gebhart/patrepeval huggingface dataset:
Ultrafast transient absorption revisited: Phase-flips, spectral fingers, and other dynamical features (2016)

We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from the optical response of an individual molecule to incident femtosecond pump and probe pulses. The resulting description makes use of pulse propagators and free molecular evolution operators to arrive at compact expressions for the several contributions to a transient-absorption signal. In this alternative description, which is physically equivalent to the conventional response-function formalism, these signal contributions are conveniently expressed as quantum mechanical overlaps between nuclear wave packets that have undergone different sequences of pulse-driven optical transitions and time-evolution on different electronic potential-energy surfaces. Using this setup in application to a simple, multimode model of the light-harvesting chromophores of PC577, we develop wave-packet pictures of certain generic features of ultrafast transient-absorption signals related to the probed-frequency dependence of vibrational quantum beats. These include a Stokes-shifting node at the time-evolving peak emission frequency, antiphasing between vibrational oscillations on opposite sides (i.e., to the red or blue) of this node, and spectral fingering due to vibrational overtones and combinations. Our calculations make a vibrationally abrupt approximation for the incident pump and probe pulses, but properly account for temporal pulse overlap and signal turn-on, rather than neglecting pulse overlap or assuming delta-function excitations, as are sometimes done.
Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation (2018)

Gut microbiota dysbiosis and metabolic dysfunction in infancy precedes childhood atopy and asthma development. Here we examined gut microbiota maturation over the first year of life in infants at high risk for asthma (HR), and whether it is modifiable by early-life Lactobacillus supplementation. We performed a longitudinal comparison of stool samples collected from HR infants randomized to daily oral Lactobacillus rhamnosus GG (HRLGG) or placebo (HRP) for 6 months, and healthy (HC) infants. Meconium microbiota of HRP participants is distinct, follows a delayed developmental trajectory, and is primarily glycolytic and depleted of a range of anti-inflammatory lipids at 6 months of age. These deficits are partly rescued in HRLGG infants, but this effect was lost at 12 months of age, 6 months after cessation of supplementation. Thus we show that early-life gut microbial development is distinct, but plastic, in HR infants. Our findings offer a novel strategy for early-life preventative interventions.
Allosterism and Cooperativity in <i>Pseudomonas aeruginosa </i>GDP-Mannose Dehydrogenase (2002)

GDP-Mannose dehydrogenase catalyzes the formation of GDP-mannuronic acid, which is the monomeric unit from which the polysaccharide alginate is formed. Alginate is secreted by the pathogenic bacterium Pseudomonas aeruginosa and is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response. We have characterized the kinetic behavior of GDP-mannose dehydrogenase in detail. The enzyme displays cooperative behavior with respect to NAD(+) binding, and phosphate and GMP act as allosteric effectors. Binding of the allosteric effectors causes the Hill coefficient for NAD(+) binding to decrease from 6 to 1, decreases K(1/2) for NAD(+) by a factor of 10, and decreases V(max) by a factor of 2. The cooperative binding of NAD(+) is also sensitive to pH; deprotonation of two residues with identical pK's of 8.0 is required for maximally cooperative behavior. The kinetic behavior of GDP-mannose dehydrogenase suggests that it must be at least hexameric under turnover conditions; however, dynamic light-scattering measurements do not provide a clear determination of the size of the active enzyme complex.
Therapeutic Plasma Exchange (1981)

Category A-1 continuing education credit is available to anyone who studies a C/E Update series and completes a written exam. Exams can be ordered from the ASCP and will be sent to participants following the appearance of the final article of each series in LABORATORY MEDICINE. After receipt of a completed answer sheet at ASCP, a certificate of credit will be awarded to each participant. An exam order form appears on page 754 in this issue.
Small molecules that bind the inner core of gp41 and inhibit HIV envelope-mediated fusion (2006)

HIV-1 enters cells by membrane fusion, mediated by the trimeric viral envelope glycoprotein gp160, which is processed by a single proteolytic cleavage into stably associated gp120 and gp41. The gp120/gp41 trimer can be triggered to undergo an irreversible conformational change. Using a protein-based assay designed to mimic the gp41 conformational change, we screened for small molecules that prevent the formation of postfusion gp41. Several compounds were identified. One set of structurally related molecules inhibited formation of a postfusion-like assembly with an IC50 of approximately 5 microM. The compounds also inhibited envelope-mediated membrane fusion in both cell-cell fusion and viral infectivity assays. Thus, our screen identifies effective fusion inhibitors. Tested against a panel of envelope proteins from primary HIV-1 isolates, the compounds inhibited fusion across a broad range of clades, including both M and T tropic strains. They bind in a highly conserved, hydrophobic pocket on the inner core of the gp41 trimer, a region previously identified as a potential inhibitor site.
Methylene Blue Binding to DNA with Alternating GC Base Sequence:  A Modeling Study (2000)

