gebhart/patrepeval huggingface dataset:
A new parallel method for molecular dynamics simulation of macromolecular systems (1994)

Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter-processor communication scales as N, the number of atoms, independent of P, the number of processors. Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this paper a new parallel method called force-decomposition for simulating macromolecular or small-molecule systems is presented. Its memory and communication costs scale as N/{radical}P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load-balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor.
Impact of complementary treatment of breast cancer patients with standardized mistletoe extract during aftercare: a controlled multicenter comparative epidemiological cohort study. (2008)

Complementary treatment with the sME HELIXOR proved to be beneficial for breast cancer patients since it significantly improved quality of life and significantly reduced persistant signs/symptoms of the disease/treatment during the validated aftercare period of approximately five years.
LOS VARONES JÓVENES EN LA CORRESPONDENCIA DE DOÑA MARÍA DE CASTILLA, REINA DE ARAGÓN * (2012)

espanolEn este articulo se estudia la mirada que una mujer culta y poderosa del siglo XV sostuvo sobre la juventud masculina. Para su elaboracion se han utilizado Registros de Cancilleria Real del Archivo de la Corona de Aragon que contienen cartas de la soberana que aportan datos sustanciosos acerca del grupo juvenil masculino en la sociedad cortesana; que guardan memoria de cuestiones problematicas estructurales de la juventud, y de las acciones y comportamientos juveniles en los que la reina actuo como reguladora. Se ha incidido especialmente en las negociaciones de dona Maria para promover a los jovenes de su entorno y se han analizado algunas de las actuaciones transgresoras juveniles (injuriar a doncellas, perturbar a viudas y huerfanos o provocar escandalos publicos) en las que la reina intervino. EnglishThis article studies the standpoint maintained by a learned and powerful 15th-century woman on male youth. It is grounded on the registers of the Royal Chancellery held at the Archive of the Crown of Aragon, which contain letters by the queen providing substantial evidence about male youth in courtly society. This documentation records structural problems concerning youth as well as the actions and attitudes of young men regarding which the queen exercised her powers. Particular attention is given to Queen Maria's negotiations in order to promote the young men in her entourage, as well as to the transgressive behaviour of the young men whose actions were the target of the Queen's direct intervention, such as abusing ladies, disturbing widows and orphans and causing public scandals.
Platelets in HIV: A Guardian of Host Defence or Transient Reservoir of the Virus? (2021)

The immune and inflammatory responses of platelets to human immunodeficiency virus 1 (HIV-1) and its envelope proteins are of great significance to both the treatment of the infection, and to the comorbidities related to systemic inflammation. Platelets can interact with the HIV-1 virus itself, or with viral membrane proteins, or with dysregulated inflammatory molecules in circulation, ensuing from HIV-1 infection. Platelets can facilitate the inhibition of HIV-1 infection <i>via</i> endogenously-produced inhibitors of HIV-1 replication, or the virus can temporarily hide from the immune system inside platelets, whereby platelets act as HIV-1 reservoirs. Platelets are therefore both guardians of the host defence system, and transient reservoirs of the virus. Such reservoirs may be of particular significance during combination antiretroviral therapy (cART) interruption, as it may drive viral persistence, and result in significant implications for treatment. Both HIV-1 envelope proteins and circulating inflammatory molecules can also initiate platelet complex formation with immune cells and erythrocytes. Complex formation cause platelet hypercoagulation and may lead to an increased thrombotic risk. Ultimately, HIV-1 infection can initiate platelet depletion and thrombocytopenia. Because of their relatively short lifespan, platelets are important signalling entities, and could be targeted more directly during HIV-1 infection and cART.
Antigenic protein from Mycobacterium leprae released in macrophages in vitro as indicator of viability of bacteria. (1990)

Peritoneal macrophages from randombred, Swiss white mice, when cultured and infected with Mycobacterium leprae for 24 hours, are able to show the presence of antigen(s) with binding affinity to antibodies present in the sera of bacteriologically positive, lepromatous leprosy patients. Such antibodies are not seen in sera from normal and healthy persons, tuberculoid leprosy patients, or long-term-treated, bacteriologically negative, lepromatous leprosy patients. The production of the antigen(s) is blocked by the anti-M leprae drug rifampin. Other mycobacteria when incubated with macrophages from mice show very little antigens in the lysate but the antigens have an equal affinity for antibodies in sera from both normal individuals and lepromatous patients. Only the lysates from macrophages exposed to live M. leprae could discriminate and could exhibit differential binding to sera from leprosy patients compared to sera from normal individuals. This antigen(s) does not have any binding ability to the monoclonal antibodies available to the antigens of M. leprae identified at present and shown to be specific to M. leprae. This indicates a separate identity of this product which has potential for further exploitation in exploring host-pathogen interactions related specifically to the leprosy infection and the tolerance of M. leprae inside cells.
Environmentally friendly bleaching of cotton using laccases (2005)

