gebhart/patrepeval huggingface dataset:
Optimal transport at finite temperature (2019)

Optimal transport (OT) has become a discipline by itself that offers solutions to a wide range of theoretical problems in probability and mathematics. Despite its appealing theoretical properties, solving the OT problem involves the resolution of a linear program whose computational cost can quickly become prohibitive whenever the size of the problem exceeds a few hundred points. The recent introduction of entropy regularization, however, has led to the development of fast algorithms for solving an approximate OT problem. The successes of those algorithms have resulted in a popularization of the applications of OT in several applied fields such as imaging sciences and machine learning, and in data sciences in general. Problems remain, however, as to the numerical convergence of those regularized approximations towards the actual OT solution. In addition, the physical meaning of this regularization is unclear. In this paper, we propose an approach to solving the discrete OT problem using techniques adapted from statistical physics. Our first contribution is to fully describe this formalism, including all the proofs of its main claims. In particular we derive a strongly concave effective free energy function that captures the constraints of the optimal transport problem at a finite temperature. Its maximum defines a pseudo distance between the two set of weighted points that are compared, which satisfies the triangular inequalities. The temperature dependent OT pseudo distance decreases monotonically to the standard OT distance, providing a robust framework for temperature annealing. Our second contribution is to show that the implementation of this formalism has the same properties as the regularized OT algorithms in time complexity, making it a competitive approach to solving the OT problem. We illustrate applications of the framework to the problem of protein fold recognition based on sequence information only.
Video super-resolution using high quality photographs (2010)

This paper introduces a technique that increases the spatial resolution of a given video. The method is built on the fundamentals of super-resolution techniques that aim to reconstruct high-resolution frames from a low-resolution input sequence. Different than classical super-resolution methods, besides using the information of adjacent frames, we take advantage of several reference high quality (resolution) photographs of the same scene. The method is purely imagebased, and does not require depth estimation. The additional information extracted from the reference photographs is used to construct several high resolution seed frames added with a constant step in the initial video sequence. Therefore, the seed frames but also the adjacent low-resolution frames provide important information to define priors that are considered in the probabilistic interpretation of the generative model. The estimated solution is obtained based on a standard maximum a posteriori (MAP) approach. Objective tests on real and synthetic video sequences demonstrate the utility and the benefits of the proposed technique over related methods.
Coordinated Cell Type–Specific Epigenetic Remodeling in Prefrontal Cortex Begins before Birth and Continues into Early Adulthood (2013)

Development of prefrontal and other higher-order association cortices is associated with widespread changes in the cortical transcriptome, particularly during the transitions from prenatal to postnatal development, and from early infancy to later stages of childhood and early adulthood. However, the timing and longitudinal trajectories of neuronal gene expression programs during these periods remain unclear in part because of confounding effects of concomitantly occurring shifts in neuron-to-glia ratios. Here, we used cell type-specific chromatin sorting techniques for genome-wide profiling of a histone mark associated with transcriptional regulation--H3 with trimethylated lysine 4 (H3K4me3)--in neuronal chromatin from 31 subjects from the late gestational period to 80 years of age. H3K4me3 landscapes of prefrontal neurons were developmentally regulated at 1,157 loci, including 768 loci that were proximal to transcription start sites. Multiple algorithms consistently revealed that the overwhelming majority and perhaps all of developmentally regulated H3K4me3 peaks were on a unidirectional trajectory defined by either rapid gain or loss of histone methylation during the late prenatal period and the first year after birth, followed by similar changes but with progressively slower kinetics during early and later childhood and only minimal changes later in life. Developmentally downregulated H3K4me3 peaks in prefrontal neurons were enriched for Paired box (Pax) and multiple Signal Transducer and Activator of Transcription (STAT) motifs, which are known to promote glial differentiation. In contrast, H3K4me3 peaks subject to a progressive increase in maturing prefrontal neurons were enriched for activating protein-1 (AP-1) recognition elements that are commonly associated with activity-dependent regulation of neuronal gene expression. We uncovered a developmental program governing the remodeling of neuronal histone methylation landscapes in the prefrontal cortex from the late prenatal period to early adolescence, which is linked to cis-regulatory sequences around transcription start sites.
Regenerative Medicine Manufacturing--A Systems Engineering Perspective (2012)

