MTS-LOF: Medical Time-Series Representation Learning via Occlusion-Invariant Features.

Medical time series data are indispensable in healthcare, providing critical insights for disease diagnosis, treatment planning, and patient management. The exponential growth in data complexity, driven by advanced sensor technologies, has presented challenges related to data labeling. Self-supervised learning (SSL) has emerged as a transformative approach to address these challenges, eliminating the need for extensive human annotation. In this study, we introduce a novel framework for Medical Time Series Representation Learning, known as MTS-LOF. MTS-LOF leverages the strengths of Joint-Embedding SSL and Masked Autoencoder (MAE) methods, offering a unique approach to representation learning for medical time series data. By combining these techniques, MTS-LOF enhances the potential of healthcare applications by providing more sophisticated, context-rich representations. Additionally, MTS-LOF employs a multi-masking strategy to facilitate occlusion-invariant feature learning. This approach allows the model to create multiple views of the data by masking portions of it. By minimizing the discrepancy between the representations of these masked patches and the fully visible patches, MTS-LOF learns to capture rich contextual information within medical time series datasets. The results of experiments conducted on diverse medical time series datasets demonstrate the superiority of MTS-LOF over other methods. These findings hold promise for significantly enhancing healthcare applications by improving representation learning. Furthermore, our work delves into the integration of Joint-Embedding SSL and MAE techniques, shedding light on the intricate interplay between temporal and structural dependencies in healthcare data. This understanding is crucial, as it allows us to grasp the complexities of healthcare data analysis.

[Upper digestive tract bleeding as a clinical presentation of non-Hodgkin's lymphoma]. / Sangrado de tubo digestivo alto como presentación clínica del linfoma no Hodgkin.

Background: Non-Hodgkin's lymphoma (NHL) is a group of malignant tumors of the nodal and extranodal lymphoid tissues, and it is associated with autoimmune diseases, mainly rheumatoid arthritis (RA). Extra nodal presentation is observed in 40%, mainly affecting the gastrointestinal tract in 3% of cases, with bleeding in the digestive tract being a rare cause of clinical presentation that requires a detailed diagnostic approach. Clinical case: 55-year-old female with a history of RA, admitted to an internal medicine service due to bleeding in the digestive tract; patient presented clinical data of deep vein thrombosis in the left pelvic limb and consumptive syndrome under study. During her approach she was identified with splenic and liver infarctions, as well as multiple lymph node conglomerates, due to which it was performed an axillary lymph node biopsy reporting neoplastic proliferation of lymphoid cells, and bone marrow aspirate with presence of lymphoplasmacytic infiltration, with which a diagnosis of stage IV non-Hodgkin lymphoma was made. Patient was sent to a third-level hospital to start treatment. Conclusions: This case shows us what has already been described in literature, which is why it is of fundamental importance to carry out a comprehensive approach of clinical findings in patients with previously identified risk factors, with the aim of achieving an etiological diagnosis that allows early therapy to improve their survival.

Introducción: el linfoma no Hodgkin (LNH) es un grupo de tumores malignos de los tejidos linfoides nodales y extranodales, y está asociado a enfermedades autoinmunes, principalmente artritis reumatoide (AR). La presentación extranodal se observa en el 40% y afecta principalmente el tracto gastrointestinal en el 3% de los casos; el sangrado de tubo digestivo es una causa rara de presentación clínica que requiere un abordaje diagnóstico detallado. Caso clínico: mujer de 55 años con antecedente de AR que ingresó a un servicio de medicina interna por sangrado de tubo digestivo; presentó datos clínicos de trombosis venosa profunda en miembro pélvico izquierdo y síndrome consuntivo en estudio. Durante su abordaje se identificó con infartos esplénicos y hepáticos, así como múltiples conglomerados ganglionares, por lo que se practicó biopsia de ganglio axilar que reportó proliferación neoplásica de células linfoides y aspirado de médula ósea con presencia de infiltración linfoplasmocitaria, con lo que se determinó diagnóstico de linfoma no Hodgkin estadio IV. La paciente fue enviada a un hospital de tercer nivel para inicio de tratamiento. Conclusiones: este caso nos muestra lo ya descrito en la literatura, por lo que es de fundamental importancia hacer un abordaje integral de los hallazgos clínicos en pacientes con factores de riesgo previamente identificados, con el objetivo de lograr un diagnóstico etiológico que permita una terapéutica temprana para mejorar su sobrevida.

