Miracle-dz/UniFAR-FTUs huggingface dataset:
Helicobacter pylori Infection in Infant Rhesus Macaque Monkeys is Associated with an Altered Lung and Oral Microbiome

Abstract Background It is estimated that more than half of the world population has been infected with Helicobacter pylori . Most newly acquired H. pylori infections occur in children before 10 years of age. We hypothesized that early life H. pylori infection could influence the composition of the microbiome at mucosal sites distant to the stomach. To test this hypothesis, we utilized the infant rhesus macaque monkey as an animal model of natural H. pylori colonization to determine the impact of infection on the lung and oral microbiome during a window of postnatal development. Results From a cohort of 4–7-month-old monkeys, gastric biopsy cultures identified 44% of animals infected by H. pylori . 16S ribosomal RNA gene sequencing of lung washes and buccal swabs from animals showed distinct profiles for the lung and oral microbiome, independent of H. pylori infection. In relative order of abundance, the lung microbiome was dominated by the phyla Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campilobacterota and Actinobacteriota while the oral microbiome was dominated by Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota. Relative to the oral cavity, the lung was composed of more genera and species that significantly differed by H. pylori status, with a total of 6 genera and species that were increased in H. pylori negative infant monkey lungs. Lung, but not plasma IL-8 concentration was also associated with gastric H. pylori load and lung microbial composition. Conclusions We found the infant rhesus macaque monkey lung harbors a microbiome signature that is distinct from that of the oral cavity during postnatal development. Gastric H. pylori colonization and IL-8 protein were linked to the composition of microbial communities in the lung and oral cavity. Collectively, these findings provide insight into how H. pylori infection might contribute to the gut-lung axis during early childhood and modulate future respiratory health.
SOCIEDADE, NATUREZA E REFORMA AGRÁRIA: ASSENTAMENTOS RURAIS E UNIDADES DE CONSERVAÇÃO NA REGIÃO DO PONTAL DO PARANAPANEMA

BEDUSCHI FILHO, L.C. (2002). Society, nature and land reform: rural planned settelments and conservation areas in Pontal do Paranapanema region. Sao Paulo, 2002. 97p. Dissertacao de Mestrado. Programa de Pos-Graduacao em Ciencia Ambiental da Universidade de Sao Paulo. The families seated in the Gleba Ribeirao Bonito, who live to the side of the Morro do Diabo State Park, are, in contrast of that we could wait, contributing, through designs articulated for a network of organizations, for the conservation of the natural features of this Unit of Conservation. The text explores the factors that condition such reality, basing itself on the theoretical contributions of the institutional economics and environmental sociology. The conclusion is that it is in construction process, in the region of the Pontal of the Paranapanema, a new institution that can contribute for the promotion of a model of regional development that includes, at the same time, the social and economic development of the seated families and the conservation of the nature.
Rotator cuff degeneration and healing after rotator cuff repair

Rotator cuff tear is a common shoulder injury that compromises both function and quality of life. Despite the prevalence of the injury and advancements in repair techniques, a significant percentage of these repairs fail. This review aims to explore the multifactorial reasons behind this failure, including the degenerative nature of the rotator cuff tendon, inherent and extrinsic factors, and the role of hypoxia in tissue degeneration. Additionally, it elucidates potential strategies for improving healing outcomes.
Structure et dynamique des jets barotropes créés pas les îles du Pacifique Sud-Ouest.

