Miracle-dz/UniFAR-FTUs huggingface dataset:
Surface temperatures are influenced by handling stress independently of corticosterone levels in wild king penguins (Aptenodytes patagonicus)

Assessing the physiological stress responses of wild animals opens a window for understanding how organisms cope with environmental challenges. Since stress response is associated with changes in body temperature, the use of body surface temperature through thermal imaging could help to measure acute and chronic stress responses non-invasively. We used thermal imaging, acute handling-stress protocol and an experimental manipulation of corticosterone (the main glucocorticoid hormone in birds) levels in breeding king penguins (Aptenodytes patagonicus), to assess: 1. the potential contribution of the Hypothalamo-Pituitary-Adrenal (HPA) axis in mediating chronic and acute stress-induced changes in adult surface temperature, 2. the influence of HPA axis manipulation on parental investment through thermal imaging of eggs and brooded chicks, and 3. the impact of parental treatment on offspring thermal’s response to acute handling. Maximum eye temperature (Teye) increased and minimum beak temperature (Tbeak) decreased in response to handling stress in adults, but neither basal nor stress-induced surface temperatures were significantly affected by corticosterone implant. While egg temperature was not significantly influenced by parental treatment, we found a surprising pattern for chicks: chicks brooded by the (non-implanted) partner of corticosterone-implanted individuals exhibited higher surface temperature (both Teye and Tbeak) than those brooded by glucocorticoid-implanted or control parents. Chick’s response to handling in terms of surface temperature was characterized by a drop in both Teye and Tbeak independently of parental treatment. We conclude that the HPA axis seems unlikely to play a major role in determining chronic or acute changes in surface temperature in king penguins. Changes in surface temperature may primarily be mediated by the Sympathetic-Adrenal-Medullary (SAM) axis in response to stressful situations. Our experiment did not reveal a direct impact of parental HPA axis manipulation on parental investment (egg or chick temperature), but a potential influence on the partner’s brooding behaviour. Highlights Experimental increase in corticosterone does not affect king penguin’s surface temperature Acute handling stress increases eye but decreases beak surface temperature in adults Acute handling decreases both eye and beak surface temperatures in young chicks Parental corticosterone treatment does not affect egg surface temperature during incubation Chicks brooded by non-implanted partners of corticosterone parents are warmer than chicks brooded by others adults.
Lupus erythematosus tumidus as a separate subtype of cutaneous lupus erythematosus

1 Bongartz T, Sutton AJ, Sweeting MJ et al. Anti-TNF antibody therapy in rheumatoid arthritis and the risk of serious infections and malignancies: systematic review and meta-analysis of rare harmful effects in randomized controlled trials. JAMA 2006; 295:2275–85. 2 Stubgen JP. Tumor necrosis factor-alpha antagonists and neuropathy. Muscle Nerve 2008; 37:281–92. 3 Mohan N, Edwards ET, Cupps TR et al. Demyelination occurring during anti-tumor necrosis factor alpha therapy for inflammatory arthritides. Arthritis Rheum 2001; 44:2862–9. 4 Palucka AK, Blanck JP, Bennett L et al. Cross-regulation of TNF and IFN-alpha in autoimmune diseases. Proc Natl Acad Sci USA 2005; 102:3372–7. 5 Yrjänäinen H, Hytönen J, Song XY et al. Anti-tumor necrosis factoralpha treatment activates Borrelia burgdorferi spirochetes 4 weeks after ceftriaxone treatment in C3H ⁄He mice. J Infect Dis 2007; 195:1489– 96. 6 Zeidner N, Dreitz M, Belasco D, Fish D. Suppression of acute Ixodes scapularis-induced Borrelia burgdorferi infection using tumor necrosis factor-alpha, interleukin-2, and interferon-gamma. J Infect Dis 1996; 173:187–95. 7 Molin S, Ruzicka T, Prinz JC. Borreliosis mimicking lupus-like syndrome during infliximab treatment. Clin Exp Dermatol 2010 Feb 22 [Epub ahead of print]. 8 Prinz JC, Kutasi Z, Weisenseel P et al. Borrelia-associated early-onset morphea: a particular type of scleroderma in childhood and adolescence with high titer antinuclear antibodies? Results of a cohort analysis and presentation of three cases. J Am Acad Dermatol 2009; 60:248–55.
AutoPeptideML: A study on how to build more trustworthy peptide bioactivity predictors

