Miracle-dz/UniFAR-FTUs huggingface dataset:
REGULATION OF ANTIBODY FORMATION BY SERUM ANTIBODY

Rabbits were immunized to two antigens and 18–55 days later exchange transfusion was performed using blood of rabbits immunized to one antigen only. By this means, serum antibody levels to one antigen were reduced 50–84% while maintaining serum antibody levels to the second antigen. After exchange, serum antibody levels of the removed antibody rose rapidly for 24–48 hr and then more slowly, reaching peak titers an average of 8 days later. The peak titer was 48–222% higher than the preexchange titer. The specificity of this rebound excluded as a cause nonspecific changes in Ig levels. Passive administration of antibody to a third antigen 4–7 days before the exchange indicated that re-equilibration of preformed antibody was not a major factor in the rebound. A change in the ratio of IgM to IgG antibodies as a cause of an increased neutralization titer in the postexchange sera was also excluded. It was therefore suggested that a change in the rate of antibody formation had occurred, although other changes in the quality of serum antibody were not excluded.
EFFECTS OF SEVERE WINTER CONDITIONS ON PERFORMANCE OF FEEDLOT STEERS

An analysis of 7 yr of monthly records on a total of 1,970 steers from the University of Saskatchewan feedlot at Saskatoon was conducted to determine the effects of climate on steer performance. During the months of December, January and February (mean monthly temperature −17 C), average daily gain fell to 70% of the average recorded over the remainder of the year. Production efficiency was also severely affected. The feed required per unit of gain and the metabolizable energy intake per unit of gain during winter were, respectively, 149 and 140% of the mean requirements from March to November. These effects were not caused by differences in weight, maturity or energy intake of the steers. Animal performance appeared to be related to climatic factors over the entire annual range. Average daily gain and feed per unit gain were significantly correlated with mean ambient temperatures (r = 0.74 and −0.85, respectively), days below −23 C (r = −0.74 and 0.86), windchill (r = −0.73 and 0.82) and dewpoint (r = 0.
The role of Rif1 in telomere length regulation is separable from its role in origin firing

To examine the established link between DNA replication and telomere length, we tested whether firing of telomeric origins would cause telomere lengthening. We found that RIF1 mutants that block Protein Phosphatase 1 (PP1) binding activated telomeric origins but did not elongate telomeres. In a second approach, we found overexpression of ΔN-Dbf4 and Cdc7 increased DDK activity and activated telomeric origins, yet telomere length was unchanged. We tested a third mechanism to activate origins using the sld3-A mcm5-bob1 mutant that deregulates the pre-replication complex, and again saw no change in telomere length. Finally, we tested whether mutations in RIF1 that cause telomere elongation would affect origin firing. We found that neither rif1-Δ1322 nor rif1HOOK affected firing of telomeric origins. We conclude that telomeric origin firing does not cause telomere elongation, and the role of Rif1 in regulating origin firing is separable from its role in regulating telomere length.
Identiﬁcation of Plant Species using Image Analysis

Preservation and maintenance of biodiversity data is in need for automation. We pro-pose ﬁrst results of an automated and model-free approach to the species identiﬁcation of herbarium sheets kept in herbaria worldwide. Methodologically, our approach relies on the detection and description of so called keypoints and their classiﬁcation into species-characteristic categories. First results on a set of four fern species show recognition accuracies between 96% and 100%.
Temperatures Selected and Avoided by Fish at Various Acclimation Temperatures

Temperatures selected and avoided by 13 fish species, evaluated at decreasing increments of 3 C from 30 to 6 C, declined as the acclimation temperature decreased from summer to winter. As acclimation levels declined the difference between acclimation and selected temperatures increased for centrarchids and cyprinids, whereas the difference between these two temperatures increased for trout above and below the 18 C level of acclimation. Bluegill (Lepomis macrochirus) and spotted bass (Micropterus punctulatus) selected the highest temperatures at all acclimation levels, followed by channel catfish (Ictalurus punctatus), green sunfish (Lepomis cyanellus), smallmouth bass (Micropterus dolomieui), spotfin shiner (Notropis spilopterus), and other cyprinids. Rainbow (Salmo gairdneri) and brook (Salvelinus fontinalis) trout selected the lowest temperatures. A linear regression of the selection vs. the acclimation temperatures was plotted for cyprinids, centrarchids, and salmonids.As the acclimation temperature wa.
Infection-Related Hospitalization in Heart Failure With Reduced Ejection Fraction