Les observations et les modeles globaux ont montre que l'ecoulement vers l'ouest du Courant Equatorial Sud est perturbe par la topographie complexe du Pacifique Sud-Ouest. Il se concentre en jets zonaux associes aux iles de Fidji, Vanuatu et Nouvelle-Caledonie. Ce travail de these est motive par la comprehension des processus non-lineaires et des effets topographiques. Une simulation regionale a haute resolution, a ete realisee. L'effort de validation du modele a permis de mettre a jour un probleme de diffusion diapycnale trop forte. Ce probleme numerique a ete resolu , ce qui permet desormais de preserver la structure thermohaline de grande echelle et l'integrite de la solution dynamique regionale. La solution obtenue montre la presence de jets intenses avec des recirculations dans le sillage des iles et une tendance des jets a etre devies vers le nord en abordant les iles principales : Nouvelle-Caledonie, Vanuatu, Fidji. Des bilans de vorticite de l'ecoulement permettent de mettre en evidence la predominance des effets topographiques sur la circulation du Pacifique Sud-Ouest, bien que ces derniers soient en partie compenses par la baroclinicite et l'advection non lineaire. Les non-linearites sont importantes pour les recirculations dans le sillage des iles. L'augmentation de la resolution conduit a des jets plus etroits et a une " vidange " des jets au sud des iles au profit de ceux au nord. Le Pacifique Sud-Ouest etant considere comme une region clef dans la modulation decennale du climat, ce travail tend a affirmer la necessite de prendre en compte plus finement les effets topographiques du Pacifique Sud-Ouest dans les modeles d'ocean globaux et de climat.
Pretrained transformer models for predicting the withdrawal of drugs from the market

Abstract Motivation The process of drug discovery is notoriously complex, costing an average of 2.6 billion dollars and taking ∼13 years to bring a new drug to the market. The success rate for new drugs is alarmingly low (around 0.0001%), and severe adverse drug reactions (ADRs) frequently occur, some of which may even result in death. Early identification of potential ADRs is critical to improve the efficiency and safety of the drug development process. Results In this study, we employed pretrained large language models (LLMs) to predict the likelihood of a drug being withdrawn from the market due to safety concerns. Our method achieved an area under the curve (AUC) of over 0.75 through cross-database validation, outperforming classical machine learning models and graph-based models. Notably, our pretrained LLMs successfully identified over 50% drugs that were subsequently withdrawn, when predictions were made on a subset of drugs with inconsistent labeling between the training and test sets. Availability and implementation The code and datasets are available at https://github.com/eyalmazuz/DrugWithdrawn.
Small proteins in bacteria – Big challenges in prediction and identification

Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo‐seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.
The Bovine Ex Vivo Retina: A Versatile Model for Retinal Neuroscience

Purpose The isolated ex vivo retina is the standard model in retinal physiology and neuroscience. During isolation, the retina is peeled from the retinal pigment epithelium (RPE), which plays a key role in the visual cycle. Here we introduce the choroid-attached bovine retina as an in vivo–like model for retinal physiology. We find that—in the bovine eye—the choroid and retina can be peeled from the sclera as a single thin sheet. Importantly, the retina remains tightly associated with the RPE, which is sandwiched between the retina and the choroid. Furthermore, bovine tissue is readily available and cheap, and there are no ethical concerns related to the use of animals solely for research purposes. Methods We combine multi-electrode array and single-cell patch-clamp recordings to characterize light responses in the choroid-attached bovine ex vivo retina. Results We demonstrate robust and consistent light responses in choroid-attached preparations. Importantly, light responses adapt to different levels of background illumination and rapidly recover from photobleaching. The choroid-attached retina is also thin enough to permit targeted electrophysiological recording from individual retinal neurons using standard differential interference contrast microscopy. We also characterize light responses and membrane properties of bovine retinal ganglion cells and compare data obtained from bovine and murine retinas. Conclusions The choroid-attached retinal model retains the advantages of the isolated retina but with an intact visual cycle and represents a useful tool to elucidate retinal physiology.
Electrode Montage Induced Changes in Air-Conducted Ocular Vestibular-Evoked Myogenic Potential

