Miracle-dz/UniFAR-FTUs huggingface dataset:
Cattle herd inspections and fly trapping for the detection of the Old World screw-worm fly (Chrysomya bezziana).

OBJECTIVES To compare the sensitivity of inspections of cattle herds and adult fly trapping for detection of the Old World screw-worm fly (OWS). PROCEDURES The incidence of myiases on animals and the number of OWS trapped with LuciTrap®/Bezzilure were measured concurrently on cattle farms on Sumba Island (Indonesia) and in peninsular Malaysia (two separate periods for the latter). The numbers of animal inspections and traps required to achieve OWS detection at the prevalent fly densities were calculated. RESULTS On Sumba Island, with low-density OWS populations, the sensitivity of herd inspections and of trapping for OWS detection was 0.30 and 0.85, respectively. For 95% confidence of detecting OWS, either 45 inspections of 74 animals or trapping with 5 sets of 4 LuciTraps for 14 days are required. In Malaysia, at higher OWS density, herd inspections of 600 animals (twice weekly, period 1) or 1600 animals (weekly, period 2) always detected myiases (sensitivity = 1), while trapping had sensitivities of 0.89 and 0.64 during periods 1 and 2, respectively. For OWS detection with 95% confidence, fewer than 600 and 1600 animals or 2 and 6 LuciTraps are required in periods 1 and 2, respectively. CONCLUSIONS Inspections of cattle herds and trapping with LuciTrap and Bezzilure can detect OWS populations. As a preliminary guide for OWS detection in Australia, the numbers of animals and traps derived from the Sumba Island trial should be used because the prevailing conditions better match those of northern Australia.
Emerging Evidence for a Direct Link between EAAT-Associated Anion Channels and Neurological Disorders

Excitatory amino acid transporters (EAATs) are membrane proteins that control excitatory synaptic transmission in the brain ([Bergles et al., 1999][1]; [Danbolt, 2001][2]; [Robinson and Jackson, 2016][3]). As classical secondary active transporters, which use the energy stored within ion gradients
Ethanol blocks adenosine uptake via inhibiting the nucleoside transport system in bronchial epithelial cells.

BACKGROUND Adenosine uptake into cells by nucleoside transporters plays a significant role in governing extracellular adenosine concentration. Extracellular adenosine is an important signaling molecule that modulates many cellular functions via 4 G-protein-coupled receptor subtypes (A(1), A(2A), A(2B), and A(3)). Previously, we demonstrated that adenosine is critical in maintaining airway homeostasis and airway repair and that airway host defenses are impaired by alcohol. Taken together, we hypothesized that ethanol impairs adenosine uptake via the nucleoside transport system. METHODS To examine ethanol-induced alteration on adenosine transport, we used a human bronchial epithelial cell line (BEAS-2B). Cells were preincubated for 10 minutes in the presence and absence of varying concentrations of ethanol (EtOH). In addition, some cells were pretreated with S-(4-Nitrobenzyl)-6-thioinosine (100 microM: NBT), a potent adenosine uptake inhibitor. Uptake was then determined by addition of [(3)H]-adenosine at various time intervals. RESULTS Increasing EtOH concentrations resulted in increasing inhibition of adenosine uptake when measured at 1 minute. Cells pretreated with NBT effectively blocked adenosine uptake. In addition, short-term EtOH revealed increased extracellular adenosine concentration. Conversely, adenosine transport became desensitized in cells exposed to EtOH (100 mM) for 24 hours. To determine the mechanism of EtOH-induced desensitization of adenosine transport, cAMP activity was assessed in response to EtOH. Short-term EtOH exposure (10 minutes) had little or no effect on adenosine-mediated cAMP activation, whereas long-term EtOH exposure (24 hours) blocked adenosine-mediated cAMP activation. Western blot analysis of lysates from unstimulated BEAS-2B cells detected a single 55 kDa band indicating the presence of hENT1 and hENT2, respectively. Real-time RT-PCR of RNA from BEAS-2B revealed transcriptional expression of ENT1 and ENT2. CONCLUSIONS Collectively, these data reveal that acute exposure of cells to EtOH inhibits adenosine uptake via a nucleoside transporter, and chronic exposure of cells to EtOH desensitizes the adenosine transporter to these inhibitory effects of ethanol. Furthermore, our data suggest that inhibition of adenosine uptake by EtOH leads to an increased extracellular adenosine accumulation, influencing the effect of adenosine at the epithelial cell surface, which may alter airway homeostasis.
Binding of Procollagen C-Proteinase Enhancer-1 (PCPE-1) to Heparin/Heparan Sulfate

