Miracle-dz/UniFAR-FTUs huggingface dataset:
Thermal shock susceptibility and regrowth of Pseudomonas aeruginosa biofilms

Abstract Biofilms on implanted medical devices cause thousands of patients each year to undergo multiple surgeries to remove and replace the implant, driving billions of dollars in increased health care costs due to the lack of viable treatment options for in situ biofilm eradication. Remotely activated localised heating is under investigation to mitigate these biofilms; however, little is known about the temperatures required to kill the biofilms. To better understand the required parameters this study investigated the thermal susceptibility of biofilms as a function of their fluidic and chemical environment during growth, as well as their propensity for regrowth following thermal shock. Pseudomonas aeruginosa biofilms were cultured in shaker plate fluidic conditions in four different growth media, then thermally shocked at various temperatures and exposure times. Biofilms were re-incubated to determine their regrowth potential following thermal shocks of various intensities. Results indicate that growth media has little impact on thermal susceptibility, while fluidic conditions strongly influence susceptibility to modest thermal shocks. This effect disappears, however, with increasingly aggressive shocks, reducing biofilm populations by up to 5 orders of magnitude. Regrowth studies indicate a critical post-shock bacterial loading (∼103 CFU/cm2) below which the biofilms were no longer viable, while biofilms above that loading slowly regrew to their previous population density.
Head-Impact-Measurement Devices: A Systematic Review.

CONTEXT With an estimated 3.8 million sport- and recreation-related concussions occurring annually, targeted prevention and diagnostic methods are needed. Biomechanical analysis of head impacts may provide quantitative information that can inform both prevention and diagnostic strategies. OBJECTIVE To assess available head-impact devices and their clinical utility. DATA SOURCES We performed a systematic search of the electronic database PubMed for peer-reviewed publications, using the following phrases: accelerometer and concussion, head impact telemetry, head impacts and concussion and sensor, head impacts and sensor, impact sensor and concussion, linear acceleration and concussion, rotational acceleration and concussion, and xpatch concussion. In addition to the literature review, a Google search for head impact monitor and concussion monitor yielded 15 more devices. STUDY SELECTION Included studies were performed in vivo, used commercially available devices, and focused on sport-related concussion. DATA EXTRACTION One author reviewed the title and abstract of each study for inclusion and exclusion criteria and then reviewed each full-text article to confirm inclusion criteria. Controversial articles were reviewed by all authors to reach consensus. DATA SYNTHESIS In total, 61 peer-reviewed articles involving 4 head-impact devices were included. Participants in boxing, football, ice hockey, soccer, or snow sports ranged in age from 6 to 24 years; 18% (n = 11) of the studies included female athletes. The Head Impact Telemetry System was the most widely used device (n = 53). Fourteen additional commercially available devices were presented. CONCLUSIONS Measurements collected by impact monitors provided real-time data to estimate player exposure but did not have the requisite sensitivity to concussion. Proper interpretation of previously reported head-impact kinematics across age, sport, and position may inform future research and enable staff clinicians working on the sidelines to monitor athletes. However, head-impact-monitoring systems have limited clinical utility due to error rates, designs, and low specificity in predicting concussive injury.
Convergence Along Mean Flows

We develop a technique of multiple scale asymptotic expansions along mean flows and a corresponding notion of weak multiple scale convergence. These are applied to homogenize convection dominated parabolic equations with rapidly oscillating, locally periodic coefficients and $\mathcal{O}(\eps^{-1})$ mean convection term. Crucial to our analysis is the introduction of a fast time variable, $\tau=\frac{t}{\eps}$, not apparent in the heterogeneous problem. The effective diffusion coefficient is expressed in terms of the average of Eulerian cell solutions along the orbits of the mean flow in the fast time variable. To make this notion rigorous, we use the theory of ergodic algebras with mean value.
Variations in muscle chemical composition, pH, and protein extractability among eight different broiler crosses.

