gebhart/patrepeval huggingface dataset:
Molecular asymmetries in actin dynamics drive left‐right organogenesis (2016)

The embryonic heart tube arises from bilaterally symmetric populations of cells in the anterior lateral plate mesoderm (LPM). These bilateral progenitors undergo epithelial maturation and migrate as coherent sheets of cells that fuse at the midline to form the linear heart tube, which exhibit left‐right asymmetry. Here, we explore the dynamics of the actin cytoskeleton in coordinating the morphogenesis of the LPM during heart tube formation in zebrafish using a fluorescent reporter of actin dynamics, LifeAct‐GFP. Multiphoton time‐lapse microscopy coupled with quantitative analysis of 4‐dimensional data (x,y,z,t) reveal a number of dynamics in actin polymerization within the LPM that is suggestive of differential force exertion from the LPM cells as they undergo morphogenesis. These actin dynamics are asymmetrically distributed and are dependent on both Nodal signaling and tissue‐tissue interaction. The asymmetries can be uncoupled genetically and are required for leftward placement of the heart tube. Taken together, these data suggest that the LPM exerts multiple cellular traction forces as it undergoes midline migration and morphogenesis to form a leftward positioned linear heart tube.
Oxidation Reactions in CO2:  Academic Exercise or Future Green Processes? (2003)

Conducting oxidation reactions using CO2 as the solvent is a promising strategy for creation of greener chemical processes that are also economical, as CO2 and water are probably the only solvents that can be used in oxidation reactions without the formation of any solvent byproducts. However, it must be noted that the promise of CO2-based oxidation still dwarfs the actual realization of CO2-based oxidation processes. Nevertheless, there is extensive literature on the use of CO2 as the solvent for the oxidation of cyclohexane (adipic acid synthesis), cumene oxidation (phenol synthesis), and epoxidation (propylene oxide synthesis). In all of these studies, knowledge of the phase behavior is crucial toward understanding the effects of pressure and temperature on reaction outcomes. To date, much of the research in this field has involved simply using CO2 as a "drop-in" replacement for a conventional organic solvent; it will be interesting in the future to see if the use of CO2 can be combined with innovations in catalyst and reactor design to create truly green oxidation processes where the use of CO2 is not merely tolerated but truly supports process and chemistry innovation.
Complex intrachromosomal rearrangement in the process of amplification of the L-myc gene in small-cell lung cancer. (1992)

The L-myc gene was first isolated from a human small-cell lung cancer (SCLC) cell line on the basis of its amplification and sequence similarity to c-myc and N-myc. A new mechanism of L-myc activation which results from the production of rlf-L-myc fusion protein was recently reported. On the basis of our earlier observation of a rearrangement involving amplified L-myc in an SCLC cell line, ACC-LC-49, we decided to investigate this rearrangement in detail along with the structure of L-myc amplification units in five additional SCLC cell lines. We report here the identification of a novel genomic region, termed jal, which is distinct from rlf and is juxtaposed to and amplified with L-myc during the process of DNA amplification of the region encompassing L-myc. Long-range analysis using pulsed-field gel electrophoresis revealed that the amplified L-myc locus is involved in highly complex intrachromosomal rearrangements with jal and/or rlf. Our results also suggest that the simultaneous presence of rearrangements both in rlf intron 1 and in regions immediately upstream of L-myc may be necessary for the expression of rlf-L-myc chimeric transcripts.
Comparison of inhibitory activities of various antiretroviral agents against particle-derived and recombinant human immunodeficiency virus type 1 reverse transcriptases (1989)

Several known antiretroviral agents were tested for their ability to inhibit the activities of human immunodeficiency virus type 1 reverse transcriptase purified from virions or from a recombinant Escherichia coli strain. The recombinant reverse transcriptase, a polypeptide of 66 kilodaltons, showed inhibition profiles indistinguishable from those of the virion-derived enzyme with all tested compounds, except for suramin and two dextran sulfates. These were more inhibitory to the recombinant enzyme, presumably because the E. coli-derived enzyme was more highly purified. The relative ease with which large quantities of recombinant enzyme can be prepared should facilitate the large-scale screening and identification of new potential inhibitors of the human immunodeficiency virus type 1 reverse transcriptase.
New Architectures for Designed Catalysts: Selective Oxidation using AgAu Nanoparticles on Colloid‐Templated Silica (2017)

