Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat-Mediated Responses of Zooplankton to Decreasing Light in Two Temperate Lakes Undergoing Long-Term Browning

Increases in dissolved organic matter and the consequent “browning” of some lakes in recent decades are reducing water transparency to both ultraviolet and photosynthetically active radiation with important, but poorly understood ecosystem-level consequences for zooplankton grazers. The prevailing resource-based unimodal hypothesis posits that nutrients in dissolved organic matter stimulate primary production in clear-water lakes, while shading by dissolved organic matter inhibits primary production in browner lakes, with zooplankton responses following the patterns of their food resources. Support for this hypothesis derives primarily from short-term experiments, space-for-time analyses, and modeling studies. Here we use three decades of long-term monitoring data from two temperate lakes to assess zooplankton responses to changes in not only resources (chlorophyll) as drivers of change, but also light-related habitat variables (ultraviolet and photosynthetically active radiation, surface and deep-water temperatures, deep-water dissolved oxygen, and pH). The study lakes include one clear-water lake and one browner lake, both of which have experienced long-term browning. Given that zooplankton depth distribution and body size can vary with water transparency, color, and temperature, we test for responses in not only overall zooplankton abundance, but also in vertical distribution and body size. We also examine the ability of the relationship between short-term interannual variation in the driver vs. response variables to predict long-term zooplankton trends. The primary responses of zooplankton were strong changes in abundance that varied with taxon and life history stage in response to habitat variables rather than food resources. Only two groups showed vertical distribution responses, and they trended toward deeper distributions with browning. There was no significant change in body size ratio. The directionality of the response of zooplankton abundance to interannual variability in the driver variables was consistent with those observed in the long-term trends for 33 of 80 comparisons (41%), though only three of those (4%) had statistically significant short-term interannual variability relationships. We conclude that habitat-related changes associated with browning in lakes have important consequences for zooplankton community structure with stronger effects in clear-water lakes than in browner lakes, and that even at the whole-lake scale short-term data are generally not adequate to predict long-term responses.
Comparative Analysis of T-Cell Responses to Aquaporin-4 and Myelin Oligodendrocyte Glycoprotein in Inflammatory Demyelinating Central Nervous System Diseases

Autoantibodies against aquaporin-4 (AQP4-Ab) and myelin oligodendrocyte glycoprotein (MOG-Ab) are associated with rare central nervous system inflammatory demyelinating diseases like neuromyelitis optica spectrum disorders (NMOSD). Previous studies have shown that not only antibodies, but also autoreactive T-cell responses against AQP4 are present in NMOSD. However, no study has yet analyzed the presence of MOG reactive T-cells in patients with MOG antibodies. Therefore, we compared AQP4 and MOG specific peripheral T-cell response in individuals with AQP4-Ab (n = 8), MOG-Ab (n = 10), multiple sclerosis (MS, n = 8), and healthy controls (HC, n = 14). Peripheral blood mononuclear cell cultures were stimulated with eight AQP4 and nine MOG peptides selected from previous studies and a tetanus toxoid peptide mix as a positive control. Antigen-specific T-cell responses were assessed using the carboxyfluorescein diacetate succinimidyl ester proliferation assay and the detection of granulocyte macrophage colony-stimulating factor (GM-CSF), interferon (IFN)-ɤ and interleukin (IL)-4, IL-6, and IL-17A in cell culture supernatants. Additionally, human leukocyte antigen (HLA)-DQ and HLA-DR genotyping of all participants was performed. We classified a T-cell response as positive if proliferation (measured by a cell division index ≥3) was confirmed by the secretion of at least one cytokine. Reactivity against AQP4 peptides was observed in many groups, but the T-cell response against AQP4 p156-170 was present only in patients with AQP4-Ab (4/8, 50%) and absent in patients with MOG-Ab, MS and HC (corrected p = 0.02). This AQP4 p156-170 peptide specific T-cell response was significantly increased in participants with AQP4-Ab compared to those without [Odds ratio (OR) = 59.00, 95% confidence interval-CI 2.70–1,290.86]. Moreover, T-cell responses against at least one AQP4 peptide were also more frequent in participants with AQP4-Ab (OR = 11.45, 95% CI 1.24–106.05). We did not observe any significant differences for the other AQP4 peptides or any MOG peptide. AQP4-Ab were associated with HLA DQB1*02 (OR = 5.71, 95% CI 1.09–30.07), DRB1*01 (OR = 9.33, 95% CI 1.50–58.02) and DRB1*03 (OR = 6.75, 95% CI = 1.19–38.41). Furthermore, HLA DRB1*01 was also associated with the presence of AQP4 p156-170 reactive T-cells (OR = 31.67, 95% CI 1.30–772.98). To summarize, our findings suggest a role of AQP4-specific, but not MOG-specific T-cells, in NMOSD.
LRRK2 and α-Synuclein: Distinct or Synergistic Players in Parkinson’s Disease?

