% confidence interval 52–65%) moderate amyloid], than men [62% (95% confidence interval 52–73%) high and 44% (95% confidence interval 35–53%) moderate amyloid]. Overall, the hazard and absolute risk of dementia varied considerably by predictor group. The absolute risk of dementia associated with predictors characteristic of Alzheimer’s disease was greater in women than men while at the same time the combination of APOE ɛ4 non-carrier with normal amyloid was more protective in women than men. This set of findings may be attributed in part to different biological effects and in part to lower mortality rates in women.
How common are high-risk coronavirus contacts? A video-observational analysis of outdoor public place behavior during the COVID-19 pandemic

Epidemiological evidence and recommendations from the World Health Organization suggest that close face-to-face interactions pose a particular coronavirus transmission risk. The real-life prevalence and nature of such high-risk contacts are understudied, however. Here, we video-observed high-risk contacts in outdoor public places in Amsterdam, the Netherlands, during the COVID-19 pandemic. We found that high-risk contacts were relatively uncommon: Of the 7,813 individuals observed, only 20 (0.26%) displayed high-risk contacts. Further, we qualitatively examined the 20 high-risk contacts identified and found that they occurred disproportionally between affiliated persons engaged in affiliative behaviors. We discuss the potential public health implications of the relatively low incident rate of high-risk contacts.
Self-assembled nanoparticle-enzyme aggregates enhance functional protein production in pure transcription-translation systems

Cell-free protein synthesis systems (CFPS) utilize cellular transcription and translation (TX-TL) machinery to synthesize proteins in vitro. These systems are useful for multiple applications including production of difficult proteins, as high-throughput tools for genetic circuit screening, and as systems for biosensor development. Though rapidly evolving, CFPS suffer from some disadvantages such as limited reaction rates due to longer diffusion times, significant cost per assay when using commercially sourced materials, and reduced reagent stability over prolonged periods. To address some of these challenges, we conducted a series of proof-of-concept experiments to demonstrate enhancement of CFPS productivity via nanoparticle assembly driven nanoaggregation of its constituent proteins. We combined a commercially available CFPS that utilizes purified polyhistidine-tagged (His-tag) TX-TL machinery with CdSe/CdS/ZnS core/shell/shell quantum dots (QDs) known to readily coordinate His-tagged proteins in an oriented fashion. We show that nanoparticle scaffolding of the CFPS cross-links the QDs into nanoaggregate structures while enhancing the production of functional recombinant super-folder green fluorescent protein and phosphotriesterase, an organophosphate hydrolase; the latter by up to 12-fold. This enhancement, which occurs by an undetermined mechanism, has the potential to improve CFPS in general and specifically CFPS-based biosensors (faster response time) while also enabling rapid detoxification/bioremediation through point-of-concern synthesis of similar catalytic enzymes. We further show that such nanoaggregates improve production in diluted CFPS reactions, which can help to save money and extend the amount of these costly reagents. The results are discussed in the context of what may contribute mechanistically to the enhancement and how this can be applied to other CFPS application scenarios.
Age-associated B cells in viral infection

Age-associated B cells (ABCs) are a recently identified, unique B cell population that displays both protective and pathogenic characteristics, depending on the context. A major role of ABCs is to protect from viral infection. ABCs expand during an array of viral infections and display various functional capacities, including secretion of antibodies and activation of T cells. Following resolution of infection, ABCs appear to persist and play a crucial role in memory and recall responses. Here, we review the currently understanding of ABCs in the antiviral response in both humans and mice. We discuss avenues for future research, including the impact of sex on the ABC population and heterogeneity of ABCs between contexts.
Pentosan polysulfate regulates hepcidin 1-facilitated formation and function of osteoclast derived from canine bone marrow