Abstract Invited for the cover of this issue are the groups of Joanna Aizenberg and Cynthia M. Friend from Harvard University, Cambridge, USA. The image depicts a templated silica matrix decorated with AuAg nanoparticles catalyzing the oxidative coupling of methanol to form methyl formate. Read the full text of the article at 10.1002/chem.201704552 .
Determination of Haloacetic Acids in Water by LC/MS (2004)

Introduction oacetic acids (HAAs) are disinfection byproducts (DBPs) of the chlorination of drinking water. Dichloroacetic acid and trichloroacetic acid are animal carcinogens. We present an ion-pair HPLC and negative electrospray ionization mass spectrometry (ESI-MS) method with a “function-switching” feature for analysis of all 9 haloacetic acids, monochloroacetic acid (MCAA), dichloroacetic acid (DCAA), monobromoacetic acid (MBAA), bromochloroacetic acid (BCAA), dibromoacetic acid (DBAA), bromodichloroacetic acid (BDCAA), trichloroacetic acid (TCAA), chlorodibromoacetic acid (CDBAA), and tribromoacetic acid (TBAA). JEOL MassCenter™ software can switch different MS settings by the time course. This “function-switching” feature enables each HAA to be analyzed under its optimized MS conditions so that the highest sensitivity can be achieved. Using triethylamine (TEA) as an ion-pairing reagent, a good HPLC separation of all 9 HAAs has been achieved. The optimized MS conditions for each HAA were evaluated.
Structure-Guided Engineering of a Multimeric Bacteriophage-Encoded Endolysin PlyC (2019)

Emerging antibiotic resistance has become a global health threat. One alternative to antibiotics is bacteriophage-encoded endolysins. Endolysins are peptidoglycan hydrolases produced at the end of the bacteriophage replication cycle resulting in bacterial cell lysis and progeny bacteriophage release. Endolysins are also capable of destroying the Gram-positive bacterial peptidoglycan when applied externally as recombinant proteins. These enzymes typically consist of an enzymatically active domain (EAD) and a separate cell wall binding domain (CBD). Studies have shown therapeutic efficacy of endolysins in vitro and in vivo, with no resistance developed to date. An endolysin from the streptococcal C1 phage, known as PlyC, has the highest activity of any endolysin reported. It also has a unique multimeric structure consisting of one activity subunit (PlyCA) harboring two synergistically acting catalytic domains, GyH and CHAP, and eight identical binding subunits (PlyCB) forming an octameric ring. Groups A, C, and E streptococci as well as Streptococcus uberis are sensitive to the lytic activities of PlyC. In order to harness the potent activity of PlyC for use against other bacteria, we sought to change/extend the host range of PlyC by engineering PlyCB and PlyCA, respectively. We first used a structure-guided mutagenesis method to obtain the single PlyCB monomer subunit, PlyCBK40A E43A (PlyCBm), aiming to study the binding mechanism of PlyCB. Via fluorescence microscopy and binding assays, we determined that PlyCBm retained the host range of the octamer with a much lower binding affinity, which suggests the PlyCB octamer binds concurrently to a specific epitope on the bacterial surface resulting in a tight, stable interaction. Thus, it is not feasible to change/extend the PlyC host range via engineering PlyCB. Next, we proposed a novel design to engineer PlyCA. We successfully created two chimeric endolysins, ClyX-1 and ClyX-2, possessing the synergistic activity of the GyH and CHAP catalytic domains, but extended the host range to include, Streptococcus pneumoniae, Group B streptococci, Streptococcus mutans, and Enterococcus faecalis, all strains previously insensitive to PlyC. Finally, we tested a novel hypothesis that a positively charged catalytic domain could display lytic activity in a CBD-independent manner resulting in a broad host range. Using the PlyC CHAP domain as a model, we converted the net surface charge of the CHAP domain from negative three to positive one through positive seven. Notwithstanding the range of charges, our mutant CHAP domains did not show lytic activity in a CBD-independent manner, suggesting that other factors, like surface charge distribution, need to be considered in such a way of engineering.
Reduced Competitive Repopulation Capacity of Multipotential Hematopoietic Stem Cells in the Bone Marrow of Friend Virus-infected Fv2-resistant Mice (2017)