Objectives: Stimulus and recording parameters are pivotal for shaping the ocular vestibular-evoked myogenic potential (oVEMP). In the last decade, several attempts were made to identify the optimum electrode placement site to improve the oVEMP responses. A vast majority of these found larger response amplitudes for alternate electrode montages like belly-tendon (BT), chin-referenced (CR), and/or sternum-referenced montages than the clinically used infra-orbital montage. However, no study has yet compared all alternate electrode montages in a simultaneous recording paradigm to eliminate other confounding factors. Also, no study has compared all of them for their test–retest reliability, waveform morphology, and signal-to-noise ratio. Therefore, the decision on which among these electrode montages is best suited for oVEMP acquisition remains opaque. The present study aimed to investigate the effects of various electrode montages on oVEMP’s response parameters and to determine the test–retest reliability of each of these in clinically healthy individuals using a simultaneous recording paradigm. Design: This study had a within-subject experimental design. Fifty-five young healthy adults (age range: 20–30 years) underwent contralateral oVEMP recording using infra-orbital, BT, chin-referenced, and sternum-referenced electrode montages simultaneously using a four-channel evoked potential system. Results: BT montage had a significantly shorter latency, larger amplitude, higher signal-to-noise ratio, and better morphology than other alternate montages (p < 0.008). Further, all electrode montages of the current study showed fair/moderate to excellent test–retest reliability. Conclusions: By virtue of producing significantly better response parameters than the other electrode montages, BT montage seems better suited to the recording of oVEMP than the known electrode montages thus far.
Optimizing aortic valve prosthesis selection in patients with obesity: Institutional experience with multidisciplinary perspective

Background Aortic valve diseases are life-threatening conditions with increasing prevalence worldwide. Risk factors include gender, age, hypertension, dyslipidemia, and type 2 diabetes. Obesity is closely related to these risk factors and has been linked to a higher risk of developing aortic valve diseases. However, there is no specific guideline for managing aortic valve disease in patients with obesity, and the choice of valve type remains uncertain. Methods A total of 130 patients with obesity who met the inclusion criteria underwent surgical aortic valve replacement. The patients were divided into two groups based on the type of prosthesis used. Among the study cohort, 50 patients received a bioprosthetic valve, while 80 patients received a mechanical valve. We compared these groups in terms of perioperative characteristics and follow-up results. Statistical significance was determined using a p-value threshold of 0.05. Results There were no significant differences in age, gender, body mass index, or cardiac comorbidities between the two groups. Preoperative blood results and echo findings also showed no significant differences. Intraoperative characteristics and postoperative outcomes, including mortality and acute kidney injury, did not differ significantly between the groups. In addition, BHVG patients had shorter ICU stays compared to MHVG patients without significance. Conclusion Deliberate consideration is crucial when selecting valves for obese patients, particularly those with class II obesity. This is due to the potential influence of obesity on valve types, as well as the need to account for the possibility of bariatric surgery and its potential effects.
Impact of KRAS Mutations and Co-mutations on Clinical Outcomes in Pancreatic Ductal Adenocarcinoma

The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 PDAC patients (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p<0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2–3.0, p=0.006] and 22 months [HR: 1.7, 95% CI 1.3–2.3, p<0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2–2.4, p=0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05–2.99, p=0.04). Similar findings were observed in the external validation cohort (PanCAN’s Know Your Tumor® dataset, n=408).
Increasing the uptake of 18F‐fluorodeoxyglucose in the left hippocampus after 4 weeks of bright light exposure in healthy participants: A randomized controlled study