Parkinson’s disease (PD) is the most common neurodegenerative movement disorder, characterized by prominent degeneration of dopaminergic neurons in the substantia nigra and aggregation of the protein α-synuclein within intraneuronal inclusions known as Lewy bodies. Ninety percent of PD cases are idiopathic while the remaining 10% are associated with gene mutations that affect cellular functions ranging from kinase activity to mitochondrial quality control, hinting at a multifactorial disease process. Mutations in LRRK2 and SNCA (the gene coding for α-synuclein) cause monogenic forms of autosomal dominant PD, and polymorphisms in either gene are also associated with increased risk of idiopathic PD. Although Lewy bodies are a defining neuropathological feature of PD, an appreciable subset of patients with LRRK2 mutations present with a clinical phenotype indistinguishable from idiopathic PD but lack Lewy pathology at autopsy, suggesting that LRRK2-mediated PD may occur independently of α-synuclein aggregation. Here, we examine whether LRRK2 and α-synuclein, as mediators of neurodegeneration in PD, exist in common or distinct pathways. Specifically, we review evidence from preclinical models and human neuropathological studies examining interactions between the two proteins. Elucidating the degree of interplay between LRRK2 and α-synuclein will be necessary for treatment stratification once effective targeted disease-modifying therapies are developed.
10% Higher Rowing Power Outputs After Flexion-Extension-Cycle Compared to an Isolated Concentric Contraction in Sub-Elite Rowers

The resulting muscular performance is considered notably higher during a stretch shortening cycle (SSC) compared to an isolated concentric contraction. Thus, the present study examined the occurrence and magnitude of rowing performance enhancement after a flexion–extension cycle (FEC) of the legs compared to both concentric contractions only and isometric pre-contraction. Therefore, 31 sub-elite male rowers (age: 25 ± 6 years, height: 1.90 ± 0.02 m, weight: 91 ± 10 kg, weekly training volume: 11.4 ± 5.3 h/week, rowing experience: 7.1 ± 2.7 years) randomly completed (a) isolated concentric rowing strokes (DRIVE), (b) single FEC-type rowing strokes (SLIDE-DRIVE), and (c) rowing strokes with an isometric pre-contraction (ISO-DRIVE). The resulting rowing power (Prow), leg power (Pleg), and work per stroke (WPS) were recorded using motion-capturing, force, and rotation sensors. Comparison of DRIVE and SLIDE-DRIVE revealed significantly (p < 0.05) higher Prow (+11.8 ± 14.0%), Pleg (+19.6 ± 26.7%), and WPS (+9.9 ± 10.5%) during SLIDE-DRIVE. Compared to ISO-DRIVE, Pleg (+9.8 ± 26.6%) and WPS (+6.1 ± 6.7%) are again significantly (p < 0.05) higher for SLIDE-DRIVE. In conclusion, notably higher work and power outputs (compared to an isolated concentric contraction) during FEC rowing referred to an underlying SSC. Future ultrasound studies should elucidate whether a real SSC on the muscle tendon unit level account for these performance enhancements.
Eomes Expression Defines Group 1 Innate Lymphoid Cells During Metastasis in Human and Mouse