Supplemental Digital Content is available in the text. Background: Hospitalization is a common adverse event in people with heart failure and reduced ejection fraction, yet is often not primarily due to decompensated heart failure (HF). We investigated the long-term prognosis following infection-related hospitalization. Methods: We conducted a prospective observational cohort study of 711 people with heart failure and reduced ejection fraction recruited from 4 specialist HF clinics in the United Kingdom. All hospitalization episodes (n=1568) were recorded and categorized as primarily due to decompensated HF, other cardiovascular disease, infection-related, or other noncardiovascular disease. Survival was determined after the first hospitalization. Results: During 2900 patient-years of follow-up, there were a total of 14 686 hospital days. At least one hospitalization occurred in 467 people (66%); 25% of first hospitalizations were primarily due to infection and these were not associated with typical signs including tachycardia and pyrexia. Compared with other categories of hospitalization, infection-related was associated with older age, lower serum albumin, higher blood neutrophil counts, and greater prevalence of chronic obstructive pulmonary disease at recruitment. Median survival after first infection-related hospitalization was 18.6 months, comparable to that after first decompensated HF hospitalization, even after age-sex adjustment. The burden of all-cause rehospitalization was comparable irrespective of the category of first hospitalization, but infection more commonly caused re-hospitalization after index infection hospitalization. Conclusions: Infection is a common driver of hospitalization in heart failure and reduced ejection fraction and often presents without classical signs. It is associated with high mortality rates, comparable to decompensated HF, and a major burden of rehospitalization caused by recurrent episodes of infection.
Deep-sea demersal fish and fisheries

Setting the stage. Diversity and distribution of deep demersal fish. Morphological and life history adaptations. Aspects of fish production: general considerations and feeding. Aspects of fish production: growth and reproduction. Adding a trophic link: exploitation beyond the shelf. The ecology of fisheries. Pandora's box: reflections on the future.
Pmp22 Super-enhancer Deletion Causes Tomacula Formation and Conduction Block in Peripheral Nerves.

Copy number variation of the peripheral nerve myelin gene Peripheral Myelin Protein 22 (PMP22) causes multiple forms of inherited peripheral neuropathy. Duplication of a 1.4 Mb segment surrounding this gene in chromosome 17p12 (c17p12) causes the most common form of Charcot-Marie-Tooth disease, CMT type 1A (CMT1A), while the reciprocal deletion of this gene causes a separate neuropathy termed Hereditary Neuropathy with Liability to Pressure Palsies (HNPP). PMP22 is robustly induced in Schwann cells in early postnatal development, and several transcription factors and their cognate regulatory elements have been implicated in coordinating the gene's proper expression. We previously found that a distal super-enhancer domain was important for Pmp22 expression in vitro, with particular impact on a Schwann cell-specific alternative promoter. Here, we investigate the consequences of deleting this super-enhancer in vivo. We find that loss of the super-enhancer in mice reduces Pmp22 expression throughout development and into adulthood, with greater impact on the Schwann cell-specific promoter. Additionally, these mice display tomacula formed by excessive myelin folding, a pathological hallmark of HNPP, as have been previously observed in heterozygous Pmp22 mice as well as sural biopsies from patients with HNPP. Our findings demonstrate a mechanism by which smaller copy number variations, not including the Pmp22 gene, are sufficient to reduce gene expression and phenocopy a peripheral neuropathy caused by the HNPP-associated deletion encompassing PMP22.
Inhibitors of DNA Glycosylases as Prospective Drugs

DNA glycosylases are enzymes that initiate the base excision repair pathway, a major biochemical process that protects the genomes of all living organisms from intrinsically and environmentally inflicted damage. Recently, base excision repair inhibition proved to be a viable strategy for the therapy of tumors that have lost alternative repair pathways, such as BRCA-deficient cancers sensitive to poly(ADP-ribose)polymerase inhibition. However, drugs targeting DNA glycosylases are still in development and so far have not advanced to clinical trials. In this review, we cover the attempts to validate DNA glycosylases as suitable targets for inhibition in the pharmacological treatment of cancer, neurodegenerative diseases, chronic inflammation, bacterial and viral infections. We discuss the glycosylase inhibitors described so far and survey the advances in the assays for DNA glycosylase reactions that may be used to screen pharmacological libraries for new active compounds.
Predictive coding as a unifying principle for explaining a broad range of brightness phenomena

