Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative analysis of structure and strength of vitelline membrane and physical parameters of yolk of ostrich, emu, and greater rhea eggs

Abstract In this study, we analyzed selected morphological traits of eggs, as well as structure, strength, and protein composition of the vitelline membrane (VM) of ostrich, emu, and greater rhea eggs. Ninety eggs (30 for species) were analyzed for the following parameters: egg weight, yolk weight, yolk ratio, and yolk index. In addition, pH value, water activity, consistency index, and flow behavior index were determined. The strength of VM was measured using the TA.HDPlus Texture Analyzer. Micrograph images were taken via a scanning electron microscope. Polyacrylamide gel electrophoresis was conducted under denaturing conditions. Ostrich eggs were characterized by the highest egg and yolk weight compared with those of emu and greater rhea eggs, whereas emu eggs had the highest yolk ratio compared with those of ostrich and greater rhea eggs (P > 0.05). Yolk content differed among the species in terms of water activity; it was found to be higher in emu eggs than in ostrich and greater rhea eggs (P > 0.05). Based on flow curves, yolks of the ratites were classified as pseudoplastic non‐Newtonian fluids. The consistency index was significantly higher in yolks of ostrich and emu than that of greater rhea eggs, whereas the VM of yolks of greater rhea eggs was the most resistant (had the highest breaking force = 26.4 g). All species differed significantly regarding the structure of VM, the outer layer (OL) in particular, which was found to constitute fibers of various thicknesses that were differently arranged. Fibers of the OL of the VM of emu, whose fibers were the least differentiated but formed the most compact network, were the most diverse in characterization. An electropherogram of the VM of ostrich revealed 11 primary protein bands: 6 for the OL and 5 for the inner layer (IL), that of emu revealed 9 bands: 5 for the OL and 4 for the IL, and that of greater rhea revealed 10 bands: 6 for the OL and 4 for the IL.
Nanoelectromechanical systems from carbon nanotubes and graphene

Carbon nanotubes and graphene have many interesting properties. To exploit the properties in applications their synthesis and incorporation in devices has to be understood and controlled. This thesis is based on experimental studies on synthesis of carbon nanotubes and fabrication of nanoelectromechanical systems from carbon nanotubes and graphene. Vertically aligned nanotube arrays with heights over 800 µm have been grown using acetylene with iron as catalyst on alumina support using thermal chemical vapor deposition. By varying the partial pressure of acetylene it was found that the addition-rate of carbon was proportional to the coverage of acetylene molecules on the catalyst nanoparticle. In certain conditions the macroscopic pattern of the catalyst areas influenced the microscopic properties of the carbon nanotubes. It was shown that the initial carbon-precursor flow conditions could determine the number of walls produced. The amount of carbon incorporated into nanotubes was constant but regions that experienced less carbon precursor gas flow due e.g. to depletion, produced longer but fewer-walled nanotubes. Arrays of vertically aligned nanotubes were shown to deflect as a single unit under electrostatic actuation, making possible the fabrication of varactors. Measurements of deflection were used to determine an eff ective Young's modulus of 6(+- 4) MPa. The capacitance of such a device could be reproducibly changed by more than 20 %. Devices based on the nanoelectromechanical properties of few-layer graphene were fabricated and characterized. Electrostatic actuation of buckled beams and membranes led to a "snap-through" switching at a critical applied voltage. By characterizing this behavior for diff erent sizes and geometries of membranes, it was possible to extract the bending rigidity of bilayered graphene, yielding a value of 35(+20,-15) eV. CNTFETs with suspended graphene gates were fabricated. It was shown that a moveable graphene gate could control the conductance of the carbon nanotube and improve the switching characteristics. Inverse sub-threshold slope down to 53 mV per decade were measured at 100 K. The experimental data were compared with theoretical simulations and it was inferred that the subthreshold slope could be improved beyond the thermal limit by improving the design of the device.
Integrated Networking, Caching, and Computing for Connected Vehicles: A Deep Reinforcement Learning Approach