Bright light therapy (BLT) has been used to treat seasonal affective disorders, depression, and bipolar depression; however, the precise mechanism remains unclear. Neurogenesis in the human brain occurs in the hippocampal dentate gyrus (DG). Stress-induced structural remodeling in the adult hippocampus provides a cellular basis for understanding the impairment of neural plasticity in the human hippocampus in depression. Antidepressant treatment both restores neurogenesis in the hippocampus and serves to normalize behavior in depression animal models, suggesting that deficits in neurogenesis of hippocampus can act as a potential target for depression therapies. Thus, we hypothesized that bright light (BL) may induce neurogenesis in the human hippocampus, especially in the DG. We previously reported that 5-day BL significantly increased the uptake of F-fluorodeoxyglucose (FDG) in the right olfactory cortex, however significant metabolic change did not detect in the hippocampus. The limitations of our previous study are the lack of the direct evidence for neurogenesis and a short duration of BL. Therefore, we previously conducted a randomized controlled trial that revealed a 4-week period of BL in healthy participants resulted in an increase in the volume of the left hippocampal DG-head. This research letter used and analyzed the data of F-FDG positron emission tomography (PET), which was performed simultaneously with magnetic resonance imaging in the previous study.
Use of chemicals in aquaculture in Asia. Proceedings of the Meeting on the Use of Chemicals in Aquaculture in Asia, 20-22 May 1996; Tigbauan, Iloilo, Philippines.

AQUACHEM was funded by the Government of the Philippines through SEAFDEC Aquaculture Department, the Food and Agriculture Organization of the United Nations, and the Canadian International Development Agency through the ASEAN-Canada Fund. Dr. Efren Ed. C. Flores, former Chief of SEAFDEC AQD, laid down the ground-work for the smooth conduct of the meeting as well as solicited funds to support data gathering and travel of some participants from the ASEAN countries. We thank Milagros T. Castanos and Renelle Ivy Y. Adan of the Development Communications Unit, SEAFDEC, who helped in the lay-out of this proceedings.
Changes in the degree of substitution of HES in vivo and their influence on methods for determining HES concentrations in plasma

Objective The degree of substitution (DS) of HES describes the average proportion of substituted glucose molecules in a starch molecule. Although no quantitative studies of the in vivo behavior of the DS have been conducted so far, most pharmacokinetic studies to date have measured HES concentrations using the enzymatic method. This method assumes that at any point in time after an infusion, the DS in a serum remains constant and is identical to the DS in the infused solution. In the present study, we examined the changes in the DS of HES 130/0.42 in vivo in an animal model and compared two methods of measuring HES concentrations in plasma (the enzymatic and the o-Toluidine method). Methodology We randomized 22 pigs into 2 groups. After induction of anesthesia, the pigs received 500 ml or 1000 ml of HES 130/0.42 (Tetraspan®). The DS was measured directly after the infusion, then after 30, 60, 120 and 240 minutes. In determining the DS, the hydroxyethyl starch was extracted from the plasma and hydrolyzed with hydrochloric acid to form non-substituted glucose and hydroxyethyl glucose. Subsequently, the concentration of free unsubstituted glucose was determined enzymatically and the total concentration of all (i.e., substituted and unsubstituted) glucose molecules was determined using the o-Toluidine method. From this, the concentration of the substituted glucose (hydroxyethyl glucose) and the DS could be calculated. In addition, the HES concentration was measured first in vitro and then in vivo at any point after the infusion by both the enzymatic method and the o-Toluidine method. Results The DS increased significantly directly after the infusion from 0.42 to 0.53 (for 500ml) or to 0.50 (for 1000ml); 4 hours later this had further increased to 0.55 and 0.54, respectively (p <0.0001). The HES concentration in vitro showed no significant difference (p = 0.17) when determined with the enzymatic and the o-Toluidine method. In contrast, the serum concentrations in vivo displayed significant differences (p<0.0001) between the two measurement methods. Immediately after the infusion of 500ml HES, the concentration measured with the o-Toluidine method was 31% higher than the one measured with the enzymatic method; 4 hours later, this discrepancy was still at 25%. For 1000 ml HES, the differences amounted to 16% and 25%, respectively. Conclusion The DS of HES in vivo increases significantly over time. As a result, an HES concentration measured with the enzymatic method in vivo will be significantly lower than the same concentration determined with the o-Toluidine method. In future pharmacokinetic studies, HES concentrations should be measured using a method that takes into account changes in the DS in vivo.
High sensitivity and wide range flexible piezoresistive sensor based on petal-shaped MOF-derived NiCo-NPC

