Miracle-dz/UniFAR-FTUs huggingface dataset:
Endobronchial Lesions in Patients Presenting with Hemoptysis

Objectives The aim of this study was to determine the incidence of endobronchial lesions in patients presenting with hemoptysis. We also aimed to characterize features that would predict whether bronchoscopy would be useful. Methods A retrospective chart review was conducted on 185 consecutive patients who presented with hemoptysis from January 1, 2006 to December 31, 2015 at Methodist Le Bonheur Healthcare–affiliated hospitals in Memphis, Tennessee. Data collection included demographic information, description of hemoptysis, imaging results, bronchoscopy results, and the final diagnosis. Results A total of 185 patients presented with hemoptysis during our study period. Of these, 14 patients were excluded because of age (younger than 18 years) and incomplete data (inadequate information about the procedure performed, lack of imaging studies, incorrect International Classification of Diseases, Ninth Revision coding). The final analysis was performed in 171 patients; 87 underwent bronchoscopy either to determine etiology or to aid in management. Most patients (73%) had mild hemoptysis, with approximately half of the patients having hemoptysis for ⩽1 day. Of 87 people who underwent bronchoscopy, 12 (13.8%) were found to have endobronchial lesions, and 35 (51.7%) patients were found to have either active bleeding or had fresh blood in their airway during bronchoscopy. Final diagnoses included pneumonia/bronchitis in 30 (18.9%) patients, malignancy in 24 (15.1 %), and anticoagulation toxicity in 23 (14.5%) patients. Conclusions Bronchoscopy should be strongly considered in patients presenting with hemoptysis, especially if it is frank blood, of >1 week’s duration, or both, because the information obtained can be vital for management. This appears to hold true even for patients who have no abnormalities seen on computed tomography chest imaging upon initial workup.
Are Local Filters Blind to Provenance? Ant Seed Predation Suppresses Exotic Plants More than Natives

The question of whether species’ origins influence invasion outcomes has been a point of substantial debate in invasion ecology. Theoretically, colonization outcomes can be predicted based on how species’ traits interact with community filters, a process presumably blind to species’ origins. Yet, exotic plant introductions commonly result in monospecific plant densities not commonly seen in native assemblages, suggesting that exotic species may respond to community filters differently than natives. Here, we tested whether exotic and native species differed in their responses to a local community filter by examining how ant seed predation affected recruitment of eighteen native and exotic plant species in central Argentina. Ant seed predation proved to be an important local filter that strongly suppressed plant recruitment, but ants suppressed exotic recruitment far more than natives (89% of exotic species vs. 22% of natives). Seed size predicted ant impacts on recruitment independent of origins, with ant preference for smaller seeds resulting in smaller seeded plant species being heavily suppressed. The disproportionate effects of provenance arose because exotics had generally smaller seeds than natives. Exotics also exhibited greater emergence and earlier peak emergence than natives in the absence of ants. However, when ants had access to seeds, these potential advantages of exotics were negated due to the filtering bias against exotics. The differences in traits we observed between exotics and natives suggest that higher-order introduction filters or regional processes preselected for certain exotic traits that then interacted with the local seed predation filter. Our results suggest that the interactions between local filters and species traits can predict invasion outcomes, but understanding the role of provenance will require quantifying filtering processes at multiple hierarchical scales and evaluating interactions between filters.
An Innovative Model for Naloxone Use Within an OTP Setting: A Prospective Cohort Study