A new strain of Trametes hirsuta was found to oxidize various cotton flavonoids. Here we show that laccases of this organism were responsible for oxidation of the flavonoids morin, luteolin, rutin and quercetin. Out of two laccases produced by T. hirsuta (60.7 and 51.0 kDa) the more prominent 60.7 kDa laccase was purified and showed K m and k cat values of 75.5, 20.9 and 49.4 μM and 72.5, 96.3 and 32.7 s−1, hours on ABTS, syringaldazide and DMP, respectively. Pretreatment of cotton with the T. hirsuta laccase resulted in a whiteness increase of 8.5%.
In Vivo Penetrating Microelectrodes for Brain Electrophysiology (2022)

In recent decades, microelectrodes have been widely used in neuroscience to understand the mechanisms behind brain functions, as well as the relationship between neural activity and behavior, perception and cognition. However, the recording of neuronal activity over a long period of time is limited for various reasons. In this review, we briefly consider the types of penetrating chronic microelectrodes, as well as the conductive and insulating materials for microelectrode manufacturing. Additionally, we consider the effects of penetrating microelectrode implantation on brain tissue. In conclusion, we review recent advances in the field of in vivo microelectrodes.
Cotrimoxazole Resistant Chancroid. (2017)

Four male young adults, after contact with prostitutes, developed clinically typical chancroid which was resistant to cotrimoxazole alone and also in combination with tetracycline. With chloramphenicol, the response was quick and complete with no untoward side effects.
Biological Baeyer–Villiger oxidation of some monocyclic and bicyclic ketones using monooxygenases from Acinetobacter calcoaceticus NCIMB 9871 and Pseudomonas putida NCIMB 10007 (1994)

A. calcoaceticus NCIMB 9871 and Ps. putida NCIMB 10007 [grown on (+)-camphor] have been utilized as biocatalysts in Baeyer–Villiger oxidations. The former microorganism oxidized the racemic ketone 6 non-selectively but transformed the dihalogeno ketone (±)-8 into optically active lactone 10 and recovered ketone. Ps. putida NCIMB 10007 oxidized the two enantiomers of the ketone 6 at different rates while both enantiomers of ketone (±)-1 were converted into lactones, one enantiomer giving 3-oxabicyclooctenone preferentially, while the other enantiomer gave 2-oxabicyclooctenone. Ps. putida NCIMB 10007 contains two quite different types of monooxygenase enzyme, one using NADH as cofactor (labelled MO1) the other employing NADPH as cofactor (labelled MO2). Monooxygenase MO1 proved to be a selective efficient biocatalyst for the oxidation of bicyclic ketones such as 1 and 6 while monooxygenase MO2 is a useful catalyst for the oxidation of cyclopentanones 15–17. Cofactor recycling was effected using dehydrogenase enzymes in preparative-scale experiments.
Influence of Tumor Location on the Composition of Immune Infiltrate and Its Impact on Patient Survival. Lessons from DCBCL and Animal Models (2012)

Diffuse large B-cell lymphomas (DLBCLs) are heterogeneous diseases growing either in nodal or extranodal locations including the central nervous system. One key issue is to decipher the prognostic value of immune cells infiltrating these tumors as DLBCLs developing in sanctuaries are more aggressive than nodal DLCBLs. Here, we summarize available data from the literature regarding the prognostic values of the different immune cell types found in these two types of human primary tumors (i.e., nodal vs brain). In nodal DLBCLs, memory T-cells and dendritic cells (DCs) densities are of good prognostic value whereas the influence of regulatory T-cells (Tregs) is less clear, in accordance with other types of cancers. Data for primary central nervous system lymphomas are very sparse for these cell types. By contrast, CD8(+) cytotoxic T-cells seem to be of poor prognosis in either location. Their presence is linked to a loss of MHC expression providing a possible immune escape mechanism for these tumors. Clearly, tumor-associated macrophages are not associated to a significant prognostic value even in the brain where they highly infiltrate the tumor. Animal models indicate some specific features of lymphoma developing in sanctuaries by comparison to splenic location, with a higher infiltration of Tregs and less DCs, most likely reflecting the immunosuppressive context of these organs. All these informations illustrate the high impact of the immune system on patient outcome, encourage the pursuit of the immune environment's analysis and of immunotherapeutic approaches.
Suprathreshold levodopa doses, dyskinesias, and disability in advanced Parkinson's disease (1998)

Reply from the Authors: We thank Drs. Horstink and Praamstra for their interest in our article. In their letter, they state that dyskinesias can be disabling and conclude that when accurate movements are required, such as when performing the pegboard test, patients are sometimes better off bradykinetic than dyskinetic. We …
Event-Related Bias Removal for Real-time Disaster Events (2020)