The developments of connected vehicles are heavily influenced by information and communications technologies, which have fueled a plethora of innovations in various areas, including networking, caching, and computing. Nevertheless, these important enabling technologies have traditionally been studied separately in the existing works on vehicular networks. In this paper, we propose an integrated framework that can enable dynamic orchestration of networking, caching, and computing resources to improve the performance of next generation vehicular networks. We formulate the resource allocation strategy in this framework as a joint optimization problem, where the gains of not only networking but also caching and computing are taken into consideration in the proposed framework. The complexity of the system is very high when we jointly consider these three technologies. Therefore, we propose a novel deep reinforcement learning approach in this paper. Simulation results with different system parameters are presented to show the effectiveness of the proposed scheme.
Patterns of range‐wide genetic variation in six North American bumble bee (Apidae: Bombus) species

The increasing evidence for population declines in bumble bee (Bombus) species worldwide has accelerated research efforts to explain losses in these important pollinators. In North America, a number of once widespread Bombus species have suffered serious reductions in range and abundance, although other species remain healthy. To examine whether declining and stable species exhibit different levels of genetic diversity or population fragmentation, we used microsatellite markers to genotype populations sampled across the geographic distributions of two declining (Bombus occidentalis and Bombus pensylvanicus) and four stable (Bombus bifarius; Bombus vosnesenskii; Bombus impatiens and Bombus bimaculatus) Bombus species. Populations of declining species generally have reduced levels of genetic diversity throughout their range compared to codistributed stable species. Genetic diversity can be affected by overall range size and degree of isolation of local populations, potentially confounding comparisons among species in some cases. We find no evidence for consistent differences in gene flow among stable and declining species, with all species exhibiting weak genetic differentiation over large distances (e.g. >1000 km). Populations on islands and at high elevations experience relatively strong genetic drift, suggesting that some conditions lead to genetic isolation in otherwise weakly differentiated species. B. occidentalis and B. bifarius exhibit stronger genetic differentiation than the other species, indicating greater phylogeographic structure consistent with their broader geographic distributions across topographically complex regions of western North America. Screening genetic diversity in North American Bombus should prove useful for identifying species that warrant monitoring, and developing management strategies that promote high levels of gene flow will be a key component in efforts to maintain healthy populations.
Multi-Drug-Resistant Gram-Negative Infections in Deployment-Related Trauma Patients.

BACKGROUND The contribution of multi-drug-resistant gram-negative bacilli infections (MDRGN-I) in patients with trauma is not well described. We present characteristics of MDRGN-Is among military personnel with deployment-related trauma (2009-2014). PATIENTS AND METHODS Data from the Trauma Infectious Disease Outcomes Study were assessed for infectious outcomes and microbial recovery. Infections were classified using standardized definitions. Gram-negative bacilli were defined as multi-drug-resistant if they showed resistance to ≥3 antibiotic classes or were producers of extended-spectrum β-lactamase or carbapenemases. RESULTS Among 2,699 patients admitted to participating U.S. hospitals, 913 (33.8%) experienced ≥1 infection event, of which 245 (26.8%) had a MDRGN-I. There were 543 MDRGN-I events (24.6% of unique 2,210 infections) with Escherichia coli (48.3%), Acinetobacter spp. (38.6%), and Klebsiella pneumoniae (8.4%) as the most common MDRGN isolates. Incidence of MDRGN-I was 9.1% (95% confidence interval [CI]: 8.0-10.2). Median time to MDRGN-I event was seven days with 75% occurring within 13 days post-trauma. Patients with MDRGN-Is had a greater proportion of blast injuries (84.1% vs. 62.5%; p < 0.0001), traumatic amputations (57.5% vs. 16.3%; p < 0.0001), and higher injury severity (82.0% had injury severity score ≥25 vs. 33.7%; p < 0.0001) compared with patients with either no infections or non-MDRGN-Is. Furthermore, MDRGN-I patients were more frequently admitted to the intensive care unit (90.5% vs. 48.5%; p < 0.0001), colonized with a MDRGN before infection (58.0% vs. 14.7%; p < 0.0001), and required mechanical ventilation (78.0% vs. 28.8% p < 0.0001). Antibiotic exposure before the MDRGN-I event was significantly higher across antibiotic classes except first generation cephalosporins and tetracyclines, which were very commonly used with all patients. Regarding outcomes, patients with MDRGN-Is had a longer length of hospitalization than the comparator group (53 vs. 18 days; p < 0.0001). CONCLUSIONS We found a high rate of MDRGN-I in our population characterized by longer hospitalization and greater injury severity. These findings inform treatment and infection control decisions in the trauma patient population.
Adaptive Randomization of Veliparib-Carboplatin Treatment in Breast Cancer.