Objectives: Unintentional opioid overdose deaths are a public health crisis, and naloxone is the most effective harm reduction tool to curb many of these deaths. There is growing evidence that take-home naloxone can prevent opioid overdose in targeted populations. The goal of this study is to measure the opioid overdose reversal rate with take-home naloxone among participants with a diagnosis of opioid use disorder (OUD) in an opioid treatment program (OTP) setting. Methods: Patients enrolled in an outpatient OTP program were eligible for this prospective cohort study between April 4, 2016 and July 4, 2016. Two hundred forty-four study participants received overdose education, instruction on how to use naloxone, and were provided with 2 doses of a take-home naloxone auto-injector kit. They were subsequently followed for 3 months. Results: Thirty-one study participants reported overdose reversals using naloxone auto-injector kits on 38 community members. All overdose reversals were heroin-related. Eighty-seven per cent of the community members reversed with naloxone were friends or relatives of the study participants. Conclusions: This study validates that naloxone is not commonly used on the index study participant, but is often used on a secondary target among people who inject drugs. The large number of overdose reversals reported in this prospective study suggests that this novel model for naloxone use may be replicated at other OTP settings to reduce opioid overdose deaths.
Using Manipulated Photographs to Identify Features of Streetscapes That May Encourage Older Adults to Walk for Transport

Experimental evidence of environmental features important for physical activity is challenging to procure in real world settings. The current study aimed to investigate the causal effects of environmental modifications on a photographed street's appeal for older adults' walking for transport. Secondly, we examined whether these effects differed according to gender, functional limitations, and current level of walking for transport. Thirdly, we examined whether different environmental modifications interacted with each other. Qualitative responses were also reported to gain deeper insight into the observed quantitative relationships. Two sets of 16 panoramic photographs of a streetscape were created, in which six environmental factors were manipulated (sidewalk evenness, traffic level, general upkeep, vegetation, separation from traffic, and benches). Sixty older adults sorted these photographs on appeal for walking for transport on a 7-point scale and reported qualitative information on the reasons for their rankings. Sidewalk evenness appeared to have the strongest influence on a street's appeal for transport-related walking. The effect of sidewalk evenness was even stronger when the street's overall upkeep was good and when traffic was absent. Absence of traffic, presence of vegetation, and separation from traffic also increased a street's appeal for walking for transport. There were no moderating effects by gender or functional limitations. The presence of benches increased the streetscape's appeal among participants who already walked for transport at least an hour/week. The protocols and methods used in the current study carry the potential to further our understanding of environment-PA relationships. Our findings indicated sidewalk evenness as the most important environmental factor influencing a street's appeal for walking for transport among older adults. However, future research in larger samples and in real-life settings is needed to confirm current findings.
Synonymous Rare Arginine Codons and tRNA Abundance Affect Protein Production and Quality of TEV Protease Variant

It has been identified that a TEV protease (TEVp) variant, TEVp5M, displays improved solubility. Here, we constructed fifteen TEVp5M variants with one or more of six rare arginine codons in the coding sequence replaced with abundant E. coli arginine codons. These codon variants expressed in either E. coli BL21 (DE3) or Rossetta (DE3) showed different solubility and activity. Supply of rare tRNAs increased the tendency of certain codon variants to form insoluble aggregates at early induction stage, as determined by the fused S-tag. About 32% increase in soluble protein production of M5 variant with four synonymously mutated arginine codons was identified in Rossetta (DE3) cells using GFP fusion reporter, comparable to that of TEVp5M. After purification, two other codon variants from both E. coli strains exhibited less activity than TEVp5M on cleaving the native or modified recognition sequence incorporated between GST and E. coli diaminopropionate ammonialyase by enzyme-coupled assay, whereas purified M5 variant showed activity similar to the TEVp5M. Supply of rare tRNAs caused the decrease of activity of TEVp5M and M5 by about 21%. Our results revealed that engineering of highly soluble TEVp variants can be achieved by the combined mutations of amino acid residues and optimization of specific rare codons, whereas simple augment of rare tRNAs abundance resulted in partial loss of activity.
Variation in the outcomes of an ant-plant system: Fire and leaf fungus infection reduce benefits to plants with extrafloral nectaries