Social media has become an important tool to share information about crisis events such as natural disasters and mass attacks. Detecting actionable posts that contain useful information requires rapid analysis of huge volume of data in real-time. This poses a complex problem due to the large amount of posts that do not contain any actionable information. Furthermore, the classification of information in real-time systems requires training on out-of-domain data, as we do not have any data from a new emerging crisis. Prior work focuses on models pre-trained on similar event types. However, those models capture unnecessary event-specific biases, like the location of the event, which affect the generalizability and performance of the classifiers on new unseen data from an emerging new event. In our work, we train an adversarial neural model to remove latent event-specific biases and improve the performance on tweet importance classification.
Rheological, potentiometric and 23Na NMR studies on pectin-calcium systems (2007)

Pectins with degree of methylation lower than 50% are able to gel in presence of divalent ions such as calcium. A phase diagram of a sodium pectinate (DM=28%) in wate, pH 7.4, and 20°C was established, evidencing three phases: sol, gel, and syneresis. From rheological experiments, the calcium concentration at the sol-gel transition was determined, [Ca2+]t/[COO−] ≈ 0.168, for a polymer concentration of 5.8 g/l and it was shown that this transition was accurately described by the scalar percolation theory. Under the same conditions, potentiometric studies showed that the binding of calcium ions seemed to be independent from physical state (sol or gel). Furthermore, this calcium binding decreased only slightly with the amount of added calcium, whereas the sodium one decreased sharply in the same time. By following the evolution of the 23Na NMR longitudinal relaxation time, and abrupt increase was found around [Ca2+]t[COO−]=0.182, which was close to the results of the rheological study.
Resolution of multiple endosomal compartments associated with the internalization of epidermal growth factor and transferrin (1987)

Morphological studies have indicated divergent pathways for the endocytosis of epidermal growth factor (EGF) and transferrin (Tf). In order to obtain biochemical evidence for the pathways associated with the endocytosis of EGF and Tf, a series of Percoll density gradients were employed to separate individual cellular components. Subcellular fractionation of murine fibroblasts exposed to a 2-min pulse of either 125I-Tf or 125I-EGF results in the detection of a total of six cellular compartments related to the internalization process of these ligands. The results of kinetic analysis of the entry of EGF into five membranous fractions is consistent with a model in which ligand is transferred sequentially from the plasma membrane through three distinct prelysosomal environments prior to reaching secondary lysosomes. Each prelysosomal compartment exhibits distinct density and temporal properties in a Percoll density gradient and may represent preexisting endocytic vesicles and/or specific domains of a continuous tubular structure, vesicularized during the process of cell disruption. In addition, the observed differential migration on Percoll density gradients of Tf and EGF containing compartments indicates that the majority of cell bound Tf segregates from EGF and enters a compartment lacking EGF within 5 min of internalization.
Neutron analysis of spent fuel storage installation using parallel computing and advance discrete ordinates and Monte Carlo techniques (2005)

In the United States, the Nuclear Waste Policy Act of 1982 mandated centralised storage of spent nuclear fuel by 1988. However, the Yucca Mountain project is currently scheduled to start accepting spent nuclear fuel in 2010. Since many nuclear power plants were only designed for -10 y of spent fuel pool storage, > 35 plants have been forced into alternate means of spent fuel storage. In order to continue operation and make room in spent fuel pools, nuclear generators are turning towards independent spent fuel storage installations (ISFSIs). Typical vertical concrete ISFSIs are -6.1 m high and 3.3 m in diameter. The inherently large system, and the presence of thick concrete shields result in difficulties for both Monte Carlo (MC) and discrete ordinates (SN) calculations. MC calculations require significant variance reduction and multiple runs to obtain a detailed dose distribution. SN models need a large number of spatial meshes to accurately model the geometry and high quadrature orders to reduce ray effects, therefore, requiring significant amounts of computer memory and time. The use of various differencing schemes is needed to account for radial heterogeneity in material cross sections and densities. Two P3, S12, discrete ordinate, PENTRAN (parallel environment neutral-particle TRANsport) models were analysed and different MC models compared. A multigroup MCNP model was developed for direct comparison to the SN models. The biased A3MCNP (automated adjoint accelerated MCNP) and unbiased (MCNP) continuous energy MC models were developed to assess the adequacy of the CASK multigroup (22 neutron, 18 gamma) cross sections. The PENTRAN SN results are in close agreement (5%) with the multigroup MC results; however, they differ by -20-30% from the continuous-energy MC predictions. This large difference can be attributed to the expected difference between multigroup and continuous energy cross sections, and the fact that the CASK library is based on the old ENDF/B-II library. Both MC and SN calculations were run in parallel on a BEOWULF PC-cluster (eight processors). Timing results indicate that the SN calculation yielded a detailed dose distribution at over 318,426 points in -164 h. Unbiased continuous energy MC required 214 h to calculate dose rates with a 1% relative error in only 18 regions on the surface of the cask. The biased A3MCNP calculations yields dose rates with -0.8% relative error in only 2.5 h on one processor. This study demonstrates that a parallel code, such as the 3-D parallel SN transport code, PENTRAN can solve a complex large problem, such as the storage cask, accurately and efficiently. Moreover, this calculation was performed on a relatively inexpensive PC-cluster. Possible inadequacies of the CASK cross section library still need to be evaluated.
A Borehole Test for Chlorinated Solvent Diffusion and Degradation Rates in Sedimentary Rock (2022)