Procollagen C-proteinase enhancer-1 (PCPE-1) is an extracellular matrix (ECM) glycoprotein that can stimulate procollagen processing by procollagen C-proteinases (PCPs) such as bone morphogenetic protein-1 (BMP-1). The PCPs can process additional extracellular protein precursors and play fundamental roles in developmental processes and assembly of the ECM. The stimulatory activity of PCPE-1 is restricted to the processing of fibrillar procollagens, suggesting PCPE-1 is a specific regulator of collagen deposition. PCPE-1 consists of two CUB domains that bind to the procollagen C-propeptides and are required for PCP enhancing activity, and one NTR domain that binds heparin. To understand the biological role of the NTR domain, we performed surface plasmon resonance (SPR) binding assays, cell attachment assays as well as immunofluorescence and activity assays, all indicating that the NTR domain can mediate PCPE-1 binding to cell surface heparan sulfate proteoglycans (HSPGs). The SPR data revealed binding affinities to heparin/HSPGs in the high nanomolar range and dependence on calcium. Both 3T3 mouse fibroblasts and human embryonic kidney cells (HEK-293) attached to PCPE-1, an interaction that was inhibited by heparin. Cell attachment was also inhibited by an NTR-specific antibody and the NTR fragment. Immunofluorescence analysis revealed that PCPE-Flag binds to mouse fibroblasts and heparin competes for this binding. Cell-associated PCPE-Flag stimulated procollagen processing by BMP-1 several fold. Our data suggest that through interaction with cell surface HSPGs, the NTR domain can anchor PCPE-1 to the cell membrane, permitting pericellular enhancement of PCP activity. This points to the cell surface as a physiological site of PCPE-1 action.
Clinicopathological Features of Gallbladder Papillary Adenocarcinoma

AbstractAlthough patients with gallbladder papillary adenocarcinoma (GBPA) appear to have better prognoses than patients with other pathological subtypes of gallbladder carcinoma (GBC), the clinicopathological features and outcomes of GBPA have not been fully explored. This study therefore analyzed the clinicopathological characteristics and outcomes of GBPA.This study included 16 patients with GBPA and 101 with gallbladder adenocarcinoma (GBA) not otherwise specified (NOS), all diagnosed pathologically after surgical resection. Clinicopathological and survival data were retrospectively collected and compared.Fever was significantly more common in GBPA (7/16 vs 10/101; P = 0.000). Serum carbohydrate antigen 19-9 level was increased in 1 of 9 patients with GBPA and 39 of 76 with GBA (P = 0.022). More patients with GBPA underwent curative resection (15/16 vs 54/101; P = 0.009). Pathologically, patients with GBPA were at much earlier tumor (T) (4 in situ, 8 T1; P = 0.000) and Tumor, Node, Metastases (TNM) stages (P = 0.000). The overall 1-, 3-, and 5-year survival rates were significantly higher in patients with GBPA (100%, 76.9%, and 76.9%, respectively), than in patients with GBA (72.2%, 38.8%, and 31.0%, respectively; P = 0.001). Preoperative jaundice (odds ratio 7.69; 95% confidence interval, 1.53–38.76; P = 0.013) was a significant prognostic factor in patients with GBA, but was no longer significant when the patients with GBA and GBPA were pooled together.The clinicopathological features of patients with GBPA differed from those in patients with GBA (not otherwise specified). Pooling of patients may mask prognostic factors in each group.
Hamming distance geometry of a protein conformational space: Application to the clustering of a 4‐ns molecular dynamics trajectory of the HIV‐1 integrase catalytic core

