Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement of Synchronization in a Hybrid Neural Circuit by Spike-Timing Dependent Plasticity

Synchronization of neural activity is fundamental for many functions of the brain. We demonstrate that spike-timing dependent plasticity (STDP) enhances synchronization (entrainment) in a hybrid circuit composed of a spike generator, a dynamic clamp emulating an excitatory plastic synapse, and a chemically isolated neuron from the Aplysia abdominal ganglion. Fixed-phase entrainment of the Aplysia neuron to the spike generator is possible for a much wider range of frequency ratios and is more precise and more robust with the plastic synapse than with a nonplastic synapse of comparable strength. Further analysis in a computational model of Hodgkin–Huxley-type neurons reveals the mechanism behind this significant enhancement in synchronization. The experimentally observed STDP plasticity curve appears to be designed to adjust synaptic strength to a value suitable for stable entrainment of the postsynaptic neuron. One functional role of STDP might therefore be to facilitate synchronization or entrainment of nonidentical neurons.
Conserving Biodiversity Efficiently: What to Do, Where, and When

Conservation priority-setting schemes have not yet combined geographic priorities with a framework that can guide the allocation of funds among alternate conservation actions that address specific threats. We develop such a framework, and apply it to 17 of the world's 39 Mediterranean ecoregions. This framework offers an improvement over approaches that only focus on land purchase or species richness and do not account for threats. We discover that one could protect many more plant and vertebrate species by investing in a sequence of conservation actions targeted towards specific threats, such as invasive species control, land acquisition, and off-reserve management, than by relying solely on acquiring land for protected areas. Applying this new framework will ensure investment in actions that provide the most cost-effective outcomes for biodiversity conservation. This will help to minimise the misallocation of scarce conservation resources.
Comparison of the Bruker Biotyper and Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems for Identification of Mycobacteria Using Simplified Protein Extraction Protocols

ABSTRACT Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has recently been described as a fast and inexpensive method for the identification of mycobacteria. Although mycobacteria require extraction prior to MALDI-TOF MS analysis, previously published protocols have been relatively complex, involving significant hands-on time and materials not often found in the clinical laboratory. In this study, we tested two simplified protein extraction protocols developed at the University of Washington (UW) and by bioMérieux (BMX) for use with two different mass spectrometry platforms (the Bruker MALDI Biotyper and the bioMérieux Vitek MS, respectively). Both extraction protocols included vortexing with silica beads in the presence of ethanol. The commercial Bruker database was also augmented with an in-house database composed of 123 clinical Mycobacterium strains. A total of 198 clinical strains, representing 18 Mycobacterium species, were correctly identified to the species level 94.9% of the time when extracted using the UW protocol and compared to the augmented database. The BMX protocol and Vitek MS system resulted in correct species-level identifications for 94.4% of these strains. In contrast, only 79.3% of the strains were identified to the species level by the nonaugmented Bruker database, although the use of a lower identification score threshold (≥1.7) increased the identification rate to 93.9%, with two misidentifications that were unlikely to be clinically relevant. The two simplified protein extraction protocols described in this study are easy to use for identifying commonly encountered Mycobacterium species.
Dynamic auxin transport patterns preceding vein formation revealed by live-imaging of Arabidopsis leaf primordia