Recent studies have attempted to uncover the role of Group 1 Innate lymphoid cells (ILCs) in multiple physiological contexts, including cancer. However, the definition and precise contribution of Group 1 ILCs (constituting ILC1 and NK subsets) to metastasis is unclear due to the lack of well-defined cell markers. Here, we first identified ILC1 and NK cells in NSCLC patient blood and differentiated them based on the expression of transcription factors, T-bet and Eomes. Interestingly, Eomes downregulation in the peripheral blood NK cells of NSCLC patients positively correlated with disease progression. Additionally, we noted higher Eomes expression in NK cells (T-bet+Eomeshi) compared to ILC1s (T-bet+Eomeslo). We asked whether the decrease in Eomes was associated with the conversion of NK cells into ILC1 using Eomes as a reliable marker to differentiate ILC1s from NK cells. Utilizing a murine model of experimental metastasis, we observed an association between increase in metastasis and Eomes downregulation in NKp46+NK1.1+ Group 1 ILCs, which was consistent to that of human NSCLC samples. Further confirmation of this trend was achieved by flow cytometry, which identified tissue-specific Eomeslo ILC1-like and Eomeshi NK-like subsets in the murine metastatic lung based on cell surface markers and adoptive transfer experiments. Next, functional characterization of these cell subsets showed reduced cytotoxicity and IFNγ production in Eomeslo ILC1s compared to Eomeshi cells, suggesting that lower Eomes levels are associated with poor cancer immunosurveillance by Group 1 ILCs. These findings provide novel insights into the regulation of Group 1 ILC subsets during metastasis, through the use of Eomes as a reliable marker to differentiate between NK and ILC1s.
Cardiorespiratory Alterations in a Newborn Ovine Model of Systemic Inflammation Induced by Lipopolysaccharide Injection

Although it is well known that neonatal sepsis can induce important alterations in cardiorespiratory control, their detailed early features and the mechanisms involved remain poorly understood. As a first step in resolving this issue, the main goal of this study was to characterize these alterations more extensively by setting up a full-term newborn lamb model of systemic inflammation using lipopolysaccharide (LPS) injection. Two 6-h polysomnographic recordings were performed on two consecutive days on eight full-term lambs: the first after an IV saline injection (control condition, CTRL); the second, after an IV injection of 2.5 μg/kg Escherichia coli LPS 0127:B8 (LPS condition). Rectal temperature, locomotor activity, state of alertness, arterial blood gases, respiratory frequency and heart rate, mean arterial blood pressure, apneas and cardiac decelerations, and heart-rate and respiratory-rate variability (HRV and RRV) were assessed. LPS injection decreased locomotor activity (p = 0.03) and active wakefulness (p = 0.01) compared to the CTRL. In addition, LPS injection led to a biphasic increase in rectal temperature (p = 0.01 at ∼30 and 180 min) and in respiratory frequency and heart rate (p = 0.0005 and 0.005, respectively), and to an increase in cardiac decelerations (p = 0.05). An overall decrease in HRV and RRV was also observed. Interestingly, the novel analysis of the representations of the horizontal and vertical visibility network yielded the most statistically significant alterations in HRV structure, suggesting its potential clinical importance for providing an earlier diagnosis of neonatal bacterial sepsis. A second goal was to assess whether the reflexivity of the autonomic nervous system was altered after LPS injection by studying the cardiorespiratory components of the laryngeal and pulmonary chemoreflexes. No difference was found. Lastly, preliminary results provide proof of principle that brainstem inflammation (increased IL-8 and TNF-α mRNA expression) can be shown 6 h after LPS injection. In conclusion, this full-term lamb model of systemic inflammation reproduces several important aspects of neonatal bacterial sepsis and paves the way for studies in preterm lambs aiming to assess both the effect of prematurity and the central neural mechanisms of cardiorespiratory control alterations observed during neonatal sepsis.
Peripapillary Vessel Density as Early Biomarker in Multiple Sclerosis

Background: To evaluate retinal vessel density (VD) in macular and in peripapillary regions in patients with recent onset of multiple sclerosis, at initial demyelinating event (IDE) and in matched relapsing-remitting multiple sclerosis (RRMS) patients. Methods: We evaluated VD in superficial capillary plexus, deep capillary plexus, choriocapillaris and radial peripapillary capillary plexus in IDE, RRMS patients and in matched healthy controls (HCs) through Optical Coherence Tomography Angiography (OCT-A). Clinical history, including history of optic neuritis, Expanded Disability Status scale and disease duration of patients were collected. Results: Thirty patients (20 with IDE and 10 with RRMS) and 15 HCs were enrolled. IDE patients showed a lower VD in radial peripapillary capillary plexus compared with controls (coeff. β = −3.578; p = 0.002). RRMS patients displayed a lower VD in both superficial capillary plexus and radial peripapillary capillary plexus compared with HCs (coeff. β = −4.955; p = 0.002, and coeff. β = −7.446; p < 0.001, respectively). Furthermore, RRMS patients showed a decreased VD in radial peripapillary capillary plexus compared with IDE patients (coeff. β = −3.868; p = 0.003). Conclusions: Peripapillary region vessel density reduction, revealed through OCT-A, might be considered as an early event in MS, and might be relevant as a biomarker of disease pathology.
Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes

Acinetobacter baumannii is an opportunistic bacterial pathogen infecting immunocompromised patients and has gained attention worldwide due to its increased antimicrobial resistance. Here, we report a comparative whole-genome sequencing and analysis coupled with an assessment of antibiotic resistance of 46 Acinetobacter strains (45 A. baumannii plus one Acinetobacter nosocomialis) originated from five hospitals from the city of Recife, Brazil, between 2010 and 2014. An average of 3,809 genes were identified per genome, although only 2,006 genes were single copy orthologs or core genes conserved across all sequenced strains, with an average of 42 new genes found per strain. We evaluated genetic distance through a phylogenetic analysis and MLST as well as the presence of antibiotic resistance genes, virulence markers and mobile genetic elements (MGE). The phylogenetic analysis recovered distinct monophyletic A. baumannii groups corresponding to five known (ST1, ST15, ST25, ST79, and ST113) and one novel ST (ST881, related to ST1). A large number of ST specific genes were found, with the ST79 strains having the largest number of genes in common that were missing from the other STs. Multiple genes associated with resistance to β-lactams, aminoglycosides and other antibiotics were found. Some of those were clearly mapped to defined MGEs and an analysis of those revealed known elements as well as a novel Tn7-Tn3 transposon with a clear ST specific distribution. An association of selected resistance/virulence markers with specific STs was indeed observed, as well as the recent spread of the OXA-253 carbapenemase encoding gene. Virulence genes associated with the synthesis of the capsular antigens were noticeably more variable in the ST113 and ST79 strains. Indeed, several resistance and virulence genes were common to the ST79 and ST113 strains only, despite a greater genetic distance between them, suggesting common means of genetic exchange. Our comparative analysis reveals the spread of multiple STs and the genomic plasticity of A. baumannii from different hospitals in a single metropolitan area. It also highlights differences in the spread of resistance markers and other MGEs between the investigated STs, impacting on the monitoring and treatment of Acinetobacter in the ongoing and future outbreaks.
The Global Attractor of the Allen-Cahn Equation on the Sphere

In this paper we study the attractor of a parabolic semiflow generated by a singularly perturbed PDE with a non-linear term given by a bistable potential, in an oval surface; the Allen-Cahn equation being a prototypical example. An additional constraint motivated by a variational principle for closed geodesics originally proposed by Poincaré arising from geometric considerations is introduced. The existence of a global attractor is established by modifying standard techniques in order to handle the constraint. Based on previous work on the elliptic case, it is known that when the perturbation parameter tends to zero, minimal energy solutions exhibit a sharp interface concentrated on a closed geodesic. We provide numerical simulations using Galerkin's method. Based on the analytical and numerical results we conjecture that, when the perturbation parameter tends to zero and for large times, the transition layers of the solutions of this PDE consists of closed geodesics or a union of arcs of such geodesics, thus characterizing the structure of the attractor.
Complex Visceral Coupling During Central Sleep Apnea in Cats

Central sleep apnea is a sudden arrest of breathing during sleep caused by the central commands to the thoracoabdominal muscles. It is a widespread phenomenon in both healthy and diseased people, as well as in some animals. However, there is an ongoing debate whether it can be considered as a pathological deviation of the respiratory function or an adaptive mechanism of an unclear function. We performed chronic recordings from six behaving cats over multiple sleep/wake cycles, which included electroencephalogram, ECG, eye movements, air flow, and thoracic respiratory muscle movements, and in four cats combined that with the registration of myoelectric activity of the stomach and the duodenum. In these experiments, we observed frequent central cessations of breathing (for 5–13 s) during sleep. Each of the sleep apnea episodes was accompanied by a stereotypical complex of somatic and visceral effects. The heart rate increased 3–5 s before the respiration arrest and strongly decreased during the absence of respiration. The myoelectric activity of the stomach and the duodenum also often demonstrated a strong suppression during the apnea episodes. The general composition of the visceral effects was stable during all periods of observation (up to 3 years in one cat). We hypothesize that the stereotypic coupling of activities in various visceral systems during episodes of central sleep apnea most likely reflects a complex adaptive behavior rather than an isolated respiratory pathology and discuss the probable function of this phenomenon.
Dynamic Stability and Trunk Control Improvements Following Robotic Balance and Core Stability Training in Chronic Stroke Survivors: A Pilot Study