Dietary Fiber and the Hippocampal Neurogenic Niche in a Model of Pelvic Radiotherapy.

We sought to determine whether radiation to the colorectum had an impact on parameters of hippocampal neurogenesis and, if so, whether it could be modulated by a fiber-rich diet. Male C57BL/6J mice were fed a diet containing bioprocessed oat bran or a fiber-free diet, starting two weeks before colorectal irradiation with 4 fractions of 8 Gray or sham-irradiation. Diets were then continued for 1, 6 or 18 weeks, whereafter parameters of hippocampal neurogenesis were analyzed and correlated to serum cytokine levels. No statistically significant changes in neuronal markers or cell proliferation were found at one week post-irradiation. Six weeks post-irradiation there was a decreased cell proliferation in the subgranular zone that appeared slightly more pronounced in irradiated animals on a fiber-free diet and increased numbers of immature neurons per mm2 dentate gyrus in the irradiated mice, with a statistically significant increase in mice on a fiber-rich diet. Microglial abundancy was similar between all groups. 18 weeks post-irradiation, a fiber-free diet had reduced the number of immature neurons, whereas irradiation resulted in an increase. Despite this, the population of mature neurons was stable. Analysis of serum cytokines revealed a negative correlation between MIP1-α and the number of immature neurons one week after irradiation, regardless of diet. Our findings show that pelvic radiotherapy has the potential to cause a long-lasting impact on hippocampal neurogenesis, and dietary interventions may modulate this impact. More in-depth studies on the relationship between irradiation-induced intestinal injury and brain health are warranted.

Cultivation of the gut bacterium Prevotella copri DSM 18205T using glucose and xylose as carbon sources.

Prevotella copri DSM18205T is a human gut bacterium, suggested as a next-generation probiotic. To utilize it as such, it is, however, necessary to grow the species in a reproducible manner. Prevotella copri has previously been reported to be highly sensitive to oxygen, and hence difficult to isolate and cultivate. This study presents successful batch cultivation strategies for viable strain inoculations and growth in both serum bottles and a stirred tank bioreactor (STR), without the use of an anaerobic chamber, as long as the cells were kept in the exponential growth phase. A low headspace volume in the STR was important to reach high cell density. P. copri utilized xylose cultivated in Peptone Yeast Xylose medium (PYX medium), resulting in a comparable growth rate and metabolite production as in Peptone Yeast Glucose medium (PYG medium) in batch cultivations at pH 7.2.Up to 5 g/L of the carbon source was consumed, leading to the production of succinic acid, acetic acid, and formic acid, and cell densities (OD620 nm ) in the range 6-7.5. The highest yield of produced succinic acid was 0.63 ± 0.05 g/g glucose in PYG medium cultivations and 0.88 ± 0.06 g/g xylose in PYX medium cultivations.

Effects of Bilberry and Oat intake on lipids, inflammation and exercise capacity after Acute Myocardial Infarction (BIOAMI): study protocol for a randomized, double-blind, placebo-controlled trial.

BACKGROUND: Bilberries from Sweden, rich in polyphenols, have shown cholesterol-lowering effects in small studies, and the cholesterol-lowering properties of oats, with abundant beta-glucans and potentially bioactive phytochemicals, are well established. Both may provide cardiometabolic benefits following acute myocardial infarction (AMI), but large studies of adequate statistical power and appropriate duration are needed to confirm clinically relevant treatment effects. No previous study has evaluated the potential additive or synergistic effects of bilberry combined with oats on cardiometabolic risk factors. Our primary objective is to assess cardioprotective effects of diet supplementation with dried bilberry or with bioprocessed oat bran, with a secondary explorative objective of assessing their combination, compared with a neutral isocaloric reference supplement, initiated within 5 days following percutaneous coronary intervention (PCI) for AMI. METHODS: The effects of Bilberry and Oat intake on lipids, inflammation and exercise capacity after Acute Myocardial Infarction (BIOAMI) trial is a double-blind, randomized, placebo-controlled clinical trial. A total of 900 patients will be randomized post-PCI to one of four dietary intervention arms. After randomization, subjects will receive beverages with bilberry powder (active), beverages with high-fiber bioprocessed oat bran (active), beverages with bilberry and oats combined (active), or reference beverages containing no active bilberry or active oats, for consumption twice daily during a 3-month intervention. The primary endpoint is the difference in LDL cholesterol change between the intervention groups after 3 months. The major secondary endpoint is exercise capacity at 3 months. Other secondary endpoints include plasma concentrations of biochemical markers of inflammation, metabolomics, and gut microbiota composition after 3 months. DISCUSSION: Controlling hyperlipidemia and inflammation is critical to preventing new cardiovascular events, but novel pharmacological treatments for these conditions are expensive and associated with negative side effects. If bilberry and/or oat, in addition to standard medical therapy, can lower LDL cholesterol and inflammation more than standard therapy alone, this could be a cost-effective and safe dietary strategy for secondary prevention after AMI. TRIAL REGISTRATION: ClinicalTrials.gov NCT03620266 . Registered on August 8, 2018.