Automated machine learning (AutoML) solutions can bridge the gap between new computational advances and their real-world applications by enabling experimental scientists to build trustworthy models. We considered the effect of different design choices in the development of peptide bioactivity binary predictors and found that the choice of negative peptides and the use of homology-based partitioning strategies when constructing the evaluation set have a significant impact on perceived model performance providing more realistic estimation of the performance of the model when exposed to new data. We also show that the use of protein language models to generate peptide representations can both simplify the computational pipelines and improve model performance, and that state-of-the-art protein language models perform similarly regardless of size or architecture. Finally, we integrate these results into an easy-to-use AutoML tool to support the development of new robust predictive models for peptide bioactivity by biologist without a strong machine learning expertise. Source code, documentation, and data are available at https://github.com/IBM/AutoPeptideML and a dedicated web-server at http://peptide.ucd. ie/AutoPeptideML.
PRE- AND POST-OPERATIVE SELF-REPORTED FUNCTION AND QUALITY OF LIFE IN WOMEN WITH AND WITHOUT GENERALIZED JOINT LAXITY UNDERGOING HIP ARTHROSCOPY FOR FEMOROACETABULAR IMPINGEMENT.

BACKGROUND Generalized joint laxity is more prevalent in women than men and may lead to poorer post-operative outcomes in select orthopedic populations. There are no studies examining peri-operative function in patients with generalized joint laxity (GJL) and femoroacetabular impingement (FAI). PURPOSE The purpose of this study was to determine the difference in perceived function and quality of life as measured by the Hip Outcome Score ADL subscale (HOS-ADL), International Hip Outcomes Tool (iHOT-33) and the Short Form 12-Item Health Survey (SF-12) in women with and without GJL prior to and six months after undergoing hip arthroscopy for FAI. STUDY DESIGN Cohort Study. METHODS Peri-operative data were collected from women with FAI from November 2011-September 2014. Lax subjects were women with laxity scores ≥4/9 on the Beighton and Horan Joint Mobility Index; Nonlax subjects were women with laxity scores <4/9. Functional outcomes were evaluated using the HOS-ADL, iHOT-33, PCS-12, and the MCS-12 pre-operatively and at 6 months post-operatively. Change scores (post-score - pre-score) were calculated for each outcome measure and compared between groups, along with pre-operative and post-operative means, using Mann-Whitney U tests. RESULTS 166 women met the inclusion criteria: Nonlax (n = 131), Lax (n = 35). There were no statistically significant differences between groups in pre-operative functional outcomes (all p > .05). Additionally, there were no statistically significant differences between groups in post-operative means or change scores, respectively, for HOS-ADL (p = .696, .358), iHOT-33 (p = .550, .705), PCS-12 (p = .713, .191), and MCS-12 (p = .751, .082). Laxity score was not associated with any post-operative functional outcome score or change score (all p > .05). CONCLUSION Women with and without generalized joint laxity do not appear to report differences in hip function in the 6-month peri-operative period before and after hip arthroscopy for FAI. LEVEL OF EVIDENCE 3.
Comparative evaluation of the mutagenicity and genotoxicity of smoke condensate derived from Korean cigarettes

