Miracle-dz/UniFAR-FTUs huggingface dataset:
Diminished Metal Accumulation in Riverine Fishes Exposed to Acid Mine Drainage over Five Decades

Bony bream (Nematalosa erebi) and black catfish (Neosilurus ater) were sampled from the fresh surface waters of the Finniss River in tropical northern Australia, along a metal pollution gradient draining the Rum Jungle copper/uranium mine, a contaminant source for over five decades. Paradoxically, populations of both fish species exposed to the highest concentrations of mine-related metals (cobalt, copper, lead, manganese, nickel, uranium and zinc) in surface water and sediment had the lowest tissue (bone, liver and muscle) concentrations of these metals. The degree of reduction in tissue concentrations of exposed populations was also specific to each metal and inversely related to its degree of environmental increase above background. Several explanations for diminished metal bioaccumulation in fishes from the contaminated region were evaluated. Geochemical speciation modeling of metal bioavailability in surface water showed no differences between the contaminated region and the control sites. Also, the macro-nutrient (calcium, magnesium and sodium) water concentrations, that may competitively inhibit metal uptake, were not elevated with trace metal contamination. Reduced exposure to contaminants due to avoidance behavior was unlikely due to the absence of refugial water bodies with the requisite metal concentrations lower than the control sites and very reduced connectivity at time of sampling. The most plausible interpretation of these results is that populations of both fish species have modified kinetics within their metal bioaccumulation physiology, via adaptation or tolerance responses, to reduce their body burdens of metals. This hypothesis is consistent with (i) reduced tissue concentrations of calcium, magnesium and sodium (macro-nutrients), in exposed populations of both species, (ii) experimental findings for other fish species from the Finniss River and other contaminated regions, and (iii) the number of generations exposed to likely selection pressure over 50 years.
Multitrophic diversity effects of network degradation

Abstract Predicting the functional consequences of biodiversity loss in realistic, multitrophic communities remains a challenge. No existing biodiversity–ecosystem function study to date has simultaneously incorporated information on species traits, network topology, and extinction across multiple trophic levels, while all three factors are independently understood as critical drivers of post‐extinction network structure and function. We fill this gap by comparing the functional consequences of simulated species loss both within (monotrophic) and across (bitrophic) trophic levels, in an ecological interaction network estimated from spatially explicit field data on tropical fecal detritus producer and consumers (mammals and dung beetles). We simulated trait‐ordered beetle and mammal extinction separately (monotrophic extinction) and the coextinction of beetles following mammal loss (bitrophic extinction), according to network structure. We also compared the diversity effects of bitrophic extinction models using a standard monotrophic function (the daily production or consumption of fecal detritus) and a unique bitrophic functional metric (the proportion of daily detritus production that is consumed). We found similar mono‐ and bitrophic diversity effects, regardless of which species traits were used to drive extinctions, yet divergent predictions when different measures of function were used. The inclusion of information on network structure had little apparent effect on the qualitative relationship between diversity and function. These results contribute to our growing understanding of the functional consequences of biodiversity from real systems and underscore the importance of species traits and realistic functional metrics to assessments of the ecosystem impacts of network degradation through species loss.
New Species of Insect Trypanosomatids from Costa Rica and the Proposal for a New Subfamily within the Trypanosomatidae

Several new species of trypanosomatids (Euglenozoa, Kinetoplastea, Trypanosomatidae), isolated from the intestines of Neotropical insects (Heteroptera), were genotyped on the basis of spliced leader RNA, and also defined phylogenetically using gene sequences of small subunit ribosomal RNA and glycosomal glyceraldehyde phosphate dehydrogenase. The taxonomic descriptions also included characterization using morphometry and electron microscopy. Our phylogenetic analyses placed the new species within the clade, previously designated “SE” for “Slowly Evolving” sequences of ribosomal RNA genes, a clade that also includes numerous monoxenous parasites of insects from the genera Crithidia, Leptomonas, and Wallaceina, as well as the dixenous genus Leishmania. Based on the high phylogenetic support for this clade, which is consistently recovered in all recent phylogenetic reconstructions, a proposal is put forward to recognize this natural taxon as a new subfamily, Leishmaniinae, within the family Trypanosomatidae.
Respiratory and cognitive mediators of treatment change in panic disorder: evidence for intervention specificity.