TutORials in Operations Research is a collection of tutorials published annually and designed for students, faculty, and practitioners. The series provides in-depth instruction on significant operations research topics and methods. INFORMS has published the series, founded by Harvey J. Greenberg, since 2005.
Bacterial–Platelet Interactions: Virulence Meets Host Defense (2010)

Platelets have historically been viewed as cell fragments that only mediate blood coagulation. Yet, platelets have as - or perhaps even more - important roles in tissue remodeling, modulation of inflammation and antimicrobial host defense. It is evident that platelets interact with prokaryotes directly and indirectly through multiple molecular and cellular mechanisms. The important roles of platelets in antibacterial host defense can be exemplified through contemporary themes in platelet immunobiology. Platelets have unambiguous structures and functions of host defense effector cells. Recent discoveries reveal platelet expression of toll-like and purinonergic receptors, which enable detection and response to bacterial infection, degranulation of an array of microbicidal peptides and coordination of other molecular and cellular host defenses. From multiple perspectives, platelets are now increasingly recognized as critical innate immune effector cells that also bridge and facilitate optimization of adaptive immunity. It follows that clinical deficiencies in platelet quantity or quality are now recognized correlates of increased risk and severity of bacterial and other infections. Along these lines, new evidence suggests that certain prokaryotic organisms may be capable of exploiting platelet interactions to gain a virulence advantage. Indeed, certain bacterial pathogens appear to have evolved highly coordinated means by which to seize opportunities to bind to surfaces of activated platelets, and exploit them to establish or propagate infection. Hence, it is conceivable that certain bacterial pathogens subvert platelet functions. From these perspectives, the net consequences of bacterial virulence versus platelet host defenses likely decide initial steps towards the ultimate result of infection versus immunity.
Substituted 2-Aminopyrimidines Selective for α7-Nicotinic Acetylcholine Receptor Activation and Association with Acetylcholine Binding Proteins (2017)

Through studies with ligand binding to the acetylcholine binding protein (AChBP), we previously identified a series of 4,6-substituted 2-aminopyrimidines that associate with this soluble surrogate of the nicotinic acetylcholine receptor (nAChR) in a cooperative fashion, not seen for classical nicotinic agonists and antagonists. To examine receptor interactions of this structural family on ligand-gated ion channels, we employed HEK cells transfected with cDNAs encoding three requisite receptor subtypes: α7-nAChR, α4β2-nAChR, and a serotonin receptor (5-HT<sub>3A</sub>R), along with a fluorescent reporter. Initial screening of a series of over 50 newly characterized 2-aminopyrimidines with affinity for AChBP showed only two to be agonists on the α7-nAChR below 10 μM concentration. Their unique structural features were incorporated into design of a second subset of 2-aminopyrimidines yielding several congeners that elicited α7 activation with EC<sub>50</sub> values of 70 nM and K<sub>d</sub> values for AChBP in a similar range. Several compounds within this series exhibit specificity for the α7-nAChR, showing no activation or antagonism of α4β2-nAChR or 5-HT3AR at concentrations up to 10 μM, while others were weaker antagonists (or partial agonists) on these receptors. Analysis following cocrystallization of four ligand complexes with AChBP show binding at the subunit interface, but with an orientation or binding pose that differs from classical nicotinic agonists and antagonists and from the previously analyzed set of 2-aminopyrimidines that displayed distinct cooperative interactions with AChBP. Orientations of aromatic side chains of these complexes are distinctive, suggesting new modes of binding at the agonist-antagonist site and perhaps an allosteric action for heteromeric nAChRs.
CDCP1 (CUB domain containing protein 1) (2013)

