Miracle-dz/UniFAR-FTUs huggingface dataset:
Inflammation patterns induced by different Burkholderia species in mice

Burkholderia pseudomallei, which causes melioidosis, a severe, mainly pulmonary disease endemic in South‐East Asia, is considered to be the most pathogenic of the Burkholderia genus. B. thailandensis, however, is considered avirulent. We determined differences in patterns of inflammation of B. pseudomallei 1026b (clinical virulent isolate), B. pseudomallei AJ1D8 (an in vitro invasion‐deficient mutant generated from strain 1026b by Tn5‐OT182 mutagenesis) and B. thailandensis by intranasally inoculating C57BL/6 mice with each strain. Mice infected with B. thailandensis showed a markedly decreased bacterial outgrowth from lungs, spleen and blood 24 h after inoculation, compared with infection with B. pseudomallei and the invasion mutant AJ1D8. Forty‐eight hours after inoculation, B. thailandensis was no longer detectable. This was consistent with elevated pulmonary cytokine and chemokine concentrations after infection with B. pseudomallei 1026b and AJ1D8, and the absence of these mediators 48 h, but not 24 h, after inoculation with B. thailandensis. Histological examination, however, did show marked pulmonary inflammation in the mice infected with B. thailandensis, corresponding with substantial granulocyte influx and raised myeloperoxidase levels. Survival experiments showed that infection with 1 × 103 cfu B. thailandensis was not lethal, whereas inoculation with 1 × 106 cfu B. thailandensis was equally lethal as 1 × 103 cfu B. pseudomallei 1026b or AJ1D8. These data show that B. pseudomallei AJ1D8 is just as lethal as wild‐type B. pseudomallei in an in vivo mouse model, and B. thailandensis is perhaps more virulent than is often recognized.
Semantic Markers in the Diagnosis of Neurodegenerative Dementias

Background: The search for early cognitive markers of Alzheimer’s disease (AD) has focused on episodic memory and spatiotemporal orientation. However, recent research suggests that semantic memory is also impaired in the preclinical stages of AD. Methods: Age- and education-matched groups of participants with AD, mild cognitive impairment, and subjective memory complaints and healthy controls were assessed with 16 cognitive tests encompassing attention, orientation, episodic and semantic memory, and language tasks. Results: The battery correctly distinguished AD patients from healthy seniors in 92% of the cases. Three semantic memory-based tasks turned out to be particularly powerful for this purpose. Conclusion: Our results suggest that semantic memory tasks should be included in the battery of tests for the evaluation of cognitively impaired patients.
Toward a psychology of harm reduction.

This article discusses 3 different strategies for dealing with the harmful consequences of drug use and other risky behaviors: We can discourage people from engaging in the behavior (prevalence reduction), we can encourage people to reduce the frequency or extent of the behavior (quantity reduction), or we can try to reduce the harmful consequences of the behavior when it occurs (harm reduction). These strategies are not mutually exclusive; this article offers a framework for integrating them. The framework is useful for examining frequent claims that harm reduction "sends the wrong message. " Opposition to harm reduction is based in part on a recognition of potential trade-offs among the strategies, but it is also fueled by several more symbolic psychological factors. Strategies for successfully integrating prevalence reduction, quantity reduction, and harm reduction are explored.
A Truncated Fragment of Src Protein Kinase Generated by Calpain-mediated Cleavage Is a Mediator of Neuronal Death in Excitotoxicity*

Background: Abnormal regulation of calpains and Src contributes to stroke-induced brain damage. Results: The abnormally activated calpains cleave Src to generate a truncated Src fragment capable of directing neurons to undergo cell death. Conclusion: A new function of Src in neuronal death is discovered. Significance: Prevention of calpain-mediated cleavage of Src is a potential therapeutic strategy to minimize stroke-induced brain damage. Excitotoxicity resulting from overstimulation of glutamate receptors is a major cause of neuronal death in cerebral ischemic stroke. The overstimulated ionotropic glutamate receptors exert their neurotoxic effects in part by overactivation of calpains, which induce neuronal death by catalyzing limited proteolysis of specific cellular proteins. Here, we report that in cultured cortical neurons and in vivo in a rat model of focal ischemic stroke, the tyrosine kinase Src is cleaved by calpains at a site in the N-terminal unique domain. This generates a truncated Src fragment of ∼52 kDa, which we localized predominantly to the cytosol. A cell membrane-permeable fusion peptide derived from the unique domain of Src prevents calpain from cleaving Src in neurons and protects against excitotoxic neuronal death. To explore the role of the truncated Src fragment in neuronal death, we expressed a recombinant truncated Src fragment in cultured neurons and examined how it affects neuronal survival. Expression of this fragment, which lacks the myristoylation motif and unique domain, was sufficient to induce neuronal death. Furthermore, inactivation of the prosurvival kinase Akt is a key step in its neurotoxic signaling pathway. Because Src maintains neuronal survival, our results implicate calpain cleavage as a molecular switch converting Src from a promoter of cell survival to a mediator of neuronal death in excitotoxicity. Besides unveiling a new pathological action of Src, our discovery of the neurotoxic action of the truncated Src fragment suggests new therapeutic strategies with the potential to minimize brain damage in ischemic stroke.
Hyperparathyroidism-jaw tumor syndrome: the HRPT2 locus is within a 0.7-cM region on chromosome 1q.