A Fiber-Rich Diet and Radiation-Induced Injury in the Murine Intestinal Mucosa.

Dietary fiber is considered a strong intestinal protector, but we do not know whether dietary fiber protects against the long-lasting mucosal damage caused by ionizing radiation. To evaluate whether a fiber-rich diet can ameliorate the long-lasting pathophysiological hallmarks of the irradiated mucosa, C57BL/6J mice on a fiber-rich bioprocessed oat bran diet or a fiber-free diet received 32 Gray in four fractions to the distal colorectum using a linear accelerator and continued on the diets for one, six or 18 weeks. We quantified degenerating crypts, crypt fission, cell proliferation, crypt survival, macrophage density and bacterial infiltration. Crypt loss through crypt degeneration only occurred in the irradiated mice. Initially, it was most frequent in the fiber-deprived group but declined to levels similar to the fiber-consuming group by 18 weeks. The fiber-consuming group had a fast response to irradiation, with crypt fission for growth or healing peaking already at one week post-irradiation, while crypt fission in the fiber-deprived group peaked at six weeks. A fiber-rich diet allowed for a more intense crypt cell proliferation, but the recovery of crypts was eventually lost by 18 weeks. Bacterial infiltration was a late phenomenon, evident in the fiber-deprived animals and intensified manyfold after irradiation. Bacterial infiltration also coincided with a specific pro-inflammatory serum cytokine profile. In contrast, mice on a fiber-rich diet were completely protected from irradiation-induced bacterial infiltration and exhibited a similar serum cytokine profile as sham-irradiated mice on a fiber-rich diet. Our findings provide ample evidence that dietary fiber consumption modifies the onset, timing and intensity of radiation-induced pathophysiological processes in the intestinal mucosa. However, we need more knowledge, not least from clinical studies, before this finding can be introduced to a new and refined clinical practice.

Dietary Oat Bran Reduces Systemic Inflammation in Mice Subjected to Pelvic Irradiation.

Patients undergoing radiotherapy to treat pelvic-organ cancer are commonly advised to follow a restricted fiber diet. However, reducing dietary fiber may promote gastrointestinal inflammation, eventually leading to deteriorated intestinal health. The goal of this study was to evaluate the influence of dietary fiber on radiation-induced inflammation. C57BL/6J male mice were fed a High-oat bran diet (15% fiber) or a No-fiber diet (0% fiber) and were either irradiated (32 Gy delivered in four fractions) to the colorectal region or only sedated (controls). The dietary intervention started at 2 weeks before irradiation and lasted for 1, 6, and 18 weeks after irradiation, at which time points mice were sacrificed and their serum samples were assayed for 23 cytokines and chemokines. Our analyses show that irradiation increased the serum cytokine levels at all the time points analyzed. The No-fiber irradiated mice had significantly higher levels of pro-inflammatory cytokines than the High-oat irradiated mice at all time points. The results indicate that a fiber-rich oat bran diet reduces the intensity of radiation-induced inflammation, both at an early and late stage. Based on the results, it seems that the advice to follow a low-fiber diet during radiotherapy may increase the risk of decreased intestinal health in cancer survivors.

Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.