Variations in muscle chemical composition, pH, and protein extractability were studied using male broilers of eight different genetic crosses of commercial strains. Three replicate groups of 24 birds of each cross were grown in floor pens using commercial corn-soybean meal diets. At 8 wk of age, three birds per replicate, weighing within 5% of the pen average, were slaughtered, scalded, defeathered, eviscerated, and chilled in ice slurries overnight. Muscles were excised from breasts and thighs, and trimmed of skin and external fat. Proximate analysis was conducted using ground muscle pooled within replicate groups. Breast muscle of all strain crosses contained more (P < or = .05) total protein (ranging from 20.7 to 23.6%) and moisture (74.6 to 75.9%), and less fat (1.0 to 2.0%) than thigh muscle, which contained 18.1 to 21.3% protein, 72.8 to 73.8% moisture, and 5.0 to 7.2% fat. The pH of breast muscle was lower (P < or = .05) than that of thigh muscle for four of the eight strains, and protein extractability of breast muscle was greater (P < or = .05) than that of thigh muscle for all strains. There were significant differences among strains in chemical composition, pH, and protein extractability for both breast and thigh muscles. The correlation between percentage protein and fat was positive in breast (r = .72, P < .05) and negative in thigh muscle (r = -.77, P < .05). However, no significant correlations were observed between the chemical constituents of breast muscle with the respective constituents of thigh muscle. (ABSTRACT TRUNCATED AT 250 WORDS)
Buprenorphine requires concomitant activation of NOP and MOP receptors to reduce cocaine consumption

Buprenorphine's clinical use is approved for the treatment of heroin addiction; however, evidence supporting its efficacy in cocaine abuse also exists. While for heroin it has been demonstrated that the effect of buprenorphine is mediated by its ability to activate μ‐opioid peptide receptor (MOP) receptors, the mechanism through which it attenuates cocaine intake remains elusive. We explored this mechanism using operant models where rodents were trained to chronically self‐administer cocaine for 2 hours daily. Buprenorphine (0.3, 1.0 and 3.0 mg/kg) given intraperitoneally 90 minutes before access to cocaine significantly and dose dependently reduced its intake. Pre‐treatment with naltrexone or with the selective nociceptin/orphanin FQ peptide (NOP) antagonist SB‐612111 did not prevent buprenorphine‐induced reduction of cocaine intake. However, when naltrexone and SB‐612111 were combined, the effect of buprenorphine on cocaine was completely prevented. To confirm that co‐activation of MOP and NOP receptors is the underlying mechanism through which buprenorphine reduces cocaine intake, three compounds, namely, AT‐034, AT‐201 and AT‐202, with a range of affinity and intrinsic activity profiles for MOP and NOP receptors, but weak ability for kappa‐opioid peptide receptor (KOP) transmission, were tested. Consistent with our hypothesis based on buprenorphine's effects, results demonstrated that AT‐034 and AT‐201, which co‐activate MOP and NOP receptors, reduced cocaine self‐administration like buprenorphine. AT‐202, which selectively stimulates NOP receptors, was not effective. Together, these data demonstrate that for buprenorphine, co‐activation of MOP and NOP receptors is essential to reduce cocaine consumption. These results open new vistas on the treatment of cocaine addiction by developing compounds with mixed MOP/NOP agonist properties.
Carbonic anhydrase‐related protein VIII is expressed in rod bipolar cells and alters signaling at the rod bipolar to AII‐amacrine cell synapse in the mammalian retina

Mutation of the gene encoding carbonic anhydrase‐related protein VIII (CAVIII) results in motor coordination deficits in mice and humans, due to loss of this protein in Purkinje cells of the cerebellum. Recent studies have indicated that the CAVIII gene, Car8, is also expressed in rod bipolar cells (RBCs), a critical glutamatergic neuron for scotopic vision. We investigated the localization of CAVIII in the mouse and macaque retina, and utilized the wdl mouse, which has a null mutation in the Car8 gene, to determine how the loss of CAVIII affects retinal signaling. CAVIII immunoreactivity was observed in RBCs, with particularly high staining intensity in the axon terminals. In addition, weaker staining was observed in a subset of cone bipolar cells and γ‐aminobutyric acid (GABA)ergic amacrine cells. Light‐evoked current and voltage responses of RBCs were not altered in the wdl mutant. However, light‐evoked current responses from the AII‐amacrine cell, a postsynaptic partner at the RBC ribbon synapse, were significantly larger, and more prolonged than in control mice. These changes could not be attributed to alterations in calcium current activation or inactivation, or to changes in the density of RBCs. Furthermore, no gross synaptic alterations were evident in the wdl mutant at the light or ultrastructural level. These data provide evidence that the CAVIII protein, which is highly conserved in vertebrates, is selectively expressed within neural circuits, and may be important for modulating retinal neurotransmission.
Strength reduction in slash pine (Pinus elliotii) wood caused by decay fungi