Hyperparathyroidism-jaw tumor syndrome (HPT-JT) is an autosomal dominant disease characterized by the development of multiple parathyroid adenomas and multiple fibro-osseous tumors of the maxilla and mandible. Some families have had affected members with involvement of the kidneys, variously reported as Wilms tumors, nephroblastomas, and hamartomas. The HPT-JT gene (HRPT2) maps to chromosome 1q25-q31. We describe further investigation of two HPT-JT families (K3304 and K3349) identified through the literature. These two expanded families and two previously reported families were investigated jointly for linkage with 21 new, closely linked markers. Multipoint linkage analysis resulted in a maximum LOD score of 7.83 (at recombination fraction 0) for markers D1S2848-D1S191. Recombination events in these families reduced the HRPT2 region to approximately 14.7 cM. In addition, two of these four study families (i.e., K3304 and K11687) share a 2.2-cM length of their (expanded) affected haplotype, indicating a possible common origin. Combining the linkage data and shared-haplotype data, we propose a 0.7-cM candidate region for HRPT2.
Precise sub-pixel estimation on area-based matching

Area-based matching is a common procedure in various fields such as image-based measurements, stereo image processing, and fluidics. Sub-pixel estimation using parabola fitting over three points with their similarity measures is also a common method to increase the resolution of matching. However, few investigations or studies concerning the characteristics of this estimation have been reported. In this paper we have analyzed the sub-pixel estimation error by using an approximate image function and three kinds of similarity measures for matching. The results illustrate some inherently problematic phenomena such as so called "pixel-locking". In addition to this, we propose a new algorithm to greatly reduce sub-pixel estimation error. This method is independent from the similarity measure and quite simple to implement. The advantage of our novel method is confirmed through experiments using three different types of images.
Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

Significance Human activities have elevated nitrogen (N) deposition and there is evidence that deposition impacts species diversity, but spatially extensive and context-specific estimates of N loads at which species losses begin remain elusive. Across a wide range of climates, soil conditions, and vegetation types in the United States, we found that 24% of >15,000 sites were susceptible to N deposition-induced species loss. Grasslands, shrublands, and woodlands were susceptible to species losses at lower loads of N deposition than forests, and susceptibility to species losses increased in acidic soils. These findings are pertinent to the protection of biodiversity and human welfare and should be considered when establishing air quality standards. Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United States, to address how edaphic and climatic conditions altered vulnerability to this stressor. In our dataset, with N deposition ranging from 1 to 19 kg N⋅ha−1⋅y−1, we found a unimodal relationship; richness increased at low deposition levels and decreased above 8.7 and 13.4 kg N⋅ha−1⋅y−1 in open and closed-canopy vegetation, respectively. N deposition exceeded critical loads for loss of plant species richness in 24% of 15,136 sites examined nationwide. There were negative relationships between species richness and N deposition in 36% of 44 community gradients. Vulnerability to N deposition was consistently higher in more acidic soils whereas the moderating roles of temperature and precipitation varied across scales. We demonstrate here that negative relationships between N deposition and species richness are common, albeit not universal, and that fine-scale processes can moderate vegetation responses to N deposition. Our results highlight the importance of contingent factors when estimating ecosystem vulnerability to N deposition and suggest that N deposition is affecting species richness in forested and nonforested systems across much of the continental United States.
Type Ibn Supernovae Show Photometric Homogeneity and Spectral Diversity at Maximum Light

Type Ibn supernovae (SNe) are a small yet intriguing class of explosions whose spectra are characterized by low-velocity helium emission lines with little to no evidence for hydrogen. The prevailing theory has been that these are the core-collapse explosions of very massive stars embedded in helium-rich circumstellar material (CSM). We report optical observations of six new SNe Ibn: PTF11rfh, PTF12ldy, iPTF14aki, iPTF15ul, SN 2015G, and iPTF15akq. This brings the sample size of such objects in the literature to 22. We also report new data, including a near-infrared spectrum, on the Type Ibn SN 2015U. In order to characterize the class as a whole, we analyze the photometric and spectroscopic properties of the full Type Ibn sample. We find that, despite the expectation that CSM interaction would generate a heterogeneous set of light curves, as seen in SNe IIn, most Type Ibn light curves are quite similar in shape, declining at rates around 0.1 mag day−1 during the first month after maximum light, with a few significant exceptions. Early spectra of SNe Ibn come in at least two varieties, one that shows narrow P Cygni lines and another dominated by broader emission lines, both around maximum light, which may be an indication of differences in the state of the progenitor system at the time of explosion. Alternatively, the spectral diversity could arise from viewing-angle effects or merely from a lack of early spectroscopic coverage. Together, the relative light curve homogeneity and narrow spectral features suggest that the CSM consists of a spatially confined shell of helium surrounded by a less dense extended wind.
A Coding Theoretical Approach to Predict Sequence Changes in H5N1 Influenza A Virus Hemagglutinin

