Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation.

Knowledge about transcription factor binding and regulation, target genes, cis-regulatory modules and topologically associating domains is not only defined by functional associations like biological processes or diseases but also has a determinative genome location aspect. Here, we exploit these location and functional aspects together to develop new strategies to enable advanced data querying. Many databases have been developed to provide information about enhancers, but a schema that allows the standardized representation of data, securing interoperability between resources, has been lacking. In this work, we use knowledge graphs for the standardized representation of enhancers and topologically associating domains, together with data about their target genes, transcription factors, location on the human genome, and functional data about diseases and gene ontology annotations. We used this schema to integrate twenty-five enhancer datasets and two domain datasets, creating the most powerful integrative resource in this field to date. The knowledge graphs have been implemented using the Resource Description Framework and integrated within the open-access BioGateway knowledge network, generating a resource that contains an interoperable set of knowledge graphs (enhancers, TADs, genes, proteins, diseases, GO terms, and interactions between domains). We show how advanced queries, which combine functional and location restrictions, can be used to develop new hypotheses about functional aspects of gene expression regulation.

Monitoring synaptic pathology in Alzheimer's disease through fluid and PET imaging biomarkers: a comprehensive review and future perspectives.

Alzheimer's disease (AD) is currently constrained by limited clinical treatment options. The initial pathophysiological event, which can be traced back to decades before the clinical symptoms become apparent, involves the excessive accumulation of amyloid-beta (Aß), a peptide comprised of 40-42 amino acids, in extraneuronal plaques within the brain. Biochemical and histological studies have shown that overaccumulation of Aß instigates an aberrant escalation in the phosphorylation and secretion of tau, a microtubule-binding axonal protein. The accumulation of hyperphosphorylated tau into intraneuronal neurofibrillary tangles is in turn correlated with microglial dysfunction and reactive astrocytosis, culminating in synaptic dysfunction and neurodegeneration. As neurodegeneration progresses, it gives rise to mild clinical symptoms of AD, which may eventually evolve into overt dementia. Synaptic loss in AD may develop even before tau alteration and in response to possible elevations in soluble oligomeric forms of Aß associated with early AD. These findings largely rely on post-mortem autopsy examinations, which typically involve a limited number of patients. Over the past decade, a range of fluid biomarkers such as neurogranin, α-synuclein, visinin-like protein 1 (VILIP-1), neuronal pentraxin 2, and ß-synuclein, along with positron emission tomography (PET) markers like synaptic vesicle glycoprotein 2A, have been developed. These advancements have facilitated the exploration of how synaptic markers in AD patients correlate with cognitive impairment. However, fluid biomarkers indicating synaptic loss have only been validated in cerebrospinal fluid (CSF), not in plasma, with the exception of VILIP-1. The most promising PET radiotracer, [11C]UCB-J, currently faces significant challenges hindering its widespread clinical use, primarily due to the necessity of a cyclotron. As such, additional research geared toward the exploration of synaptic pathology biomarkers is crucial. This will not only enable their extensive clinical application, but also refine the optimization process of AD pharmacological trials.

Exome sequencing of 20,791 cases of type 2 diabetes and 24,440 controls.

Protein-coding genetic variants that strongly affect disease risk can yield relevant clues to disease pathogenesis. Here we report exome-sequencing analyses of 20,791 individuals with type 2 diabetes (T2D) and 24,440 non-diabetic control participants from 5 ancestries. We identify gene-level associations of rare variants (with minor allele frequencies of less than 0.5%) in 4 genes at exome-wide significance, including a series of more than 30 SLC30A8 alleles that conveys protection against T2D, and in 12 gene sets, including those corresponding to T2D drug targets (P = 6.1 × 10-3) and candidate genes from knockout mice (P = 5.2 × 10-3). Within our study, the strongest T2D gene-level signals for rare variants explain at most 25% of the heritability of the strongest common single-variant signals, and the gene-level effect sizes of the rare variants that we observed in established T2D drug targets will require 75,000-185,000 sequenced cases to achieve exome-wide significance. We propose a method to interpret these modest rare-variant associations and to incorporate these associations into future target or gene prioritization efforts.