Friend virus disease in Fv-2<sup>s</sup> mice is associated with expansion of committed hematopoietic progenitors. Fv-2<sup>r</sup> mice show no expansion of either committed progenitor or pluripotential stem cell numbers.
Prevalence of extracolonic findings at virtual colonoscopy (2003)

Purpose: To determine the prevalence of extracolonic findings at virtual colonoscopy using CT scanning of the abdomen and pelvis for data acquisition.
Drug Delivery: Zero‐Order Antibiotic Release from Multilayer Contact Lenses: Nonuniform Drug and Diffusivity Distributions Produce Constant‐Rate Drug Delivery (Adv. Healthcare Mater. 3/2017) (2017)

In article 1600775, Mukerrem Cakmak and co-workers present a novel approach to zero-order constant-rate drug delivery from three-layer bimodal amphiphilic conetwork contact lenses. Combined effects of nonuniform distribution of drug loading and diffusion constants maintains low local drug concentration at the lens–fluid interface and yields zero-order drug delivery. The release rates of topical antibiotics provide constant-rate therapeutic-level delivery with appropriate oxygen permeability for at least 30 h.
Nanostructure-Mediated Thermal Therapy – The Path From Bench to Clinic (2006)

Evaluation of: Huang X, El-Sayed IH, Qian W, El-Sayed MA: Cancer cell imaging and photothermal therapy in the near-infrared region by using gold nanorods. J. Amer. Chem. Soc. 128(6), 2115–2120 (2006) [1]. A recent paper, one of several recent studies on the use of nanostructures in thermal cancer therapy, is evaluated here. Functionalized gold nanorods have been used in vitro to selectively destroy cancer cells by converting near infrared radiation to heat. Nanostructures with tunable optical properties and biologically relevant size show great promise in highly selective thermal ablation therapy. Gold nanorods coated with targeting antibodies were demonstrated to be selective agents for the detection and destruction of cancer cells. We present the results of the El-Sayed paper, compare gold nanorods with other near infrared-absorptive nanostructures and discuss challenges of nanostructure-mediated thermal therapy.
LDPC code design for OFDM channel: graph connectivity and information bits positioning (2006)

We present an optimized channel coding scheme for OFDM transmission. In the future wireless standards such IEEE 802.11n, frame error rates (FER) as low as 0.0001 are targeting. Irregular LDPC codes have excellent performance at moderate computational complexity: they are strong candidates for channel coding in such systems. In the context of an OFDM transmission, Mannoni et al. (2002) proposed to optimize the graph connectivity of the irregular LDPC code accordingly to the channel spectrum. However, their codes did not have good performance for a FER range of 0.001-0.0001. In this paper, we propose to optimize the LDPC code in two steps: first, we optimize the graph connectivity in order to get a minimum operational average SNR and therefore excellent FER; then we optimize the information bits placement accordingly to the channel. By simulation, we show that our approach provides substantial performance gain in term of FER over the existing methods (1 dB or more for FER equal to 10/sup -4/).
Phenomenological aspects of new gravitational forces. II. Static planetary potentials (1987)

Theories of quantum gravity generically predict that there are vector and scalar partners of the graviton. These bosons produce new gravitational effects which, in general, tend to cancel in matter because the vector boson produces a repulsive force, whereas a scalar boson produces an attractive force. In this paper we derive the effects which these new interactions will produce in planets. In particular, static Yukawa potential theory is elucidated for massive (nonpointlike) objects.
A series of InGaP/InGaAs HBT oscillators up to D-band (2001)

In this paper, the development of a series of fixed-frequency heterojunction bipolar transistor (HBT) oscillators from the W- to D-bands is reported. The oscillators are designed based on feedback theory with a small-signal equivalent circuit. This design method enables the achievement of high-output-power oscillators for the management of the power that is generated at the current source inside the HBT. We use a 1 /spl mu/m/spl times/10 /spl mu/m single-emitter InGaP/InGaAs HBT as an active device for each oscillator, and 50-/spl Omega/ coplanar waveguides as transmission lines and resonators. Emitter output topology is adopted to reduce the chip size. The series of oscillators achieve the oscillation frequency of 74.8-146.7 GHz. To our knowledge, the 146.7-GHz fundamental oscillation frequency is the highest oscillation frequency achieved thus far using InGaP/InGaAs HBT technology. The output power of the 146.7-GHz oscillator is -18.4 dBm. The chip size of the oscillator is 731 /spl mu/m/spl times/411 /spl mu/m.
Sonochemical Reaction of [Fe(CO)5] with 1‐Methylimidazole in An Ionic Liquid: Formation of [(1‐Methylimidazole)6FeII](PF6)2 (2004)