Self-regulatory patterning mechanisms capable of generating biologically meaningful, yet unpredictable cellular patterns offer unique opportunities for obtaining mathematical descriptions of underlying patterning systems properties. The networks of higher-order veins in leaf primordia constitute such a self-regulatory system. During the formation of higher-order veins, vascular precursors are selected from a homogenous field of subepidermal cells in unpredictable positions to eventually connect in complex cellular networks. Auxin transport routes have been implicated in this selection process, but understanding of their role in vascular patterning has been limited by our inability to monitor early auxin transport dynamics in vivo. Here we describe a live-imaging system in emerging Arabidopsis thaliana leaves that uses a PIN1:GFP reporter to visualize auxin transport routes and an Athb8:YFP reporter as a marker for vascular commitment. Live-imaging revealed common features initiating the formation of all higher-order veins. The formation of broad PIN1 expression domains is followed by their restriction, leading to sustained, elevated PIN1 expression in incipient procambial cells files, which then express Athb8. Higher-order PIN1 expression domains (hPEDs) are initiated as freely ending domains that extend toward each other and sometimes fuse with them, creating connected domains. During the restriction and specification phase, cells in wider hPEDs are partitioned into vascular and non-vascular fates: Central cells acquire a coordinated cell axis and express elevated PIN1 levels as well as the pre-procambial marker Athb8, while edge cells downregulate PIN1 and remain isodiametric. The dynamic nature of the early selection process is underscored by the instability of early hPEDs, which can result in dramatic changes in vascular network architecture prior to Athb8 expression, which is correlated with the promotion onto vascular cell fate.
Simultaneous recording of oxytocin release, milk ejection and milk flow during milking of dairy cows with and without prestimulation

Summary The effects of manual teat stimulation compared with stimulation by the liner of a conventional milking machine and the influence of milk ejection on the course of milk flow during the entire milking were investigated. Twelve cows were milked with or without prestimulation on three quarters and milk flow was recorded while intramammary pressure (IMP) was recorded in the left front quarter and blood samples for the determination of oxytocin (OT) were taken at 1 min intervals. OT concentrations increased very similarly in response to manual teat stimulation or liner stimulation and remained elevated during the entire milking procedure. Milk flow curves were generally bimodal without stimulation and not bimodal during milking after prestimulation. Milk yield was not significantly lower in milkings without than with stimulation, whereas machine-on time was prolonged and peak milk flow rate was reduced during milking without stimulation. Time to reach milk flow plateau, time to reach peak flow rate and IMP profiles were similar in both treatments if time was calculated from the start of stimulation. IMP increased similarly in response to manual or liner teat stimulation. In milkings with and without prestimulation IMP did not reach its maximum until the start of milking. In bimodal milk flow curves the second increase of milk flow occurred concomitantly with the start of IMP increase; ejection IMP generally occurred concomitantly with the milk flow plateau. In some cases during milking without prestimulation only small and transient OT release was observed. In response, IMP did not increase to its maximum and increased further in response to a stripping-related OT release. During the course of milking IMP decreased slightly because of the emptying of the three milked quarters. After the end of milking, and with OT concentrations decreasing to the premilking values, IMP again decreased slightly to another plateau, probably owing to myoepithelial relaxation. Thus the course of milk ejection, i.e. the IMP profile, influenced milk removal markedly during early milking.
Thyroid dysfunction and autoantibodies in early pregnancy are associated with increased risk of gestational diabetes and adverse birth outcomes.

CONTEXT Maternal thyroid dysfunction, especially in early pregnancy, may lead to pregnancy complications and adverse birth outcomes. Few population-based prospective studies have evaluated these effects and results are discrepant. OBJECTIVE We examined the association of thyroid function and autoimmunity in early pregnancy with adverse pregnancy and birth outcomes. SETTING AND PARTICIPANTS The study used data from the prospective mother-child cohort "Rhea" study in Crete, Greece. A total of 1170 women with singleton pregnancies participated in this analysis. Maternal serum samples in the first trimester of pregnancy were tested for thyroid hormones (TSH, free T(4), and free T(3)) and thyroid antibodies (thyroid peroxidase antibody and thyroglobulin antibody). Multivariable log-Poisson regression models were used adjusting for confounders. MAIN OUTCOME MEASURES Outcomes included gestational diabetes, gestational hypertension/preeclampsia, cesarean section, preterm delivery, low birth weight, and small-for-gestational-age neonates. RESULTS The combination of high TSH and thyroid autoimmunity in early pregnancy was associated with a 4-fold increased risk for gestational diabetes [relative risk (RR) 4.3, 95% confidence interval (CI) 2.1-8.9)] and a 3-fold increased risk for low birth weight neonates (RR 3.1, 95% CI 1.2-8.0) after adjustment for several confounders. Women positive for thyroid antibodies without elevated TSH levels in early pregnancy were at high risk for spontaneous preterm delivery (RR 1.7, 95% CI 1.1-2.8), whereas the combined effect of high TSH and positive thyroid antibodies did not show an association with preterm birth. CONCLUSIONS High TSH levels and thyroid autoimmunity in early pregnancy may detrimentally affect pregnancy and birth outcomes.
Investigation and image processing of cellular metals with highly resolving 3D microtomography (μCT)