OBJECTIVE There are numerous theories of panic disorder, each proposing a unique pathway of change leading to treatment success. However, little is known about whether improvements in proposed mediators are indeed associated with treatment outcomes and whether these mediators are specific to particular treatment modalities. Our purpose in this study was to analyze pathways of change in theoretically distinct interventions using longitudinal, moderated mediation analyses. METHOD Forty-one patients with panic disorder and agoraphobia were randomly assigned to receive 4 weeks of training aimed at altering either respiration (capnometry-assisted respiratory training) or panic-related cognitions (cognitive training). Changes in respiration (PCO₂, respiration rate), symptom appraisal, and a modality-nonspecific mediator (perceived control) were considered as possible mediators. RESULTS The reductions in panic symptom severity and panic-related cognitions and the improvements in perceived control were significant and comparable in both treatment groups. Capnometry-assisted respiratory training, but not cognitive training, led to corrections from initially hypocapnic to normocapnic levels. Moderated mediation and temporal analyses suggested that in capnometry-assisted respiratory training, PCO₂ unidirectionally mediated and preceded changes in symptom appraisal and perceived control and was unidirectionally associated with changes in panic symptom severity. In cognitive training, reductions in symptom appraisal were bidirectionally associated with perceived control and panic symptom severity. In addition, perceived control was bidirectionally related to panic symptom severity in both treatment conditions. CONCLUSION The findings suggest that reductions in panic symptom severity can be achieved through different pathways, consistent with the underlying models.
Theoretical Model for Fiber-Reinforced Polymer-Confined Concrete

Fiber-reinforced polymer (FRP) composites have found increasingly wide applications in civil engineering due to their high strength-to-weight ratio and high corrosion resistance. One important application of FRP composites is as a confining material for concrete, particularly in the strengthening or seismic retrofit of existing reinforced concrete columns by the provision of a FRP jacket. FRP confinement can enhance both the compressive strength and the ultimate strain of concrete significantly. This paper presents a new stress–strain model for FRP-confined concrete in which the responses of the concrete core and the FRP jacket as well as their interaction are explicitly considered. Such a model is often referred to as an analysis-oriented model. The key novel feature of the proposed analysis-oriented model, compared to existing models of the same kind, is a more accurate and more widely applicable lateral strain equation based on a careful interpretation of the lateral deformation characteristics of unco.
Social Simulation of Stock Markets: Taking It to the Next Level

This paper studies the use of social simulation in linking micro level investor behaviour and macro level stock market dynamics. Empirical data from a survey on individual investors' decision-making and social interaction was used to formalize the trading and interaction rules of the agents of the artificial stock market SimStockExchange. Multiple simulation runs were performed with this artificial stock market, which generated macro level results, like stock market prices and returns over time. These outcomes were subsequently compared to empirical macro level data from real stock markets. Partial qualitative as well as quantitative agreement between the simulated asset returns distributions and the asset returns distributions of the real stock markets was found.
Comparative inhibition of influenza and parainfluenza virus replication by ribavirin in MDCK cells

Actinomycin D inhibited the yield of influenza virus hemagglutinin from MDCK cells infected at high multiplicity, but had little effect on the yield of parainfluenza virus hemagglutinin. In similar hemagglutinin yield experiments, ribavirin was only slightly more active (threefold) against influenza virus than against parainfluenza virus replication. In plaque inhibition experiments, ribavirin depressed influenza virus plaque formation by 50% at a concentration of approximately 3 micrograms/ml, whereas the corresponding figure for parainfluenza viruses was threefold higher. The concentration of ribavirin demonstrating anti-influenza activity was indistinguishable for that inhibiting host cell growth. It is concluded that, unlike actinomycin D, ribavirin is unlikely to have a major effect on the provision of host cell 5-germinal methylated cap structures and the subsequent priming of influenza messenger ribonucleic acid synthesis.
Past it? HIV and older people in England, Wales and Northern Ireland