Objectives Cigarette smoking is associated with carcinogenesis owing to the mutagenic and genotoxic effects of cigarette smoke. The aim of this study was to evaluate the mutagenic and genotoxic effects of Korean cigarettes using in vitro assays. Methods We selected 2 types of cigarettes (TL and TW) as benchmark Korean cigarettes for this study, because they represent the greatest level of nicotine and tar contents among Korean cigarettes. Mutagenic potency was expressed as the number of revertants per μg of cigarette smoke condensate (CSC) total particulate matter whereas genotoxic potency was expressed as a concentration-dependent induction factor. The CSC was prepared by the International Organization for Standardization 3308 smoking method. CHO-K1 cells were used in vitro micronucleus (MNvit) and comet assays. Two strains of Salmonella typhimurium (Salmonella enterica subsp.enterica; TA98 and TA1537) were employed in Ames tests. Results All CSCs showed mutagenicity in the TA98 and TA1537 strains. In addition, DNA damage and micronuclei formation were observed in the comet and MNvit assays owing to CSC exposure. The CSC from the 3R4F Kentucky reference (3R4F) cigarette produced the most severe mutagenic and genotoxic potencies, followed by the CSC from the TL cigarette, whereas the CSC from the TW cigarette produced the least severe mutagenic and genotoxic potencies. Conclusions The results of this study suggest that the mutagenic and genotoxic potencies of the TL and TW cigarettes were weaker than those of the 3R4F cigarette. Further study on standardized concepts of toxic equivalents for cigarettes needs to be conducted for more extensive use of in vitro tests.
Even Small Visual Latencies Can Profoundly Impair Implicit Sensorimotor Learning

Short sub-100ms visual feedback latencies are common in many types of human-computer interactions yet are known to markedly reduce performance in a wide variety of motor tasks from simple pointing to operating surgical robotics. These latencies are also present in the computer-based experiments used to study the sensorimotor learning that underlies the acquisition of motor performance. Inspired by neurophysiological findings showing that cerebellar LTD and cortical LTP would both be disrupted by sub-100ms latencies, we hypothesized that implicit sensorimotor learning may be particularly sensitive to these short latencies. Remarkably, we find that improving latency by just 60ms, from 85 to 25ms in latency-optimized experiments, increases implicit learning by 50% and proportionally decreases explicit learning, resulting in a dramatic reorganization of sensorimotor memory. We go on to show that implicit sensorimotor learning is considerably more sensitive to latencies in the sub-100ms range than at higher latencies, in line with the latency-specific neural plasticity that has been observed. This suggests a clear benefit for latency reduction in computer-based training that involves implicit sensorimotor learning and that across-study differences in implicit motor learning might often be explained by disparities in feedback latency.
Heterochromatin protein 1 (HP1) of Schistosoma mansoni: non-canonical chromatin landscape and fitness effects

Heterochromatin protein 1 (HP1) is widespread in several organisms playing a role in control of gene expression by heterochromatin formation and maintenance of silent chromatin. Schistosoma mansoni is a human parasite that is responsible for Schistosomiasis, a tropical neglected disease in the tropical and subtropical areas in the world, where the intermediate host Biomphalaria glabrata is present. In this study we attempted to investigate if the SmHP1 is enriched in S. mansoni chromatin in cercariae larvae stage, compared with another larvae stage sporocysts and it’s importance for S. mansoni life cycle progression and parasite fitness. We used ChIPmentation with commercial antibody ab109028 that passed in-house quality control. Our data show that S. mansoni HP1 enrichment is non-canonical with a peak at the transcription end sites of protein coding genes. We did not find strong differences in SmHP1 chromatin landscapes between sporocysts and cercariae. Knock-down of SmHP1 in schistosomula and in vivo experiments in mice unexpectedly increased parasite fitness. Our results suggest that SmHP1 may influence chromatin structure in a non-canonical way in S. mansoni stages and may play a role in regulation of parasite fitness.
Dissecting AlphaFold’s Capabilities with Limited Sequence Information

