Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial endophytes from mangrove leaves with antibacterial and enzymatic activities

Aims: The aim of this study was to screen bacterial endophytes with antibacterial and enzyme activity from mangrove leaves of Indonesia. Methodology and results: Bacterial endophytes were isolated and evaluated for antibacterial activity against five strains of pathogenic bacteria. Enzymatic Index (EI) was measured to evaluate the production of protease, amylase and cellulase. Hemolysin test was performed on Blood Agar and the sensitivity to antibiotic was performed. Bacterial endophyte Strain 1-1 isolated from Bruguiera gymnorrhiza showed strong inhibition against Escherichia coli, Salmonella sp. , Staphylococcus aureus and Pseudomonas aeruginosa with inhibition zone of 12.6 ± 1.4, 8.8 ± 4.1, 12.5 ± 2.3 and 8.4 ± 0.9 mm respectively. Isolate 1-16 which isolated from B. gymnorrhiza exhibited antibacterial activity against E. coli and P. aeruginosa, while Isolate 6-10 isolated from Avicennia lanata exhibited strong inhibition on Salmonella sp. (13.1 ± 3.3 mm). All of those three isolates produced protease, non-haemolysin-producing strain and sensitive to gentamicin or kanamycin but resistant to ampicillin, tetracycline and chloramphenicol. Those three isolates were identified based on homology of 16S rDNA sequence. Strain 1-1 and 1-16 were identified as P. aeruginosa, while strain 6-10 identified as S. marcescens. Conclusion, significance and impact of study: This finding was showed the potential endophytic bacteria from Indonesian mangrove plants with antibacterial and enzyme production.
Effects of Salinity Stress on Growth, Mineral Nutrient Accumulation and Biochemical Parameters of Seedlings of Three Citrus Rootstocks

ABSTRACT Citrus is an important fruit crop in Bangladesh and its growth is often constrained by salt stress. A polyhouse experiment was conducted to assess salt tolerance of three citrus rootstocks. Six-month-old seedlings of three citrus rootstocks, namely pomelo, Cleopatra mandarin, and calamansi, were irrigated with six concentrations of NaCl (0.75, 3, 6, 9, 12 and 16 dS m–1) for 3 months. Seedlings of all citrus rootstocks were significantly affected by salinity of irrigation water. All growth parameters were decreased with increase in salinity level of irrigation water. Based on growth parameters, the seedlings of Cleopatra mandarin were the least affected followed by pomelo and calamansi. The seedlings of Cleopatra mandarin accumulated less Na and Cl, while calamansi accumulated the highest amount of Na and Cl. Chlorophyll content was decreased and proline content was increased with increase in salinity level of irrigation water. Proline content was the highest in the leaves of Cleopatra mandarin with 16 dS m–1 salinity level followed by pomelo and calamansi. Overall, Cleopatra mandarin and pomelo rootstocks were more tolerant to saline conditions than calamansi rootstock. The relative susceptibility of citrus species to salinity should be taken into consideration for plant breeding programs, and growing of salt-tolerant citrus rootstocks should be promoted in salt-affected soils for better productivity.
Modulation of the Tryptophan Hydroxylase 1/Monoamine Oxidase‐A/5‐Hydroxytryptamine/5‐Hydroxytryptamine Receptor 2A/2B/2C Axis Regulates Biliary Proliferation and Liver Fibrosis During Cholestasis

Serotonin (5HT) is a neuroendocrine hormone synthetized in the central nervous system (CNS) as well as enterochromaffin cells of the gastrointestinal tract. Tryptophan hydroxylase (TPH1) and monoamine oxidase (MAO‐A) are the key enzymes for the synthesis and catabolism of 5HT, respectively. Previous studies demonstrated that 5‐hydroxytryptamine receptor (5HTR)1A/1B receptor agonists inhibit biliary hyperplasia in bile‐duct ligated (BDL) rats, whereas 5HTR2B receptor antagonists attenuate liver fibrosis (LF) in mice. Our aim was to evaluate the role of 5HTR2A/2B/2C agonists/antagonists in cholestatic models.
The past, present and future of cleaner fish cognitive performance as a function of CO2 levels