The changes in the receptor binding domain of influenza A virus hemagglutinin lead to the appearance of new viral strains that evade the immune system. To prepare the future emergence of potentially dangerous outbreaks caused by divergent influenza strains including human-adapted H5N1 strains, it is imperative that we understand the rule stored in the sequence of the receptor binding domain. Information of life is stored as a sequence of nucleotides, and the sequence composed of four nucleotides seems to be a code. It is important to determine the code structure of the sequences. Once we know the code structure, we can make use of mathematical results concerning coding theory for research in life science. In this study, we applied various codes in coding theory to sequence analysis of the 220 loop in the receptor binding domain of H1, H3, H5 and H7 subtype viruses isolated from humans. Sequence diversity in the 220 loop has been observed even within the same hemagglutinin subtype. However, we found that the code structure of the 220 loop from the same subtype remains unchanged. Our results indicate that the sequences at the 220 loop have the structure of subtype-specific codes. In addition, in view of these finding, we predicted possible amino acid changes in the 220 loop of H5N1 strains that will emerge in the future. Our method will facilitate understanding of the evolutionary patterns of influenza A viruses, and further help the development of new antiviral drugs and vaccines.
Self Adaptive Safe Provisioning of Wireless Power Using DCOPs

Wireless Power Transfer (WPT) technologies aim at getting rid of cables used by consumer devices for energy provision. As long distance WPT is becoming mature, the health impact of WPT becomes increasingly important to consider. In this paper we look at how to maximize the wireless power transfer to remote devices, while maintaining a safe level of electromagnetic radiation (EMR) for humans that are in the vicinity of the energy transmitters. Classically, this problem can be described as a centralized optimization problem of finding the optimal set of safe power levels at locations of human presence. Instead, we advocate to formulate this problem as an agent-based Distributed Constraint Optimization Problem (DCOP). As a solution to this problem we introduce CoCoA_WPT, a variant of the DCOP solver CoCoA. CoCoA_WPT provides a solution of similar quality to centralized solver even for a large scale network involving over a thousand nodes. Based on CoCoA_WPT, we propose a self-adaptive charging system: Transferring Energy Safely by Self-Adaptation (TESSA). TESSA keeps the charging network safe even when it is perturbed by environmental dynamics. We show that TESSA can reach on average up to 85% of the theoretical optimal maximum total transmitted power (calculated using centralized solution) while satisfying the EMR safety constraints.
Neuroethics with regard to treatment limiting and withdrawal of nutrition and hydration in long lasting irreversible full state Apallic Syndrome and Minimal Conscious State

Introduction: Epidemiology in Europe shows constantly increasing figures for the Apallic Syndrome (AS)/Vegetative State (VS) as a consequence of advanced rescue, emergency services, intensive care treatment after acute brain damage, and high standard activating home nursing for completely dependent end stage cases secondary to progressive neurological disease. Management of patients in irreversible apallic syndrome has been the subject of sustained scientific and moral-legal debate over the last decade. Methods: Neuroethics coming more and more into consideration when neurological societies address key issues relating to AS/VS prevalence and quality management. With regard to treatment limiting and withdrawal of nutrition and hydration of patients suffering from irreversible full state Apallic Syndrome and Minimal Conscious State. Results: The overall incidence of new AS/VS full stage cases all aetiology is 0.5 - 2/ 100.000 population per year. About one third is traumatic and two thirds are non-traumatic cases. The worst prognosis might be expected from non-traumatic hypoxemic apallic syndrome. The main conceptual criticism is based on assessment and diagnosis of all different AS/VS stages based solely on behavioural findings without knowing the exact or uniform pathogenesis or neuropathologic findings. No special diagnostics, no specific medical management can be recommended for class II or III AS treatment and rehabilitation. But in United Kingdom, The Netherlands, Belgium, and Switzerland active euthanasia is now practiced in medicine taking into account the uncertainty of the right diagnose the clinical features for humanistic treatment of patients in irreversible “AS full or early , remission stages” . Discussion: As long as there is no single AS/VS specific diagnostic tool, no specific laboratory investigation regimen to be recommended neuroethical principles demands by all means a humanistic (ethical) activating nursing even in the irreversible full stage AS cases. Full acceptable is only the palliative pain therapy with renunciation of maximal therapy. Active euthanasia is a criminal act and has to be respected as such in neuroscience.
Combined ultrasound‐targeted microbubble destruction and polyethylenimine‐mediated plasmid DNA delivery to the rat retina: enhanced efficiency and accelerated expression

