gebhart/patrepeval huggingface dataset:
Chorioallantoic Morphogenesis and Formation of the Placental Villous Tree (2003)

The placenta is a highly specialized organ whose primary function is to promote the exchange of nutrients and oxygen between maternal and fetal blood, essential for survival and growth of the baby. The surface area for nutrient transport is a highly convoluted villous structure that forms by branching morphogenesis. In mice, this process begins after embryonic day 8.5, following attachment of allantoic mesoderm to the chorion, and continues through the end of gestation. Gene targeting studies in mice have identified a large number of genes that are essential for chorioallantoic development to give rise to the layer of the placenta called the labyrinth. Collectively, these studies reveal that a number of signaling pathways regulate four distinct phases of labyrinth development: chorioallantoic attachment (involving VCAM1 and its receptor alpha4 integrin, Bmp5/7, and Wnt7b, as well as the cochaperone Mrj), initiation of branching (involving the Gcm1 transcription factor to select sites of branch initiation), extension of villous branching (involving FGF, EGF, and HGF/Met signaling, through the Grb2/Sos1/Mek1/p38alpha MAPK pathway), followed by vascularization of the villous tree. The restricted expression and/or action of the signaling components indicate that a series of intercellular interactions regulate chorioallantoic development.
Nanopore Analysis of Individual RNA/Antibiotic Complexes (2011)

Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3-3.5 nm diameter pore fabricated in a 8-10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug-RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.
Words, Words, Words! (1902)

obtained the first prize of one thousand lire in the competition opened some time since by the authorities of the Palermo Conservatorio.SOFIA.-Under the title of 4 Horo-Dance,' what may be described as the first national Bulgarian opera has just been produced at the Grand Theatre.The composer is M. K. Machanyi, who, as a matter of course, has largely availed himself in his score of the folk-song element of which Bulgaria is by no means destitute.STRASSBURG.-A noteworthy performance of Eduard Grell's sixteen-part Mass (unaccompanied) took place last month at the Church of St. Thomas, under the direction of Musik-director Munch.There was a choir of seven hundred members and sixteen solo vocalists.The remarkable work of the whilom director of the Berlin Singakademie is but rarely performed, owing to the difficulties presented by it, and there was consequently a very numerous and discriminating audience on the present occasion.TERAMO.-Anew one-act Biblical opera, 4 La Figlia di Jefte,' the music by Giuseppe Righetti, has been brought out with much success at the Municipal theatre.
Recovery Increase through Water Flooding with Smart Well Technology (2001)

Abstract Water flooding is a frequently used technique to increase oil recovery after primary depletion. The presence of high permeability zones can have a large influence on the recovery, because they can cause early water breakthrough and trapping of by-passed oil. Smart well technology gives us the opportunity to counteract these effects by imposing an appropriate pressure or flow rate profile along the injection and production wells. In the current study we focus on water flooding with fully penetrating, smart, horizontal wells in 2 dimensional, horizontal reservoirs with simple, large-scale heterogeneities. The water flood is improved by changing the well profiles according to some simple algorithms that move flow paths away from the high permeability zone in order to delay water breakthrough. For all cases where early water breakthrough plays a role, it was possible to improve the water flooding process with these simple algorithms. For all these cases acceleration of production was possible. The increase in ultimate recovery obtained is very much dependent on total production time allowed. The shorter this time, the better the improvement in recovery will generally be. The increase in recovery obtained by applying the optimization algorithm varied between 0% - 20%. The delay in breakthrough time achieved by our optimization routine varied from 7-168 %. Our algorithms result in flow profiles that do not change in time. Both results from our own study and from literature show that time-varying flow profiles can at least further accelerate production. The general principle behind optimization in our cases was to reduce the difference in time of flight from injector to producer as much as possible.
Rhythm Control versus Rate Control for Atrial Fibrillation and Heart Failure (2008)