The majority of those infected and affected by HIV are younger adults. The ability of highly active antiretroviral therapies (HAART) to extend survival means that those infected when younger may reach older age, and future increases in numbers of older individuals living with HIV in England, Wales and Northern Ireland (E,W&NI) are expected. Evidence that older individuals engage in risky sexual behaviours suggests potential for HIV transmission. Data from national HIV/AIDS surveillance systems were reviewed (1997–2001). An older individual is defined as aged 45 years or over. Between 1997 and 2001, 2290 older individuals were diagnosed with HIV; 361 in 1997, rising to 648 in 2001. Heterosexual acquisition accounted for 1073 (47%) infections; 662 were male. Where reported, 666 (65%) older heterosexuals were probably infected in Africa, 144 (14%) in the United Kingdom and 113 (11%) in Asia. There were 1020 (45%) new diagnoses acquired homosexually; white (92%), infected in the United Kingdom (78%). Numbers of older individuals accessing HIV-related services more than doubled between 1997 (2488) and 2001 (5175). In 2001, 2270 (53%) were London residents. Between 1997 and 2001, among HIV-infected older individuals attending genitourinary medicine (GUM) clinics, the proportions previously undiagnosed were 60% and 82% in heterosexual males and females respectively, and for men who have sex with men (MSM), 42%. Numbers of older individuals newly diagnosed with HIV have increased in recent years. The increase in numbers of older individuals accessing HIV-related services were in excess of younger adults. A significant proportion of older HIV-infected female heterosexuals and MSM were undiagnosed. Awareness must be raised among clinicians, and an ‘aged response’ to HIV is required.
Joint source/channel coding for variable length codes

When using entropy coding over a noisy channel it is customary to protect the highly vulnerable bitstream with an error correcting code. In this paper we propose a technique which utilizes the residual redundancy at the output of the source coder to provide error protection for entropy coded systems. The proposed approach provides 4-10 dB improvement over the standard approaches at a reduced rate.
Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties

We have recently sequenced the genome of a novel thermophilic bacteriophage designated as TS2126 that infects the thermophilic eubacterium Thermus scotoductus. One of the annotated open reading frames (ORFs) shows homology to T4 RNA ligase 1, an enzyme of great importance in molecular biology, owing to its ability to ligate single-stranded nucleic acids. The ORF was cloned, and recombinant protein was expressed, purified and characterized. The recombinant enzyme ligates single-stranded nucleic acids in an ATP-dependent manner and is moderately thermostable. The recombinant enzyme exhibits extremely high activity and high ligation efficiency. It can be used for various molecular biology applications including RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE). The TS2126 RNA ligase catalyzed both inter- and intra-molecular single-stranded DNA ligation to >50% completion in a matter of hours at an elevated temperature, although favoring intra-molecular ligation on RNA and single-stranded DNA substrates. The properties of TS2126 RNA ligase 1 makes it very attractive for processes like adaptor ligation, and single-stranded solid phase gene synthesis.
Chronic manganese poisoning