The visual system is highly sensitive to spatial context for encoding luminance patterns. Context sensitivity inspired the proposal of many neural mechanisms for explaining the perception of luminance (brightness). Here we propose a novel computational model for estimating the brightness of many visual illusions. We hypothesize that many aspects of brightness can be explained by a predictive coding mechanism, which reduces the redundancy in edge representations on the one hand, while non-redundant activity is enhanced on the other (response equalization). Response equalization is implemented with a dynamic filtering process, which (dynamically) adapts to each input image. Dynamic filtering is applied to the responses of complex cells in order to build a gain control map. The gain control map then acts on simple cell responses before they are used to create a brightness map via activity propagation. Our approach is successful in predicting many challenging visual illusions, including contrast effects, assimilation, and reverse contrast. Author summary We hardly notice that what we see is often different from the physical world “outside” of the brain. This means that the visual experience that the brain actively constructs may be different from the actual physical properties of objects in the world. In this work, we propose a hypothesis about how the visual system of the brain may construct a representation for achromatic images. Since this process is not unambiguous, sometimes we notice “errors” in our perception, which cause visual illusions. The challenge for theorists, therefore, is to propose computational principles that recreate a large number of visual illusions and to explain why they occur. Notably, our proposed mechanism explains a broader set of visual illusions than any previously published proposal. We achieved this by trying to suppress predictable information. For example, if an image contained repetitive structures, then these structures are predictable and would be suppressed. In this way, non-predictable structures stand out. Predictive coding mechanisms act as early as in the retina (which enhances luminance changes but suppresses uniform regions of luminance), and our computational model holds that this principle also acts at the next stage in the visual system, where representations of perceived luminance (brightness) are created.
Physico-chemical and environmental characterisation of sediments from Cantabrian estuaries (Northern Spain)

Previous studies show that sediments of the Cantabrian estuaries (Northern Spain) contain significant concentrations of heavy metals and organic pollutants derived from intensive industrial, agricultural and urban activities. In the most polluted sediments of two estuaries (the bay of Santander and estuary of Suances), physico-chemical and environmental characterisation has been carried out. Water content, density, pH, specific surface, porosity and particle diameter distribution have been evaluated as physical parameters. Total metal contents have been analysed as inorganic parameters. Loss of ignition (LOI), phenol index and extractable organic halogens (EOX) have been determined as organic parameters. Two leachate assays have been carried out in order to evaluate the environmental behaviour of the sediments. Total availability has been analysed using the NEN 7341 test and the mobility of the pollutants has been determined using the EN 12457 leaching test at two liquid/solid ratios. The obtained results have been compared with European Union regulations. The physical parameters and inorganic compounds are very similar in the studied sediments. However, the sediments from Suances have high concentrations of LOI and EOX. The obtained correlation of the physical parameters with the particle size distribution is useful in the study of the sediment addition to ceramic process as a sediment management option. A comparison of the results obtained from the total, availability and mobility analysis of the inorganic pollutant concentrations of As, Ba, Ni, Pb and Zn present in sediments has been made, giving knowledge for the development of regulations and tools that would contribute to the integral management of the estuarine areas.
Per-protocol repeat kidney biopsy portends relapse and long-term outcome in incident cases of proliferative lupus nephritis.

OBJECTIVES In patients with LN, clinical and histological responses to treatment have been shown to be discordant. We investigated whether per-protocol repeat kidney biopsies are predictive of LN relapses and long-term renal function impairment. METHODS Forty-two patients with incident biopsy-proven active proliferative (class III/IV±V) LN from the database of the UCLouvain were included in this retrospective study. Per-protocol repeat biopsies were performed after a median [interquartile range (IQR)] time of 24.3 (21.3-26.2) months. The National Institutes of Health activity index (AI) and chronicity index (CI) scores were assessed in all biopsies. RESULTS Despite a moderate correlation between urinary protein/creatinine ratios (UPCR) and AI scores at repeat biopsy (r = 0.48; P = 0.001), 10 patients (23.8%) with UPCR < 1.0 g/g still had a high degree of histological activity (AI > 3). High AI scores (continuous) in repeat biopsies were associated with an increased probability and/or shorter time to renal relapse (n = 11) following the repeat biopsy [hazard ratio (HR) = 1.2, 95% CI: 1.1, 1.3; P = 0.007], independently of proteinuria levels. High CI scores (continuous) in repeat biopsies were associated with a sustained increase in serum creatinine levels corresponding to ≥120% of the baseline value (HR = 1.8, 95% CI: 1.1, 2.9; P = 0.016) through a median (IQR) follow-up time of 131.5 (73.8-178.2) months, being also the case for acute tubulointerstitial inflammation and interstitial fibrosis/tubular atrophy in repeat but not baseline biopsies. CONCLUSION Our results highlight the usefulness of per-protocol repeat biopsies, herein performed after a median time of 24 months from baseline, as an integral part of the treatment evaluation, also in patients showing adequate clinical response.
The JIP test: a tool to screen the capacity of plant adaptation to climate change

Abstract Adaptation and acclimation are strategies that forests enact to cope with climate change. They consist of genotypic and phenotypic adjustments that allow plants to grow and reproduce successfully in a stressful environment. Both these aspects can be actively promoted by reforestation programmes. The key phases are: (1) selection of the most suitable provenances and genotypes; (2) adoption of adequate cultural techniques in nursery; and (3) monitoring of the plantations. Physiological techniques may be useful to assist all the phases of this process. Among these, chlorophyll fluorescence-based techniques, such as the JIP test, are relevant to monitor the stress conditions and the effectiveness of the cultural practices. JIP test is a non-destructive, non-invasive, informative, very fast and inexpensive technique, and can be used to support the cultural decision.
Development of mPing‐based activation tags for crop insertional mutagenesis

Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system.
Where do the doped hole carriers reside in the new superconducting nickelates

The families of high-temperature superconductors recently welcome a new member: hole doped nickelate Nd$_{0.8}$Sr$_{0.2}$NiO$_2$ with a $\sim$15K transition temperature. To understand its emergent low-energy behaviors and experimental properties, an immediate key question is whether the superconducting hole carriers reside in oxygen as in the cuprates, or in nickel as in most nickelates. We answer this crucial question by deriving an effective interacting Hamiltonian from density functional calculation, and studying its local many-body states. Surprisingly, distinct from the expected Ni$^{2+}$ spin-triplet state found in most nickelates, the local ground state of two holes is actually a Ni-O spin-singlet state with doped hole residing greatly in oxygen. The emerged eV-scale model therefore resembles that of the cuprates, advocating further systematic experimental comparisons. Tracing the microscopic origin of this unexpected result to the lack of apical oxygen in this material, we proposed a route to increase superconducting temperature, and a possible new quantum phase transition absent in the cuprates.
Wireless power distributions in multi-cavity systems at high frequencies

The next generations of wireless networks will work in frequency bands ranging from sub-6 GHz up to 100 GHz. Radio signal propagation differs here in several critical aspects from the behaviour in the microwave frequencies currently used. With wavelengths in the millimetre range (mmWave), both penetration loss and free-space path loss increase, while specular reflection will dominate over diffraction as an important propagation channel. Thus, current channel model protocols used for the generation of mobile networks and based on statistical parameter distributions obtained from measurements become insufficient due to the lack of deterministic information about the surroundings of the base station and the receiver-devices. These challenges call for new modelling tools for channel modelling which work in the short-wavelength/high-frequency limit and incorporate site-specific details—both indoors and outdoors. Typical high-frequency tools used in this context—besides purely statistical approaches—are based on ray-tracing techniques. Ray-tracing can become challenging when multiple reflections dominate. In this context, mesh-based energy flow methods have become popular in recent years. In this study, we compare the two approaches both in terms of accuracy and efficiency and benchmark them against traditional power balance methods.
Aspect-Controlled Neural Argument Generation

We rely on arguments in our daily lives to deliver our opinions and base them on evidence, making them more convincing in turn. However, finding and formulating arguments can be challenging. In this work, we present the Arg-CTRL - a language model for argument generation that can be controlled to generate sentence-level arguments for a given topic, stance, and aspect. We define argument aspect detection as a necessary method to allow this fine-granular control and crowdsource a dataset with 5,032 arguments annotated with aspects. Our evaluation shows that the Arg-CTRL is able to generate high-quality, aspect-specific arguments, applicable to automatic counter-argument generation. We publish the model weights and all datasets and code to train the Arg-CTRL.
Deeply Cascaded U-Net for Multi-Task Image Processing

In current practice, many image processing tasks are done sequentially (e.g. denoising, dehazing, followed by semantic segmentation). In this paper, we propose a novel multi-task neural network architecture designed for combining sequential image processing tasks. We extend U-Net by additional decoding pathways for each individual task, and explore deep cascading of outputs and connectivity from one pathway to another. We demonstrate effectiveness of the proposed approach on denoising and semantic segmentation, as well as on progressive coarse-to-fine semantic segmentation, and achieve better performance than multiple individual or jointly-trained networks, with lower number of trainable parameters.
Formulating and Critically Examining the Assumptions of Global 21 cm Signal Analyses: How to Avoid the False Troughs That Can Appear in Single-spectrum Fits

The assumptions inherent to global 21 cm signal analyses are rarely delineated. In this paper, we formulate a general list of suppositions underlying a given claimed detection of the global 21 cm signal. Then, we specify the form of these assumptions for two different analyses: (1) the one performed by the team for the Experiment to Detect the Global Epoch-of-Reionization Signature (EDGES) showing an absorption trough in brightness temperature that they modeled separately from the sky foreground and (2) a new, so-called minimum assumption analysis (MAA) that makes the most conservative assumptions possible for the signal. We show fits using the EDGES analysis on various beam-weighted foreground simulations from the EDGES latitude with no signal added. Depending on the beam used, these simulations produce large false troughs because of the invalidity of the foreground model in describing the combination of beam chromaticity and the shape of the Galactic plane in the sky, the residuals of which are captured by the ad hoc flattened Gaussian signal model. On the other hand, the MAA provides robust fits by including many spectra at different time bins and allowing any possible 21 cm spectrum to be modeled exactly. We present uncertainty levels and example signal reconstructions found with the MAA for different numbers of time bins. With enough time bins, one can determine the true 21 cm signal with the MAA to <10 times the noise level.