Ocean acidification is one of the many consequences of climate change. Various studies suggest that marine organisms' behaviour will be impaired under high CO2. Here, we show that the cognitive performance of the cleaner wrasse, Labroides dimidiatus, has not suffered from the increase of CO2 from pre-industrial levels to today, and that the standing variation in CO2 tolerance offers potential for adaptation to at least 750 µatm. We acclimated cleaners over 30 days to five levels of pCO2, from pre-industrial to high future CO2 scenarios, before testing them in an ecologically relevant task—the ability to learn to prioritize an ephemeral food source over a permanent one. Fish learning abilities remained stable from pre-industrial to present-day pCO2. While performance was reduced under mid (750 µatm) and high CO2 (980 µatm) scenarios, under the former 36% of cleaners still solved the task. The presence of tolerant individuals reveals potential for adaptation, as long as selection pressure on cognitive performance is strong. However, the apparent absence of high CO2 tolerant fish, and potentially synergistic effects between various climate change stressors, renders the probability of further adaptation unlikely.
aer2vec: Distributed Representations of Adverse Event Reporting System Data as a Means to Identify Drug/Side-Effect Associations

Adverse event report (AER) data are a key source of signal for post marketing drug surveillance. The standard methodology to analyze AER data applies disproportionality metrics, which estimate the strength of drug/side-effect associations from discrete counts of their occurrence at report level. However, in other domains, improvements in predictive modeling accuracy have been obtained through representation learning, where discrete features are replaced by distributed representations learned from unlabeled data. This paper describes aer2vec, a novel representational approach for AER data in which concept embeddings emerge from neural networks trained to predict drug/side-effect co-occurrence. Trained models are evaluated for their utility in identifying drug/side-effect relationships, with improvements over disproportionality metrics in most cases. In addition, we evaluate the utility of an otherwise-untapped resource in the Food and Drug Administration (FDA) AER system – reporter designations of suspected causality – and find that incorporating this information enhances performance of all models evaluated.
Toxoplasma induces stripping of perisomatic inhibitory synapses

Infection and inflammation within the brain induces changes in neuronal connectivity and function. The intracellular protozoan parasite, Toxoplasma gondii, is one pathogen that infects the brain and can cause encephalitis and seizures. Persistent infection by this parasite is also associated with behavioral alterations and an increased risk for developing psychiatric illness, including schizophrenia. Current evidence from studies in humans and mouse models suggest that both seizures and schizophrenia result from a loss or dysfunction of inhibitory synapses. In line with this, we recently reported that persistent Toxoplasma gondii infection alters the distribution of glutamic acid decarboxylase 67 (GAD67), an enzyme that catalyzes GABA synthesis in inhibitory synapses. These changes could reflect a redistribution of presynaptic machinery in inhibitory neurons or a loss of inhibitory nerve terminals. To directly assess the latter possibility, we employed serial block face scanning electron microscopy (SBFSEM) and quantified inhibitory perisomatic synapses in neocortex and hippocampus following parasitic infection. Not only did persistent infection lead to a significant loss of perisomatic synapses, it induced the ensheathment of neuronal somata by phagocytic cells. Immunohistochemical, genetic, and ultrastructural analyses revealed that these phagocytic cells included reactive microglia. Finally, ultrastructural analysis identified phagocytic cells enveloping perisomatic nerve terminals, suggesting they may participate in synaptic stripping. Thus, these results suggest that microglia contribute to perisomatic inhibitory synapse loss following parasitic infection and offer a novel mechanism as to how persistent Toxoplasma gondii infection may contribute to both seizures and psychiatric illness. MAIN POINTS Toxoplasma-infection leads the loss of perisomatic inhibitory synapses Phagocytic microglia ensheath neuronal somata following Toxoplasma-infection Microglia contact and envelop perisomatic nerve terminals, suggesting that Toxoplasma induces synaptic stripping
Transmembrane helix 6b links proton- and metal-release pathways to drive conformational change in an Nramp transition metal transporter