Review on CDCP1 (CUB domain containing protein 1), with data on DNA, on the protein encoded, and where the gene is implicated.
Brief Communication: Intracolonlc Injection of BeG in the Rhesus Monkey (1974)

Intramucosal injection of living BCGInto the colon and rectum was well tolerated by rhesus monkeys (Macaca mulatta). Ulceration developed at Injection sites within 3 weeks after initial injection and healed spontaneously without sigulficant hemorrhage, perforation, or functional obstruction. All animals developed systemic tuberculin hypersensitivity. A second Intrarectal Injection of BCG produced indurated mucosal lesions within 24–48 hours and local ulceration within 1 week. Inadvertent extracolonic Injection of BCG produced localized abscesses and a single Instance of focal granulomatous peritonitis. No extracolonlc lesions were observed In properly inoculated animals and there was no evidence of systemic BCG infection at necropsy.
Resilience-Oriented Scheduling of Shared Autonomous Electric Vehicles: A Cooperation Framework for Electrical Distribution Networks and Transportation Sector (2023)

As autonomous electric vehicles and car-sharing services are becoming more popular, the contribution of shared autonomous electric vehicles (SAEVs) to the future of urban transportation is getting more achievable. Like conventional electric vehicles, SAEVs can provide power grids with ancillary services. This article proposes a new scheduling scheme for SAEV fleets within a cooperative plan to let power distribution networks benefit from the energy storage of vehicle batteries in recovering critical loads after a predictable extreme event. According to a long-term contract, the detailed request of the distribution system operator (DSO), together with desired constraints and perquisites, is sent to the SAEVs aggregator (SA) prior to the landfall of a predictable extreme event. Afterward, SA runs a targeted algorithm to schedule trip assignments and charging cycles of SAEVs so that the required constraints of DSO are satisfied. The SAEV participants will continue carrying passengers within the scheduled time horizon in addition to delivering energy to the distribution network at the scheduling deadline declared by DSO. This deadline is the time instant when the capacity of the SAEV fleet may be no more applicable to enhance the system preparedness against the approaching event. Numerical results illustrated that the proposed scheme helps improve the power grid resilience by delivering 2396.1 kWh of energy to the distribution network in addition to increasing the total income of each participant SAEV by about 130%. Thus, it is implied that the proposed method offers a win-win situation for both entities.
Jet Ventilation for the Excision of Vocal Cord Polyps in a Pregnant Patient (2011)

The anaesthetic management of patients presenting with laryngeal tumours and airway obstruction is difficult. We present the case of a pregnant woman at 30 weeks gestation who underwent surgical removal of two vocal cord polyps under general anaesthesia using jet ventilation
Nature versus design: the conformational propensities of d-amino acids and the importance of side chain chirality (2014)

D-amino acids are useful building blocks for de novo peptide design and they play a role in aging-related diseases associated with gradual protein racemization. For amino acids with achiral side chains, one should be able to presume that the conformational propensities of L- and D-amino acids are a reflection of one another due to the straightforward geometric inversion at the Cα atom. However, this presumption does not account for the directionality of the backbone dipole and the inverted propensities have never been definitively confirmed in this context. Furthermore, there is little known of how alternative side chain chirality affects the backbone conformations of isoleucine and threonine. Using a GGXGG host-guest pentapeptide system, we have completed exhaustive sampling of the conformational propensities of the D-amino acids, including D-allo-isoleucine and D-allo-threonine, using atomistic molecular dynamics simulations. Comparison of these simulations with the same systems hosting the cognate L-amino acids verifies that the intrinsic backbone conformational propensities of the D-amino acids are the inverse of their cognate L-enantiomers. Where amino acids have a chiral center in their side chain (Thr, Ile) the β-configuration affects the backbone sampling, which in turn can confer different biological properties.
Effects of elastic properties on the wave propagation in cancellous bones - a simulation study - (2008)