First-in-Human Phase I Clinical Trial of the Adenosine A1R/A3R Agonist AST-004 in Healthy Subjects.

BACKGROUND: AST-004 is a small-molecule adenosine A1/A3 receptor agonist that has exhibited significant cerebroprotective efficacy in preclinical models of acute ischemic stroke and traumatic brain injury. The primary objectives of this clinical phase I first-in-human study were to evaluate the safety and tolerability profile of single ascending intravenous doses in healthy subjects. The secondary objectives were to characterize the single-dose pharmacokinetic profiles in plasma, cerebrospinal fluid (CSF), and urine. METHODS: In part 1 of the study, AST-004 was administered in ascending dose cohorts of 5, 25, 50, 75, and 100 mg, with 6 subjects in each cohort receiving the study drug and 2 receiving placebo. In part 2, all 12 subjects received a 100 mg IV infusion of the study drug followed by a single CSF collection per subject via lumbar puncture at 20, 40, or 60 minutes after infusion. RESULTS: A total of 42 subjects received AST-004, with no severe or serious adverse events observed. Twelve of these subjects experienced a treatment-emergent adverse event, the most frequent across groups being headache. In part 2, pharmacokinetic analyses confirmed that AST-004 was distributed in the CSF, with the CSF-to-plasma ratio increasing over the 3 timepoints sampled. The mean half-life was 1.1 to 1.4 hours for doses of 25 to 100 mg, and the geometric mean maximum plasma concentration obtained in the highest dosing cohort (100 mg) was 2232±428 ng/mL. CONCLUSIONS: AST-004 was safe and well-tolerated at plasma concentrations 3 to 8× higher than those associated with significant efficacy in astrocyte's preclinical primate stroke efficacy studies, with CSF concentrations highest at the 60-minute collection timepoint, the last timepoint tested. This study supports additional clinical investigations, including evaluation of an extended infusion to support the phase 2 program in stroke and traumatic brain injury.

Identifying patterns to uncover the importance of biological pathways on known drug repurposing scenarios.

BACKGROUND: Drug repurposing plays a significant role in providing effective treatments for certain diseases faster and more cost-effectively. Successful repurposing cases are mostly supported by a classical paradigm that stems from de novo drug development. This paradigm is based on the "one-drug-one-target-one-disease" idea. It consists of designing drugs specifically for a single disease and its drug's gene target. In this article, we investigated the use of biological pathways as potential elements to achieve effective drug repurposing. METHODS: Considering a total of 4214 successful cases of drug repurposing, we identified cases in which biological pathways serve as the underlying basis for successful repurposing, referred to as DREBIOP. Once the repurposing cases based on pathways were identified, we studied their inherent patterns by considering the different biological elements associated with this dataset, as well as the pathways involved in these cases. Furthermore, we obtained gene-disease association values to demonstrate the diminished significance of the drug's gene target in these repurposing cases. To achieve this, we compared the values obtained for the DREBIOP set with the overall association values found in DISNET, as well as with the drug's target gene (DREGE) based repurposing cases using the Mann-Whitney U Test. RESULTS: A collection of drug repurposing cases, known as DREBIOP, was identified as a result. DREBIOP cases exhibit distinct characteristics compared with DREGE cases. Notably, DREBIOP cases are associated with a higher number of biological pathways, with Vitamin D Metabolism and ACE inhibitors being the most prominent pathways. Additionally, it was observed that the association values of GDAs in DREBIOP cases were significantly lower than those in DREGE cases (p-value < 0.05). CONCLUSIONS: Biological pathways assume a pivotal role in drug repurposing cases. This investigation successfully revealed patterns that distinguish drug repurposing instances associated with biological pathways. These identified patterns can be applied to any known repurposing case, enabling the detection of pathway-based repurposing scenarios or the classical paradigm.

Tracking neuroinflammatory biomarkers in Alzheimer's disease: a strategy for individualized therapeutic approaches?