The natural resistance-associated macrophage protein (Nramp) family encompasses transition metal and proton co-transporters found in organisms from bacteria to humans. Recent structures of Deinococcus radiodurans (Dra)Nramp in multiple conformations revealed the intramolecular rearrangements required for alternating access. Here we demonstrate that two parallel cytoplasm-accessible networks of conserved hydrophilic residues in DraNramp—one lining the wide intracellular vestibule for metal release, the other forming a narrow proton-transport pathway—are essential for metal transport. We further show that mutagenic or post-translational modifications of transmembrane helix (TM) 6b, which structurally links these two pathways, impedes normal conformational cycling and metal transport. TM6b contains two highly conserved histidines, H232 and H237. Different mutagenic perturbations for H232, just below the metal-binding site along the proton-exit route, differentially affect DraNramp’s conformational state, suggesting H232 serves as a pivot point for conformational change. In contrast, any tested replacement for H237, lining the metal-exit route, locks the transporter in a transport-inactive outward-closed state. We conclude that these two histidines, and TM6b more broadly, help trigger the bulk rearrangement to the inward-open state upon metal binding and facilitate the return of the empty transporter to an outward-open state upon metal release.
Mitochondria biogenesis in the synapse is supported by local translation

Synapses are the regions of the neuron that enable the transmission and propagation of action potentials on the cost of high energy consumption and elevated demand for mitochondrial ATP production. The rapid changes in local energetic requirements at dendritic spines imply the role of mitochondria in the maintenance of their homeostasis. Using global proteomic analysis supported with complementary experimental approaches, we show that an important pool of mitochondrial proteins is locally produced at the synapse indicating that mitochondrial biogenesis takes place locally to maintain the pool of functional mitochondria in axons and dendrites. Furthermore, we show that stimulation of synaptoneurosomes induces the local synthesis of mitochondrial proteins that are transported to the mitochondria and incorporated into the protein supercomplexes of the respiratory chain. Synopsis Mitochondria biogenesis in the synapse is supported by local translation Mitochondrial proteins represent a large pool of proteins synthesized locally at the synapse Newly synthesized mitochondrial proteins are imported into the mitochondria and incorporated into the respiratory chain complexes Uncoupling of mitochondria and blocking mitochondrial import inhibits incorporation of de novo synthesized proteins into the mitochondrial protein complexes
The Tensile Strength of Full-Thickness Skin: A Laboratory Study Prior to Its Use as Reinforcement in Parastomal Hernia Repair

Purpose: Parastomal hernia is a common complication of an enterostoma. Current methods of repair have high recurrence rates and are associated with severe complications. Autologous full-thickness skin as reinforcement may reduce the recurrence and complication rates. This study aims to investigates the tensile strength of full-thickness skin; information that is essential if we are to proceed with clinical trials on humans. Methods: Full-thickness skin samples from 12 donors were tested for tensile strength, as well as the load tolerated by a suture through the skin. Strips of skin were cut out and stretched until breaking point. Sutures were made through skin samples and traction applied until either the tissue or the suture gave way. All done while recording the forces applied using a dynamometer. Identical tests were carried out on commercially available synthetic and biologic graft material for comparison. Results: The full-thickness skin strips had a median tensile strength of 604 N/cm. This tensile strength was significantly higher than that of the compared materials evaluated in this study. In full-thickness skin, the suture, or tissue endured a median force of 67 N before giving way, which was as high as, or higher than similar sutures through the compared materials. Conclusions: The tensile strength of full-thickness skin vastly exceeds the physiological forces affecting the abdominal wall, and sutures through skin endure high loads before giving way. The tensile strength of a full-thickness skin graft and the strength of sutures through this material will not limit its use for reinforcement in parastomal hernia repair.
The present scenario, challenges, and future anticipation of traditional mongolian medicine in China