Abstract Interactions between species are evolutionary malleable and may suffer changes in small timescales. Environmental disturbances, such as fire, can deeply affect species interactions, but how they influence the outcome of a mutualistic interaction has yet to be studied. In order to test the hypothesis that an environmental disturbance, in this case fire, may produce differences in the outcome of the association of ants with the extrafloral-nectaries-bearing plant Qualea multiflora Mart. (Myrtales: Vochysiaceae), a previous study was replicated, but this time after fire incidence, at the same study site and with the same plant species. Eight ant species visited Q. multiflora , and the most abundant genera were Crematogaster , Cephalotes , and Camponotus . Herbivores were found in branches with and without ants with no statistical difference, but foliar herbivory was always higher in branchs where ants were absent. Leaves were infested by fungi, and fungi spots were higher in branches where ants were present. Compared to the previous study, it was clearly observed that ant benefits to Q. multiflora varied over time. The most common ant species still protected leaves against chewing herbivores, but a new kind of leaf damage appeared, namely fungi spots. Data also support that ants may be acting as vectors of fungi spores on plants, as ant visited branches had higher fungus incidence than non-visited branches. Fire is a major source of disturbance in tropical savannas, and we suggest that it can cause strong variation in the outcomes of interactions between ants and plants with extrafloral nectaries in the Brazilian tropical savanna.
Interactions between frugivorous bats (Chiroptera: Phyllostomidae) and Piper tuberculatum (Piperaceae) in a tropical dry forest in Valle del Cauca, Colombia.

In any ecosystem, fruits are resources that vary in time and space as well as in nutritional content. Coexistence of species from a trophic guild depends on the division and use of resources. Therefore, the organisms that depend on them as a food source, tend to show a certain degree of specialization. This way, understanding the factors that influence the dynamics of seed dispersal is important for the regeneration and conservation of tropical ecosystems. Our aim was to determine variation in consumption of Piper tuberculatum by fruit bat assemblages in the village of Robles (Jamundí, Valle del Cauca, Colombia). P. tuberculatum is a resource used not only by wildlife but also by people in the village of Robles. Bats were captured in mist nets between June and November 2014, their feces were collected, and the length of the forearm, wing area, leg length and mass were recorded. At the Universidad del Valle seed laboratory, fecal samples were washed, and their content determined. Of the 14 species captured, Sturnira lilium, Carollia brevicauda, Carollia perspicillata and Artibeus lituratus showed signs of having consumed P. tuberculatum. Sturnira lilium was the main consumer of P. tuberculatum fruits, with the greatest number of consumption events of fruit from this plant species, whereas the other bats showed more diversified consumption events. The greatest niche overlap was recorded between C. brevicauda and C. perspicillata, species that showed similar sizes (i.e., wing area and forearm length) followed by S. lilium and C. perspicillata. In contrast, A. lituratus showed the least niche overlap with the other three fruit bats captured. In conclusion, Sturnira lilium showed an interaction Sturnira-Piper, which is the result of low Solanum availability, and this bat species was the largest consumer of P. tuberculatum in the region.
Lethal Fighting in Nematodes Is Dependent on Developmental Pathway: Male-Male Fighting in the Entomopathogenic Nematode Steinernema longicaudum

Aggressive encounters occur between competitors (particularly males) throughout the animal kingdom, and in some species can result in severe injury and death. Here we describe for the first time lethal interactions between male nematodes and provide evidence that the expression of this behaviour is developmentally controlled. Males of the entomopathogenic nematode Steinernema longicaudum coil around each other, resulting in injuries, paralysis and frequently death. The probability of death occurring between pairs of males was affected by the developmental pathway followed, being much greater among males that had passed through the infective juvenile (IJ, or dauer) stage than among males that had not. Post-IJ males are found only in newly colonised hosts, typically with few competing males present. Killing those few competitors may secure valuable resources (both females and a host cadaver for nourishment of offspring). Non-IJ males develop in subsequent generations within a host cadaver, where the presence of many closely related male competitors increases the risk:benefit ratio of fighting. Thus, passage through the IJ stage primes males for enhanced aggression in circumstances where this is more likely to result in increased reproductive success. Fighting occurred between males developing in mixed-sex social groups, indicating that it is an evolved trait and not an abnormal response to absence of females. This is supported by finding high mortality of males, but not of females, across a range of population densities in insect cadavers. We propose that these nematodes, with their relatively simple organization, may be a useful model for studies of aggression.
A Single Serine Residue Determines Selectivity to Monovalent Metal Ions in Metalloregulators of the MerR Family