BACKGROUND: Recent trials of anti-amyloid-ß (Aß) monoclonal antibodies, including lecanemab and donanemab, in early Alzheimer disease (AD) showed that these drugs have limited clinical benefits and their use comes with a significant risk of serious adverse events. Thus, it seems crucial to explore complementary therapeutic approaches. Genome-wide association studies identified robust associations between AD and several AD risk genes related to immune response, including but not restricted to CD33 and TREM2. Here, we critically reviewed the current knowledge on candidate neuroinflammatory biomarkers and their role in characterizing the pathophysiology of AD. MAIN BODY: Neuroinflammation is recognized to be a crucial and contributing component of AD pathogenesis. The fact that neuroinflammation is most likely present from earliest pre-stages of AD and co-occurs with the deposition of Aß reinforces the need to precisely define the sequence and nature of neuroinflammatory events. Numerous clinical trials involving anti-inflammatory drugs previously yielded unfavorable outcomes in early and mild-to-moderate AD. Although the reasons behind these failures remain unclear, these may include the time and the target selected for intervention. Indeed, in our review, we observed a stage-dependent neuroinflammatory process in the AD brain. While the initial activation of glial cells counteracts early brain Aß deposition, the downregulation in the functional state of microglia occurs at more advanced disease stages. To address this issue, personalized neuroinflammatory modulation therapy is required. The emergence of reliable blood-based neuroinflammatory biomarkers, particularly glial fibrillary acidic protein, a marker of reactive astrocytes, may facilitate the classification of AD patients based on the ATI(N) biomarker framework. This expands upon the traditional classification of Aß ("A"), tau ("T"), and neurodegeneration ("N"), by incorporating a novel inflammatory component ("I"). CONCLUSIONS: The present review outlines the current knowledge on potential neuroinflammatory biomarkers and, importantly, emphasizes the role of longitudinal analyses, which are needed to accurately monitor the dynamics of cerebral inflammation. Such a precise information on time and place will be required before anti-inflammatory therapeutic interventions can be considered for clinical evaluation. We propose that an effective anti-neuroinflammatory therapy should specifically target microglia and astrocytes, while considering the individual ATI(N) status of patients.

Factors influencing the health-related quality of life of older men and women living with HIV in Spain.

The number of older people living with HIV (OPLHIV) is increasing worldwide. However, little is known about the factors that better predict their health-related quality of life (HRQoL). We administered the validated WHOQoL-HIV BREF questionnaire to 247 Spanish OPLHIV (192 men and 55 women). In addition to the six domains of the questionnaire, we constructed a seventh domain as theaverage of punctuations of all domains. Multivariable Poisson regression models with robust estimates by sex were constructed for the seven domains (14 in total). The best-subset selection method together with Mallow's Cp metric was used to select the model factors. The percentage of variability explained by Poisson models ranged from15-38% for men and 29-70% for women. The analysis showed that women were most affected by ageing (four domains), mobility impairments (five domains), and mental disorders (five domains). The factors with the greatest negative influence on men were heterosexuality (six domains), mental disorders (six domains), being single (five domains), and poverty risk (three domains). Physical activity was found to improve HRQoL in both men (six domains) and women (four domains). Future OPLHIV programmes would benefit from considering sex specific HRQoL factors. This could also improve the cost-effectiveness of interventions.

Impact of Vancomycin trough levels monitoring on uncomplicated methilcillin-resistant Staphylococcus aureus bacteremia in chronic kidney disease on hemodialysis, retrospective cohort.

BACKGROUND: CKD patients on hemodialysis (HD) with Staphylococcus aureus (SA) bacteremia present high morbidity, mortality and increased risk of MRSA. Vancomycin is the antibiotic of choice in these cases, it has a narrow therapeutic margin and inadequate dosage generates a risk of toxicity, therefore, the recommendation is to dosage it through serum levels. METHODS: This is a retrospective cohort study in 3 hospitals of third level of complexity in the city of Medellin in which there were differences in the measurement and implementation of vancomycin25 dosage based on trough levels (VL) in patients with chronic kidney disease on hemodialysis (CKD- HD) with uncomplicated bacteremia based infection by methilcillin-resistant Staphyloccocus aureus (MRSA). The primary outcome was the composite of hospital mortality, clinical response (fever, hemodynamic instability and altered consciousness), complications associated with bacteremia, or bacteriological response failure (positive cultures at first week follow-up) at 7 days. The composite variables were analyzed individually as secondary outcomes. RESULTS: The main unadjusted outcome (OR 1.3, CI 0.6 - 2.7) and adjusted for age, Charlson index, loading dose, initial dose, dosing frequency and MIC to vancomycin (OR 1.2, CI 0.5 - 2.7). Regarding adjusted secondary outcomes: clinical response (OR 1.4 CI 0.3 - 5.8), death (OR 1.3 CI 0.3 - 4.6) and complications (OR 0.9, CI 0.37 - 2.2). CONCLUSIONS: We conclude that the measurement of trough levels in patients with HD-CKD does not modify the composite outcome. The main limitation is the sample size and type of study, randomized control trials may be required to confirm the results presented.