Small wood specimens selected from slash pine (Pinus elliotii )trees at three growth rates (fast, medium, and slow) were inoculated with brown-rot and white-rot fungi and then evaluated for work to maximum load (WML), modulus of rupture (MOR), and modulus of elasticity (MOE). The experimental variables studied included a brown-rot fungus (Gloeophyllum trabeum) and a white-rot fungus (Trametes versicolor) and six exposure periods (2, 4, 6, 8, 10, and 12 weeks) in which weight loss measurements were recorded. All samples were tested for nondestructive MOE (MOEsw) prior to static bending and the results were compared via regression analyses. There were significant differences in weight loss, WML, MOR, and MOE reductions due to tree growth rate and decay periods. The weight loss, WML, MOR, and MOE losses of all three growth rate classes treated with brown-rot fungi were greater than those exposed to white-rot fungi with the exception of very early decay (i.e., 2 weeks after inoculation). The mechanical property reduction was greater for fast grown wood than that of slow grown wood. As expected, strength decreased as exposure time to the fungi increased. The specimens exposed to brown-rot decay showed most of the strength reduction in the initial 6 weeks and after 10 weeks. The samples inoculated with the white-rot fungi showed a continual slight strength reduction for the entire 12 weeks. The results showed that the ratio of the loss in mechanical properties compared to weight loss were 7.2: 1 for WML, 6.4: 1 for MOR, and 3.8: 1 for MOE, for slash pine sapwood exposed to G. trabeum, and that of wood specimens exposed to T. versicolor were 3.0: 1 for WML, 2.2: 1 for MOR, and 4.1: 1 for MOE. Regression analysis indicated good correlations between MOEsw and static bending MOE after the 12 week exposure period.
Silicon Carbide Whiskers Interference on Silicon Nitride Based Composite

Silicon nitride based composite has been prepared, using a direct mixture process as alternative route. Silicon carbide whiskers were mixed directly to silicon nitride based powders containing yttrium and neodymium oxide as sintering aids. Uniaxial hot pressing was used to prepare sintered samples. Crystalline phases were identified using x-ray diffractometry. Intergranular phases were analyzed using Scanning Electron Microscopy. Some mechanical properties (microhardness and fracture toughness) were also evaluated. The obtained high values of fracture toughness were correlated to the activation of toughening mechanisms, such as crack bridging and crack deflection.
Counting Homomorphisms to Trees Modulo a Prime

Many important graph-theoretic notions can be encoded as counting graph homomorphism problems, such as partition functions in statistical physics, in particular independent sets and colourings. In this article, we study the complexity of #pHOMSTOH, the problem of counting graph homomorphisms from an input graph to a graph H modulo a prime number p. Dyer and Greenhill proved a dichotomy stating that the tractability of non-modular counting graph homomorphisms depends on the structure of the target graph. Many intractable cases in non-modular counting become tractable in modular counting due to the common phenomenon of cancellation. In subsequent studies on counting modulo 2, however, the influence of the structure of H on the tractability was shown to persist, which yields similar dichotomies. Our main result states that for every tree H and every prime p the problem #pHOMSTOH is either polynomial time computable or #pP-complete. This relates to the conjecture of Faben and Jerrum stating that this dichotomy holds for every graph H when counting modulo 2. In contrast to previous results on modular counting, the tractable cases of #pHOMSTOH are essentially the same for all values of the modulo when H is a tree. To prove this result, we study the structural properties of a homomorphism. As an important interim result, our study yields a dichotomy for the problem of counting weighted independent sets in a bipartite graph modulo some prime p. These results are the first suggesting that such dichotomies hold not only for the modulo 2 case but also for the modular counting functions of all primes p.
Neuromuscular control of wingbeat kinematics in Anna's hummingbirds (Calypte anna)