Stroke survivors show greater postural oscillations and altered muscular activation compared to healthy controls. This results in difficulties in walking and standing, and in an increased risk of falls. A proper control of the trunk is related to a stable walk and to a lower falling risk; to this extent, rehabilitative protocols are currently working on core stability. The main objective of this work was to evaluate the effectiveness of trunk and balance training performed with a new robotic device designed for evaluation and training of balance and core stability, in improving the recovery of chronic stroke patients compared with a traditional physical therapy program. Thirty chronic stroke patients, randomly divided in two groups, either underwent a traditional rehabilitative protocol, or a robot-based program. Each patient was assessed before and after the rehabilitation and at 3-months follow-up with clinical and robot-based evaluation exercises focused on static and dynamic balance and trunk control. Results from clinical scores showed an improvement in both groups in balance and trunk control. Robot-based indices analysis indicated that the experimental group showed greater improvements in proprioceptive control, reactive balance and postural control in unstable conditions, compared to the control group, showing an improved trunk control with reduced compensatory strategies at the end of the training. Moreover, the experimental group had an increased retention of the benefits obtained with training at 3 months follow up. These results support the idea that such robotic device is a promising tool for stroke rehabilitation.
Retinal and Brain Organoids: Bridging the Gap Between in vivo Physiology and in vitro Micro-Physiology for the Study of Alzheimer’s Diseases

Recent progress in tissue engineering has led to increasingly complex approaches to investigate human neurodegenerative diseases in vitro, such as Alzheimer’s disease, aiming to provide more functional and physiological models for the study of their pathogenesis, and possibly the identification of novel diagnostic biomarkers and therapeutic targets. Induced pluripotent stem cell-derived cortical and retinal organoids represent a novel class of in vitro three-dimensional models capable to recapitulate with a high similarity the structure and the complexity of the native brain and retinal tissues, thus providing a framework for better mimicking in a dish the patient’s disease features. This review aims to discuss progress made over the years in the field of in vitro three-dimensional cell culture systems, and the benefits and disadvantages related to a possible application of organoids for the study of neurodegeneration associated with Alzheimer’s disease, providing a promising breakthrough toward a personalized medicine approach and the reduction in the use of humanized animal models.
Psychometric Properties and Configural Invariance of the Polish – Language Version of the 20-Item Toronto Alexithymia Scale in Non-clinical and Alcohol Addict Persons

Aim The development and assessment of the psychometric properties of the Polish-language version of the Toronto Alexithymia Scale (Bagby et al., 1994a, b) is described in this article. The aim of this study was to translate the TAS – 20 into Polish and establish the psychometric properties of this instrument evaluating alexithymia. Materials and Methods Data were collected via self-report measures from a total sample of 676 participants: a total of 180 participants (115 males and 65 females) diagnosed with alcohol dependence, and 496 control group (347 males and 149 females). Results Confirmatory factor analyses found the factor structure of the original English-language TAS 20 for the three subscales translated into Polish: Difficulty in Identifying Feeling (DIF); Difficulty in Describing Feeling (DDF); Externally Oriented Thinking (EOT). All three subscales showed good internal consistency in non-clinical group and two subscales, DIF and DDF in alcohol addict group. Several EOT items loaded poorly on their intended factor. Conclusion The results from the present study indicate that the Polish version of the TAS - 20 is a reliable and valid measure of alexithymia with good levels of internal consistency, homogeneity, and construct validity. We conclude that the TAS-20 has, for the most part, adequate psychometric properties, though interpretation should focus only on the total scale score and DIF and DDF subscales, especially in clinical groups.