Frailty and Cancer Prognosis.

PURPOSE OF REVIEW: This review aims to summarize the current evidence regarding the prognostic role of frailty in older patients diagnosed with cancer and to explore the evidence regarding its prognostic implications in cancer survivors. RECENT FINDINGS: Frailty has been consistently associated with mortality/overall survival, postoperative complications, short- and long-term postoperative mortality, length of stay, among other adverse health-related outcomes in several oncological contexts. The possible association between frailty and treatment toxicity has been less explored, however most studies suggest frailty is a predictor of treatment induced toxicity. In addition, in cancer survivors, frailty is a risk factor for cardiovascular disease, incident type 2 diabetes mellitus, mortality, altered cognitive performance and increased symptom severity. Due to its usefulness in establishing prognosis and informing treatment decision making, it is expected that frailty screening and assessment will continue to gain popularity as part of the pretreatment evaluation of older patients with cancer.

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing.

Common genetic contributions to autism spectrum disorder (ASD) reside in risk gene variants that individually have minimal effect sizes. As environmental factors that perturb neurodevelopment also underlie idiopathic ASD, it is crucial to identify altered regulators that can orchestrate multiple ASD risk genes during neurodevelopment. Cytoplasmic polyadenylation element binding proteins 1-4 (CPEB1-4) regulate the translation of specific mRNAs by modulating their poly(A)-tails and thereby participate in embryonic development and synaptic plasticity. Here we find that CPEB4 binds transcripts of most high-confidence ASD risk genes. The brains of individuals with idiopathic ASD show imbalances in CPEB4 transcript isoforms that result from decreased inclusion of a neuron-specific microexon. In addition, 9% of the transcriptome shows reduced poly(A)-tail length. Notably, this percentage is much higher for high-confidence ASD risk genes, correlating with reduced expression of the protein products of ASD risk genes. An equivalent imbalance in CPEB4 transcript isoforms in mice mimics the changes in mRNA polyadenylation and protein expression of ASD risk genes and induces ASD-like neuroanatomical, electrophysiological and behavioural phenotypes. Together, these data identify CPEB4 as a regulator of ASD risk genes.

Impact of a multimodal effort re-education programme on functionality, physical performance, and functional capacity in cancer patients with dyspnoea: a randomised experimental study.

BACKGROUND: In recent years, there has been a significant increase in the survival rates of cancer patients. However, this has also led to an increase in side effects, such as dyspnoea, which can negatively impact of patients. We propose a programme for re-educating effort. The main objective is to test the effectiveness of this programme in improving respiratory symptoms and functionality in cancer patients. METHODOLOGY: Experimental, prospective, longitudinal, randomised study with a parallel fixed-assignment scheme (CG-IG). The patients were selected from the Medical Oncology Service of the University Hospital Complex of Salamanca (CAUSA), Spain. Two parallel intervention programmes were designed for the two study groups (Conventional Clinical Practice-Effort Re-education Programme). Primary variables: dyspnoea (MRC), functionality (Barthel); secondary variables: physical performance (SPPB) and functional capacity (ECOG) and the socio-demographic variables (age, sex, anatomopathological diagnosis, and number of treatment lines). RESULTS: The study sample consisted of 182 patients, with 12 excluded, resulting in a final sample size of n = 170. Sex distribution (CG: 52.9% male and 47.1% female; IG: 49.4% male and 50.6% female). The primary oncological diagnosis was lung cancer, and the most frequent tumour stages were III and IV. Statistically significant differences were found between the IG and CG scores (p < 0.001, d = 0.887, 95% CI) and between the IG and CG scores (p = 0.004, d = 0.358, 95% CI), indicating that the IG performed better. CONCLUSION: The results of this study support the beneficial effects of an exercise re-education programme, carried out by an interdisciplinary team in improving the autonomy of oncology patients with dyspnoea. TRIAL REGISTRATION: The clinical trial was registered in ClinicalTrials.gov (NCT04186754). (03 September 2019).