Abstract The ionic liquid 1‐butyl‐3‐methylimidazolium hexafluorophosphate, (BMI + )(PF 6 − ), has been used as a solvent in the sonochemical reaction of 1‐methylimidazole and [Fe(CO) 5 ] at 40−50 °C under air. The reaction afforded [(1‐methylimidazole) 6 Fe II ](PF 6 ) 2 , the structure of which was determined at 293 K by single‐crystal X‐ray diffraction methods. The salt crystallizes in the trigonal space group P $\bar 3$ with unit‐cell parameters of a = 11.4603(16) Å, c = 8.0172(11) Å, and Z = 1. The crystals showed twinning by merohedry, which was accounted for in the structure determination and refinement calculations. All the 1‐methylimidazole ligands are equivalent, with a Fe−N bond length of 2.204(3) Å. Mössbauer spectroscopy confirmed the presence of Fe 2+ . (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Growth Regulation in Crop Plants with New Types of Triazole Compounds1) (1987)

Abstract BAS 110 … W and BAS 111 … W are introduced as new triazole‐type plant growth regulators. Most probably, the principal mode of action of both compounds consists in reducing the endogenous levels of biologically active gibberellins, thereby inducing shorter stems. The risk of lodging can be reduced in particular by BAS 110 … W in cereals and by BAS 111 … W in oilseed rape. Apart from this, pronounced increases in seed yield are obtained which are most probably due to the following effects: improved canopy structure, delayed senescence of leaves, improved partitioning of assimilates, enhanced root growth, reduced fungal infections and a lowered susceptibility to low temperatures and drought.
Novel vaccines for allergen-specific immunotherapy (2020)

Molecular allergy diagnosis is useful for the prescription and monitoring of AIT and may improve the success of AIT. Results with molecular allergy vaccines and by passive immunization with allergen-specific IgG antibodies indicate the importance of allergen-specific IgG capable of blocking allergen recognition by IgE and IgE-mediated allergic inflammation as important mechanism for the success of AIT. New molecular vaccines may pave the road towards prophylactic allergen-specific vaccination.
A note on BIC in mixed-effects models (2014)

The Bayesian Information Criterion (BIC) is widely used for variable selection in mixed effects models. However, its expression is unclear in typical situations of mixed effects models, where simple definition of the sample size is not meaningful. We derive an appropriate BIC expression that is consistent with the random effect structure of the mixed effects model. We illustrate the behavior of the proposed criterion through a simulation experiment and a case study and we recommend its use as an alternative to various existing BIC versions that are implemented in available software.
Requirement of spermidine for developmental transitions in Aspergillus nidulans (2002)

Deletion of the spermidine synthase gene in the fungus Aspergillus nidulans results in a strain, deltaspdA, which requires spermidine for growth and accumulates putrescine as the sole polyamine. Vegetative growth but not sporulation or sterigmatocystin production is observed when deltaspdA is grown on media supplemented with 0.05-0.10 mM exogenous spermidine. Supplementation of deltaspdA with >/= 0.10 mM spermidine restores sterigmatocystin production and >/= 0.50 mM spermidine produces a phenotype with denser asexual spore production and decreased radial hyphal growth compared with the wild type. DeltaspdA spores germinate in unsupplemented media but germ tube growth ceases after 8 h upon which time the spores swell to approximately three times their normal diameter. Hyphal growth is resumed upon addition of 1.0 mM spermidine. Suppression of a G protein signalling pathway could not force asexual sporulation and sterigmatocystin production in deltaspdA strains grown in media lacking spermidine but could force both processes in deltaspdA strains supplemented with 0.05 mM spermidine. These results show that increasing levels of spermidine are required for the transitions from (i) germ tube to hyphal growth and (ii) hyphal growth to tissue differentiation and secondary metabolism. Suppression of G protein signalling can over-ride the spermidine requirement for the latter but not the former transition.
Supplementary Figure 6 from A Human Breast Cell Model of Preinvasive to Invasive Transition (2023)