BACKGROUND The genetic and clinical heterogeneity of breast cancer makes the identification of effective therapies challenging. We designed I-SPY 2, a phase 2, multicenter, adaptively randomized trial to screen multiple experimental regimens in combination with standard neoadjuvant chemotherapy for breast cancer. The goal is to match experimental regimens with responding cancer subtypes. We report results for veliparib, a poly(ADP-ribose) polymerase (PARP) inhibitor, combined with carboplatin. METHODS In this ongoing trial, women are eligible for participation if they have stage II or III breast cancer with a tumor 2.5 cm or larger in diameter; cancers are categorized into eight biomarker subtypes on the basis of status with regard to human epidermal growth factor receptor 2 (HER2), hormone receptors, and a 70-gene assay. Patients undergo adaptive randomization within each biomarker subtype to receive regimens that have better performance than the standard therapy. Regimens are evaluated within 10 biomarker signatures (i.e., prospectively defined combinations of biomarker subtypes). Veliparib-carboplatin plus standard therapy was considered for HER2-negative tumors and was therefore evaluated in 3 signatures. The primary end point is pathological complete response. Tumor volume changes measured by magnetic resonance imaging during treatment are used to predict whether a patient will have a pathological complete response. Regimens move on from phase 2 if and when they have a high Bayesian predictive probability of success in a subsequent phase 3 neoadjuvant trial within the biomarker signature in which they performed well. RESULTS With regard to triple-negative breast cancer, veliparib-carboplatin had an 88% predicted probability of success in a phase 3 trial. A total of 72 patients were randomly assigned to receive veliparib-carboplatin, and 44 patients were concurrently assigned to receive control therapy; at the completion of chemotherapy, the estimated rates of pathological complete response in the triple-negative population were 51% (95% Bayesian probability interval [PI], 36 to 66%) in the veliparib-carboplatin group versus 26% (95% PI, 9 to 43%) in the control group. The toxicity of veliparib-carboplatin was greater than that of the control. CONCLUSIONS The process used in our trial showed that veliparib-carboplatin added to standard therapy resulted in higher rates of pathological complete response than standard therapy alone specifically in triple-negative breast cancer. (Funded by the QuantumLeap Healthcare Collaborative and others; I-SPY 2 TRIAL ClinicalTrials.gov number, NCT01042379.).
Looking at genetic structure and selection signatures of the Mexican chicken population using single nucleotide polymorphism markers

Abstract Genetic variation enables both adaptive evolutionary changes and artificial selection. Genetic makeup of populations is the result of a long‐term process of selection and adaptation to specific environments and ecosystems. The aim of this study was to characterize the genetic variability of México's chicken population to reveal any underlying population structure. A total of 213 chickens were sampled in different rural production units located in 25 states of México. Genotypes were obtained using the Affymetrix Axiom® 600 K Chicken Genotyping Array. The Identity by Descent (IBD) and the principal components analysis (PCA) were performed by SVS software on pruned single nucleotide polymorphisms (SNPs). ADMIXTURE analyses identified 3 ancestors and the proportion of the genetic contribution of each of them has been determined in each individual. The results of the Neighbor‐Joining (NJ) analysis resulted consistent with those obtained by the PCA. All methods utilized in this study did not allow a classification of Mexican chicken in distinct clusters or groups. A total of 3,059 run of homozygosity (ROH) were identified and, being mainly short in length (<4 Mb), these regions are indicative of a low inbreeding level in the population. Finally, findings from the ROH analysis indicated the presence of natural selective pressure in the population of Mexican chicken. The study indicates that the Mexican chicken clearly appear to be a unique creole chicken population that was not subjected to a specific artificial selection. Results provide a genetic knowledge that can be used as a basis for the genetic management of a unique and very large creole population, especially in the view of using it in production of hybrids to increase the productivity and economic revenue of family farming agriculture, which is widely present in México.
Efficacy of splint therapy for the management of temporomandibular disorders: a meta-analysis