Some very small parts from regular cellular (spherical) metals were investigated in a strength test, which was done inside the (mu) CT machine with resolutions down to 5 micrometers . The aim was to inspect the behavior of the walls of cellular metals under load, and to find out how the buckling or breaking starts. The results are needed for theoretical calculations, which will be used to predict the behavior of large structures of these materials. Also the pore size and pore size distribution for cellular metals is calculated and a method to separate walls and nodes is presented. CT insights of cellular metals as well as investigations of data by means of image processing is shown.
Optimizing targeted vaccination across cyber–physical networks: an empirically based mathematical simulation study

Targeted vaccination, whether to minimize the forward transmission of infectious diseases or their clinical impact, is one of the ‘holy grails’ of modern infectious disease outbreak response, yet it is difficult to achieve in practice due to the challenge of identifying optimal targets in real time. If interruption of disease transmission is the goal, targeting requires knowledge of underlying person-to-person contact networks. Digital communication networks may reflect not only virtual but also physical interactions that could result in disease transmission, but the precise overlap between these cyber and physical networks has never been empirically explored in real-life settings. Here, we study the digital communication activity of more than 500 individuals along with their person-to-person contacts at a 5-min temporal resolution. We then simulate different disease transmission scenarios on the person-to-person physical contact network to determine whether cyber communication networks can be harnessed to advance the goal of targeted vaccination for a disease spreading on the network of physical proximity. We show that individuals selected on the basis of their closeness centrality within cyber networks (what we call ‘cyber-directed vaccination’) can enhance vaccination campaigns against diseases with short-range (but not full-range) modes of transmission.
Parametric Bandits: The Generalized Linear Case

We consider structured multi-armed bandit problems based on the Generalized Linear Model (GLM) framework of statistics. For these bandits, we propose a new algorithm, called GLM-UCB. We derive finite time, high probability bounds on the regret of the algorithm, extending previous analyses developed for the linear bandits to the non-linear case. The analysis highlights a key difficulty in generalizing linear bandit algorithms to the non-linear case, which is solved in GLM-UCB by focusing on the reward space rather than on the parameter space. Moreover, as the actual effectiveness of current parameterized bandit algorithms is often poor in practice, we provide a tuning method based on asymptotic arguments, which leads to significantly better practical performance. We present two numerical experiments on real-world data that illustrate the potential of the GLM-UCB approach.
Leaf Size, Sapling Allometry, and Corner's Rules: Phylogeny and Correlated Evolution in Maples (Acer)

We studied the evolution of leaf size, sapling canopy allometry, and related traits in 17 Acer species growing in the understory of temperate deciduous forests, using parsimony methods, randomization tests, and independent contrasts calculated on idena phylogeny inferred from nuclear ribosomal internal transcribed spacer (ITS) sequences. Bivariate correlations and multivariate analyses indicated two independent suites of coevolving traits, and the results were robust over a range of alternative phylogenies. The first suite consisted of strong positive correlations among twig thickness, leaf size, inflorescence length, and branch spacing (Corner's rules). Seed size and mature height were also weakly corre‐ lated with these traits. The second suite reflected aspects of sapling crown allometry, including crown size, stem diameter, and total leaf area, which appear to be related to shade tolerance. There was a weak negative correlation between sapling crown size and mavegetative ture height, but no correlation with leaf or seed size. Most correlattion were similar in magnitude for ahistorical and independent contrasts analyses, and discrepancies between these two measures were greater in traits with lower levels of convergent evolution. The evolutionary correlations among twig, leaf, seed, inflorescence, and canopy dimensions emphasize the need for integrated theories of evolution and function of these disparate traits.
Development and application of an algorithm for detecting Phaeocystis globosa blooms in the Case 2 Southern North Sea waters