ABSTRACT MerR metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. The sensor protein binds the inducer metal ion by using two conserved cysteine residues at the C-terminal metal-binding loop (MBL). Divalent metal ion sensors, such as MerR and ZntR, require a third cysteine residue, located at the beginning of the dimerization (α5) helix, for metal coordination, while monovalent metal ion sensors, such as CueR and GolS, have a serine residue at this position. This serine residue was proposed to provide hydrophobic and steric restrictions to privilege the binding of monovalent metal ions. Here we show that the presence of alanine at this position does not modify the activation pattern of monovalent metal sensors. In contrast, GolS or CueR mutant sensors with a substitution of cysteine for the serine residue respond to monovalent metal ions or Hg(II) with high sensitivities. Furthermore, in a mutant deleted of the Zn(II) exporter ZntA, they also trigger the expression of their target genes in response to either Zn(II), Cd(II), Pb(II), or Co(II). IMPORTANCE Specificity in a stressor's recognition is essential for mounting an appropriate response. MerR metalloregulators trigger the expression of specific resistance systems upon detection of heavy metal ions. Two groups of these metalloregulators can be distinguished, recognizing either +1 or +2 metal ions, depending on the presence of a conserved serine in the former or a cysteine in the latter. Here we demonstrate that the serine residue in monovalent metal ion sensors excludes divalent metal ion detection, as its replacement by cysteine renders a pan-metal ion sensor. Our results indicate that the spectrum of signals detected by these sensors is determined not only by the metal-binding ligand availability but also by the metal-binding cavity flexibility.
Energy intake, energy required and mortality in an older population

Abstract Objectives The present study evaluated the association between energy intake, energy required and mortality in older adults. Design A cohort study with a mean of 10·67 (sd 4·74) years of follow-up. Participants completed a 24 h dietary recall. Energy required per day was computed by BMR. Deaths through 2006 were identified from the National Death Index. A Cox regression was used to estimate the hazard ratios (HR) of quantiles of energy intake and energy required on all-cause and CVD mortality, adjusting for demographics, socio-economic status and co-morbidity. Setting The National Health and Nutrition Examination Survey (NHANES) III, 1988–1994. Subjects A total of 4846 participants aged 60 years or above were analysed. Results Within the follow-up period, there were a total of 2954 deaths (61·0 %), 51·9 % were caused by CVD. Relative to those in quartile 1 of energy intake, only quartile 4 was associated with all-cause mortality and CVD mortality with HR of 0·86 (95 % CI 0·77, 0·96, P=0·006) and 0·76 (95 % CI 0·65, 0·89, P=0·001), respectively. On the other hand, relative to those in quartile 1 of energy required, all quartiles of participants had a lower risk of all-cause mortality and CVD mortality. The interaction effects between energy intake and energy required with all-cause and CVD mortality were insignificant (P=0·70 and 0·61, respectively). Conclusions Independent of energy required, higher energy intake was associated with lower HR of both all-cause and CVD mortality in older adults.
utocrine role of endogenous interleukin‐18 on inflammatory cytokine generation by human neutrophils