Temporomandibular disorders (TMD) are a group of clinical problems affecting temporomandibular joint (TMJ), myofascial muscles and other related structures. Splint therapy is the most commonly used approach to treatment of TMD, but its effectiveness is remains unclear. We therefore conducted a meta-analysis to evaluate the effectiveness of splint therapy for TMD in adults. The electronic databases PubMed, EMBASE, Cochrane Library, and ClinicalTrials.gov were searched for reports published up to March 31, 2016. Thirteen eligible studies involving 538 patients were identified. The results indicated that splint therapy increased maximal mouth opening (MMO) for patients with a MMO <45mm and reduced pain intensity measured using the visual analogue scale (VAS) for patients with TMD without specific description (TMDSD). Splint therapy also reduced the frequency of painful episodes for patients with TMJ clicking. No publication bias was observed, as determined with Egger's test for all outcomes. On the basis of this evidence, we recommend the use of splints for the treatment and control of TMD in adults.
Capecitabine in locally advanced anal cancer, do we need randomised evidence?

ABSTRACT Introduction: Standard treatment for locally advanced anal cancer is chemoradiotherapy with mitomycin C and fluorouracil. However, infusional fluorouracil requires central venous catheter placement potentiating risk of infection and thrombosis. Capecitabine which is an oral tumor activated fluoropyrimidine carbamate is an established treatment alternative to infusional fluorouracil for patients with gastrointestinal cancers. Areas covered: This review examines and discusses the current evidence for substitution of Capecitabine for infusional fluorouracil in locally advanced anal cancer. Two phase II studies, one phase I study and three retrospective reviews were identified. The rate of complete response and locoregional control with the use of Capecitabine in all of these studies ranged from 77% to 89.1% and 79% to 94% respectively, and these results are comparable with prior pivotal studies. The main toxicity with radiation and Capecitabine is radiation dermatitis occurring in 23% to 63% of patients. Despite high rates of radiation dermatitis, treatment completion rates were high, suggesting that it is a well tolerated protocol. Expert commentary: Capecitabine has been used widely in other gastrointestinal cancers, including rectal cancer in chemo-radiotherapy protocols, with proven efficacy and safety and could be a reasonable treatment alternative to fluorouracil in locally advanced anal cancer.
Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills

A long-standing goal in artificial intelligence is creating agents that can learn a variety of different skills for different problems. In the artificial intelligence subfield of neural networks, a barrier to that goal is that when agents learn a new skill they typically do so by losing previously acquired skills, a problem called catastrophic forgetting. That occurs because, to learn the new task, neural learning algorithms change connections that encode previously acquired skills. How networks are organized critically affects their learning dynamics. In this paper, we test whether catastrophic forgetting can be reduced by evolving modular neural networks. Modularity intuitively should reduce learning interference between tasks by separating functionality into physically distinct modules in which learning can be selectively turned on or off. Modularity can further improve learning by having a reinforcement learning module separate from sensory processing modules, allowing learning to happen only in response to a positive or negative reward. In this paper, learning takes place via neuromodulation, which allows agents to selectively change the rate of learning for each neural connection based on environmental stimuli (e.g. to alter learning in specific locations based on the task at hand). To produce modularity, we evolve neural networks with a cost for neural connections. We show that this connection cost technique causes modularity, confirming a previous result, and that such sparsely connected, modular networks have higher overall performance because they learn new skills faster while retaining old skills more and because they have a separate reinforcement learning module. Our results suggest (1) that encouraging modularity in neural networks may help us overcome the long-standing barrier of networks that cannot learn new skills without forgetting old ones, and (2) that one benefit of the modularity ubiquitous in the brains of natural animals might be to alleviate the problem of catastrophic forgetting.
Characterization of an Abiraterone Ultraresponsive Phenotype in Castration-Resistant Prostate Cancer Patient-Derived Xenografts