For diagnosing osteoporosis, ultrasonic systems are considered a powerful tool, because ultrasonic waves strongly depend on the elasticity and structure of cancellous bones. We have reported the separation of longitudinal waves into fast and slow waves, a phenomenon that is strongly connected to the alignment of bone trabeculae.In order to understand this complicated wave propagation, we have simulated the wave propagations with the finite-difference time-domain (FDTD) method using three-dimensional X-ray CT images of actual cancellous bones. In this simulation, the effects of elastic properties in the solid portions are important. One idea is to adopt the experimentally observed ultrasonic properties of cortical bone. However, we should remind the possible problems like the elasticity difference between cancellous and cortical bones, individual differences, and anisotropy. In this study, then, we have investigated the influences of elastic properties, Poisson's ratio, and densities of solid portion (trabeculae). As a result, we confirmed that the small changes give strong influences on not only the wave speed but also the amplitudes of fast and slow waves. The influence on the amplitudes seems to come from the changes of acoustic impedance of trabeculae. The results show the importance of elastic properties in the simulation.
Polycaprolactone Thin-Film Micro- and Nanoporous Cell-Encapsulation Devices (2015)

Cell-encapsulating devices can play an important role in advancing the types of tissue available for transplantation and further improving transplant success rates. To have an effective device, encapsulated cells must remain viable, respond to external stimulus, and be protected from immune responses, and the device itself must elicit a minimal foreign body response. To address these challenges, we developed a micro- and a nanoporous thin-film cell encapsulation device from polycaprolactone (PCL), a material previously used in FDA-approved biomedical devices. The thin-film device construct allows long-term bioluminescent transfer imaging, which can be used for monitoring cell viability and device tracking. The ability to tune the microporous and nanoporous membrane allows selective protection from immune cell invasion and cytokine-mediated cell death in vitro, all while maintaining typical cell function, as demonstrated by encapsulated cells' insulin production in response to glucose stimulation. To demonstrate the ability to track, visualize, and monitor the viability of cells encapsulated in implanted thin-film devices, we encapsulated and implanted luciferase-positive MIN6 cells in allogeneic mouse models for up to 90 days. Lack of foreign body response in combination with rapid neovascularization around the device shows promise in using this technology for cell encapsulation. These devices can help elucidate the metrics required for cell encapsulation success and direct future immune-isolation therapies.
Whole genome microarray analysis, from neonatal blood cards (2009)

Together, these data suggest that DNA obtained from less than 10% of a standard neonatal blood specimen, stored dry for several years on a Guthrie card, can support a program of genome-wide neonatal genetic testing.
A Systematic Review of Experimental Strategies Aimed at Improving Motor Function after Acute and Chronic Spinal Cord Injury (2015)

While various approaches have been proposed in clinical trials aimed at improving motor function after spinal cord injury in humans, there is still limited information regarding the scope, methodological quality, and evidence associated with single-intervention and multi-intervention approaches. A systematic review performed using the PubMed search engine and the key words "spinal cord injury motor recovery" identified 1973 records, of which 39 were selected (18 from the search records and 21 from reference list inspection). Study phase ( clinicaltrials.org criteria) and methodological quality (Cochrane criteria) were assessed. Studies included proposed a broad range of single-intervention (encompassing cell therapies, pharmacology, electrical stimulation, rehabilitation) (encompassing cell therapies, pharmacology, electrical stimulation, rehabilitation) and multi-intervention approaches (that combined more than one strategy). The highest evidence level was for Phase III studies supporting the role of multi-intervention approaches that contained a rehabilitation component. Quality appraisal revealed that the percentage of selected studies classified with high risk of bias by Cochrane criteria was as follows: random sequence generation = 64%; allocation concealment = 77%; blinding of participants and personnel = 69%; blinding of outcome assessment = 64%; attrition = 44%; selective reporting = 44%. The current literature contains a high proportion of studies with a limited ability to measure efficacy in a valid manner because of low methodological strength in all items of the Cochrane risk of bias assessment. Recommendations to decrease bias are discussed and include increased methodological rigor in the study design and recruitment of study participants, and the use of electrophysiological and imaging measures that can assess functional integrity of the spinal cord (and may be sufficiently sensitive to detect changes that occur in response to therapeutic interventions).
Resistencia a antibióticos en bacterias del ácido láctico y bifidobacterias (2009)