While mapping algal blooms from space is now well-established, mapping undesirable algal blooms in eutrophicated coastal waters raises further challenge in detecting individual phytoplankton species. In this paper, an algorithm is developed and tested for detecting Phaeocystis globosa blooms in the Southern North Sea. For this purpose, we first measured the light absorption properties of two phytoplankton groups, P. globosa and diatoms, in laboratory-controlled experiments. The main spectral difference between both groups was observed at 467 nm due to the absorption of the pigment chlorophyll c3 only present in P. globosa, suggesting that the absorption at 467 nm can be used to detect this alga in the field. A Phaeocystis-detection algorithm is proposed to retrieve chlorophyll c3 using either total absorption or water-leaving reflectance field data. Application of this algorithm to absorption and reflectance data from Phaeocystis-dominated natural communities shows positive results. Comparison with pigment concentrations and cell counts suggests that the algorithm can flag the presence of P. globosa and provide quantitative information above a chlorophyll c3 threshold of 0.3 mg m−3 equivalent to a P. globosa cell density of 3 × 106 cells L−1. Finally, the possibility of extrapolating this information to remote sensing reflectance data in these turbid waters is evaluated.
Targeted Delivery of Pulmonary Arterial Endothelial Cells Overexpressing Interleukin-8 Receptors Attenuates Monocrotaline-Induced Pulmonary Vascular Remodeling

Objective—Interleukin-8 (IL-8) receptors IL8RA and IL8RB (IL8RA/B) on neutrophil membranes bind to IL-8 with high affinity and play a critical role in neutrophil recruitment to sites of injury and inflammation. This study tested the hypothesis that administration of rat pulmonary arterial endothelial cells (ECs) overexpressing IL8RA/B can accelerate the adhesion of ECs to the injured lung and inhibit monocrotaline-induced pulmonary inflammation, arterial thickening and hypertension, and right ventricular hypertrophy. Approach and Results—The treatment groups included 10-week-old ovariectomized Sprague-Dawley rats that received subcutaneous injection of PBS (vehicle), a single injection of monocrotaline (monocrotaline alone, 60 mg/kg, SC), monocrotaline followed by intravenous transfusion of ECs transduced with the empty adenoviral vector (null-EC), and monocrotaline followed by intravenous transfusion of ECs overexpressing IL8RA/B (1.5×106 cells/rat). Two days or 4 weeks after monocrotaline treatment, endothelial nitric oxide synthase, inducible nitric oxide synthase, cytokine-induced neutrophil chemoattractant-2&bgr; (IL-8 equivalent in rat), and monocyte chemoattractant protein-1 expression, neutrophil and macrophage infiltration into pulmonary arterioles, and arteriolar and alveolar morphology were measured by histological and immunohistochemical techniques. Proinflammatory cytokine/chemokine protein levels were measured by Multiplex rat-specific magnetic bead–based sandwich immunoassay in total lung homogenates. Transfusion of ECs overexpressing IL8RA/B significantly reduced monocrotaline-induced neutrophil infiltration and proinflammatory mediator (IL-8, monocyte chemoattractant protein-1, inducible nitric oxide synthase, cytokine-induced neutrophil chemoattractant, and macrophage inflammatory protein-2) expression in lungs and pulmonary arterioles and alveoli, pulmonary arterial pressure, and pulmonary arterial and right ventricular hypertrophy and remodeling. Conclusions—These provocative findings suggest that targeted delivery of ECs overexpressing IL8RA/B is effective in repairing the injured pulmonary vasculature.
Ossiculoplasty: A Prospective Study of 80 Cases