Protein structure prediction, a fundamental challenge in computational biology, aims to predict a protein’s 3D structure from its amino acid sequence. This structure is pivotal for elucidating protein functions, interactions, and driving innovations in drug discovery and enzyme engineering. AlphaFold, a powerful deep learning model, has revolutionized this field by leveraging phylogenetic information from multiple sequence alignments (MSAs) to achieve remarkable accuracy in protein structure prediction. However, a key question remains: how well does AlphaFold understand protein structures? This study investigates AlphaFold’s capabilities when relying primarily on high-quality template structures, without the additional information provided by MSAs. By designing experiments that probe local and global structural understanding, we aimed to dissect its dependence on specific features and its ability to handle missing information. Our findings revealed AlphaFold’s reliance on sterically valid C-β atoms for correctly interpreting structural templates. Additionally, we observed its remarkable ability to recover 3D structures from certain perturbations. Collectively, these results support the hypothesis that AlphaFold has learned an accurate local biophysical energy function. However, this function seems most effective for local interactions. Our work significantly advances understanding of how deep learning models predict protein structures and provides valuable guidance for researchers aiming to overcome limitations in these models.
The Solanum lycopersicum WRKY3 Transcription Factor SlWRKY3 Is Involved in Salt Stress Tolerance in Tomato

Salinity threatens productivity of economically important crops such as tomato (Solanum lycopersicum L.). WRKY transcription factors appear, from a growing body of knowledge, as important regulators of abiotic stresses tolerance. Tomato SlWRKY3 is a nuclear protein binding to the consensus CGTTGACC/T W box. SlWRKY3 is preferentially expressed in aged organs, and is rapidly induced by NaCl, KCl, and drought. In addition, SlWRKY3 responds to salicylic acid, and 35S::SlWRKY3 tomatoes showed under salt treatment reduced contents of salicylic acid. In tomato, overexpression of SlWRKY3 impacted multiple aspects of salinity tolerance. Indeed, salinized (125 mM NaCl, 20 days) 35S::SlWRKY3 tomato plants displayed reduced oxidative stress and proline contents compared to WT. Physiological parameters related to plant growth (shoot and root biomass) and photosynthesis (stomatal conductance and chlorophyll a content) were retained in transgenic plants, together with lower Na+ contents in leaves, and higher accumulation of K+ and Ca2+. Microarray analysis confirmed that many stress-related genes were already up-regulated in transgenic tomatoes under optimal conditions of growth, including genes coding for antioxidant enzymes, ion and water transporters, or plant defense proteins. Together, these results indicate that SlWRKY3 is an important regulator of salinity tolerance in tomato.
The Bacterial Regulatory Protein H-NS A Versatile Modulator of Nucleic Acid Structures

Abstract The small DNA binding protein HNS is attracting broad interest for its profound involvement in the regulation of bacterial physiology. It is involved in the regulation of many genes in response to a changing environment and functions in the adaptation to many different kinds of stress. Many HNScontrolled genes, including the hns gene itself, are further linked to global regulatory networks. HNS thus plays a key role in maintaining bacterial homeostasis under conditions of a rapidly changing environment. In this review we summarize recent results from combined biochemical and biophysical efforts which have yielded new insights into the threedimensional structure and function of HNS. The protein consists of two distinct domains separated by an unstructured linker region, and the structural details available today have helped to understand how these domains may interact with each other or with ligand molecules. Functional studies have, in addition, revealed mechanistic clues for the various HNS activities, like temperature or growth phasedependent regulation. Important elements for the specific regulatory activities of HNS comprise different modes of DNA binding, protein oligomerization, the competition with other regulators and the fact that the topology of the target DNA is modulated during complex formation. The distinctive ability to recognize nucleic acid structures in combination with other proteins also explains HNSdependent posttranscriptional activities where the interaction with defined RNA structures and the interference with RNA/protein complexes during mRNA translation are crucial for regulation. Thus, protein/protein interactions, in combination with the recognition and modulation of nucleic acid structures, are key elements of the different mechanisms which make HNS such a versatile regulator.
ASSOCIATION BETWEEN RENAL FUNCTION AND COGNITIVE PERFORMANCE IN ELDERLY COMMUNITY‐DWELLING MEN WITHOUT DEMENTIA