In patients with atrial fibrillation and congestive heart failure, a routine strategy of rhythm control does not reduce the rate of death from cardiovascular causes, as compared with a rate-control strategy. (ClinicalTrials.gov number, NCT00597077.)
Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks (2017)

Carbapenem-resistant Enterobacteriaceae (CRE) are among the most severe threats to the antibiotic era. Multiple different species can exhibit resistance due to many different mechanisms, and many different mobile elements are capable of transferring resistance between lineages. We prospectively sampled CRE from hospitalized patients from three Boston-area hospitals, together with a collection of CRE from a single California hospital, to define the frequency and characteristics of outbreaks and determine whether there is evidence for transfer of strains within and between hospitals and the frequency with which resistance is transferred between lineages or species. We found eight species exhibiting resistance, with the majority of our sample being the sequence type 258 (ST258) lineage of Klebsiella pneumoniae There was very little evidence of extensive hospital outbreaks, but a great deal of variation in resistance mechanisms and the genomic backgrounds carrying these mechanisms. Local transmission was evident in clear phylogeographic structure between the samples from the two coasts. The most common resistance mechanisms were KPC (K. pneumoniae carbapenemases) beta-lactamases encoded by bla<sub>KPC2</sub>, bla<sub>KPC3</sub>, and bla<sub>KPC4</sub>, which were transferred between strains and species by seven distinct subgroups of the Tn4401 element. We also found evidence for previously unrecognized resistance mechanisms that produced resistance when transformed into a susceptible genomic background. The extensive variation, together with evidence of transmission beyond limited clonal outbreaks, points to multiple unsampled transmission chains throughout the continuum of care, including asymptomatic carriage and transmission of CRE. This finding suggests that to control this threat, we need an aggressive approach to surveillance and isolation.
Rapid and sensitive detection of Mycobacterium leprae using a nested-primer gene amplification assay (1990)

By using a set of four nested oligonucleotide primers, a two-step polymerase chain reaction assay for the detection and identification of Mycobacterium leprae that does not require the use of radioactivity labeled hybridization probes was developed. The nested-primer procedure amplified a 347-base-pair product from M. leprae genomic DNA. No amplification products were produced from DNAs of 19 other Mycobacterium species, 19 non-Mycobacterium species, mouse cells, or human cells. Minor amplification products were observed with three additional Mycobacterium species, i.e., "M. lufu", M. simiae, and M. smegmatis. These products were easily distinguished from the M. leprae product by size and restriction enzyme cleavage patterns. The assay could amplify the 347-base-pair product from samples containing as little as 3 fg of M. leprae genomic DNA--the amount of DNA in a single bacillus. The assay also amplified target sequences in crude lysates of M. leprae bacilli isolated from tissue biopsy specimens from infected animals and humans. The entire assay, from sample preparation to data analysis, can be completed in less than 8 h.
Engineered vascularized bone grafts (2010)

Clinical protocols utilize bone marrow to seed synthetic and decellularized allogeneic bone grafts for enhancement of scaffold remodeling and fusion. Marrow-derived cytokines induce host neovascularization at the graft surface, but hypoxic conditions cause cell death at the core. Addition of cellular components that generate an extensive primitive plexus-like vascular network that would perfuse the entire scaffold upon anastomosis could potentially yield significantly higher-quality grafts. We used a mouse model to develop a two-stage protocol for generating vascularized bone grafts using mesenchymal stem cells (hMSCs) from human bone marrow and umbilical cord-derived endothelial cells. The endothelial cells formed tube-like structures and subsequently networks throughout the bone scaffold 4-7 days after implantation. hMSCs were essential for stable vasculature both in vitro and in vivo; however, contrary to expectations, vasculature derived from hMSCs briefly cultured in medium designed to maintain a proliferative, nondifferentiated state was more extensive and stable than that with hMSCs with a TGF-beta-induced smooth muscle cell phenotype. Anastomosis occurred by day 11, with most hMSCs associating closely with the network. Although initially immature and highly permeable, at 4 weeks the network was mature. Initiation of scaffold mineralization had also occurred by this period. Some human-derived vessels were still present at 5 months, but the majority of the graft vasculature had been functionally remodeled with host cells. In conclusion, clinically relevant progenitor sources for pericytes and endothelial cells can serve to generate highly functional microvascular networks for tissue engineered bone grafts.
The PPAR-gamma agonist pioglitazone protects cortical neurons from inflammatory mediators via improvement in peroxisomal function (2012)