Introduction: The use of ossicular graft material in ossicular chain reconstruction has significantly improved hearing results hearing after tympanoplasty and tympanomastoid surgery for chronic otitis media. Today, otologists have a wide array of tools from which to choose, but may find it difficult to know which middle ear implant works best. Materials and Methods: A prospective study of 80 patients who underwent ossiculoplasty was performed in the ear, nose, and throat (ENT) department at a tertiary health care facility from 2011 to 2013. Patients with chronic suppurative otitis media with an air-bone gap (ABG) of >25 dB with ossicular involvement were included in the study. Total ossicular replacement prosthesis (TORP), partial ossicular replacement prosthesis (PORP), and refashioned incus were used. Success was defined as ABG <25 dB on postoperative Day 90. Results: The majority patients were of middle age with moderate conductive hearing loss. Incus was the most susceptible ossicle. Overall success rate in this study was 80.0% with an average change of 15.76 dB in ABG. Conclusion: With continuing advances in our understanding of middle ear mechanics, the results of ossiculoplasty are improving and results can be very rewarding in experienced hands. Severity of preoperative ear discharge, preoperative mastoid cellularity, presence of disease, and surgical procedure proved to be significant prognostic factors. Autograft incus and PORP fared better when the malleus handle was present while TORP gave better results when the malleus handle was eroded.
Flaring Activity of Sgr A*: Expanding Hot Blobs

Kavli Institute for Astrophysics and Space Research, MIT, Cambridge, MA 02139-4307E-mail:fkb@space.mit. eduSgr A* is considered to be a massive black hole at the Galactic center and is known to be variablein radio, millimeter, near-IR and X-rays. Recent multi-wavelength observing campaigns show asimultaneous X-ray and near-IR ﬂare, as well as sub-millimeter and near-IR ﬂares from Sgr A*. The ﬂare activity is thought to be arising from the innermost region of Sgr A*. We have recentlyargued that the duration of ﬂares in near-IR and submillimeter wavelengths implies that the burstof emission expands and cools on a dynamical time scale before the ﬂares leave Sgr A*. Thedetection of radio ﬂares with a time delay in the range of 20 an d 40 minutes between 7 and 12mmpeak emission implies adiabatic expansion of a uniform, spherical hot blob due to ﬂare activity.We suspect that this simple outﬂow picture shows some of the c haracteristics that are known totake place in microquasars, thus we may learn much from comparative study of Sgr A* and itsenvironment vs. microquasars.VI Microquasar Workshop: Microquasars and BeyondSeptember 18-22 2006Societa del Casino, Como, Italy
Red colored IgG4 caused by vitamin B12 from cell culture media combined with disulfide reduction at harvest

While many antibody therapeutics are formulated at low concentration (~10–20 mg/mL) for intravenous administration, high concentration (> 100 mg/mL) formulations may be required for subcutaneous delivery in certain clinical indications. For such high concentration formulations, product color is more apparent due to the higher molecular density across a given path-length. Color is therefore a product quality attribute that must be well-understood and controlled, to demonstrate process consistency and enable clinical trial blinding. Upon concentration of an IgG4 product at the 2000 L manufacturing scale, variability in product color, ranging from yellow to red, was observed. A small-scale experimental model was developed to assess the effect of processing conditions (medium composition and harvest conditions) on final bulk drug substance (BDS) color. The model was used to demonstrate that, for two distinct IgG4 products, red coloration occurred only in the presence of disulfide reduction-mediated antibody dissociation. The red color-causing component was identified as vitamin B12, in the hydroxocobalamin form, and the extent of red color was correlated with the cobalt (vitamin B12) concentration in the final pools. The intensity of redness in the final BDS was modulated by changing the concentration of vitamin B12 in the cell culture media.