Conflict of Interest: The editor in chief has reviewed the conflict of interest checklist provided by the authors and has determined that the authors have no financial or any other kind of personal conflicts with this paper. Author Contributions: Dr. Vázquez-Valdez developed the conceptualization and design of the study, performed the analyses, and interpreted the data. He wrote the manuscript under the supervision of Drs. Aguilar-Navarro and Ávila-Funes. The coauthors certify that they have participated substantially in the conceptualization and design of this work, the analysis of the data, and the writing of the manuscript. They have reviewed the final version of the manuscript and approved it for publication. Sponsor’s Role: None.
Perception of congruent and incongruent audiovisual speech stimuli

Previous studies of audiovisual (AV) speech integration have used behavioral methods to examine perception of congruent and incongruent AV speech stimuli. Such studies have investigated responses to a relatively limited set of the possible incongruent combinations of AV speech stimuli. A central issue for examining a wider range of incongruent AV speech stimuli is developing a systematic method for alignment that will work with a wide variety of segments. In the present study, we investigated the use of three different landmarks (consonant-onset, vowel-onset, and minimum distance) for aligning incongruent AV stimuli. Acoustic /ba/ or /la/ syllables were dubbed onto eight visual Consonant-/a/ syllables that spanned different places and manners of articulation. The AV stimuli were presented to ten participants. Results indicated that the effect of alignment landmark was not significant. The distance measures were found to be related to visual influence. Acoustic /ba/ tokens were more influenced by visual stimuli than acoustic /la/ tokens. Visual influence on the acoustic /ba/ tokens was mainly of the McGurk-type and/or of voicing confusion; while visual influence on the acoustic /la/ tokens was mainly of the combination type (/ba/ + /la/ = /bla/).
The turning winds with height thermal advection rainfall diagnostic: why does it work in the tropics?

For decades forecasters in the Queensland Regional Forecast Office of the Australian Bureau of Meteorology have been using winds that turn with height as a rainfall diagnostic, with good success in the subtropics and tropics. The diagnostic is based on the relationship between thermal advection (with its implied isentropic ascent or descent) and geostrophic winds that turn with height. This paper demonstrates that the above relationship also holds for gradient winds that turn with height, which suggests the relationship should be true for any slowly evolving pressure anomalies. Furthermore, it explains why the diagnostic is successful at low latitudes for most heavy rain bearing mesoscale and larger systems, including tropical depressions, tropical lows, monsoon depressions, tropical cyclones, and hybrid tropical/baroclinic storms such as the often destructive East Coast Low that forms off the eastern coast of Australia. Equations are derived to demonstrate the relationship between thermal advection and turning gradient winds with height, and the implications of each term are discussed. As with the geostrophic relationship the sign of the thermal advection is determined by the rotation direction, with anticyclonic (cyclonic) turning with height representing warm (cold) air advection and isentropic ascent (descent). In the geostrophic wind relationship the thermal advection magnitude is proportional to the Coriolis acceleration, whereas in the gradient wind relationship the thermal advection magnitude is proportional to the sum of the Coriolis and centrifugal acceleration terms. Alternative forms of the diagnostic are proposed that incorporate the additional centrifugal acceleration.
Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging

The bone marrow is the organ responsible for blood production. Diverse non-hematopoietic cells contribute essentially to hematopoiesis. However, these cells and their spatial organization remain largely uncharacterized as they have been technically challenging to study in humans. Here, we used fresh femoral head samples and performed single-cell RNA sequencing (scRNA-Seq) to profile 29,325 enriched non-hematopoietic bone marrow cells and discover nine transcriptionally distinct subtypes. We next employed CO-detection by inDEXing (CODEX) multiplexed imaging of 18 individuals, including both healthy and acute myeloid leukemia (AML) samples, to spatially profile over one million single cells with a novel 53-antibody panel. We discovered a relatively hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, niche for early hematopoietic stem and progenitor cells. We used our atlas to predict cell type labels in new bone marrow images and used these predictions to uncover mesenchymal stromal cell (MSC) expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. Our work represents the first comprehensive, spatially-resolved multiomic atlas of human bone marrow and will serve as a reference for future investigation of cellular interactions that drive hematopoiesis.