Protein structures can be encoded into binary sequences (Gabarro‐Arpa et al., Comput Chem 2000;24:693–698 ) these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space in two halves. Thus, the information encoded in the binary sequences is also used to characterize the regions of conformational space visited by the system. We apply this distance and their associated geometric structures to the clustering and analysis of conformations sampled during a 4‐ns molecular dynamics simulation of the HIV‐1 integrase catalytic core. The cluster analysis of the simulation shows a division of the trajectory into two segments of 2.6 and 1.4 ns length, which are qualitatively different: the data points to the fact that equilibration is only reached at the end of the first segment. The Hamming distance is compared also to the r.m.s. deviation measure. The analysis of the cases studied so far shows that under the same conditions the two measures behave quite differently, and that the Hamming distance appears to be more robust than the r.m.s. deviation. Proteins 2002;47:169–179. © 2002 Wiley‐Liss, Inc.
Experimental Demonstration of Complex Image Theory and Application to Position Measurement

Measurements of the magnetoquasistatic fields generated from a magnetic dipole (an electrically small current loop) located above the Earth are presented and compared to calculations using complex image theory. With a horizontal (i.e., the surface normal parallel to the Earth) emitting loop located at a height of h and a copolarized horizontal receiving loop located at a height of z ≥ 0, coupling between the dipoles was measured for distances up to 50 m along a direction perpendicular to the surface normal axes of the loops. Inverting the theoretical expressions to estimate the distance from measured field values resulted in peak and rms distance estimation errors of 23.01 and 11.74 cm, respectively, for distances between 1.3 and 34.2 m. Received signals were not strongly affected by the proximity of a group of people even when the line of sight was obstructed.
Cognition and Synaptic-Plasticity Related Changes in Aged Rats Supplemented with 8- and 10-Carbon Medium Chain Triglycerides

Previous studies have shown that cognition is improved by providing AD patients with an alternate energy source: ketones derived from either ketogenic diet or supplementation with medium chain triglycerides (MCT). Recently, data on the neuroprotective capacity of MCT‐derived medium chain fatty acids (MCFA) suggest octanoic and decanoic acid have direct, cognition‐enhancing properties unrelated to ketone production.
Mesopelagic N2 Fixation Related to Organic Matter Composition in the Solomon and Bismarck Seas (Southwest Pacific)

Dinitrogen (N2) fixation was investigated together with organic matter composition in the mesopelagic zone of the Bismarck (Transect 1) and Solomon (Transect 2) Seas (Southwest Pacific). Transparent exopolymer particles (TEP) and the presence of compounds sharing molecular formulae with saturated fatty acids and sugars, as well as dissolved organic matter (DOM) compounds containing nitrogen (N) and phosphorus (P) were higher on Transect 1 than on Transect 2, while oxygen concentrations showed an opposite pattern. N2 fixation rates (up to ~1 nmol N L-1 d-1) were higher in Transect 1 than in Transect 2, and correlated positively with TEP, suggesting a dependence of diazotroph activity on organic matter. The scores of the multivariate ordination of DOM molecular formulae and their relative abundance correlated negatively with bacterial abundances and positively with N2 fixation rates, suggesting an active bacterial exploitation of DOM and its use to sustain diazotrophic activity. Sequences of the nifH gene clustered with Alpha-, Beta-, Gamma- and Deltaproteobacteria, and included representatives from Clusters I, III and IV. A third of the clone library included sequences close to the potentially anaerobic Cluster III, suggesting that N2 fixation was partially supported by presumably particle-attached diazotrophs. Quantitative polymerase chain reaction (qPCR) primer-probe sets were designed for three phylotypes and showed low abundances, with a phylotype within Cluster III at up to 103 nifH gene copies L-1. These results provide new insights into the ecology of non-cyanobacterial diazotrophs and suggest that organic matter sustains their activity in the mesopelagic ocean.
A WRKY Gene from Creosote Bush Encodes an Activator of the Abscisic Acid Signaling Pathway*

The creosote bush (Larrea tridentata) is a xerophytic evergreen C3 shrub thriving in vast arid areas of North America. As the first step toward understanding the molecular mechanisms controlling the drought tolerance of this desert plant, we have isolated a dozen genes encoding transcription factors, including LtWRKY21 that encodes a protein of 314 amino acid residues. Transient expression studies with the GFP-LtWRKY21 fusion construct indicate that the LtWRKY21 protein is localized in the nucleus and is able to activate the promoter of an abscisic acid (ABA)-inducible gene, HVA22, in a dosage-dependent manner. The transactivating activity of LtWRKY21 relies on the C-terminal sequence containing the WRKY domain and a N-terminal motif that is essential for the repression activity of some regulators in ethylene signaling. LtWRKY21 interacts synergistically with ABA and transcriptional activators VP1 and ABI5 to control the expression of the HVA22 promoter. Co-expression of VP1, ABI5, and LtWRKY21 leads to a much higher expression of the HVA22 promoter than does the ABA treatment alone. In contrast, the Lt-WRKY21-mediated transactivation is inhibited by two known negative regulators of ABA signaling: 1-butanol, an inhibitor of phospholipase D, and abi1-1, a dominant negative mutant protein phosphatase. Interestingly, abi1-1 does not block the synergistic effect of LtWRKY21, VP1, and ABI5 co-expression, indicating that LtWRKY21, VP1, and ABI5 may form a complex that functions downstream of ABI1 to control ABA-regulated expression of genes.
Three paradigms for viewing decision biases