Photoactive methylene blue is one of the most efficient singlet oxygen generating dyes. It binds to DNA and induces photosensitized reactions which can be used for sequence-specific cleavage of the DNA backbone. Photophysical data obtained for methylene blue in complexes with DNA indicate different binding modes of the dye depending on base sequences. In this study, the binding of methylene blue to a double-stranded decamer with an alternating GC sequence has been investigated by structural modeling and force field based energy calculations. Solvation and desolvation effects have been treated using an electrostatic continuum model. For each of the three possible binding modes (intercalation and minor and major groove binding), a search of the configurational space resulted in six model structures which were selected by the criterion of lowest total energies. The differences of estimated energies are only a few kilocalories per mole, but suggest a preference for symmetric intercalation at the 5‘-CpG-3‘ or 5‘-GpC-3‘ steps. Asymmetric intercalation and minor and major groove binding appear to be less favorable. This result is compatible with published circular dichroism data. An energetic analysis of the model structures gives detailed insight into the interactions involved in the stabilization of the complex and clearly shows the importance of solvent contributions in selecting the most probable structure from an ensemble of structural alternatives.
Scaling a convolutional neural network based Flower counting application in a distributed GPU cluster (2019)

Taking advantage of modern data acquisition techniques, the researchers of P2IRC located at the University of Saskatchewan developed an application to monitor the status of the flower growth during different phases of the blooming period and the yield prediction of canola crops. Though the application could predict the near accurate number of flowers in a few scenarios, its inability to function under challenging situations such as misinterpreting sun reflection or dust along the roadside as flowers have motivated the researchers to find an alternative approach of counting flowers. In addition to being a more accurate version, another goal is for the new application to be faster to infer the number of flowers and scalable in distributed environments. \n\nPutting these goals in mind, in this thesis, a Convolutional neural network (CNN) based flower counting application is developed and evaluated taking inspiration from two other previous works where CNN was used for counting heads in dense crowds and predicting the number of bacterial cells from medical imagery. In addition to that, the application addresses the performance and the accuracy goals previously mentioned. Two challenges of using the neural network are (a) the training needs a large volume of data to converge to a low error and (b) the training is computationally expensive and it takes longer time to complete. \n\nTo address the first challenge, experiments were run with both "ground truth" estimated using a modified version of the previous flower counter, and ground truth from manual annotation. To address the problem of long training time, two distributed versions of the proposed application were created based on two different distributed architectures called Parameter Server and Ring-AllReduce. Moreover, a detailed explanation of the proposed CNN's architecture along with its memory footprints and GPU utilization is also organized as an in-depth case study to help trace the model's memory consumption during training.\n\nFrom different sets of experiments, the new flower counter application is observed more accurate than its previous version and both implementations of its distributed versions successfully reduced the total completion time as a result of being linearly scalable when more workers are added to run the training. The Ring-AllReduce version performed slightly better than the Parameter Server, but the differences were not substantial.
Expression and Quorum Sensing Regulation of Type III Secretion System Genes of Vibrio harveyi during Infection of Gnotobiotic Brine Shrimp (2015)

Type III secretion systems enable pathogens to inject their virulence factors directly into the cytoplasm of the host cells. The type III secretion system of Vibrio harveyi, a major pathogen of aquatic organisms and a model species in quorum sensing studies, is repressed by the quorum sensing master regulator LuxR. In this study, we found that during infection of gnotobiotic brine shrimp larvae, the expression levels of three type III secretion operons in V. harveyi increased within the first 12h after challenge and decreased again thereafter. The in vivo expression levels were highest in a mutant with a quorum sensing system that is locked in low cell density configuration (minimal LuxR levels) and lowest in a mutant with a quorum sensing system that is locked in the high cell density configuration (maximal LuxR levels), which is consistent with repression of type III secretion by LuxR. Remarkably, in vivo expression levels of the type III secretion system genes were much (> 1000 fold) higher than the in vitro expression levels, indicating that (currently unknown) host factors significantly induce the type III secretion system. Given the fact that type III secretion is energy-consuming, repression by the quorum sensing master regulators might be a mechanism to save energy under conditions where it does not provide an advantage to the cells.
SCA-1 Identifies the Tumor-Initiating Cells in Mammary Tumors of BALB-neuT Transgenic Mice (2008)