SINCE COWPER’S FIRST DESCRIPTION,^ human chronic manganese poisoning has been the subject of many reports and several reviews.2-6 The aim of most publications seems to have been the definition of the clinical picture of this disease in relation to various environmental factors. The clinical picture has consisted of both psychiatric and neurological manifestations, the most crippling of which have been related to the extrapyramidal system.6 The environmental factors investigated have included the physical characteristics of dusts inhaled by manganese miners as well as some chemical properties of ores which have induced the disease in high incidence. Consequently, chelating agents have been introduced in the management of this disease.8 The present study was undertaken after consideration of some disease states in which abnormal metabolism of metals is correlated with chronic disturbances of the brain. Such correlations are particularly striking in lead encephalopathy and Wilson’s disease. In both diseases the respective presence of high tissue concentrations of leadQJ0 and of copperll seems essential to the induction and, perhaps, to the progression of the symptomatology. It seemed reasonable to investigate chronic manganese poisoning with these precedents in mind. The present publication is the initial report of studies on this problem. It develops arguments in favor of the thesis that chronic manganese poisoning may diverge significantly from the aforementioned diseases. If further substantiated by analytical evidence, these
LKB1 Is Required for the Development and Maintenance of Stereocilia in Inner Ear Hair Cells in Mice

The LKB1 gene, which encodes a serine/threonine kinase, was discovered to play crucial roles in cell differentiation, proliferation, and the establishment of cell polarity. In our study, LKB1 conditional knockout mice (Atoh1-LKB1-/- mice) were generated to investigate LKB1 function in the inner ear. Tests of auditory brainstem response and distortion product otoacoustic emissions revealed significant decreases in the hearing sensitivities of the Atoh1-LKB1-/- mice. In Atoh1-LKB1-/- mice, malformations of hair cell stereocilliary bundles were present as early as postnatal day 1 (P1), a time long before the maturation of the hair cell bundles. In addition, we also observed outer hair cell (OHC) loss starting at P14. The impaired stereocilliary bundles occurred long before the presence of hair cell loss. Stereociliary cytoskeletal structure depends on the core actin-based cytoskeleton and several actin-binding proteins. By Western blot, we examined actin-binding proteins, specifically ERM (ezrin/radixin/moesin) proteins involved in the regulation of the actin cytoskeleton of hair cell stereocilia. Our results revealed that the phosphorylation of ERM proteins (pERM) was significantly decreased in mutant mice. Thus, we propose that the decreased pERM may be a key factor for the impaired stereocillia function, and the damaged stereocillia may induce hair cell loss and hearing impairments. Taken together, our data indicates that LKB1 is required for the development and maintenance of stereocilia in the inner ear.
Prognostic impact of immune microenvironment in laryngeal and pharyngeal squamous cell carcinoma: Immune cell subtypes, immuno-suppressive pathways and clinicopathologic characteristics

Background Immune system affects prognosis of various malignancies. Anti-immune pathways like PD-L1 and CTLA4 are used by the tumor to overcome immune system and they serve as immunotherapy targets. The immune microenvironment of head-and-neck squamous cell carcinoma (SCCHN) has not been sufficiently studied. Patients and Methods 152 SCCHN were immunohistochemically studied for the expression of CD3, CD8, CD57, CD4, granzyme b, CD20, CD163, S100, PD-L1, CTLA4 and CXCR4. Results CD3, CD8, CD57 and stromal S100 higher density is a good prognostic factor (p=0.02, 0.01, 0.02, 0.03 respectively). CTLA4 tumor expression is a poor prognostic factor (p=0.05). The rest immune cells do not affect prognosis. CD3 and CD8 density does not correlate with clinicopathological factors or p16/p53 expression, while CD57 and CD4 higher density is associated with the absence of distant metastases (p=0.03 and 0.07, respectively). Higher CD20 and S100 density is associated with lower T stage (p=0.04 and 0.03, respectively). PD-L1 expression is higher in CD3, CD8, and CD163 infiltrated tumors and in histologically more aggressive tumors. Response to neoadjuvant chemotherapy is better in highly CD3 infiltrated tumors and in tumors with less intraepithelial macrophages. Conclusion Rich T-lympocytic and dendritic cell response is a good prognostic factor in SCCHN, whereas tumors expressing CTLA4 show poor prognosis. PDL1 expression does not affect prognosis, but it is expressed in histologically more aggressive tumors and in T-cells rich tumors. Response to induction chemotherapy is better in tumors less infiltrated by macrophages and mostly infiltrated by T cells.
Considerations of Budget Allocation for Sequential Parameter Optimization (SPO)