The objective was to study the present scenario, challenges, and future anticipation of traditional Mongolian medicine (TMM) in China. The literature was retrieved using various sources of information such as meetings with TMM experts, research and review articles, national health databases, and government websites and authoritative papers. Health care using TMM, TMM education and research, and the pharmaceutical industry of TMM has been improved by implementing TMM growth policies. TMM has been extensively used for health care in Mongolia and in various regions of China including Beijing. The national education system of China contains a stream of TMM education. There is a yearly increase in research productivity in the field of TMM due to extensive research funding by the government. The rapidly growing pharmaceutical industry of TMM has provided more availability of TMM to more patients. The literature search revealed good preservation and development of TMM in China, urging the need to take steps for the promotion of its spread and development in China and worldwide.
The story of a Rohingya refugee: becoming a community psychosocial volunteer

Following violence in Arakan State in Myanmar in August 2017, many Rohingya refugees arrived in Bangladesh with tremendous mental trauma. They also arrived with health problems, along with psychosocial distress shaped by their experiences in Myanmar. Mental health conditions and psychosocial problems have made life more precarious than ever to them. To come to another country (Bangladesh) and to adjust here was a major change to their lives. However, people can also be resilient in the face of adversities and some are able to continue and thrive in the context of perspective hardship. In this personal reflection, the first author, Mr. Arafat Uddin, shares his experiences as a community psychosocial volunteer at the makeshift refugee camps in Bangladesh. He describes his own experience as a Rohingya refugee and shares his personal experience of becoming a psychosocial volunteer. He has also reflects on his role as a community psychosocial volunteer, discusses the challenges he faces, describes perceptions of the community around his work, and shares his future expectations. In the last part of this piece, Hasna Sumi, a female Bangladeshi psychologist with UNHCR, describes her experiences in training and supervising community psychosocial volunteers. This personal reflection contains the life history of Arafat Uddin as told to Hasna Akter Sumi, Psychosocial Associate with UNHCR’s Mental Health and Psychosocial Support team in Cox’s Bazar. When the call for papers for this special issue was launched, Sumi had the idea to record a life story from the perspective of a Rohingya refugee. She works closely with a team of Rohingya psychosocial volunteers and asked who among them would volunteer to share their story. Arafat willingly came forward. Sumi and Arafat sat together on 29th April and 2nd May 2019 in camp 4 in Kutupalong Mega Camp. They spoke in the Rohingya language. Arafat told his story while Sumi wrote it down in an English version. The various drafts of this article were discussed with Arafat and he has given his consent to publish this story.
Emotional distress among Rohingya refugees in Malaysia

Malaysia hosts over 175,000 refugees or asylum seekers who are registered with the United Nations High Commissioner for Refugees, over half of whom are ethnically Rohingya. Economic, social and health challenges are common among refugees residing in countries of asylum such as Malaysia with limited legal rights and uncertainty regarding the future. This study examined emotional distress among a sample of 115 Rohingya refugees living in urban areas within Malaysia. We utilised both quantitative and qualitative methods to assess psychosocial wellbeing. After measuring emotional distress with the Refugee Health Screener-15, we examined socio-demographic and environmental characteristics associated with distress scores. We then examined open-ended responses to qualitative questions regarding perceptions of difficulties refugees experience in Malaysia as well as perspectives on needed assistance. Findings indicated that emotional distress was widespread among this sample. Age was associated with higher rates of distress, while gender, time in Malaysia, employment and other measured factors were not associated with distress. Qualitative themes emphasised challenges with income, documentation and concerns regarding global conflict. Findings point to the need for services that address economic needs as well as reducing distress, in addition to policy challenges that will enable stability and security for Rohingya refugees.
Hypoxia during incubation does not affect aerobic performance or haematology of Atlantic salmon (Salmo salar) when re-exposed in later life