SCOPE: The molecular mechanisms underlying the cholesterol-lowering properties of oats are only partly known. To study possible pathways involved, we investigated gene expressions in the liver and small intestine of mice fed oats. METHOD AND RESULTS: Cholesterol and bile acids were analyzed in plasma and feces from LDL-receptor deficient (LDLr-/- ) mice fed Western diet with wholegrain oats. A transcriptome analysis of mRNA from liver and jejunum was performed together with quantitative RT-PCR. Oat-fed mice had lower levels of plasma lipids and increased levels of bile acids and cholesterol in feces compared with controls. Two hundred thirty nine genes in jejunum and 25 genes in liver were differentially expressed (FDR corrected p < 0.05). The most affected biological process in jejunum was lipid biosynthesis and regulation. The apical sodium-dependent bile acid transporter (ASBT, Slc10a) and the intracellular bile acid binding protein (Fabp6) were both upregulated, whereas small heterodimer partner-1 (Shp-1) and apolipoprotein CII (Apoc2) were downregulated. CONCLUSIONS: Whole oats attenuated responses typically induced by high-fat diet. Increased expression of genes for intestinal bile acid uptake following oat consumption suggests retention in the gut lumen rather than decreased uptake capacity as cause for the increased bile acid excretion and the concomitant reduction of plasma cholesterol.

Design of a potentially prebiotic and responsive encapsulation material for probiotic bacteria based on chitosan and sulfated ß-glucan.

HYPOTHESIS: Chitosan and sulfated oat ß-glucan are materials suitable to create a prebiotic coating for targeted delivery to gastrointestinal system, using the layer by layer technology. EXPERIMENT: Quartz crystal microbalance with dissipation (QCM-D), spectroscopic ellipsometry (SE) and atomic force microscopy (AFM) were used to assess the multilayer formation capacity and characterize the resulting coatings in terms of morphology and material properties such as structure and rigidity. The coating of colloidal materials was proven, specifically on L. acidophilus bacteria as measured by changes in the bacterial suspension zeta potential. Viability of coated cells was shown using plate counting method. The coatings on solid surfaces were examined after exposure to mimics of gastrointestinal fluids and a commercially available ß-glucanase. FINDINGS: Successful build-up of multilayers was confirmed with QCM-D and SE. Zeta potential values proved the coating of cells. There was 2 log CFU/mL decrease after coating cells with four alternating layers of chitosan and sulfated ß-glucan when compared to viability of uncoated cells. The coatings were partially degraded after exposure to simulated intestinal fluid and restructured as a result of ß-glucanase treatment, mimicking enzymes present in the microflora of the human gut, but seemed to resist acidic gastric conditions. Therefore, coatings of chitosan and sulfated ß-glucan can potentially be exploited as carriers for probiotics and delicate nutraceuticals.

An oat bran-based beverage reduce postprandial glycaemia equivalent to yoghurt in healthy overweight subjects.

An acute meal study was performed to determine postprandial glucose and insulin responses after consumption of two fermented oat bran-based beverages (with and without exopolysaccharides) and yoghurt. This randomized, single-blind, within-subject study included 18 healthy, overweight participants. Four breakfast meals, including a reference meal, were tested; all meals contained 50 g of available carbohydrates, but differed in energy and macronutrient composition. All experimental meals reduced the postprandial glucose response compared with the reference meal. The oat drinks as well as the yoghurt elicited higher early (0-15 min) insulin responses, but the overall insulinaemia were similar to the reference meal. A new food product containing fermented liquid oat bran and milk reduced the postprandial blood glucose response as efficiently as yoghurt after a high-glycaemic index white wheat bread meal, but the presence of microbial exopolysaccharides did not affect the outcome.

Effects of oat bran, processed to different molecular weights of beta-glucan, on plasma lipids and caecal formation of SCFA in mice.

In the present study, we evaluated the cholesterol-lowering effects of different oat bran (OB) preparations, differing regarding their peak molecular weight (MWp) of beta-glucans (2348, 1311, 241, 56, 21 or < 10 kDa), in C57BL/6NCrl mice. The diets were designed to be atherogenic (0.8 % cholesterol and 0.1 % cholic acid), and they reflected the Western diet pattern (41 % energy fat). All OB preparations that were investigated significantly reduced plasma cholesterol when compared with a cellulose-containing control diet, regardless of the molecular weight of beta-glucan. Moreover, the difference in viscous properties between the processed OB (from 0.11 to 17.7 l/g) did not appear to play a major role in the cholesterol-lowering properties. In addition, there was no correlation between the molecular weight of beta-glucan and the amount of propionic acid formed in caecum. Interestingly, however, there was a significant correlation between the ratio of (propionic acid+butyric acid)/acetic acid and the MWp of beta-glucans: the ratio increased with increasing molecular weight. The results of the present study suggest that the molecular weights and viscous properties of beta-glucan in oat products may not be crucial parameters for their cholesterol-lowering effects.