Obviously, it is not a good idea to apply an optimization algorithm with wrongly specified parameter settings, a situation which can be avoided by applying algorithm tuning. Sequential tuning procedures are considered more efficient than single-stage procedures. [1] introduced a sequential approach for algorithm tuning that has been successfully applied to several real-world optimization tasks and experimental studies. The sequential procedure requires the specification of an initial sample size k. Small k values lead to poor models and thus poor predictions for the subsequent stages, whereas large values prevent an extensive search and local fine tuning. This study analyzes the interaction between global and local search in sequential tuning procedures and gives recommendations for an adequate budget allocation. Furthermore, the integration of hypothesis testing for increasing effectiveness of the latter phase is investigated.
Large carnivores make savanna tree communities less thorny

Understanding how predation risk and plant defenses interactively shape plant distributions is a core challenge in ecology. By combining global positioning system telemetry of an abundant antelope (impala) and its main predators (leopards and wild dogs) with a series of manipulative field experiments, we showed that herbivores’ risk-avoidance behavior and plants’ antiherbivore defenses interact to determine tree distributions in an African savanna. Well-defended thorny Acacia trees (A. etbaica) were abundant in low-risk areas where impala aggregated but rare in high-risk areas that impala avoided. In contrast, poorly defended trees (A. brevispica) were more abundant in high- than in low-risk areas. Our results suggest that plants can persist in landscapes characterized by intense herbivory, either by defending themselves or by thriving in risky areas where carnivores hunt. Changes to thorny plant defenses and high predator risk for impala determine density and distribution of savanna trees. A thorny defense keeps grazers at bay Fear and avoidance of predators are known to influence how and where herbivore prey species, such as impala, forage. This in turn has cascading effects on plant morphologies and communities. Plants, however, have their own defenses, and so may not just be hapless victims of the predator-prey “dance. ” Ford et al. found that thorny Acacia trees are more common in areas where impala experience a low risk of predation by wild dogs. A related Acacia, without thorns, is most abundant in areas where risk of predation is high, and so the number of hungry impala is low. Science, this issue p. 346
Prefrontal Function Engaging in External-Focused Attention in 5- to 6-Month-Old Infants: A Suggestion for Default Mode Network

The present study used functional near-infrared spectroscopy (fNIRS) to measure 5- to 6-month-old infants’ hemodynamic response in the prefrontal cortex (PFC) to visual stimuli differing in saliency and social value. Nineteen Japanese 5- to 6-month-old infants watched video clips of Peek-a-Boo (social signal) performed by an anime character (AC) or a human, and hand movements without social signal performed by an AC. The PFC activity of infants was measured by 22-channel fNIRS, while behaviors including looking time were recorded simultaneously. NIRS data showed that infants’ hemodynamic responses in the PFC generally decreased due to these stimuli, and the decrease was most prominent in the frontopolar (FP), covering medial PFC (MPFC), when infants were viewing Peek-a-Boo performed by an AC. Moreover, the decrease was more pronounced in the dorsolateral PFC (DLPFC) when infants were viewing Peek-a-Boo performed by an AC than by a human. Accordingly, behavioral data revealed significantly longer looking times when Peek-a-Boo was performed by an AC than by a human. No significant difference between Peek-a-Boo and non-Peek-a-Boo conditions was observed in either measure. These findings indicate that infants at this age may prefer stimuli with more salient features, which may be more effective in attracting their attentions. In conjunction with our previous findings on responses to self-name calling in infants of similar age, we hypothesize that the dynamic function of the MPFC and its vicinity (as part of default mode network (DMN): enhanced by self-focused stimuli, attenuated by externally focused stimuli), which is consistently observed in adults, may have already emerged in 5- to 6-month-old infants.