Cancer stem cells, initiating and sustaining the tumor process, have been isolated in human and murine breast cancer using different cell markers. In the present study, we aimed to evaluate the presence and characteristics of stem/tumor-initiating cells in the model of the mouse mammary neoplasia driven by the activated form of rat Her-2/neu oncogene (BALB-neuT mice). For this purpose, we generated tumor spheres from primary spontaneous BALB-neuT tumors. Tumor sphere cultures were characterized for clonogenicity, self-renewal, and ability to differentiate in epithelial/myoepithelial cells of the mammary gland expressing basal and luminal cytokeratins and alpha-smooth muscle actin. In addition, tumor spheres were more resistant to doxorubicin compared with parental tumor cells. In the attempt to identify a selected marker for the sphere-generating cells, we found that Sca-1(+) cells, present in tumors or enriched in mammospheres, and not CD24(+) or CD29(+) cells, were responsible for the sphere generation in vitro. Moreover, cells from the tumor spheres showed an increased tumor-generating ability in respect to the epithelial tumor cells. Sca-1(+) sorted cells or clonal mammospheres derived from a Sca-1(+) cell showed a superimposable tumor-initiating ability. The data of the present study indicate that a Sca-1(+) population derived from mammary BALB-neuT tumors is responsible for sphere generation in culture and for initiating tumors in vivo.
Pelvic Floor Muscle Dysfunction (2008)

In Brief Pelvic floor muscle dysfunction is a problem that affects women of all ages. The disorder can present as chronic pelvic pain, dyspareunia, rectal pain, chronic constipation, lower back pain, and a wide array of other complaints. As a result of the various presenting symptoms, patients with pelvic floor muscle dysfunction are seen by a variety of health care workers, including obstetrician-gynecologists, urogynecologists, urologists, colorectal surgeons, orthopedic surgeons, physical therapists, chiropractors, pain management specialists, psychotherapists, and others. The purpose of this review is to discuss the etiology, symptomatology, associated conditions, diagnostic tools, and treatment options for this condition. The supportive function of the female pelvic floor is generally achieved by a combination of multiple components working together in a highly coordinated, specialized fashion. This intricate unit is made up of bones, ligaments, muscles, connective tissue, visceral organs, nerves, and vessels. These components are involved in a wide variety of functions that range from simple acts, such as sitting, standing, and walking to more complicated ones, such as child birth, micturition, and defecation. The dynamic capacity of the pelvic floor can be traumatized by a number of events and this can lead to pelvic floor dysfunction. It is important to review the anatomy and function of the pelvic floor, and recognize potential causes for damage and options for treatment when there is dysfunction. Pelvic floor muscle dysfunction is a condition that can exist on its own or in association with other conditions. It is frequently unrecognized because many health care providers are not specifically looking for it as a potential cause for patient complaints. Treatment usually involves a multidisciplinary approach.
Expression of Naked Plasmid DNA Injected into the Afferent and Efferent Vessels of Rodent and Dog Livers (1997)

A variety of reporter genes within plasmid constructs were injected into the afferent and efferent vessels of the liver in mice, rats, and dogs. Efficient plasmid expression was obtained following delivery via the portal vein, the hepatic vein, and the bile duct. The use of hyperosmotic injection solutions and occlusion of the blood outflow from the liver substantially increased the expression levels. Combining these surgical approaches with improved plasmid vectors enabled uncommonly high levels of foreign gene expression in which over 15 microg of luciferase protein/liver was produced in mice and over 50 microg in rats. Equally high levels of beta-galactosidase (beta-Gal) expression were obtained, in that over 5% of the hepatocytes had intense blue staining. Expression of luciferase or beta-Gal was evenly distributed in hepatocytes throughout the entire liver when either of the three routes were injected. Peri-acinar hepatocytes were preferentially transfected when the portal vein was injected in rats. These levels of foreign gene expression are among the highest levels obtained with nonviral vectors. Repetitive plasmid administration through the bile duct led to successive events of foreign gene expression. The integration of these findings into laboratory and clinical protocols is discussed.
Experimental and theoretical investigations of coherent OFDR with semiconductor laser sources (1994)

Experimental and theoretical investigations of coherent optical-frequency-domain reflectometry using semiconductor laser sources are presented. Good agreement was found between the analysis of the signal-to-noise ratio due to the phase noise and the experimental results. The sensitivity limit due to the quantum noise is also described. Limitations due to the nonlinearity in the optical frequency sweep produced by the thermal-response time of the laser and mode hopping are investigated and compared with experimental results. Two interferometric methods to characterize the thermal-response time of the laser and their implementations are described. The effects of mode hopping in the optical-frequency sweep are compared to numerical simulations. A simple formula to predict the position of spurious peaks due to mode hopping are presented. A spatial resolution of 400 /spl mu/m over 10 cm was obtained by correcting the nonlinearity in the optical-frequency sweep by using an auxiliary interferometer. The Rayleigh backscattering was observed for the first time over more than 400 m of fiber using a DFB laser coupled to an external cavity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cooperative Processes Governing Formation of Small Pentanuclear Lanthanide(III) Nanoclusters and Energy Transport within and between Them (2001)