Abstract We present a new field measurement and numerical interpretation method (combined termed “test”) to parameterize the diffusion of trichloroethene (TCE) and its biodegradation products (DPs) from the matrix of sedimentary rock. The method uses a dual‐packer system to interrogate a low‐permeability section of the rock matrix adjacent to a previously contaminated borehole and uses the borehole monitoring history to establish the pretest condition. TCE and its DPs are removed from the groundwater between the packers at the onset of the testing. The parameters estimated by fitting a radial diffusion model to the concentration history and borehole concentration data, also termed back diffusion, are the tortuosity factor and sorption coefficients of TCE and DPs in the rock matrix and the TCE and DP biodegradation rate coefficients in the borehole. We demonstrate the equipment design and the interpretive method using a borehole accessing the gray mudstone at a TCE contaminated site in the Newark Basin. In this test, both nonreactive (bromide) and reactive (trichlorofluoroethene) tracers are used to constrain the estimated parameters; however, the bromide tracer was not needed to estimate the parameters in this test. The parameters estimated from the field test are consistent with values measured independently in laboratory experiments using field samples of similar lithology. From the interpretation, we compute the TCE and DP concentration distributions in the rock matrix prior to the test to illustrate how the results can be used to enhance understanding of contaminant distribution in the rock matrix.
Measurement of ocular parameters under various directions of gaze (2006)

Lid angles and aperture size are important factors for fitting and on-eye performance of contact lenses. In particular, toric and translating bifocal lenses rely on predictable interaction with the eyelid for successful positioning and orientation. Traditionally, lid assessment and fitting evaluation is performed under slit lamp observation. Observations are limited to primary gaze and nasal or temporal directions. Quantification of lid parameters and lens positioning is subjective and depended on the skill of the practitioner. No commercial instrument is available off the shelf, which would be suitable to measure objectively ocular parameters and/or contact lens positioning under different directions of gaze. This is the likely reason why only one study has been published in which ocular characteristics for different gaze angles were obtained [1]. However, only a limited number of parameters and gaze directions were investigated. Almost all contact lenses are designed for and assessed under primary gaze. Considering that patients constantly change their gaze while wearing contact lenses, the quantification of contact lens movement and changes in ocular parameters with eye movement can contribute substantially to the understanding of lens performance and thereby lead to improved lens designs. This is of particular importance for toric and translating bifocal lenses. Their complex optical and topographical design requires precise positioning, orientation and movement with changes in gaze direction in order to provide adequate vision. Baron [2] suggested that the lower eyelid is the most important factor for lens movement of translating bifocal lenses, but questions still remained on the complete dynamics of on eye behaviour. For toric contact lenses, the rotational orientation is more important than vertical translation to obtain optimum visual correction. Most toric lenses feature a prism ballast design. Blinking movements, mainly of the upper eyelid, interact with the wedge like shape and squeeze the thick part downwards. It has been observed that the upper eyelid does not move in a straight downward movement, but also twists slightly to close the temporal side first [3]. Precise quantification of this motion and how it affects the contact lens movement have not been reported. A new instrument was designed and constructed to provide objective measurements of ocular parameters.
Antibiotic resistance plasmid composition and architecture in Escherichia coli isolates from meat (2021)

Resistance plasmids play a crucial role in the transfer of antimicrobial resistance from the veterinary sector to human healthcare. In this study plasmids from foodborne Escherichia coli isolates with a known (ES)BL or tetracycline resistance were sequenced entirely with short- and long-read technologies to obtain insight into their composition and to identify driving factors for spreading. Resistant foodborne E. coli isolates often contained several plasmids coding for resistance to various antimicrobials. Most plasmids were large and contained multiple resistance genes in addition to the selected resistance gene. The majority of plasmids belonged to the IncI, IncF and IncX incompatibility groups. Conserved and variable regions could be distinguished in each of the plasmid groups. Clusters containing resistance genes were located in the variable regions. Tetracycline and (extended spectrum) beta-lactamase resistance genes were each situated in separate clusters, but sulphonamide, macrolide and aminoglycoside formed one cluster and lincosamide and aminoglycoside another. In most plasmids, addiction systems were found to maintain presence in the cell.