Decisions can, and do, go wrong: a doctor misdiagnoses a patient's illness; a new product fails in the marketplace; a military commander mistakenly engages a civilian aircraft. Undesirable outcomes, however, do not necessarily imply faulty decision making; consider General Hod's decision to shoot down a Libyan airliner (described at the end of the last chapter). Even though the aircraft turned out not to be on a hostile mission, his conclusion that it was hostile might have been justified by the information he had at the time, by his efforts to gather further relevant data, and by the costs of a terrorist incident. It can also happen, of course, that a bad decision works out well. It is natural, then, for psychologists to look for a way of evaluating the decision itself, or the process that led to the decision, as distinct from its outcomes: to point, for example, at false prior beliefs, inappropriate priorities, shaky inferences from data, or even logical inconsistencies, rather than simply a bad outcome. A widely accepted research paradigm in psychology (e.g., Kahneman, Slovic, and Tversky, 1982) has taken Bayesian decision theory as the standard by which reasoning is to be judged, and has identified pervasive patterns of error, called biases, in laboratory performance. According to these researchers, unaided decision processes employ rules of thumb (or "heuristics") that under many (but not all) conditions lead to "severe and systematic errors" (Tversky and Kahneman, 1974). The bottom line of this research has been a rather pessimistic view of human reasoning. To illustrate, let us extrapolate some of the laboratory results on biases and their interpretation to a hypothetical physician: ! In assessing the probability that she will encounter cases of diseases A, B, and C among her patients, the physician may rely on the ease with which she can recall or imagine instances of each disease. This is the so-called "availability heuristic", postulated by Tversky and Kahneman (1973). Availability may be influenced by factors like the recency or salience of the physician's own experiences, which do not reflect the true relative frequencies of the diseases in the relevant population. In estimating a quantity, such as the required length of treatment for disease B, the doctor may first generate her best guess, then adjust it upwards and downwards to allow for uncertainty, e.g., 10 days plus or minus 2. This is the "anchoring and adjustment" heuristic. According …
Predictive coding-based deep dynamic neural network for visuomotor learning

This study presents a dynamic neural network model based on the predictive coding framework for perceiving and predicting the dynamic visuo-proprioceptive patterns. In our previous study [1], we have shown that the deep dynamic neural network model was able to coordinate visual perception and action generation in a seamless manner. In the current study, we extended the previous model under the predictive coding framework to endow the model with a capability of perceiving and predicting dynamic visuo-proprioceptive patterns as well as a capability of inferring intention behind the perceived visuomotor information through minimizing prediction error. A set of synthetic experiments were conducted in which a robot learned to imitate the gestures of another robot in a simulation environment. The experimental results showed that with given intention states, the model was able to mentally simulate the possible incoming dynamic visuo-proprioceptive patterns in a top-down process without the inputs from the external environment. Moreover, the results highlighted the role of minimizing prediction error in inferring underlying intention of the perceived visuo-proprioceptive patterns, supporting the predictive coding account of the mirror neuron systems. The results also revealed that minimizing prediction error in one modality induced the recall of the corresponding representation of another modality acquired during the consolidative learning of raw-level visuo-proprioceptive patterns.
Initiation, Progression, and Sustained Waterpipe Use: A Nationally Representative Longitudinal Study of U.S. Young Adults