Leishmania mexicana: identification and characterization of an aspartyl proteinase activity.

An aspartyl proteinase activity was detected in the soluble fraction (SF) of Leishmania mexicana promastigotes by the use of the synthetic substrate benzoyl-Arg-Gly-Phe-Phe-Leu-4-methoxy-beta-naphthylamide selective for Cathepsin D like aspartyl-proteinases. This peptide was hydrolyzed with an apparent K(m) of 2.3+/-0.3 microM. The classic inhibitor of aspartyl-proteinases, diazo-acetyl-norleucinemethylester (DAN) inhibited the proteolytic activity with an IC(50) of 400 microM. The soluble fraction degraded (in absence of thiol groups) human fibrinogen with a specific activity of 533 U/mg protein. When tested for the ability to inhibit the "in vitro" proliferation of L. mexicana promastigotes, DAN showed concentration dependent anti-proliferative effects with a LD(50) of 466 microM at 48 h, with a significant fall in this value to 22 microM after 72 h. This is the first characterization of an aspartyl-proteinase activity in Leishmania, calling for further studies directed towards the physiologic role of these enzymes in the parasite. The anti-proliferative effect of its inhibition makes this enzyme a putative new target for the development of leishmanicidal drugs.

Characterization of a novel cAMP-binding, cAMP-specific cyclic nucleotide phosphodiesterase (TcrPDEB1) from Trypanosoma cruzi.

Trypanosoma cruzi, the causative agent of Chagas disease, encodes a number of different cAMP-specific PDE (phosphodiesterase) families. Here we report the identification and characterization of TcrPDEB1 and its comparison with the previously identified TcrPDEB2 (formerly known as TcPDE1). These are two different PDE enzymes of the TcrPDEB family, named in accordance with the recent recommendations of the Nomenclature Committee for Kinetoplast PDEs [Kunz, Beavo, D'Angelo, Flawia, Francis, Johner, Laxman, Oberholzer, Rascon, Shakur et al. (2006) Mol. Biochem. Parasitol. 145, 133-135]. Both enzymes show resistance to inhibition by many mammalian PDE inhibitors, and those that do inhibit do so with appreciable differences in their inhibitor profiles for the two enzymes. Both enzymes contain two GAF (cGMP-specific and -stimulated phosphodiesterases, Anabaena adenylate cyclases and Escherichia coli FhlA) domains and a catalytic domain highly homologous with that of the T. brucei TbPDE2/TbrPDEB2 family. The N-terminus+GAF-A domains of both enzymes showed significant differences in their affinities for cyclic nucleotide binding. Using a calorimetric technique that allows accurate measurements of low-affinity binding sites, the TcrPDEB2 N-terminus+GAF-A domain was found to bind cAMP with an affinity of approximately 500 nM. The TcrPDEB1 N-terminus+GAF-A domain bound cAMP with a slightly lower affinity of approximately 1 muM. The N-terminus+GAF-A domain of TcrPDEB1 did not bind cGMP, whereas the N-terminus+GAF-A domain of TcrPDEB2 bound cGMP with a low affinity of approximately 3 muM. GAF domains homologous with those found in these proteins were also identified in related trypanosomatid parasites. Finally, a fluorescent cAMP analogue, MANT-cAMP [2'-O-(N-methylanthraniloyl)adenosine-3',5'-cyclic monophosphate], was found to be a substrate for the TcPDEB1 catalytic domain, opening the possibility of using this molecule as a substrate in non-radioactive, fluorescence-based PDE assays, including screening for trypanosome PDE inhibitors.

Trypanosome cyclic nucleotide phosphodiesterase 2B binds cAMP through its GAF-A domain.