Factors Predicting Prolonged Mechanical Ventilation in Guillain-Barré Syndrome.

BACKGROUND: Up to 30% of patients with Guillain-Barré syndrome require mechanical ventilation and 5% die due to acute complications of mechanical ventilation. There is a considerable group of patients that will need prolonged mechanical ventilation (considered as >14 days) and should be considered for early tracheostomy. The objective of this study is to identify risk factors for prolonged mechanical ventilation. METHODS: We prospectively analyzed patients with Guillain-Barré diagnosis with versus without prolonged mechanical ventilation. We considered clinical and electrophysiological characteristics and analyzed factors associated with prolonged mechanical ventilation. RESULTS: Three hundred and three patients were included; 29% required mechanical ventilation. When comparing the groups, patients with prolonged invasive mechanical ventilation (IMV) have a lower score on the Medical Research Council score (19.5 ± 16.2 vs 27.4 ± 17.5, p = 0.03) and a higher frequency of dysautonomia (42.3% vs 19.4%, p = 0.037), as well as lower amplitudes of the distal compound muscle action potential (CMAP) of the median nerve [0.37 (RIQ 0.07-2.25) vs. 3.9 (RIQ1.2-6.4), p = <0.001] and ulnar nerve [0.37 (RIQ0.0-3.72) vs 1.5 (RIQ0.3-6.6), p = <0.001], and higher frequency of severe axonal damage in these nerves (distal CMAP ≤ 1.0 mV). Through binary logistic regression, severe axonal degeneration of the median nerve is an independent risk factor for prolonged IMV OR 4.9 (95%CI 1.1-21.5) p = 0.03, AUC of 0.774, (95%CI 0.66-0.88), p = < 0.001. CONCLUSIONS: Severe median nerve damage is an independent risk factor for prolonged mechanical ventilation.

Effect of calcium soaps from garlic (Allium sativum) and willow (Salix babylonica) extracts on nematode loads, nutrient intake and digestibility, nitrogen balance and rumen fermentation kinetics in dairy goats.

The objective of this study was to determine the effect of dietary calcium soaps from garlic (Allium sativum) and willow (Salix babylonica) extracts on nematode loads, nutrient intake and digestibility, nitrogen balance and rumen fermentation kinetics in dairy goats. Nine adult non-lactating Saanen goats were grouped into a complete randomized block design with 3 treatments (n = 3) over a period of 28 d. Animals were fed a diet based on alfalfa hay and a concentrate that was supplemented (65 g/kg DM) with calcium soaps of safflower (control), garlic or willow. Intake of dry matter (DM), organic matter (OM) and neutral detergent fiber (NDF) were not affected by dietary calcium soaps. However, the highest digestibility of DM and OM were observed in willow supplemented goats. In vitro gas kinetics and fermentation profile were not affected by diets. Results from fecal egg count indicated a reduction in total count, Haemonchus spp. and Trychostrongylus spp. for both garlic and willow compared to control. Our results suggest that calcium soaps of garlic or willow extracts can be used to reduce gastrointestinal parasites in goats without compromising productive traits or rumen function.

Contribution of Mine-Derived Airborne Particulate Matter to Ca, Fe, Mn and S Content and Distribution in the Lichen Punctelia hypoleucites Transplanted to Bajo de la Alumbrera Mine, Catamarca (Argentina).