SUMMARY Hummingbirds can maintain the highest wingbeat frequencies of any flying vertebrate – a feat accomplished by the large pectoral muscles that power the wing strokes. An unusual feature of these muscles is that they are activated by one or a few spikes per cycle as revealed by electromyogram recordings (EMGs). The relatively simple nature of this activation pattern provides an opportunity to understand how motor units are recruited to modulate limb kinematics. Hummingbirds made to fly in low-density air responded by moderately increasing wingbeat frequency and substantially increasing the wing stroke amplitude as compared with flight in normal air. There was little change in the number of spikes per EMG burst in the pectoralis major muscle between flight in normal and low-density heliox (mean=1.4 spikes cycle−1). However the spike amplitude, which we take to be an indication of the number of active motor units, increased in concert with the wing stroke amplitude, 1.7 times the value in air. We also challenged the hummingbirds using transient load lifting to elicit maximum burst performance. During maximum load lifting, both wing stroke amplitude and wingbeat frequency increased substantially above those values during hovering flight. The number of spikes per EMG burst increased to a mean of 3.3 per cycle, and the maximum spike amplitude increased to approximately 1.6 times those values during flight in heliox. These results suggest that hummingbirds recruit additional motor units (spatial recruitment) to regulate wing stroke amplitude but that temporal recruitment is also required to maintain maximum stroke amplitude at the highest wingbeat frequencies.
Development and Validation of a Deep Learning System for Diabetic Retinopathy and Related Eye Diseases Using Retinal Images From Multiethnic Populations With Diabetes

Importance A deep learning system (DLS) is a machine learning technology with potential for screening diabetic retinopathy and related eye diseases. Objective To evaluate the performance of a DLS in detecting referable diabetic retinopathy, vision-threatening diabetic retinopathy, possible glaucoma, and age-related macular degeneration (AMD) in community and clinic-based multiethnic populations with diabetes. Design, Setting, and Participants Diagnostic performance of a DLS for diabetic retinopathy and related eye diseases was evaluated using 494 661 retinal images. A DLS was trained for detecting diabetic retinopathy (using 76 370 images), possible glaucoma (125 189 images), and AMD (72 610 images), and performance of DLS was evaluated for detecting diabetic retinopathy (using 112 648 images), possible glaucoma (71 896 images), and AMD (35 948 images). Training of the DLS was completed in May 2016, and validation of the DLS was completed in May 2017 for detection of referable diabetic retinopathy (moderate nonproliferative diabetic retinopathy or worse) and vision-threatening diabetic retinopathy (severe nonproliferative diabetic retinopathy or worse) using a primary validation data set in the Singapore National Diabetic Retinopathy Screening Program and 10 multiethnic cohorts with diabetes. Exposures Use of a deep learning system. Main Outcomes and Measures Area under the receiver operating characteristic curve (AUC) and sensitivity and specificity of the DLS with professional graders (retinal specialists, general ophthalmologists, trained graders, or optometrists) as the reference standard. Results In the primary validation dataset (n = 14 880 patients; 71 896 images; mean [SD] age, 60.2 [2.2] years; 54.6% men), the prevalence of referable diabetic retinopathy was 3.0%; vision-threatening diabetic retinopathy, 0.6%; possible glaucoma, 0.1%; and AMD, 2.5%. The AUC of the DLS for referable diabetic retinopathy was 0.936 (95% CI, 0.925-0.943), sensitivity was 90.5% (95% CI, 87.3%-93.0%), and specificity was 91.6% (95% CI, 91.0%-92.2%). For vision-threatening diabetic retinopathy, AUC was 0.958 (95% CI, 0.956-0.961), sensitivity was 100% (95% CI, 94.1%-100.0%), and specificity was 91.1% (95% CI, 90.7%-91.4%). For possible glaucoma, AUC was 0.942 (95% CI, 0.929-0.954), sensitivity was 96.4% (95% CI, 81.7%-99.9%), and specificity was 87.2% (95% CI, 86.8%-87.5%). For AMD, AUC was 0.931 (95% CI, 0.928-0.935), sensitivity was 93.2% (95% CI, 91.1%-99.8%), and specificity was 88.7% (95% CI, 88.3%-89.0%). For referable diabetic retinopathy in the 10 additional datasets, AUC range was 0.889 to 0.983 (n = 40 752 images). Conclusions and Relevance In this evaluation of retinal images from multiethnic cohorts of patients with diabetes, the DLS had high sensitivity and specificity for identifying diabetic retinopathy and related eye diseases. Further research is necessary to evaluate the applicability of the DLS in health care settings and the utility of the DLS to improve vision outcomes.
Long-Range Interactions Within a Nonnative Protein