Supplementary Figure 6 from A Human Breast Cell Model of Preinvasive to Invasive Transition
The implications of damage to the lateral femoral condyle on medial unicompartmental knee replacement (2010)

With medial unicompartmental osteoarthritis (OA) there is occasionally a full-thickness ulcer of the cartilage on the medial side of the lateral femoral condyle. It is not clear whether this should be considered a contraindication to unicompartmental knee replacement (UKR). The aim of this study was to determine why these ulcers occur, and whether they compromise the outcome of UKR. Case studies of knees with medial OA suggest that cartilage lesions on the medial side of the lateral condyle are caused by impingement on the lateral tibial spine as a result of the varus deformity and tibial subluxation. Following UKR the varus and the subluxation are corrected, so that impingement is prevented and the damaged part of the lateral femoral condyle is not transmitting load. An illustrative case report is presented. Out of 769 knees with OA of the medial compartment treated with the Oxford UKR, 59 (7.7%) had partial-thickness cartilage loss and 20 (2.6%) had a full-thickness cartilage deficit on the medial side of the lateral condyle. The mean Oxford Knee Score (OKS) at the last follow-up at a mean of four years was 41.9 (13 to 48) in those with partial-thickness cartilage loss and 41.0 (20 to 48) in those with full-thickness loss. In those with normal or superficially damaged cartilage the mean was 39.5 (5 to 48) and 39.7 (8 to 48), respectively. There were no statistically significant differences between the pre-operative OKS, the final review OKS or of change in the score in the various groups. We conclude that in medial compartment OA, damage to the medial side of the lateral femoral condyle is caused by impingement on the tibial spine and should not be considered a contraindication to an Oxford UKR, even if there is extensive full-thickness ulceration of the cartilage.
Characteristics of workloads used in high performance and technical computing (2007)

This paper provides a systematic comparison of various characteristics of computationally-intensive workloads. Our analysis focuses on standard HPC benchmarks and representative applications. For the selected workloads we provide a wide range of characterizations based on instruction tracing and hardware counter measurements.
A Dual Embryonic Origin for Vertebrate Mechanoreceptors (1994)

Neuromasts, the mechanoreceptors of the lateral line system of fishes and aquatic amphibians, have previously been thought to develop exclusively from embryonic epidermal placodes. Use of fate mapping techniques shows that neuromasts of the head and body of zebrafish, Siamese fighting fish, and Xenopus are also derived from neural crest. Neural crest migrates away from the neural tube in developing vertebrates to form much of the peripheral nervous system, pigment cells, and skeletal elements of the head. The data presented here demonstrate that neuromasts are derived from both neural crest and epidermal placodes.
Margaret Thatcher, c’est la de Gaulle des Anglais (Interview) (2013)

Premier paragraphe :\nUn service religieux a été célébré mercredi 17 avril dans la cathédrale Saint-Paul de Londres pour l’ex-premier ministre britannique.\nLes opposants se sont faits discrets et n’ont provoqué aucun incident lors du passage de l’imposant cortège funèbre à travers Londres.
Coupling Between Colloidal Assemblies Can Drive a Bistable‐to‐Oscillatory Transition (2019)

Abstract We present a model to describe oscillations and collective behavior in a heterogeneous system of active colloidal clusters whose motility and interactions are driven by an oscillatory chemical reaction, as motivated by experimental observations of collective behavior in silver phosphate clusters under UV light in the presence of hydrogen peroxide, where spatio‐temporal correlations in cluster behavior are presumably modulated by diffusive communication between clusters. A generic model for a single bistable cluster becomes oscillatory upon introduction of inter‐cluster interactions that relate to localized emission or consumption of diffusing species. Multi‐cluster simulations capture the qualitative features in the experimentally observed spatio‐temporal correlations in the oscillations of nearby clusters. Since the model is generic and does not rely upon a particular chemical mechanism, it can be applied to other active matter systems exhibiting collective behavior, where interactions between bistable entities can drive collective oscillations.