The aim of this work was to relate the contribution of mine-derived airborne particulate matter to Ca, Fe, Mn and S content and distribution in Punctelia hypoleucites transplanted to Bajo de la Alumbrera, an important open-pit mine in Catamarca, Argentina. Lichen samples were transplanted to four monitoring sites: two sites inside the mine perimeter and two sites outside the mine. After three months, elemental distribution in samples was analyzed by microparticle-induced X-ray emission (microPIXE), and elemental concentration was determined by specific techniques: Ca and Fe by instrumental neutron activation analysis, Mn by inductively coupled plasma atomic emission spectrometry and S by a turbidimetric method. A differential distribution of S and Ca in thalli transplanted in-mine sites was detected compared to that of samples transplanted outside-mine sites. An overlap of Fe and S in the upper cortex of the apothecium section was observed, leading to infer a mineral association of both elements. Similar association was observed for Ca and S. In addition to these results, the significantly higher concentration detected for S and Mn in in-mine site samples suggests a contribution of Fe, S, Ca and Mn of mining origin to the content and distribution of these elements in P. hypoleucites. MicroPIXE complemented with Mössbauer spectroscopy analysis determined the presence of pyrite particles together with other iron-bearing minerals displaying different degrees of oxidation. These results point to a mining origin of the airborne particulate matter trapped by the lichen thalli transplanted to Bajo de la Alumbrera. These findings indicate that P. Hypoleucites acts as an excellent air quality biomonitor in the Bajo de la Alumbrera mine area.

Application of Machine Vision Techniques in Low-Cost Devices to Improve Efficiency in Precision Farming.

In the context of recent technological advancements driven by distributed work and open-source resources, computer vision stands out as an innovative force, transforming how machines interact with and comprehend the visual world around us. This work conceives, designs, implements, and operates a computer vision and artificial intelligence method for object detection with integrated depth estimation. With applications ranging from autonomous fruit-harvesting systems to phenotyping tasks, the proposed Depth Object Detector (DOD) is trained and evaluated using the Microsoft Common Objects in Context dataset and the MinneApple dataset for object and fruit detection, respectively. The DOD is benchmarked against current state-of-the-art models. The results demonstrate the proposed method's efficiency for operation on embedded systems, with a favorable balance between accuracy and speed, making it well suited for real-time applications on edge devices in the context of the Internet of things.

Experimental Study of White Light Interferometry in Mach-Zehnder Interferometers Based on Standard Single Mode Fiber.

In this work, we experimentally analyzed and demonstrated the performance of an in-line Mach-Zehnder interferometer in the visible region, with an LED light source. The different waist diameter taper and asymmetric core-offset interferometers proposed used a single-mode fiber (SMF). The visibility achieved was V = 0.14 with an FSR of 23 nm for the taper MZI structure and visibilities of V = 0.3, V = 0.27, and V = 0.34 with FSRs of 23 nm, 17 nm, and 8 nm and separation lengths L of 2.5 cm, 4.0 cm, and 5.0 cm between the core-offset structure, respectively. The experimental investigation of the response to the temperature sensor yielded values from 50 °C to 300 °C; the sensitivity obtained was 3.53 a.u./°C, with R2 of 0.99769 and 1% every 1 °C in the transmission. For a range of 50 °C to 150 °C, 20.3 pm/°C with a R2 of 0.96604 was obtained.

From the Microbiome to the Electrome: Implications for the Microbiota-Gut-Brain Axis.

The gut microbiome plays a fundamental role in metabolism, as well as the immune and nervous systems. Microbial imbalance (dysbiosis) can contribute to subsequent physical and mental pathologies. As such, interest has been growing in the microbiota-gut-brain brain axis and the bioelectrical communication that could exist between bacterial and nervous cells. The aim of this study was to investigate the bioelectrical profile (electrome) of two bacterial species characteristic of the gut microbiome: a Proteobacteria Gram-negative bacillus Escherichia coli (E. coli), and a Firmicutes Gram-positive coccus Enterococcus faecalis (E. faecalis). We analyzed both bacterial strains to (i) validate the fluorescent probe bis-(1,3-dibutylbarbituric acid) trimethine oxonol, DiBAC4(3), as a reliable reporter of the changes in membrane potential (Vmem) for both bacteria; (ii) assess the evolution of the bioelectric profile throughout the growth of both strains; (iii) investigate the effects of two neural-type stimuli on Vmem changes: the excitatory neurotransmitter glutamate (Glu) and the inhibitory neurotransmitter γ-aminobutyric acid (GABA); (iv) examine the impact of the bioelectrical changes induced by neurotransmitters on bacterial growth, viability, and cultivability using absorbance, live/dead fluorescent probes, and viable counts, respectively. Our findings reveal distinct bioelectrical profiles characteristic of each bacterial species and growth phase. Importantly, neural-type stimuli induce Vmem changes without affecting bacterial growth, viability, or cultivability, suggesting a specific bioelectrical response in bacterial cells to neurotransmitter cues. These results contribute to understanding the bacterial response to external stimuli, with potential implications for modulating bacterial bioelectricity as a novel therapeutic target.