Hepcidin which is the crucial regulator of iron homeostasis, produced in the liver in response to anemia, hypoxia, or inflammation. Recent studies have suggested that hepcidin and iron metabolism are involved in osteoporosis by inhibiting osteoblast function and promoting osteoclastogenesis. Pentosan polysulfate (PPS) is a heparin analogue and promising novel therapeutic for osteoarthritis (OA). This study was undertaken to determine whether PPS inhibits hepcidin-facilitated osteoclast (OC) differentiation and iron overload. Canine (n = 3) bone marrow mononuclear cells were differentiated to OC by macrophage colony-stimulating factor and receptor-activator of nuclear factor kappaB ligand with the treatment of hepcidin1 (200, 400, 800, 1200 nmol/L) and PPS (1, 5, 10, 20, 40 μg/mL). Differentiation and function of OC were accessed using tartrate-resistant acid phosphate staining and bone resorption assay while monitoring ferroportin1 (FPN1) and iron concentration by immunocytochemistry. Gene expression of OC for cathepsin K (CTK), matrix metallopeptidase-9, nuclear factor of activated-T-cells cytoplasmic 1 and FPN1 was examined. Hepcidin1 showed significant enhancement of OC number at 800 nmol/L (p<0.01). PPS impeded hepcidin-facilitated OC at 1, 5 and 10 μg/mL and reduction of resorption pits at 5 and 10 μg/mL (p< 0.01). All OC specific genes were downregulated with PPS, specifically in significant manner with CTK at higher concentrations. However, heparin induced FPN1 internalization and degradation was inhibited at higher concentrations of PPS while restoring iron-releasing capability of OC. We demonstrate for the first time that PPS is a novel-inhibitor of hepcidin-facilitated OC formation/function which might be beneficial for treatment of OA and osteoporosis.
Use of oral polio vaccine and the incidence of COVID-19 in the world

Background Several live attenuated vaccines were shown to provide temporary protection against a variety of infectious diseases through stimulation of the host innate immune system. Objective To test the hypothesis that countries using oral polio vaccine (OPV) have a lower cumulative number of cases diagnosed with COVID-19 per 100,000 population (CP100K) compared with those using only inactivated polio vaccine (IPV). Methods In an ecological study, the CP100K was compared between countries using OPV vs IPV. We used a random-effect meta-analysis technique to estimate the pooled mean for CP100K. We also used negative binomial regression with CP100K as the dependent variable and the human development index (HDI) and the type of vaccine used as independent variables. Results The pooled estimated mean CP100K was 4970 (95% CI 4030 to 5900) cases per 100,000 population for countries using IPV, significantly (p<0.001) higher than that for countries using OPV—1580 (1190 to 1960). Countries with higher HDI prefer to use IPV; those with lower HDI commonly use OPV. Both HDI and the type of vaccine were independent predictors of CP100K. Use of OPV compared to IPV could independently decrease the CP100K by an average of 30% at the mean HDI of 0.72. Conclusions Countries using OPV have a lower incidence of COVID-19 compared to those using IPV. This might suggest that OPV may either prevent SARS-CoV-2 infection at individual level or slow down the transmission at the community level.
Spatially Constrained ICA Enables Robust Detection of Schizophrenia from Very Short Resting-state fMRI

Resting-state functional network connectivity (rsFNC) has shown utility for identifying characteristic functional brain patterns in individuals with psychiatric and mood disorders, providing a promising avenue for biomarker development. However, several factors have precluded widespread clinical adoption of rsFNC diagnostics, namely the lack of standardized approaches for capturing comparable and reproducible imaging markers across individuals, as well as the disagreement on the amount of data required to robustly detect intrinsic connectivity networks (ICNs) and diagnostically relevant patterns of rsFNC. Here, we investigate the robustness of (1) subject-specific ICNs standardized to an a priori network template via spatially constrained ICA (scICA), and (2) rsFNC differences between schizophrenia and control groups with respect to the length of the fMRI. Our results suggest clinical rsFMRI scans, when decomposed with scICA, could potentially be shortened to just 2–4 minutes without significant loss of individual rsFNC information or classification performance of longer scan lengths. Clinical Relevance - This work shows diagnostically relevant rsFNC patterns for schizophrenia can be identified from just 2–4 minutes of rsfMRI using an scICA approach. These results can influence future work in neuroimaging biomarker development.
A network of transcription factors governs the dynamics of NODAL/Activin transcriptional responses

ABSTRACT SMAD2, an effector of the NODAL/Activin signalling pathway, regulates developmental processes by sensing distinct chromatin states and interacting with different transcriptional partners. However, the network of factors that controls SMAD2 chromatin binding and shapes its transcriptional programme over time is poorly characterised. Here, we combine ATAC-seq with computational footprinting to identify temporal changes in chromatin accessibility and transcription factor activity upon NODAL/Activin signalling. We show that SMAD2 binding induces chromatin opening genome wide. We discover footprints for FOXI3, FOXO3 and ZIC3 at the SMAD2-bound enhancers of the early response genes, Pmepa1 and Wnt3, respectively, and demonstrate their functionality. Finally, we determine a mechanism by which NODAL/Activin signalling induces delayed gene expression, by uncovering a self-enabling transcriptional cascade whereby activated SMADs, together with ZIC3, induce the expression of Wnt3. The resultant activated WNT pathway then acts together with the NODAL/Activin pathway to regulate expression of delayed target genes in prolonged NODAL/Activin signalling conditions. This article has an associated First Person interview with the first author of the paper.