Concern for antibiotic resistance carriage in beneficial and commensal microorganisms involved in feed and food fermentations or included in foods as probiotics is based on the possibility of the genetic resistance determinants to be transferred from these organisms to pathogens through the food chain (either during food processing or during intestinal transit). As part of a European project within the VI Framework Programme (Assessment and Critical Evaluation of Antibiotic Resistance Transferability in the Food Chain, ACE-ART), our group has been analysing the resistance/susceptibility profiles of lactic acid bacteria and bifidobacteria strains isolated from traditional cheeses and from the human gastrointestinal tract of healthy individuals to several antibiotics of clinical use. A majority of the tested strains were found to be susceptible to all antibiotics or intrinsically resistant to some of them (these having little or no ability to spread). However, a few strains showed atypical resistance levels, which were compatible with horizontal acquisition and capable of transfer. In these cases, the encoding genes were analysed to understand the molecular basis of the resistance and the mechanisms and pathways of dissemination. Among the detected genes we can mention tet(M) and tet(W) encoding tetracycline resistance and erm(B) coding for erythromycin resistance.
An ADC-Less RRAM-Based Computing-in-Memory Macro With Binary CNN for Efficient Edge AI (2023)

Resistive random-access memory (RRAM) based non-volatile computing-in-memory (nvCIM) has been regarded as a promising solution to enable efficient data-intensive artificial intelligence (AI) applications on resource-limited edge systems. However, existing weighted-current summation-based nvCIM suffers from device non-idealities and significant time, storage, and energy overheads when processing high-precision analog signals. To address these issues, we propose a 3T2R digital nvCIM macro for a fully hardware-implemented binary convolutional neural network (HBCNN), focusing on accelerating edge AI applications at low weight precision. By quantizing the voltage-division results of RRAMs through inverters, the 3T2R macro provides a stable rail-to-rail output without analog-to-digital converters or sensing amplifiers. Moreover, both batch normalization and sign activation are integrated on-chip. The hybrid simulation results show that the proposed 3T2R digital macro achieves an 86.2% (95.6%) accuracy on the CIFAR-10 (MNIST) dataset, corresponding to a 4.7% (1.9%) accuracy loss compared to the software baselines, which also feature a peak energy efficiency of 51.3 TOPS/W and a minimum latency of 8 ns, realizing an energy-efficient, low-latency, and robust AI processor.
Sequential Versus Nonsequential Measurement of Density and Affinity of Dopamine D2 Receptors with [11C]raclopride: Effect of Methamphetamine (2003)

The multiple ligand concentration assays (MLCRA) method provides researchers with the ability to measure in vivo receptor characteristics in a stable condition. Measurements of the density and affinity of the dopamine D2 receptors with [11C]raclopride, using a sequential method (three scans throughout 1 day) or a nonsequential method (three scans spread over several weeks but at the same time of the day), yield similar values. However, after an acute challenge with drugs that affect dopamine neurotransmission, the concentration of endogenous ligand may vary over the course of the in vivo sequential MLCRA. Combined PET-microdialysis studies after acute amphetamine showed that during the imaging time frame the concentrations of extracellular dopamine vary widely, but that nonetheless the decrease in raclopride binding potential is sustained and nearly constant over time. These observations apparently contradict the simple competitive displacement model if the changes in extracellular concentration are taken to reflect necessarily comparable changes at the binding sites. To understand the effect of the delay between drug administration and start-to-end of data acquisition on the MLCRA results, we compared the outcomes of the sequential and nonsequential methods after methamphetamine. Comparison of the binding potential, density, and affinity of D2 receptors in both experimental conditions revealed good concordance between the data sets, suggesting that methamphetamine produces sustained and stable increases in synaptic dopamine.