Syntheses, lanthanide quantitative analyses, mass spectrometry and luminescence spectroscopy, and decay dynamics of crystals containing pentanuclear hetero-lanthanide(III) nanoclusters [(Ln'(5-x)Ln(x))(NO(3))(6)(mu(5)-OH)(mu(4)-L)(2)] (0 < or = x < or = 5), Ln' = Eu or Tb; Ln = La-Nd, Sm-Ho (hereafter Ln'(5-x) Ln(x)) were undertaken in search of information on factors governing self-assembly processes by which the clusters are formed and electronic interactions within and between them. The data obtained are consistent with the self-assembly of Ln'(5-x) Ln(x) nanoclusters being a concerted process featuring a profound expression of complementarity among mutually bridging [Ln(mu(4)-L](-) and [Ln(NO(3))(2)](+) components. The energy transport regime in crystals of Eu(5-x) Ln(x) is in the dynamic regime when x = 0 or Ln = La and, at 293 K, Ln = Dy, despite the presence of two crystallographically different Eu(3+) coordination environments which give rise to a doublet in the excitation and emission spectra of Eu(3+)((5)D(0)). The luminescence decay behavior of Eu(3+)((5)D(0)) in Eu(5-x) Ln(x) (Ln = Dy (for 77 K), Sm) is intermediate between the static and dynamic limits and reveals extensive electronic coupling among lanthanide ions, including many-body processes at relatively high Dy(3+) or Sm(3+) concentrations.
Lip motion capture and its application to 3-D molding (2002)

It is essential for machine lip reading to process not only static images but also moving images. This paper proposes a method, which is named Optical Snakes, for lip motion extraction from moving images using the cooperation between the active contour models called Snakes and the optical flow. The effectiveness of the method is demonstrated by the extraction of a series of lip contours from time-varying images without any markers, and by the analysis of lip contours for machine lip reading. Some real products which characterize a speaker's pronunciation are made from the lip motion data by a photoforming system. It is demonstrated that the real products are better than the virtual products on a computer display for the evaluation of shapes. The application of lip motion to molding would lead to a new method for the analysis of lip motion and the training of pronunciation.
Restoring Dystrophin Expression in Duchenne Muscular Dystrophy Muscle (2011)

The identification of the Duchenne muscular dystrophy gene and protein in the late 1980s led to high hopes of rapid translation to molecular therapeutics. These hopes were fueled by early reports of delivering new functional genes to dystrophic muscle in mouse models using gene therapy and stem cell transplantation. However, significant barriers have thwarted translation of these approaches to true therapies, including insufficient therapeutic material (eg, cells and viral vectors), challenges in systemic delivery, and immunological hurdles. An alternative approach is to repair the patient's own gene. Two innovative small-molecule approaches have emerged as front-line molecular therapeutics: exon skipping and stop codon read through. Both approaches are in human clinical trials and aim to coax dystrophin protein production from otherwise inactive mutant genes. In the clinically severe dog model of Duchenne muscular dystrophy, the exon-skipping approach recently improved multiple functional outcomes. We discuss the status of these two methods aimed at inducing de novo dystrophin production from mutant genes and review implications for other disorders.
Synthetic Studies on Norrisolide:  Enantioselective Synthesis of the Norrisane Side Chain (1999)

Norrisolide (1) belongs to a family of marine diterpenes that are characterized by the assembly of a bicyclic core with a unique and highly oxygenated side chain (norrisane side chain). As a prelude to the synthesis of 1, we present herein a short, efficient, and enantioselective synthesis of the norrisane side chain 4. The synthetic route toward 4 departs from d-mannose and is short (11 steps), efficient, and enantioselective.
Force-Field Compensation in a Manual Tracking Task (2010)

This study addresses force/movement control in a dynamic "hybrid" task: the master sub-task is continuous manual tracking of a target moving along an eight-shaped Lissajous figure, with the tracking error as the primary performance index; the slave sub-task is compensation of a disturbing curl viscous field, compatibly with the primary performance index. The two sub-tasks are correlated because the lateral force the subject must exert on the eight-shape must be proportional to the longitudinal movement speed in order to perform a good tracking. The results confirm that visuo-manual tracking is characterized by an intermittent control mechanism, in agreement with previous work; the novel finding is that the overall control patterns are not altered by the presence of a large deviating force field, if compared with the undisturbed condition. It is also found that the control of interaction-forces is achieved by a combination of arm stiffness properties and direct force control, as suggested by the systematic lateral deviation of the trajectories from the nominal path and the comparison between perturbed trials and catch trials. The coordination of the two sub-tasks is quickly learnt after the activation of the deviating force field and is achieved by a combination of force and the stiffness components (about 80% vs. 20%), which is a function of the implicit accuracy of the tracking task.