Trypanosoma brucei, the causative agent of sleeping sickness in humans and livestock, expresses at least three cAMP-specific class I phosphodiesterases (PDEs), all of which are essential for survival of the parasite. These PDEs have either one or two N-terminal GAF domains, which in other proteins function as signaling domains. However, neither the functional roles nor ligands for these domains in trypanosome PDEs are known. The present study shows that TbPDE2B, which contains two tandem GAF domains, binds cAMP with high affinity through its GAF-A domain. A purified recombinant N terminus + GAF-A domain binds cAMP with an affinity (Ki) of approximately 16 nM. It also binds cGMP but with a 15-fold lower affinity of approximately 275 nM. The TbPDE2B holoenzyme has a somewhat lower affinity (approximately 55 nM) for cAMP but a greatly lower affinity (approximately 10 microM) for cGMP. This suggests that both the selectivity and affinity for a ligand can be determined not only by the nature of the binding domain but also by the adjacent domains. Additionally, binding of cAMP to the holoenzyme showed positive cooperativity, with a Hill coefficient value of 1.75. However, binding of cGMP to the holoenzyme did not show any cooperativity, suggesting differences in the conformational changes caused by binding of these two cyclic nucleotides with the protein. Point mutation of a key predicted binding site residue (T317A) resulted in a complete loss of high affinity cAMP binding. This mutation increased the apparent Km of the mutant enzyme for substrate without altering the Vmax. A truncated catalytic domain construct of TbPDE2B also exhibited an increased Km, strongly suggesting that cAMP binding to the GAF-A domain can regulate TbPDE2B by allowing the full activity of the enzyme to be expressed. These properties of the GAF-A domain of TbPDE2B thus suggest that it could be a new target for anti-trypanosomal drugs.

Cloning and characterization of a cAMP-specific phosphodiesterase (TbPDE2B) from Trypanosoma brucei.

Here we report the cloning, expression, and characterization of a cAMP-specific phosphodiesterase (PDE) from Trypanosoma brucei (TbPDE2B). Using a bioinformatic approach, two different expressed sequence tag clones were identified and used to isolate the complete sequence of two identical PDE genes arranged in tandem. Each gene consists of 2,793 bases that predict a protein of 930 aa with a molecular mass of 103.2 kDa. Two GAF (for cGMP binding and stimulated PDEs, Anabaena adenylyl cyclases, and Escherichia coli FhlA) domains, similar to those contained in many signaling molecules including mammalian PDE2, PDE5, PDE6, PDE10, and PDE11, were located N-terminal to a consensus PDE catalytic domain. The catalytic domain is homologous to the catalytic domain of all 11 mammalian PDEs, the Dictyostelium discoideum RegA, and a probable PDE from Caenorhabditis elegans. It is most similar to the T. brucei PDE2A (89% identity). TbPDE2B has substrate specificity for cAMP with a K(m) of 2.4 microM. cGMP is not hydrolyzed by TbPDE2B nor does this cyclic nucleotide modulate cAMP PDE activity. The nonselective PDE inhibitors 3-isobutyl-1-methylxanthine, papaverine and pentoxifyline are poor inhibitors of TbPDE2B. Similarly, PDE inhibitors selective for the mammalian PDE families 2, 3, 5, and 6 (erythro-9-[3-(2-hydroxynonyl)]-adenine, enoximone, zaprinast, and sildenafil) were also unable to inhibit this enzyme. However, dipyridamole was a reasonably good inhibitor of this enzyme with an IC50 of 27 microM. cAMP plays key roles in cell growth and differentiation in this parasite, and PDEs are responsible for the hydrolysis of this important second messenger. Therefore, parasite PDEs, including this one, have the potential to be attractive targets for selective drug design.

Fosfodiesterasas de nucleótidos cíclicos: diversidad, clasificación, estructura y función / Cyclic nucleotide phosphodiesterases: diversity, classification, structure and function

During the last years there have been major advances in the knowledge of cyclic nucleotide phosphodiesterases. Particularly, referred to the presence of multiple different isozymes. Seven different phosphodiesterase gene families, have been described in mammalian tissues, containing several distinct genes, most of them expressed in different tissues as functionally unique splice variants. This article includes various aspects of the currently accepted nomenclature, structure and function of each family of phosphodiesterases. Finally, a brief discussion of the presence and role of these enzymes in the cell proliferation and differentiation processes, in parasites of the Trypanosmatidae family, is provided