Due to the advantages of high porosity, excellent conductivity, and tunable morphology, carbonized metal-organic framework (C-MOF) is expected to become an ideal material for constructing high-performance flexible pressure sensor. Herein, to achieving the suitable morphology of C-MOF for piezoresistive sensors, a rapid thermal process (RTP) was used for carbonization of NiCo-MOF, and the petal-shaped NiCo alloy nanoparticles/nanoporous carbon composites (NiCo-NPCs) were obtained. Compared with NiCo-NPCs carbonized by common thermal process (CTP), NiCo-NPCs carbonized by RTP exhibit a modified morphology with smaller particle size and larger most frequent pore diameter. Due to the modified morphology, the piezoresistive sensor with RTP-carbonized NiCo-NPCs has a high sensitivity of 62.13 kPa–1 at 0–3 kPa, which is 3.46 times higher than that of the sensor with CTP-carbonized NiCo-NPCs. Meanwhile, the sensor shows an ultra-wide range of 1000 kPa, excellent cycle stability (>4000 cycles), and fast response/recovery time of 25/44 ms. Furthermore, the application of the sensor in dynamic loading test, airflow monitoring, voice recognition, and gesture detection demonstrates its great application prospects. In short, this work investigates the application of carbonized NiCo-MOFs in flexible pressure sensors, and provides a new strategy to improve the performance of piezoresistive sensors with porous carbon derived from MOFs.
Association of the time of day of EVT with clinical outcomes and benefit from successful recanalization after stroke

Experimental and neuroimaging studies suggest an influence of the time of day on acute infarct growth, but whether this could inform patient selection for acute treatments is uncertain. In a multicenter cohort of 9357 stroke patients undergoing endovascular treatment, morning treatment (05:00–10:59) was associated with lowest 90‐day mRS scores (adjusted odds ratio, 1.27 [95% CI, 1.08–1.47]; p = 0.004). The association between successful recanalization and outcome was stronger in morning compared to evening‐treated patients (pia = 0.046) with treatment benefit persisting until 24 h for morning‐treated compared to 11.5 h for evening‐treated patients suggesting that the time of day might inform patient selection for EVT.
Effect of Leuprolide Acetate, a GnRH Agonist, on Neuroinflammation and Anxiety-Like Behavior after Mild Hypoxic-Ischemic Encephalopathy in Rat Model

Background: Mild hypoxic-ischemic encephalopathy (HIE) is a condition that predisposes to negative outcomes such as neuroanatomical injury, mood disorders, and motor or cognitive disabilities. The neuroinflammation plays an important role in the neurological damage; therefore, reducing it could provide neuroprotection. The leuprolide acetate (LA) has shown to have neuroregenerative and immunomodulator properties in other nervous system injuries. Objective: The aim of this study was to evaluate the immunomodulatory effect of LA in the acute phase of mild HIE and its effects in motor activity and behavior in a subacute phase. Method: Forty-five Wistar rats on postnatal day 7 were divided into Sham, HIE treated with saline solution (HIE-SS), and HIE-LA. The HIE was performed cutting of the right carotid artery followed by 60 min of hypoxia. The expression of the inflammatory cytokines interleukin (IL)-1β, tumor necrosis factor (TNF)-α, interferon (IFN)-γ, and the chemokine CXCL-1 were evaluated 72 h after HIE by RT-qPCR and the motor activity and behavior were evaluated by open field test at postnatal day 33. Results: HIE-SS animals showed increased expression of IL-1β, TNF-α, IFN-γ, and CXCL-1 genes in injured tissue. However, the HIE-LA group exhibited similar expression levels of IL-1β and TNF-α to the Sham group, while IFN-γ and CXCL-1 mRNA expression were attenuated with LA treatment. LA treatment also prevented anxiety-like behavior in the open field test. Conclusion: Treatment with LA partially reverses HIE-induced neuroinflammation and prevents anxiety-like behavior in neonatal rats.