Response of a pan-European fish index (EFI+) to multiple pressures in rivers across Spain.

Rivers are ecosystems highly threatened by human activities and fish are an invaluable tool to measure and communicate environmental degradation and restoration. Fish bioassessment is crucial but notoriously difficult in Mediterranean-climate streams for a number of reasons, including low local species richness, faunas with high spatial turnover and generalist species, and scarcity of reference sites. In this study, we conducted the most comprehensive test of the pan-European fish index (EFI+) in the Iberian Peninsula, analysing its response to multiple anthropogenic pressures. We compiled a database, which we provide online, with 2970 electrofishing samples across Spain, involving 100,732 fish of 69 species. Principal component analyses of many quantitative variables were used to create new synthetic anthropogenic pressure indices. Correlation and multiple linear regression analyses were used to test the relationship between these pressures and the fish index (EFI+) and its four individual metrics scores (i.e., density of species intolerant to oxygen depletion, density of fish ≤150 mm of species intolerant to habitat degradation, richness of species of rheophilic reproduction habitat, and density of species of lithophilic reproduction habitat). We also obtained the same models but including the river basin district to test for spatial or methodological differences. Our results indicate that both the EFI+ index and its individual metrics respond to various anthropogenic pressures. These pressures explained about 36% of the variance of EFI+ values. Notably, downstream and mainstream reaches with higher agricultural or urban land uses, increased hydrologic alteration, and water and habitat quality impairment exhibited lower EFI+ values. Although less variance was explained for the individual metrics than for the fish index, they responded as expected to the different pressures. For instance, the richness of rheophilic species and the number of lithophilic fish decreased with hydrologic alteration, while the number of fish intolerant to oxygen depletion decreased with water quality impairment. Similar correlations were observed when river basin district was included in the model, but with higher explained variation and greater significance of the pressures. While it is possible to develop regional indices with more metrics and a stronger correlation with anthropogenic pressures, EFI+ is the only fish index that has been validated throughout the Spanish peninsular territory. Our results support the use of EFI+ in intercalibration exercises across Spain until better regional indices are developed.

Nonfunctional Incomplete Infected Ureteral Duplication in a French Bulldog.

A 7 yr old female French bulldog exhibited recurrent purulent vulvar discharge following an episode of pyometra treated by ovariohysterectomy. The diagnosis of ureteral duplication was established through a combination of ultrasonography, computed tomography scanning, and cystoscopy/vaginoscopy. Despite initial medical intervention, the dog's clinical condition did not improve. Consequently, surgical treatment was pursued to remove the duplicated ureter while preserving the integrity of the urinary tract. Resection of the duplicated ureter was performed from the kidney to the bladder, and the blind ends left in place in the kidney and in the bladder wall were omentalized. Histopathological analysis confirmed the presence of the duplicated ureter. Postoperatively, the dog made a full recovery with no complications or urinary tract dysfunction. Long-term follow-up (11 mo) revealed complete resolution of all clinical signs. Ureteral duplication should be included in the differential diagnosis of vulvar purulent discharge in dogs. Removal of the abnormal ureter resulted in complete resolution of the clinical signs. This case underscores the importance of individualized treatment plans for ureteral duplications in dogs and the potential for successful surgical treatment in selected cases.

An information-theoretic approach to basis-set fitting of electron densities and other non-negative functions.

The numerical ill-conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater-type functions is overcome by using the (extended) Kullback-Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non-negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non-negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non-negative basis functions. We present a fixed-point iteration method for optimizing the Kullback-Leibler divergence and compare it to conventional gradient-based optimization methods. These algorithms are released through the free and open-source BFit package, which also includes a L2-norm squared optimization routine applicable to any square-integrable scalar function.