Collectively, these observations provide evidence that modulation of PPAR-gamma activity and peroxisomal function by pioglitazone attenuates both NO and hydrogen peroxide-mediated neuronal and axonal damage suggesting a new therapeutic approach to protect against neurodegenerative changes associated with neuroinflammation.
Real-Time Beat Estimation Using Feature Extraction (2003)

This paper presents a novel method for the estimation of beat interval from audio files. As a first step, a feature extracted from the waveform is used to identify note onsets. The estimated note onsets are used as input to a beat induction algorithm, where the most probable beat interval is found. Several enhancements over existing beat estimation systems are proposed in this work, including methods for identifying the optimum audio feature and a novel weighting system in the beat induction algorithm. The resulting system works in real-time, and is shown to work well for a wide variety of contemporary and popular rhythmic music. Several real-time music control systems have been made using the presented beat estimation method.
Towards a single-chip, implantable RFID system: is a single-cell radio possible? (2009)

We present an overview of progress towards single-chip RFID solutions. To date heterogeneous integration has been appropriate for non-biological systems. However, for in-vivo sensors and even drug delivery systems, a small form factor is required. We discuss fundamental limits on the size of the form factor, the effect of the antenna, and propose a unified single-chip RFID solution appropriate for a broad range of biomedical in-vivo device applications, both current and future. Fundamental issues regarding the possibility of single cell RF radios to interface with biological function are discussed.
Water clusters: Untangling the mysteries of the liquid, one molecule at a time (2001)

Extensive terahertz laser vibration-rotation-tunneling spectra and mid-IR laser spectra have been compiled for several isotopomers of small (dimer through hexamer) water clusters. These data, in conjunction with new theoretical advances, quantify the structures, force fields, dipole moments, and hydrogen bond rearrangement dynamics in these clusters. This new information permits us to systematically untangle the intricacies associated with cooperative hydrogen bonding and promises to lead to a more complete molecular description of the liquid and solid phases of water, including an accurate universal force field.
Chemotherapy for Elderly Patients With Advanced Non-Small-Cell Lung Cancer: The Multicenter Italian Lung Cancer in the Elderly Study (MILES) Phase III Randomized Trial (2003)

The combination of vinorelbine plus gemcitabine is not more effective than single-agent vinorelbine or gemcitabine in the treatment of elderly patients with advanced NSCLC.
Cyclic tetramolecular complexes of monoclonal antibodies: A new type of cross‐linking reagent (1986)

A simple and efficient procedure for the construction of bifunctional molecules is described and their use in a variety of applications documented. This procedure is based on our observation that mouse IgG1 monoclonal antibodies, when mixed with equimolar amounts of a high-affinity rat monoclonal antibody specific for mouse IgG1, yield uniform cyclic tetramolecular complexes each consisting of two mouse and two rat antibodies as shown by gel electrophoresis and electron microscopy. When solutions of two mouse antibodies (e.g. a and b) are mixed prior to the formation of complexes with the rat antibody, stable bispecific (a X b) complexes together with monospecific (a X a and b X b) complexes are obtained. Bispecific complexes prepared in this way were able to efficiently bind peroxidase to cell surface antigens, and to bind red blood cells to selected nucleated cell types present in heterogeneous populations. Tetrameric antibody complexes are more easily prepared than bispecific antibodies or bifunctional antibodies produced by transfection of myelomas with recombinant genes. They also have the advantage that the antigen-binding properties of the bivalent monoclonal antibodies are not compromised. Tetrameric antibody complexes thus represent a powerful new type of cross-linking reagent that may have a wide spectrum of applications in biology and medicine.
Degradation of Misfolded Endoplasmic Reticulum Glycoproteins in Saccharomyces cerevisiae Is Determined by a Specific Oligosaccharide Structure (1998)