Neutrophils are key players of innate immunity and influence inflammatory and immune reactions through the production of numerous cyto‐kines. Interleukin‐18 (IL‐18) is known to stimulate several neutrophil responses, and recent evidence sug‐gests that neutrophils might represent a source of IL‐18. Here, we show that neutrophils constitutively produce both IL‐18 and its antagonist, IL‐18BP. Cell activation does not affect IL‐18BP release but leads to an increased gene expression and secretion of IL‐18, a process that depends on NF‐κB activation. Moreover, endogenous IL‐18 feeds back on the neutrophils to augment cytokine generation in lipopolysaccharide‐treated cells. Accordingly, exogenous IL‐18 can induce the gene expression and release of several inflamma‐tory cytokines in neutrophils, including its own expression. We finally report that IL‐18 activates the p38 MAPK, MEK/ERK, and PI3K/Akt pathways in neutro‐phils. The IKK cascade is also activated by IL‐18, resulting in IκB‐α degradation, NF‐κB activation, and RelA phosphorylation. Accordingly, these pathways contribute to the generation of inflammatory cytokines in IL‐18‐stimulated neutrophils. By contrast, the phos‐phorylation and DNA‐binding activity of various STAT proteins were not induced by IL‐18. Collectively, our results unveil new interactions between IL‐18 and neutro‐phils and further support a role for these cells in influencing both innate and adaptive immunity. —Fortin, C. F. , Ear, T. , McDonald, P. P. Autocrine role of endogenous interleukin‐18 on inflammatory cytokine generation by human neutrophils. FASEB J. 23, 194‐203 (2009)
Statistical analysis of structural determinants for protein–DNA‐binding specificity

DNA‐binding proteins play critical roles in biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific (HS) to nonspecific (NS). Alterations of DNA‐binding specificity, due to either genetic variation or somatic mutations, can lead to various diseases. In this study, a comparative analysis of protein–DNA complex structures was carried out to investigate the structural features that contribute to binding specificity. Protein–DNA complexes were grouped into three general classes based on degrees of binding specificity: HS, multispecific (MS), and NS. Our results show a clear trend of structural features among the three classes, including amino acid binding propensities, simple and complex hydrogen bonds, major/minor groove and base contacts, and DNA shape. We found that aspartate is enriched in HS DNA binding proteins and predominately binds to a cytosine through a single hydrogen bond or two consecutive cytosines through bidentate hydrogen bonds. Aromatic residues, histidine and tyrosine, are highly enriched in the HS and MS groups and may contribute to specific binding through different mechanisms. To further investigate the role of protein flexibility in specific protein–DNA recognition, we analyzed the conformational changes between the bound and unbound states of DNA‐binding proteins and structural variations. The results indicate that HS and MS DNA‐binding domains have larger conformational changes upon DNA‐binding and larger degree of flexibility in both bound and unbound states. Proteins 2016; 84:1147–1161. © 2016 Wiley Periodicals, Inc.
Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus

Zika virus–specific antibodies isolated from a single infected patient show postexposure protection in mice and reveal targets for therapy. Stopping Zika virus in its tracks Zika virus is a global concern because of its association with fetal microcephaly and neurological complications, and there are no approved countermeasures. In new work, Wang et al. isolated 13 antibodies from a patient infected with Zika virus, two of which (Z3L1 and Z23) showed potent neutralizing activity without cross-reactivity to dengue virus strains 1 to 4. Moreover, the Z3L1 and Z23 antibodies conferred postexposure protection against Zika virus in a murine model. Structural studies indicated that the antibodies bound to different viral epitopes, suggesting that these antibodies could be used as a therapeutic cocktail. The 2015–2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and countermeasures are needed to treat and prevent ZIKV infection. We report the isolation of 13 specific human monoclonal antibodies from a single patient infected with ZIKV. Two of the isolated antibodies (Z23 and Z3L1) demonstrated potent ZIKV-specific neutralization in vitro without binding or neutralizing activity against strains 1 to 4 of dengue virus, the closest relative to ZIKV. These two antibodies provided postexposure protection to mice in vivo. Structural studies revealed that Z23 and Z3L1 bound to tertiary epitopes in envelope protein domain I, II, or III, indicating potential targets for ZIKV-specific therapy. Our results suggest the potential of antibody-based therapeutics and provide a structure-based rationale for the design of future ZIKV-specific vaccines.