Gene therapy has potential in the treatment of refractory retinal diseases. It is important to develop an effective delivery system in the retina. The present study aimed to investigate the efficacy and safety of ultrasound (US)‐targeted microbubble destruction (UTMD)‐mediated polyethylenimine (PEI) to the rat retina.
iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology

The ever-increasing scientific literature and the exponential growth of large-scale molecular data have prompted active research in biological text mining to facilitate literature-based curation of molecular databases. Meanwhile, systems biology and bio-ontologies are emerging as critical tools in biological research where complex data in disparate resources are generated, integrated and analyzed. Both rely on literature for data annotation and analysis. The challenges facing us are to develop broadly utilized text mining tools and systems, and to bring together developer and user communities for system development and evaluation. We describe a framework for linking text mining tools with ontology and systems biology, extending from a previously developed text mining resource, iProLINK. We focus on molecular and ontological resources, including genes/proteins, protein-protein interaction (PPI), and Protein Ontology. The framework consists of two major components: a user interface for text mining of PPI from an integrated tool server and software modules to allow text mining outputs to be created, ranked, and used by the community. Use cases are presented for assessing the gaps and making recommendations for future development.
Analysis of hematologic alterations, immune responses and metallothionein gene expression in Nile tilapia (Oreochromis niloticus) exposed to silver nanoparticles

Abstract In this study, Nile tilapia (Oreochromis niloticus) fingerlings were used as a model to examine acute and chronic toxicity of silver nanoparticles (AgNP). Expression levels of metallothionein (MT) transcripts in fish exposed to 0, 1 or 100 mg AgNP/kg fish were investigated by quantitative real-time RT-PCR. The results showed MT expression levels were significantly decreased 0.3–0.7-fold in the liver and spleen of fish exposed to 1 or 100 mg AgNP/kg after 6–48 h. In contrast, during this period, MT mRNA expression levels were increased 2–3-fold in the head kidney of the fish exposed to either level of AgNP. Investigations of effects of AgNP on the fish immune responses and hematological parameters revealed that phagocytic activity, the amount of red blood cells (RBC) and the percent hematocrit (%Hct) in fish exposed to AgNP were decreased significantly 1 week after exposure, especially those exposed to 100 mg AgNP/kg. Fish immunized with Streptococcus agalactiae vaccine and simultaneously exposed to 100 mg AgNP/kg presented decreased antibody titers during the early phase. Lastly, a challenge test showed that vaccinated fish exposed to AgNP, regardless of concentration, remained protected against S. agalactiae infection, with a lower mortality (10–20%) compared to 70% in control fish. These findings indicated that expression patterns of the MT gene in the liver, spleen and head kidney at different timepoints could be used to assess acute and chronic exposure of Nile tilapia to AgNP. Additionally, changes in innate immune responses and hematological parameters in fish may prove useful for evaluation of AgNP toxicity. Data obtained in this study strongly support the use of Nile tilapia as an animal model to potentially serve as a bio-indicator of environment contamination caused by AgNP.
Trunk movement in Parkinson's disease during rising from seated position

Parkinson's disease (PD) is associated with particular difficulties rising from a seated position. Little is known about the mechanisms of sit‐to‐stand in this condition. We sought to define trunk movement during sit‐to‐stand in a group of patients with PD. Six patients and seven normal volunteers were studied using a six camera ELITE motion analysis system (BTS, Milan, Italy), which permitted data collection in the coronal, sagittal, and transverse planes. Retroreflective markers were positioned along the spine at C7, T3, T6, T9, T12, L3, and the sacrum. Whole‐trunk kinematics and the movement at the six different trunk markers were recorded during rising. PD patients have a significantly greater degree of trunk flexion than controls, showing a significant increase in angular velocity of the trunk in the sagittal plane. The total range of movement of trunk rotation was significantly smaller in the PD group, but lateral movement in the trunk was greater than normal. These data suggest that patients with early PD compensate for their difficulties rising from a chair by generating greater trunk flexion at higher angular velocity, thus developing greater forward momentum. This process results in a decrease in the duration of the unstable transitional phase of sit‐to‐stand, allowing PD patients to reach the upright position as easily and safely as possible. Small rotational movements are an effective way to maintain the centre of mass within the base of support during sit‐to‐stand. This mechanism appears to be denied to the PD patients who may use increased movements in the coronal plane as an alternative strategy. © 2002 Movement Disorder Society