In Saccharomyces cerevisiae, transfer of N-linked oligosaccharides is immediately followed by trimming of ER-localized glycosidases. We analyzed the influence of specific oligosaccharide structures for degradation of misfolded carboxypeptidase Y (CPY). By studying the trimming reactions in vivo, we found that removal of the terminal alpha1,2 glucose and the first alpha1,3 glucose by glucosidase I and glucosidase II respectively, occurred rapidly, whereas mannose cleavage by mannosidase I was slow. Transport and maturation of correctly folded CPY was not dependent on oligosaccharide structure. However, degradation of misfolded CPY was dependent on specific trimming steps. Degradation of misfolded CPY with N-linked oligosaccharides containing glucose residues was less efficient compared with misfolded CPY bearing the correctly trimmed Man8GlcNAc2 oligosaccharide. Reduced rate of degradation was mainly observed for misfolded CPY bearing Man6GlcNAc2, Man7GlcNAc2 and Man9GlcNAc2 oligosaccharides, whereas Man8GlcNAc2 and, to a lesser extent, Man5GlcNAc2 oligosaccharides supported degradation. These results suggest a role for the Man8GlcNAc2 oligosaccharide in the degradation process. They may indicate the presence of a Man8GlcNAc2-binding lectin involved in targeting of misfolded glycoproteins to degradation in S. cerevisiae.
Whole‐Blood Viscosity, Hematocrit and Plasma Protein in Normal Subjects at Different Ages (1971)

Abstract Whole‐blood viscosity was measured at six fixed shear rates with a cone‐plate viscometer. The 90 healthy subjects were evenly divided as to sex in three age groups from 15 to 80 years. They were selected by the criteria: normal haematocrit, erythrocyte sedimentation rate, serum creatinine concentration, and degree of intravascular erythrocyte aggregation evaluated by con‐junctival biomicroscopy; and free of disease affecting known rheological properties of the blood. The viscosity was higher in males than in females. Age was not consistently related to whole‐blood viscosity except that women of the oldest age group had a higher whole‐blood viscosity at two isolated shear rates than women in the youngest group and the plasma fibrinogen concentration was higher in the old than in the young women. A stepwise regression analysis of rheological factors and whole‐blood viscosity showed that the hematocrit had by far the closest relation to the whole‐blood viscosity at all shear rates. In the order of decreasing influence were the alpha‐globulins, fibrinogen, and serum albumin. There was a sex difference in that the whole‐blood viscosity of men was related to the concentration of alphas‐globulin, whereas in women the relation was to the alphai‐globulin.
Milk products and substitutes (1992)

Abstract Refinements in the techniques used for incorporation of fat and spray drying have improved the nutritional value of milk substitutes. The significance of these developments in protein separation and evaporation/spray drying technology are demonstrated in the new range of substitutes for colostrum which not only have a high nutritional value but also contain active immunoglobulins. Whilst milk replacers still remain a necessary outlet for excess skim milk powder production, progress has been made in the quality of novel ingredients available. The effect of European Community policy on the formulations used has been to divide milk replacers into two groups, those which do, and those which do not, contain at least 500 g/kg skim milk powder. A whole range of products based on high protein whey powders has been developed in order to replace skim milk protein in milk replacers. Differences in these whey products reflect the method of manufacture and this has repercussions on their nutritional value. The benefits of ultrafiltration technology, developed for the human food industry, have recently become available to the whey-based milk replacer market. Although the majority of milk substitutes are used for feeding calves, specific products have been developed for other species. Milk substitutes for lambs were introduced in the 1970s but there has been little commercial incentive for the use of alternatives to skim milk protein in the United Kingdom. Sow milk replacers are a more recent innovation and have taken advantage of developments in whey processing technology.
Chiral Recognition of Helical Metal Complexes by Modified Cyclodextrins (2001)