Background: Waterpipe tobacco smoking (WTS) is increasing in popularity despite evidence of harm and potential for dependence. Intervention development has been hampered by a lack of longitudinal, nationally representative data on usage patterns and factors independently associated with WTS initiation. Therefore, we aimed to characterize key transitions between WTS states in a nationally representative group of young adults, with particular attention to factors independently associated with initiation. Methods: Participants were randomly selected from a national probability-based panel representing 97% of the United States. A total of 1,785 adults ages 18 to 30 at baseline completed two Web-based surveys 18 months apart in 2013 and 2014. Assessments included knowledge of waterpipe tobacco smoke composition, positive and negative attitudes toward WTS, normative beliefs, intention to use waterpipe, and WTS behavior. We used multivariable logistic regression to assess the association between predictive factors and subsequent WTS initiation. Results: In fully adjusted models, overall knowledge about toxicants associated with WTS was not associated with subsequent WTS initiation. Similarly, negative attitudes and normative beliefs were not associated with WTS uptake. However, baseline positive attitudes were strongly and significantly associated with WTS initiation [adjusted OR (AOR) = 1.7; 95% confidence interval (CI), 1.2–2.3]. Similarly, baseline intention to use WTS was strongly associated with subsequent initiation (AOR = 7.0; 95% CI, 3.5–13.7). Conclusions: Prevention efforts may be most successful if they target individuals with clear intentions to use WTS and challenge positive attitudes surrounding WTS. Impact: Surveillance of WTS trajectories will help inform health care and policy surrounding this emerging risk behavior among U.S. young adults. Cancer Epidemiol Biomarkers Prev; 26(5); 748–55. ©2017 AACR.
Effects of light-, self-, and tack-curing on degree of conversion and physical strength of dual-cure resin cements.

PURPOSE To evaluate the polymerization degree of conversion (DC) and physical strength of dual-cure cements with tack-curing, and compare them to those with light-curing and self-curing resins. METHODS Four dual-cure resin cements were evaluated by DC and diametral tensile strength (DTS) tests with three different polymerization methods: Light-cure (photo-polymerization 40 seconds, self-curing 30 minutes); Self-cure (self-curing 30 minutes); and Tack-cure (photo-polymerization 3 seconds, self-curing 30 minutes). Polymerization degree of conversion was determined using Fourier transform infrared spectroscopy, and calculated based on the ratio changes of aliphatic-to-aromatic C=C IR absorption peaks before and after polymerized. Specimens for DTS (n = 10) were prepared using circular molds (6.0 mm in diameter and 3.0 mm in height) and tested after 24-hour water storage. Data were analyzed by two-way ANOVA. Multiple post-hoc pairwise comparisons were performed by t-test when significant effects were found across the factors (α = 0.05). Results: The Self-cure groups had slow initial curing rate, resulting in the lower DC than both the Light-cure and Tack-cure groups. After 30 minutes of polymerization, only in the RelyX Ultimate group, light-curing resulted in higher DC than tack-curing, which resulted in higher DC than self-curing (P < 0.05). The self-cure of resin cements resulted in a significantly lower DTS only for RelyX Ultimate cement (P < 0.05). There was no significantly different DTS between the Tack-cure and Light-cure groups for all of the resin cements. For all of the three curing modes, RelyX Ultimate cements had the lowest DTS among the four cements tested in this study.
Inhibition of fms‐like tyrosine kinase 3 alleviates experimental arthritis by reducing formation of dendritic cells and antigen presentation

TKs are intracellular signaling molecules essential for cell homeostasis. Inhibition of TKs is used in treatment of malignancies and diabetes mellitus. The present study evaluated the role of Flt3 in antigen‐induced arthritis. Mice were immunized with mBSA, and arthritis was induced by an i.a. injection of mBSA. Treatment with the Flt3 inhibitor sunitinib was started together with mBSA immunization or together with the induction of arthritis. The mBSA‐injected joints were evaluated morphologically for signs of synovitis and bone/cartilage destruction. Markers of bone metabolism and antibody responses were measured by ELISA. Maturation of DCs in the bone marrow and spleen was evaluated by flow cytometry. Sunitinib treatment reduced the intensity of synovitis and the incidence of bone destruction. The reduction in bone destruction was seen when the treatment was started at the time of immunization or at the time of arthritis induction. The antiarthritic effect was achieved by inhibition of DCs, reduction of antibody production, and bone metabolism. Inhibition of Flt3 is a potent antiarthritic mechanism reducing antigen presentation, synovial inflammation, and bone resorption. Down‐regulation of TKs may be a useful tool in the treatment of human RA.