Abstract Hypoxia in aquatic ecosystems is becoming increasingly prevalent, potentially reducing fish performance and survival by limiting the oxygen available for aerobic activities. Hypoxia is a challenge for conserving and managing fish populations and demands a better understanding of the short- and long-term impacts of hypoxic environments on fish performance. Fish acclimate to hypoxia via a variety of short- and long-term physiological modifications in an attempt to maintain aerobic performance. In particular, hypoxia exposure during early development may result in enduring cardio-respiratory modifications that affect future hypoxia acclimation capacity, yet this possibility remains poorly investigated. We incubated Atlantic salmon (Salmo salar) in normoxia (~100% dissolved oxygen [DO, as percent air saturation]), moderate hypoxia (~63% DO) or cyclical hypoxia (100–25% DO daily) from fertilization until 113 days post-fertilization prior to rearing all groups in normoxia for a further 8 months. At ~11 months of age, subsets of each group were acclimated to hypoxia (50% DO) for up to 44 days prior to haematology, aerobic metabolic rate and hypoxia tolerance measurements. Hypoxia exposure during incubation (fertilization to 113 days post-fertilization) did not affect the haematology, aerobic performance or hypoxia tolerance of juvenile salmon in later life. Juveniles acclimated to hypoxia increased maximum aerobic metabolic rate and aerobic scope by ~23 and ~52%, respectively, when measured at 50% DO but not at 100% DO. Hypoxia-incubated juveniles also increased haematocrit and haemoglobin concentration but did not affect acute hypoxia tolerance (critical oxygen level and DO at LOE). Thus, while Atlantic salmon possess a considerable capacity to physiologically acclimate to hypoxia by improving aerobic performance in low oxygen conditions, we found no evidence that this capacity is influenced by early-life hypoxia exposure.
Characterization of an old municipal landfill (Grindsted, Denmark) as a groundwater pollution source: landfill history and leachate composition

Investigations into the pollution of groundwater from old landfills have, in most cases, focused on delineating the pol lution plume rather than on the landfill as a source of ground water pollution. Landfills often cover large areas and spatial variations in leachate composition within the landfill may have great impact on the location of the main pollution plume in the downstream aquifer. The history of the Grind sted Landfill in Denmark was investigated using aerial photo graphs and interviews. On the basis of the aerial photographs, waste volume and age of the different areas of the landfill were evaluated. A pronounced variability in leachate compo sition was observed in the 31 leachate wells installed through the waste. The spatial variability was analysed by statistical methods, and a semivariogram model was able to describe the variability both on small and large scale. The spatial varia tions in leachate composition are very important for locating the main source of the groundwater pollution and for selec tion of cost-effective remedial action activities.
A Pilot Study Investigating Changes in Capillary Hemodynamics and Its Modulation by Exercise in the APP-PS1 Alzheimer Mouse Model

Dysfunction in neurovascular coupling that results in a mismatch between cerebral blood flow and neuronal activity has been suggested to play a key role in the pathogenesis of Alzheimer’s disease (AD). Meanwhile, physical exercise is a powerful approach for maintaining cognitive health and could play a preventive role against the progression of AD. Given the fundamental role of capillaries in oxygen transport to tissue, our pilot study aimed to characterize changes in capillary hemodynamics with AD and AD supplemented by exercise. Exploiting two-photon microscopy, intrinsic signal optical imaging, and magnetic resonance imaging, we found hemodynamic alterations and lower vascular density with AD that were reversed by exercise. We further observed that capillary properties were branch order-dependent and that stimulation-evoked changes were attenuated with AD but increased by exercise. Our study provides novel indications into cerebral microcirculatory disturbances with AD and the modulating role of voluntary exercise on these alterations.