Purpose: To identify the molecular signature associated with abiraterone acetate (AA) response and mechanisms underlying AA resistance in castration-resistant prostate cancer patient-derived xenografts (PDXs). Experimental Design: SCID mice bearing LuCaP 136CR, 77CR, 96CR, and 35CR PDXs were treated with AA. Tumor volume and prostate-specific antigen were monitored, and tumors were harvested 7 days after treatment or at end of study for gene expression and immunohistochemical studies. Results: Three phenotypic groups were observed based on AA response. An ultraresponsive phenotype was identified in LuCaP 136CR with significant inhibition of tumor progression and increased survival, intermediate responders LuCaP 77CR and LuCaP 96CR with a modest tumor inhibition and survival benefit, and LuCaP 35CR with minimal tumor inhibition and no survival benefit upon AA treatment. We identified a molecular signature of secreted proteins associated with the AA ultraresponsive phenotype. Upon resistance, AA ultraresponder LuCaP 136CR displayed reduced androgen receptor (AR) signaling and sustainably low nuclear glucocorticoid receptor (nGR) localization, accompanied by steroid metabolism alteration and epithelial–mesenchymal transition phenotype enrichment with increased expression of NF-κB–regulated genes; intermediate and minimal responders maintained sustained AR signaling and increased tumoral nGR localization. Conclusions: We identified a molecular signature of secreted proteins associated with AA ultraresponsiveness and sustained AR/GR signaling upon AA resistance in intermediate or minimal responders. These data will inform development of noninvasive biomarkers predicting AA response and suggest that further inhibition along the AR/GR signaling axis may be effective only in AA-resistant patients who are intermediate or minimal responders. These findings require verification in prospective clinical trials. Clin Cancer Res; 23(9); 2301–12. ©2016 AACR.
Comparison of Model-Based Indices of Cerebral Autoregulation and Vasomotor Reactivity Using Transcranial Doppler versus Near-Infrared Spectroscopy in Patients with Amnestic Mild Cognitive Impairment

We recently introduced model-based “physiomarkers” of dynamic cerebral autoregulation and CO2 vasomotor reactivity as an aid for diagnosis of early-stage Alzheimer’s disease (AD) [1], where significant impairment of dynamic vasomotor reactivity (DVR) was observed in early-stage AD patients relative to age-matched controls. Milder impairment of DVR was shown in patients with amnestic mild cognitive impairment (MCI) using the same approach in a subsequent study [2]. The advocated approach utilizes subject-specific data-based models of cerebral hemodynamics to quantify the dynamic effects of resting-state changes in arterial blood pressure and end-tidal CO2 (the putative inputs) upon cerebral blood flow velocity (the putative output) measured at the middle cerebral artery via transcranial Doppler (TCD). The obtained input-output models are then used to compute model-based indices of DCA and DVR from model-predicted responses to an input pressure pulse or an input CO2 pulse, respectively. In this paper, we compare these model-based indices of DVR and DCA in 46 amnestic MCI patients, relative to 20 age-matched controls, using TCD measurements with their counterparts using Near-Infrared Spectroscopy (NIRS) measurements of blood oxygenation at the lateral prefrontal cortex in 43 patients and 22 age-matched controls. The goal of the study is to assess whether NIRS measurements can be used instead of TCD measurements to obtain model-based physiomarkers with comparable diagnostic utility. The results corroborate this view in terms of the ability of either output to yield model-based physiomarkers that can differentiate the group of aMCI patients from age-matched healthy controls.