Chirality of metal complexes M(phen)3(n+) (M = Ru(II), Rh(III), Fe(II), Co(II), and Zn(II), and phen = 1,10-phenanthroline) is recognized by heptakis(6-carboxymethylthio-6-deoxy)-beta-cyclodextrin heptaanion (per-CO2(-)-beta-CD) and hexakis(2,3,6-tri-O-methyl)-alpha-cyclodextrin (TMe-alpha-CD) in D2O. The binding constant (K) for the Delta-Ru(phen)3(2+) complex of per-CO2(-)-beta-CD (K = 1250 M(-1)) in 0.067 M phosphate buffer at pD 7.0 is approximately 2 times larger than that for the Lambda-isomer (590 M(-1)). Definite effects of inorganic salts on stability of the complexes indicate a large contribution of Coulomb interactions to complexation. The fact that hydrophilic Ru(bpy)3(2+) (bpy = 2,2'-bipyridine) does not form a complex with per-CO2(-)-beta-CD suggests the importance of inclusion of the guest molecule into the host cavity for forming a stable ion-association complex. The positive entropy change for complexation of Ru(phen)3(2+) with per-CO2(-)-beta-CD shows that dehydration from both the host and the guest occurs upon complexation. Similar results were obtained with trivalent Rh(phen)3(3+) cation. Pfeiffer effects were observed in complexation of racemic Fe(phen)3(2+), Co(phen)3(2+), and Zn(phen)3(2+) with per-CO2(-)-beta-CD with enriched Delta-isomers. Native cyclodextrins such as alpha-, beta-, and gamma-cyclodextrins as well as heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin do not interact with Ru(bpy)3(2+). However, hexakis(2,3,6-tri-O-methyl)-alpha-cyclodextrin (TMe-alpha-CD) interacts with Ru(phen)3(2+) and Ru(bpy)3(2+) and discriminates between the enantiomers of these metal complexes. The K values for the Delta- and Lambda-Ru(phen)3(2+) ions are 54 and 108 M(-1), respectively. Complexation of the Delta- and Lambda-isomers of Ru(phen)3(2+) with TMe-alpha-CD is accompanied by negative entropy changes, suggesting that cationic Ru(phen)3(2+) is shallowly included into the cavity of the neutral host through van der Waals interactions. The Delta-enantiomer, having a right-handed helix configuration, fits the primary OH group side of per-CO2(-)-beta-CD (SCH2CO2(-) side) well, while the Lambda-enantiomer, having a left-handed helix configuration, is preferably bound to the secondary OH group side of TMe-alpha-CD. The asymmetrically twisted shape of a host cavity seems to be the origin of chiral recognition by cyclodextrin.
Site-Specific Drug Carriers (1986)

Site-specific drug carriers are required to exclusively deliver drug molecules to difficult targets within the body. They should do so in a form which protects the drug and host from one another. This contribution reviews the reasons for drug targeting, and describes some of the features required of two types of carrier system, i.e., particulates and soluble (bio)conjugates.
Orthogonal LTE Two-Tier Cellular Networks (2011)

In previous works, Vandermonde-subspace frequency division multiplexing (VFDM) has been shown to promote overlay networks by enabling a secondary transmitter to cancel its interference to a primary receiver, while simultaneously transmitting useful information to its own receiver at nonnegligible rates. Interference cancelation is achieved by exploiting the null-space of the channel from the secondary transmitter to the primary receiver. In the wake of a global deployment of the third generation partnership project's (3GPP) long term evolution (LTE), one of the open questions of VFDM concerns its applicability in a primary LTE-orthogonal frequency division multiple access (OFDMA) multi-user setting. In this work, we address this question by extending VFDM to the multi-user scenario where the primary system employs OFDMA, such as LTE. We show that by using at the secondary system a similar precoder structure to the ones previously studied, we are able to cancel the interference towards multiple primary receivers while still achieving acceptable rates for the secondary system.