Protein folding and unfolding are coupled to a range of biological phenomena, from the regulation of cellular activity to the onset of neurodegenerative diseases. Defining the nature of the conformations sampled in nonnative proteins is crucial for understanding the origins of such phenomena. We have used a combination of nuclear magnetic resonance (NMR) spectroscopy and site-directed mutagenesis to study unfolded states of the protein lysozyme. Extensive clusters of hydrophobic structure exist within the wild-type protein even under strongly denaturing conditions. These clusters involve distinct regions of the sequence but are all disrupted by a single point mutation that replaced residue Trp62 with Gly located at the interface of the two major structural domains in the native state. Thus, nativelike structure in the denatured protein is stabilized by the involvement of Trp62 in nonnative and long-range interactions.
Effective Design of Multifunctional Peptides by Combining Compatible Functions

Multifunctionality is a common trait of many natural proteins and peptides, yet the rules to generate such multifunctionality remain unclear. We propose that the rules defining some protein/peptide functions are compatible. To explore this hypothesis, we trained a computational method to predict cell-penetrating peptides at the sequence level and learned that antimicrobial peptides and DNA-binding proteins are compatible with the rules of our predictor. Based on this finding, we expected that designing peptides for CPP activity may render AMP and DNA-binding activities. To test this prediction, we designed peptides that embedded two independent functional domains (nuclear localization and yeast pheromone activity), linked by optimizing their composition to fit the rules characterizing cell-penetrating peptides. These peptides presented effective cell penetration, DNA-binding, pheromone and antimicrobial activities, thus confirming the effectiveness of our computational approach to design multifunctional peptides with potential therapeutic uses. Our computational implementation is available at http://bis.ifc. unam.mx/en/software/dcf.
Decline in Search Speed and Verbal Memory Over 26 Years of Midlife in a British Birth Cohort

Background: Cognitive capabilities change in later life, although their onset and rate of decline, and how they are shaped by lifetime socioeconomic position, childhood cognition and adult health status are all unclear. Methods: From the Medical Research Council National Survey of Health and Development, we analysed 3,192 participants undergoing one or more cognitive assessments at ages 43, 53, 60–64 and 69. Linear mixed models described cognitive trajectories, adjusting for factors across the life course. Results: For both search speed and verbal memory, better performance at age 43 (the intercept) was associated with higher paternal and own education, childhood cognition, and adult occupational class. For search speed, the trajectory was best described as a quadratic function (decline of 45.6 letters/5-years + 4.6 letters). Verbal memory showed a linear decline of 0.20 words/5-years between ages 43 and 60 and a steeper linear decline of 0.95 words/5-years between ages 60 and 69. Decline in verbal memory in the latter period was steeper in those with higher educational achievements at age 26 (additional 0.28 words/5-years for highest attainment). Conclusions: Decline in verbal memory and search speed across midlife is evident, though with different non-linear trajectories. By implication, pathways to cognitive impairment and dementia in older age may have their origins in this period.